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Researchers Help Answer the Question of which is Healthier for you…White or Wheat Bread?

wheat bread, white bread, metabolism

Despite being the topic of many discussions, it is still unclear how different types of bread effect different people. In a recent study published in Cell Metabolism, scientists unearth the answer to the infamous question; which is healthier, white or wheat bread?

Researchers at Weizmann Institute decided to tackle this question and performed a randomized trial of 20 healthy individuals to compare the differences in how processed white bread and whole wheat bread affect the body. Prior to the study, participants consumed about 10% of their calories from bread. During the study, participants were split into two groups and were asked to consume around 25% of their calories from either white bread or freshly supplied whole wheat bread for a week. After 2 weeks without bread, the participant groups were reversed, where the white bread group now ate wheat and vice versa. Researchers had studied the participants’ health effects, glucose levels, essential minerals (Calcium, Magnesium, etc.) levels, fat and cholesterol levels, kidney and liver enzymes, and several inflammation and tissue damage markers, before, during, and after the experiment. Scientists also measured each participant’s microbiome before the study and throughout it. Interestingly, the initial conclusion of the study showed that there were no clinically significant differences between the two types of bread in any of the initially measured parameters. However; after taking a deeper look, researchers discovered that different participants had different glycemic responses to the different types of bread. Some of the participants had a better glycemic response to the white processed bread and some participants had a better response to the wheat. This study shows that people can tell which food is a better fit for them based on their individual microbiome, strengthening the argument that nutritional values should be determined on a case by case and not one size fits all.

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Bread Affects Clinical Parameters and Induces Gut Microbiome-Associated Personal Glycemic Responses (June 2017).

New Study Shows that Certain Foods Can Play a Role in Starving Cancer

prostate cancer, turmeric, apple peels

A new study published in Precision Oncology, discusses a novel plant-based chemical agent screen that was able to show which agents, singly or in combination, were able to inhibit tumor growth in mice.

Researchers used a novel analytical approach to screen a number of plant-based chemical library to discover specific combinations that lead to shrinking of prostate tumors. Some research has been conducted in the past that has highlighted the effect of natural chemicals found in plants as potential therapies. Green tea, turmeric, and apple peels have been found to minimize risk factors for cancer and inflammation. Using these principles, scientists screened a library of 142 natural chemical compounds and then tested these compounds on mouse and human cell lines to observe which agents inhibited prostate cancer cell growth alone or in combination. The most promising chemical agents were then tested in animal models. Interestingly, ursolic acid found in apple peels and rosemary, curcumin found in turmeric, and resveratrol, found in red grapes and berries had the most prominent effect in shrinking prostate tumor volumes. Scientists were able to determine that these chemicals work in combination to modulate glutamine metabolism in cancer cells by blocking their uptake of glutamine, thus successfully starving cancer cells of an important nutrient needed for growth. This study hopes to identify synergistic combinations of natural chemicals for a different therapeutic approach to prostate cancer in conjunction with traditional treatment methods.

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Lodi, Alessia, et al. "Combinatorial treatment with natural compounds in prostate cancer inhibits prostate tumor growth and leads to key modulations of cancer cell metabolism." npj Precision Oncology 1.1 (2017): 18.

New Technology Allows Researchers to Decode and Predict what a Subject is Seeing

fMRI, Neural Network, artificial intelligence

A new tool that combines using fMRI signals and a network-based artificial intelligence called, Deep Neural Network AI, allows researchers to interpret what subjects are seeing, remembering, imagining, and even dreaming.

In the past, researchers attempting to unlock the human mind have had to extensively catalog each subject’s unique brain patterns to match them to a small number of images using fMRIs. As one can imagine the process was time consuming, expensive, and not at all foolproof. Recently a study in Nature Communications has shown the use of a neural network-based artificial intelligence to decode and predict what a person is seeing or imagining. The research team use an artificial intelligence program called the Deep Neural Network (DNN) to decode brain activity patterns. Brain activity patterns can be translated into signal patterns of stimulated neurons in the DNN. When a test subject and the DNN are shown the same image, certain visual areas in the brain can decode the image the same way the respective layers within the DNN can, thus showing a homology between the human brain and the AI. The DNN can decode an image by taking the neural network patterns seen in a test subject and comparing them with image data from a large database. Scientists hope this new technology can help connect neuroscience with artificial intelligence and one day open the door to a deeper understanding of the human brain.

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Generic decoding of seen and imagined objects using hierarchical visual features (May 2017)

How Demands of Females Changed the DNA of a Species

finches, evolution, sexual selection

Charles Darwin, the “Father of Evolution” explained the process of natural selection, where an organism better adapts to an environment in order to survive and reproduce. This process is the major driver for the evolution of species. Interesting, scientists have discovered a new driver for evolution in a group of birds closely related to finches. Females.

Darwin wrote about a process called sexual selection, where the preferences in color and pattern from a specific gender leads to the evolution of a different species of seedeaters. These finches have the same behavior and diet, but the males look completely different. Researchers from Cornell University and the Cornell Lab of Orthinology, investigated nine species of southern capuchino seedeaters doing full genomes for each one. Interestingly, scientists observed less than 0.3% difference in the DNA between species and the greatest variations appeared in genes that play a role in regulating melanin. Researchers also noted that the change in color patterns in males did not seem to give on species any survival advantage over one another. The patterns themselves seems to be dictated by female mating choices. There is still more research that needs to be done in selection sexual, but this study is one of the first examples to show it in action.

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Repeated divergent selection on pigmentation genes in a rapid finch radiation (May 2017)

How Medieval Religious Rules Drove the Evolution of the Chicken

chicken, evolution, ancient DNA

Chickens were domesticated over 6,000 years ago from Asian jungle fowl. They have acquired several traits over the years to make them more valuable to humans (appearance, reduced aggression, etc.) but the history of the evolution of these traits was unknown. A team of scientists were able to combine ancient DNA and statistical modeling to show how religion played a role in the evolution of the chicken.

Researchers were able to extract DNA from ancient chicken bones used statistical modeling to pinpoint precise timeframes that correlate with ecological and cultural shifts in history. Scientists were able to identify several traits that distinguish the domesticated chickens from their more wild relatives and were able to study their genetic evolution. The results showed that around 1000 AD, there were strong selection pressures that caused some genetic variations between the fowls. During that time, Christian edicts encouraged fasting to exclude the consumption of four legged animals, thus causing an increased demand for poultry. Scientists discovered two genetic variants domesticated chickens have in two genes: the thyroid-stimulating hormone receptor (TSHR), which is connected to the loss of seasonal reproduction and a loss of aggression, and the beta-carotene dioxygenase 2 (BCD02), which effects the pigmentation of chickens. By analyzing ancient and modern chicken DNA, scientists were able to pinpoint the origin of selection and the strength of this selection. The selection for the TSHR gene began in 920 AD, which coincides with an increase in chicken consumption across Northern Europe. The Christian fasting practices did not include birds and eggs, possibly leading to selective pressures on TSHR to allow chickens to be raised in closer confines. This study helps to pave the way for a better understanding of patterns of genomic variation and the mechanisms responsible for driving them.

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Inferring allele frequency trajectories from ancient DNA indicates that selection on a chicken gene coincided with changes in medieval husbandry practices (April 2017)

Antibiotic-Resistant Microbes Date back 450 Million Years Ago

antibiotic-resistant, microbes,enterococci

Antibiotic resistance is a major public health concern worldwide. This fact prompted a group of scientists to perform a study that sheds light on evolutionary history of these “superbugs.”

Antibiotic resistant microbes are a major problem in hospitals. About 5% of hospital patients end up fighting infections that arise during their stay. Some of these microbes are resistant to almost every antibiotic. Enterococci are the leading hospital “superbugs,” so researchers wanted to investigate how these microbes evolved to become nearly indestructible. In a study published in Cell, scientists were able to analyze the genomes and behaviors of all species of enterococci and found that they were naturally resistant to dryness, starvation, disinfectants, and many antibiotics. Enterococci live in the intestines of most land animals and is likely they lived in the intestines of extinct animals, such as dinosaurs. Research shows that bacteria arose about 4 billion years ago on Earth. When the first animals emerged in the sea, about 542 million years ago, bacteria learned to live in and on them. As animals crawled to onto land about 100 million years later, bacteria came with them. Even after mass extinctions such as the dinosaurs, bacteria such as enterococci was able to withstand dryness and starvation. Researchers were able to show discover what genes enterococci inherited hundreds of millions years ago that enable them to become resistant to drying out, starvation, disinfectants, and antibiotics. Scientists hope this research can help researchers design new types of antibiotics and disinfectants against enterococci.

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Tracing the Enterococci from Paleozoic Origins to the Hospital (May 2017)

New Methods to Improve Chronic Pain

chronic pain, caffeine, sleep

Chronic pain affects millions of people around the World and cost billions of dollars in pain medication every year. In a new study published in Nature Medicine, scientists have shown there are techniques, more natural and cost effective, than constant medication.

Scientists found that caffeine and sleep provides more relief to chronic pain sufferers than standard pain medications such as ibuprofen and morphine. Most chronic pain patients suffer from disrupted sleep patterns and/or use constant pain management medications. Therefore, researchers wanted to study how disrupted sleep cycles, pain medications, and pain sensitivity affect mice. The mice were sleep deprived for 6 or 12 hours for 5 consecutive days by entertaining them with toys and activities. Scientists then tested pain sensitivity using controlled amounts of heat, cold, pressure, or capsaicin. The mice were given pain medications such as ibuprofen or morphine, but researchers observed that these drugs did not block sleep-loss induced pain hypersensitivity. Interestingly, when caffeine and other drugs to promote wakefulness on sleep-deprived mice, they were able to block hypersensitivity. Researchers believe this study suggests that patients with chronic pain might benefit from better sleep-promoting medications at night couple with wakefulness medications during the day to improve pain management.

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Decreased alertness due to sleep loss increases pain sensitivity in mice (June 2017)

A New Discovery to Help Combat Mid-Life Obesity

Obesity, weight loss, DNA-PK

Recently, a team of researchers have discovered an enzyme that could help in the battle against mid-life obesity. This new discovery is redefining current notions of why people gain weight as they age and could pave the way for more effective weight loss medicines.

Typically, a lack of exercise at mid-life (30-60 years) is usually attributed to life style choices, but a new study is showing that this could be attributed to an overactive enzyme that promotes weight gain. This study recently published in Cell Metabolism, scientists used mice to test the role this enzyme plays in obesity. In one experimental group of mice, they administered an inhibitor against the enzyme in question and feed the mice a diet of high-fat foods. In the control group of mice, they withheld the inhibitor and feed the mice a diet of high-fat foods. Researchers were able to show a 40% reduction in weight gain in the group the received the inhibitor, indicating that this enzyme is playing a role in weight gain. This enzyme is DNA-dependent protein kinase, DNA-PK, and its activity increases with age. DNA-PK promotes the conversion of nutrients to fat and decreases the number of mitochondria, which are used to convert fat into energy to fuel the body. Scientists believe that inhibiting the activity of DNA-PK could possibly become a new type of weight loss medication.

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DNA-PK Promotes the Mitochondrial, Metabolic, and Physical Decline that Occurs During Aging (May 2017)

Is Running Contagious?

exercise, contagious, running

Exercise behavior has long been a difficult puzzle to decipher, but a recent study has suggested that running is a socially contagious behavior. Scientists have performed a large scale big data report to show how much we exercise and how we exercise is partly determined by those around us. In a study published in Nature Communications, scientists took data from a worldwide social network devoted to sharing measured exercise routines every day over the course of five years from over 1 million runners across the globe. Scientist measured exactly how often, far and fast each runner had exercised for that day and mapped out their progress and compared it to the progress of the virtual friends of that runner. Using the data, researchers started to see correlations, friends tended to display similar training patterns day to day even if they were separated geographically.

Interestingly, another correlation observed was that men generally ran longer or faster if their male or female virtual friends had done likewise. However, women usually only altered their exercise routine based on the training routines of their female friends. Researchers also found out that whether and how much we exercise can depend to a surprising extent to our responses to other's training. Therefore, if you exercise, then it is likely that you will cause your friends to exercise more. The results also suggest one practical piece of advice: if you wish to improve your performance, you want to become virtual friends with people who are a bit faster than you are.

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Exercise contagion in a global social network (Apr 2017)

New Signal to Accelerate Healing Using Stem Cells

stem cells, HGFA, and wound healing

Accelerated healing isn't just for the comics. A new study published in Cell Reports discusses how priming the body before an injury can increase the speed of tissue repair and recovery. This primed state is called an "Alert" state and it is activated by a critical signal. This study builds upon a previous report that showed upon an injury, the body's adult stem cells in uninjured areas become primed or alert. These alert stem cells have an enhanced potential to repair the injured tissue area. In a recent publication in Cell Reports, scientists found the signal that alerts stem cells and showed how this signal can serve as a potential therapy treatment to improve healing. Researchers identified an enzyme called Hepatocyte Growth Factor Activator (HGFA) as the signal. HGFA is abundant in the blood and is inactive, but upon an injury, HGFA becomes activated and HGFA signaling can alert stem cells to get ready to heal.

Scientists wanted to test the ability of HGFA to alert stem cells before an injury; therefore, they injected active HGFA into mice that would receive a skin or muscle injury a couple days later. Amazingly these mice healed faster, with some interesting after effects. The mice who received the HGFA injection actually began exercising sooner and regrew their fur better than the mice who did not receive the HGFA booster. Researchers hope these findings could one day lead to a therapeutic booster that helps improve recovery time to injuries and help those with impaired healing. Thus, one day making it possible for everyone to become a modern day superhero.

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HGFA Is an Injury-Regulated Systemic Factor that Induces the Transition of Stem Cells into GAlert (Apr 2017)

New Mechanism Reveals how Stress Controls Hemoglobin Levels in Blood

Blood, Hemoglobin, and stress

Stress is a part of life and understanding how our bodies react under stressful situations is essential to our survival. In certain stress induced situations where oxygen is less, the body reacts by producing more hemoglobin in our blood to carry oxygen. Recently, scientists have found a link between a cellular stress signal and globin genes.

In order to produce hemoglobin, the DNA of the globin gene is transcribed into a long RNA molecule. The RNA molecule contains several segments that need to be spliced out in order to be translated into protein. Now, researchers have published a finding that indicates that an intracellular stress signal is responsible for the splicing of RNA for globin genes. Scientists believe that the hemoglobin gene itself, is activated from an intracellular stress signal. In cells the enzyme, Protein Kinase R (PKR), that is responsible for RNA splicing of the globin RNA remains silenced until a specific RNA structure activates it. Once PKR is activated, it will in turn phosphorylate eIF2-alpha, which in turn leads to a block in protein synthesis, a known stress response. Interestingly, the phosphorylated eIF2-alpha is necessary to form machinery to splice globin RNA. Once the globin RNA has been spliced, the mature RNA form can inactivate PKR, thus leading to protein synthesis. This novel finding shows that stress and our ability to mount different stress responses is essential for our survival.

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PKR activation and eIF2α phosphorylation mediate human globin mRNA splicing at spliceosome assembly (May 2017)

Scientists Unveil New CRISPR-based Diagnostic Platform

anti-aging, aging, DNA repair

Scientists from the Broad Institute of MIT and Harvard in collaboration with other scientific and medical institutions, have discovered a new highly sensitive diagnostic tool. This tool uses a CRISPR enzyme protein that targets RNA instead of DNA. This new technique is sensitive enough to detect a single target molecule of RNA or DNA and has the potential to transform the field of public health around the World.

In the study published in Science, researchers have demonstrated how a RNA-targeting CRISPR enzyme can function as a highly sensitive detector of RNA and/or DNA molecules. This new diagnostic tool is named SHERLOCK (Specific-High-sensitivity Enzymatic Reporter unlocking). In a previous publication, Zhang and colleagues described Cas13a (previously known as C2c2) as the RNA-targeting CRISPR enzyme that can be programmed to cleave specific RNA targets and can remain active after cleaving its intended target to cleave non-targeting RNAs. Scientists wanted to discovery a way to harness this RNA cleaving enzyme for future applications. In a collaborative effort, researchers were able to design a synthetic paper-based test that uses body heat to amplify levels of DNA or RNA in test samples. Once the DNA or RNA molecules have been amplified, the team used a second step amplification stem to convert the DNA to RNA which lead to the millionth-fold increase of sensitivity of the CRISPR-RNA targeting enzyme, Cas13a. This SHERLOCK diagnostic tool has a wide range of applications such as detecting antibiotic resistance genes, distinguishing between genetic sequences of African and American Zika viruses, discriminating between specific types of bacteria, identifying cancerous mutations in stimulated cell-free DNA fragments, and more. And scientists say that it is just the beginning of what this tool can do.

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Nucleic acid detection with CRISPR-Cas13a/C2c2 (April 2017)

Scientist Discover a Revolutionary Regulator that Could be the Key to Reversing Aging

anti-aging, aging, DNA repair

A newly discovered metabolite involved in DNA repair seems to be the key in reversing aging. Scientists tested the effect of this metabolite on cells from old mice which were exposed to radiation. A cell's ability to repair DNA damage from ageing or radiation declines as we age. Surprisingly, scientists found that the cells of the old mice were indistinguishable from the cells of young, healthy mice after treatment.

This metabolite was identified as NAD+ and it is naturally present in cells and it functions as a key regulator in protein-protein interactions that control DNA repair. Researchers have shown that NAD+ binds to the NHD (Nudix homology domain) of DBC1 (deleted in breast cancer 1) and prevents it from inhibiting PARP1 [poly(adenosine diphosphate-ribose) polymerase], a key DNA repair protein. By treating mice with a NAD+ precursor booster, scientists saw improvement in a cell's ability to repair DNA damage caused by radiation or old age. Researchers are hoping that this discovery could possibly help aid in preparing astronauts for a four year mission to Mars, since astronauts experience accelerated ageing from cosmic radiation.

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A conserved NAD+ binding pocket that regulates protein-protein interactions during aging (March 2017)

Scientists are Using Plants to Form Human Stem Cell Scaffolds

scaffolds, synthetic biology, stem cells

Nature has always been a source of inspiration for science, and now scientists are using plants to help revolutionize stem cell research. Researchers have developed a new method using plants, such as parsley and orchids, to form three-dimensional scaffold for stem cells. The technique involves taking the decellularized husks of certain plants and transforming them into miniature three-dimensional structures to become useful for biomedical applications.

Scientists say this new approach depends on cellulose and the treatment of these husks with chemicals to enhance the attachment and growth of human stem cells. The stem cells seeded into the scaffold tend to align themselves along the pattern of the miniature structure's shape. This process creates the ideal scaffold for human stem cells to attach and thrive on since they are sensitive to topography. The goal of this study to help overcome the limitations current methods, such as 3-D printing, face when creating structures for biomedical applications.

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Biomanufacturing Seamless Tubular and Hollow Collagen Scaffolds with Unique Design Features and Biomechanical Properties (Jan 2017)

New Drug to Fight Aggressive Form of Prostate Cancer

prostate cancer, CXCL12, HMGB1

Prostate cancer is the second leading cause of cancer-related deaths in the United States for men. This statistic has driven scientists all over the World to find new life-saving treatments. Recently, scientists have discovered a new way to eradicate invasive prostate cancers in mice using a drug to boost innate immunity.

Researchers observed that using Cabozantinib, a tyrosine kinase inhibitor drug, caused the protstate cancer cells within the tumor to release CXCL12 and HMGB1, two chemical signals, in order to entice neutrophils to infiltrate and destroy the tumor. This is the first demonstration of using this type of inhibitor to activate an innate anti-tumor immune response. This immune response lead to complete eradication of invasive poorly differentiated prostate cancer tumors in mice. Interestingly, researchers discovered the key to this study is the release of the neutrophil-attracting chemical signals. When scientists used drugs to block production of CXCL12 and HMGB1, Cabozantinib no longer had an effect on the cancer cells. Researchers hope this study will open the door to combinatorial cancer immunotherapies that focus on the innate and adaptive immune systems together to fight the disease.

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Cabozantinib Eradicates Advanced Murine Prostate Cancer by Activating Anti-Tumor Innate Immunity (Mar 2017)

Why are pandas black and white?

Giant panda and pandas

Giant pandas have distinct black and white fur patterns; but why is that? In order to investigate this question, a research team from University of California, Davis in collaboration with California State University decided to take a closer look at panda behavior. This team found that pandas actually use their coloring for not one, but two distinct functions! In order to investigate further, scientists looked at each part of a panda's body as an independent area. This led scientists to try to match these different regions to various ecological and behavioral varibales to determine their function.

The study found that the white region of the panda's body is to help them hide in snowy habitats and the dark regions on the body are to help them hide in the shade. Pandas have a limited diet of bamboo, which means they are unable to store fat to hibernate during the winter. Therefore, they are active year around to travel where their food is, which range from tropical forests to snowy moutains. Scientists however, found a different function for a panda's head markings. These features are believed to be used for communication. Researchers suggest the dark ears may convey a sense of ferocity to warn predators and the dark eye patches help them to recognize one another or to signal aggression to other pandas. Who knew?

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Why is the giant panda black and white? (February 2017)

Cold or Flu? Proteins in Your Nose Can Tell the Difference

Cold, Influenza, Flu, and Runny nose

Differentiating between a cold or a flu virus might become the key to saving a life. Thousands of people die every year due to seasonal influenza viruses. Scientists have now identified a group of proteins that can be used to distinguish between a cold or flu. These proteins are also detected by a non-traditional method, your nose. Using mucous from a patient's inflamed nose passage, researchers were about to detect with 86% accuracy whether a infection was coming from a cold or flu virus. Researchers first conducted a proteomic study which identified 438 unique proteins between patients that were infected with  influenza A/H3N2 or human rhinovirus. Scientists then noticed that in patients infected with H3N2, these proteins' expressions were altered and their functions were dysregulated. These proteins are involved in acute inflammatory response and innate immune response.

Currently, most patients are given antibotics, which don't benefit patients with viral infections. Health care providers however, are limited by lack of tools to help distinguish between a bacterial infection, where antibotics are appropriate and viral infections, where they are less helpful. Researchers hope to be able to provide clinicians with a noninvasive diagnostic test to help distinguish between cold and viral infections.

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Nasopharyngeal Protein Biomarkers of Acute Respiratory Virus Infection

Heated CRISPR Patent Dispute Settled

CRISPR, Cas9, CRISPR Patent

CRISPR/Cas9 is a genome editing technique that has repurposed a bacterial immune system to easily and precisely edit DNA. The discovery of this breakthrough technology and it's advances has lead to a heated patent ownership dispute. This ownership battle was between the University of California Berkley (UC) with scientist Dr. Jennifer Doudna and her collaborator Dr. Emmanuelle Charpentier, who discovered that CRISPR/Cas9 could be used as a genome editing tool, and the Broad Institute (Broad) with scientist Dr. Feng Zhang, who discovered using CRISPR to edit genomes in mouse and human cells.

The patent board ruled in favor of the Broad Institute stating that the Board party persuaded them "that the parties claim patentable distinct subject matter." This decision means that the patent board did not find the revolutionary work by Doudna and colleagues all encompassing as to make later advances, such as Zhang discovery to use CRISPR in higher-order cells, obvious. This debate began in January 2016 when UC initiated an interference proceeding to claim that their patent awarded in May 2012 for the CRISPR/Cas9 technology was the same invention patent awarded to Broad in April 2014. The Broad Institute holds about 13 patents that encompass essentially all uses of CRISPR/Cas9 in mammalian cells. UC challenged those patents as being foundational the same invention of Doudna and colleagues. UC is expected to appeal the patent board's decision and experts say that is to be expected given the extremely high stakes. If CRISPR will be used in the future to treat genetic disorders or in agriculture to create biofuels, then patent holders can be expected to be a part of multi-billion dollar markets in the near future. As the saying goes, "the battle may be over but the war has just begun."

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A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity (June 2012)

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Multiplex genome engineering using CRISPR/Cas systems (February 2013)

New method for drug screening: Organs-on Chips

Organs-on-Chips, Drug Screening, and micro-organs

Modeling human organs on a small scale has been a major bottleneck for researchers. Now scientists have discovered a way to recreate three-dimensional structures of tissues, that are completely vascularized on an industry standard 96 well plate. How do these micro-organs work?

Researchers have been able to establish multiple micro-organs that are able to incorporate perfused micro-vessels. The survival of these tissues are dependent on a vascular network that can deliver nutrients through a blood subsite. The 96 well plate can hold a variety of micro-tissues such as brain, heart, pancreas, tumors, etc. and can use the same vascular system to supply nutrients to every tissue by hydrostatic pressure. Utilizing a panel of FDA-approved anti-cancer drugs and human colon cancer, scientists were able to identify drugs that were anti-angiogenic and/or anti-tumor. These miniature tissues are better able to reproduce human drug responses than previous models.

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A vascularized and perfused organ-on-a-chip platform for large-scale drug screening applications (January 2017)

A new 3-D Bioprinter prototype can print completely functional human skin

3D bioprinter, 3D printing, and Skin

Scientists have presented a new prototype for a 3-D bioprinter that can print properly functioning human skin. The printed skin replicates the natural structure of skin, as well as its properties. Researchers have also shown the printed skin is adequate for transplanting to patients or to be used in research. How does this bioprinter work exactly?

Experts say that bioinks are the key to 3-D bioprinting. In the example of printing skin, injections are used instead of cartridges and biological components are used instead of colored inks. Researchers show that the bioprinted skin replicates the natural structure of skin. It contains an external epidermis with its stratum corneum, an inner deeper dermis layer, and a final layer that consists of fibroblasts that produce collagen. There are two processes to produce skin tissue: 1) Stock cells are used to create allogeneic skin on a large scale for industrial processes and 2) A patient's own cells can be used to create autologous skin for therapeutic purposes. This new development is currently in the phase of being approved by different European regulatory agencies to guarantee that the printed skin is adequate to be used for transplantations on patients.

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3D bioprinting of functional human skin: production and in vivo analysis (December 2016)

A new study shows that intestinal bacteria can accelerate the development of Alzheimer's disease

Alzheimer's Disease, Gut Bacteria, Beta-amyloid, and Intestinal bacteria

Numerous studies have implicated the involvement of intestinal microbiota in a number of brain disorders but the connection between gut bacteria and Alzheimer's has remained elusive. A new study using healthy and diseased mice has shown that the presence of certain gut bacteria can lead to the development of Alzheimer's disease. How is this possible?

Researchers observed that mice with Alzheimer's disease have a different composition of intestinal bacteria as compared to healthy mice. Surprisingly, the diseased mice that lacked certain types of intestinal bacteria actually showed significantly smaller amounts beta-amyloid plaque in the brain. Interestingly, when scientists transferred intestinal flora from diseased mice to germ free mice, these mice developed more beta-amyloid plaques in the brain as compared to the germ free mice who received gut bacteria from healthy mice. By continuing to study the role of gut bacteria in Alzheimer's disease, researchers hope to one day test new types of preventative and therapeutic strategies based on modulating intestinal bacteria.

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Reduction of Abeta amyloid pathology in APPPS1 transgenic mice in the absence of gut microbiota (February 2017)

Consumption of hot chili peppers could be the key to a longer lifespan, a new research study finds

Hot chili peppers, TRP channels, Transient Receptor Potential Channels

For hundreds of years peppers and spices have thought to be beneficial to one's health by helping to combat disease. Recently, a new study has corroborated a large population study conducted in China that found that the consumption of hot red chili peppers is associated with a longer lifespan. How exactly? Researchers have found that people who consume red hot chili peppers show a 13% reduction in total mortality—primarily in deaths caused by heart disease or stroke.

Using survey data collected from more than 16,000 Americans over a 23 year time span, researchers found that consumers of hot chili peppers tended to have lower HDL-cholesterol and consume more vegetables and meats. The exact mechanism of how peppers delay mortality is not known, but scientists speculate that Transient Receptor Potential (TRP) channels, which are the primary receptors for capsaicin, may be responsible. Capsaicin is believed to play a role in cellular and molecular mechanisms that modulate coronary blood flow and prevent obesity. Capsaicin is also known to possess antimicrobial properties that may be inadvertently affecting the gut microbiota.

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The Association of Hot Red Chili Pepper Consumption and Mortality: A Large Population-Based Cohort Study (January 2017)

Scientists have developed a method to control protein activities within a live cell using light

Protein Expression, Protein Activity, Optogenetic, and chemogenetic

Proteins are instrumental to all cellular functions and therefore, are often the focal point of many research studies. Scientists have developed a new method of controlling protein activity in a cell using a common tool: light. The technique uses light to activate and deactivate a wide range of proteins throughout the cell without altering their function. This study builds on a technology, known as optogenetics, which allows scientists to use light to activate and deactivate proteins that in turn can activate or deactivate specific brain cells. Though revolutionary, this technique did have its limitations. Only a limited number of proteins could be controlled and these proteins were mislocalized within the cell making it difficult to study their original functions.

Scientists wanted to expand on this technique, and thus revised it to control a wide range of proteins without changing their function. A new study published in Science, shows that researchers can now take a protein and modify it with switch that can activate or deactivate a protein almost anywhere in the cell using light. This new technique will allow scientists to study how a protein's activity effects cell behavior in versatile and fast acting way. The publishing scientists use a computational approach to determine how to modify a protein without effecting it's function. The protein can then be modified with several controls that can be changed to respond to light intensity and timing irradiation. This new technique allows researchers to study proteins in living systems or to manipulate proteins in order to study a wide range of diseases-- all with the flick of a switch.

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Engineering extrinsic disorder to control protein activity in living cells (December 2016).

Newly discovered neural connection between brainstem and prefrontal cortex keeps instincts under control

Instincts, brainstem, instinctive behavior

Controlling one's impulses is never an easy task. So how do we do it? Instincts are driven by the brainstem and the prefrontal cortex helps to keep these instincts in check. But the connection between these two regions has eluded scientists until now. Researchers have recently found the connection in mice brains and believe this knowledge will help elucidate pathways for mental disorders. In a study recently published in Nature Neuroscience, scientists have identified which neuronal projections prevent social animals from acting on impulse alone. This connection is between the brainstem, in the PAG region, and the prefrontal cortex and scientists can trace the connection between neurons from one region to another.

Using mice, researchers found that mice continually beaten by another mouse show a weakened connection between the brainstem and the prefrontal cortex, which leads to the mice acting more "fearful". Scientists then used drugs to block the same connection and were able to obtain the same "fear" response in mice. This work may have implications in understanding mental and mood disorders, which can be linked to problems with the prefrontal cortex function and/or maturation.

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Prefrontal cortical control of a brainstem social behavior circuit (January 2017)

Ultrafast imaging has captured energy transfer in Photosynthesis

Photosynthesis imaging, Photosystem II, Photosynthesis

Scientists have captured the speed of crucial processes in Photosynthesis for the first time using ultrafast imaging. Researchers have also solved a decades old debate on which chemical process within Photosynthesis is the fastest. During Photosynthesis, plants harvest light and use water and carbon dioxide to produce fuel. The chemical process using light energy to split water into hydrogen and oxygen is done by the enzyme, Photosystem II. The 'antennae' gathers light energy. The light energy then travels to the reaction center of the Photosystem II enzyme and is used to strip electrons from water in a process called charge separation. Initially, it was thought that the process of charge separation was the slowest step in Photosynthesis when compared to other processes such as, the transfer of energy along the antennae.

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Since 2001, however, some suggestions have begun to surface that the transfer of energy step is actually the slowest, but it could not be proven. However, now using ultrafast imaging, scientists have shown that the process of harvesting light and transfer of the energy along the antennae is indeed, the slowest step. Researchers have used electronic excitation that uses small crystals of the Photosystem II to capture the images. The resulting movie shows the path of excited electrons across minute sections of the system. This new research will enable scientists to accurately replicate the process of Photosynthesis and facilitate production of biofuels.

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Ultrafast infrared observation of exciton equilibration from oriented single crystals of Photosystem II (December 2016)

New Ebola vaccine is 100% effective in protecting patients

Ebola vaccine, Ebola, Ebola vaccine discovery

The Ebola virus has killed over 11,000 people in West Africa since 2014. But thankfully, a new research study shows the experimental rVSV-ZEBOV Ebola vaccine is 100% effective against the Ebola virus. During the research trials of the vaccine, researchers and the World Health Organization made some unconventional decisions in an effort to save as many lives as possible. In 2015, an experimental vaccine trial was conducted in Guinea. Initially, only randomized individuals over the age of 18 and in contact with patients who had recently contracted Ebola, had received the vaccine. Patients were vaccinated either immediately or after three weeks. The preliminary results were quite promising, and so, the World Health Organization in conjunction with Guinea's Ministry of Health decided to stop the trail and distribute to the vaccine to everyone who needed it.

Researchers followed up with patients on 3, 14, 21, 42, 63, and 84 days after receiving the vaccine and there were no recorded cases of Ebola. There are multiple strains of the Ebola virus, usually named after the region they were discovered in. This vaccine targets the Zaire group Ebola virus and offers cross protection for similar strains, but it does not offer protection for all strains of the virus. Researchers plan to stop the transmission of the virus by vaccinating groups of people who are in close contact with an Ebola patient. The same strategy was employed to eradicate smallpox. The Ebola vaccine was originally developed in Canada and is now currently owned by Merck, Sharp & Dohme. The company has ensured that thousands of doses of the vaccine will be available in case of a new Ebola outbreak.

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Efficacy and effectiveness of an rVSV-vectored vaccine in preventing Ebola virus disease: final results from the Guinea ring vaccination, open-label, cluster-randomised trial (Ebola Ça Suffit!) (December 2016)

Scientists suggest that the food we eat influences gene regulation

Cellular Metabolism, gene regulation in yeast, and yeast genome

A research study, published in Nature Microbiology, is suggesting that the food we eat, may influence gene expression. Scientists have used yeast, as a model organism, to show how altering metabolism can affect the regulation of genes. The implications of this finding suggest that cellular metabolism plays a dynamic role in cells and this could help explain how certain individuals react differently to treatment drugs. Genes can be regulated by other genes, regions of DNA, DNA-interacting proteins, and epigenetic modifiers. Metabolism is the process of chemical reactions needed to maintain cells. It works in two directions, one to breakdown nutrients to provide energy and the second to produce essential compounds for cellular processes. Some studies have suggested that the metabolic network is a novel player in gene regulation controlled by biochemical reactions that occur when nutrients such as sugars, amino acids, fatty acids, and vitamins are available.

In order to understand how metabolism is playing a role in gene regulation, scientists manipulated the levels of metabolites in yeast cells and examined how this affected ten genes and their products. Researchers observed that nine out of the ten genes, as well as their products, were affected by the changes in these metabolite levels. These affects were seen in the background dependent gene expression and occurred predominantly through masking or suppression of transcriptional interactions epistatically. These results have a wide range of implications ranging from how cancer cells develop certain genetic mutations that change the metabolic network in those cells to how some individuals respond to certain drugs and others do not. Again, because of the start of the New Year and New Year's resolutions that pertain to diet decisions, we wanted to bring attention to this topic.

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The metabolic background is a global player in Saccharomyces gene expression epistasis (February 2016)

Can too much protein lead to cancer?

Insulin-Like Growth Factor Receptor 1, high protein diet, IGF-1

Proteins are essential for a person's diet because they provide amino acids that are used throughout the body. Most people associate high protein diets with muscle build and weight loss. But is too much protein bad for you? Scientists and medical professionals say yes. In a study published in Cell Metabolism, researchers have shown a link between increased Insulin-like Growth Factor Receptor 1 (IGF-1) expression and high protein intake. They observed raised cancer and diabetes mortality rates in younger individuals who consumed more protein in their diet. The same researchers also showed increased tumor progression in mice with high protein diets and high IGF-1 expression.

Nutritionists advise an average adult woman should consume about 46 grams of protein per day and the average adult male should consume about 56 grams. However, with the availability of protein powders, supplements, products, etc., most people are consuming more protein than their bodies can process. Experts have shown that the body can only absorb and utilize a certain amount of protein per day and robbing the body of other essential macronutrients (such as whole grains, fats, fruits, and vegetables) can be detrimental. Large population studies have shown an association between high protein diets with an increased incidence of cancer, heart disease, diabetes, increased kidney disease, and other illnesses. Some nutritionists and skeptics dismiss these concerns stating there is not adequate evidence to support these claims. Nutritionists have seen people lose weight on high protein diets and say there is a distinction between minimally required and optimal intake level when it comes to protein. Either way, nutritionists do advise that the source of protein is important, and advise individuals to avoid artificially produced proteins. Since the New Year ushers in a number of New Year resolution diets, we thought it would be pertinent to refresh this topic in hopes of providing helpful information.

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Low protein intake is associated with a major reduction in IGF-1, cancer, and overall mortality in the 65 and younger but not older population (March 2014).

Relationship between birth year and Flu infection

influenza pandemic, hemagglutinin imprinting

A major influenza pandemic has the potential to kill large numbers of people but is there a pattern to influenza infections? A recent report suggests that the first influenza attack that a child suffers can impact their lifelong immunity against the influenza virus. When a person is exposed to a flu virus, the immune system creates antibodies to target hemagglutin, receptor proteins located on the surface of the virus. Each virus differs from each other based on the hemagglutin proteins. A new study published in Science discovered if a person was primarily exposed to a particular influenza strain as a child, it will determine which avian-flu strains they will be protected against in future infections. The effect is due to "immunological imprinting" which appears to occur during first exposure to the virus and is difficult to reverse.

By studying the mortality patterns caused by two avian-origin influenza A (Bird Flu) viruses, H5N1 and H7N9, scientists noticed an interesting phenomenon - children exposed to the H1 or H2 subtype of influenza rarely succumbed to H5N1 (and H1 or H2 virus) as an adult but were highly sensitive to H7N9 (an H3 subtype). The inverse was also true where children exposed to H3 subtype of influenza were protected again H7N9, but were susceptible to H5N1. Scientists hope this mathematical model will help predict the protective effect of imprinting and help determine the age distribution and severity of future pandemics.

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Potent protection against H5N1 and H7N9 influenza via childhood hemagglutinin imprinting (November 2016)

Growing organs in lab

organoid cultures, miniature organs

Organoids are miniature organs grown in lab from a person's stem cells. To form an organoid, stem cells are grown inside gels that contain a mix of biomolecules that promote stem cell renewal and differentiation. The role of these gels is to mimic the natural environment of the stem cells which provides them with the extracellular matrix (ECM) necessary for growth. Currently organoids are difficult to grow in lab in a controlled manner. A new study published in Nature seems to have addressed the problem by developing a hydrogel that provides a controllable way to grow organoids.

The researchers use modular synthetic hydrogel networks to define the key ECM parameters that govern intestinal stem cell (ISC) expansion and organoid formation, and show that separate stages of the process require different mechanical environments and ECM components. This approach overcomes many limitations of current organoid cultures and greatly expands their applicability in basic and clinical research. Miniature organs retain key aspects of their real-life biology and can be used to study diseases or test drugs before moving to human trials.

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Designer matrices for intestinal stem cell and organoid culture (November 2016)

Discovery of a plant thermometer

Phytochromes, Arabidopsis, Cellular temperature gauge

Plants are highly responsive to temperature, being able to distinguish temperature differences as low as 1℃. But the molecular mechanisms behind temperature perception in plants was not clear. Researchers have now associated phytochromes with this function. In a study published in Science, researchers describe a major thermosensory role of phytochromes (red light receptors) during the night.

In their active state, phytochromes bind DNA to restrict plant growth. During day time, sunlight activates phytochromes to slow plant growth. When in shade, phytochromes are quickly inactivated, allowing plants to grow faster and reach sunlight. At night, the functional dynamics of phytochromes are different. Instead of a rapid deactivation at nights, phytochromes gradually change from their active state to inactive state in a process called dark reversion. And the rate at which phytochromes revert to their inactive state at nights is a direct gauge of temperature. The lower the temperature, the slower phytochromes revert to inactivity and so they spend more time in their active, growth-suppressing state. This is why plant growth in winter is much slower. When it gets warmer, dark reversion is accelerated allowing accelerated plant growth. This discovery could potentially allow the breeding of crops that are resilient to thermal stress and climate change.

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Phytochromes function as thermosensors in Arabidopsis (October 2016)

Facebook for longer life

Facebook, Social integration, Reduced mortality

Strong social ties have been associated with human longevity and social interactions are increasingly moving to the online world. Using longitudinal statistical models of 12 million social media profiles, researchers associate online social integration with lower mortality risk. In other words, people with stronger social networks live longer not just based on their offline networks but also based on the strength of their online networks. Interacting online seems to be healthy when in moderation and when it is supplemented by offline interactions. On the other extreme, spending excessive time online with little connectivity in the offline world shows a negative association.

To conduct this study researchers matched California Facebook users with vital records from the California Department of Public Health. They studied user online activity over 6 months and compared the activity of the survivors to those who had died. The analyses suggested that, in a given year, the average Facebook user is about 12% less likely to die than a non-user. People with average or large social networks (top 30%-50%), lived longer than those with smaller networks (bottom 10%). Facebook users with highest levels of offline social integration (measured by those who posted pictures) had greater longevity. Researchers also looked at the direction of friendship requests and observed that Facebook users who accepted the most friendship requests lived longer while there was no observable relationship for those who initiated the request. While individual or larger policy recommendations cannot be based on this work, the researchers hope that subsequent research will lead to a better understanding of online social experiences and their protective impacts on health.

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Online social integration is associated with reduced mortality risk (November 2016)

How much water a day should you drink really?

Swallowing inhibition, fluid intake, water intoxication, hyponatremia

Water intake in humans is a crucial behavior that ensures species survival by maintaining fluid balance in the body. A recent study in humans confirms the presence of a swallowing inhibition after excess liquid consumption, that can prevent water intoxication and even death. This was tested using rating of swallowing effort and measuring regional brain responses using functional magnetic resonance imaging (fMRI), as participants prepared to swallow liquid while they were thirsty and after they had consumed excess liquid.

Effort ratings proved the existence of swallowing inhibition and a 3 fold increase in effort after excess liquid intake, which meant that participants had to overcome some sort of resistance. Addition of sugar to water had very little effect on effort before or after excess liquid intake. Regional brain responses increased in the motor cortex, prefrontal cortices, posterior parietal cortex, striatum and thalamus after overdrinking, relative to thirst. Ratings of swallowing effort were correlated with activity in the right prefrontal cortex and pontine regions in the brainstem, suggesting these areas were involved in overriding the swallowing inhibition so drinking could occur as instructed. Drinking excess water puts body in danger of water intoxication or hyponatremia (abnormally low sodium levels in the blood) and the practical recommendation based on these findings is to drink according to thirst rather than have an elaborate schedule.

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Overdrinking, swallowing inhibition, and regional brain responses prior to swallowing (October 2016)

Molecular mechanisms behind temperature sensing revealed

rate of temperature change, TRPA1

The ability to sense rate of temperature change is a critical survival response. However, the molecular mechanisms behind temperature sensing were unknown, until now. A new study reports the role of a TRP channel, whose activity responds to the rate of temperature increase. To carry out this study researchers developed fruit fly models which exhibited different behavioral responses to rapid and gradual rises in temperature respectively. The researchers found that a rapid 25oF temperature change caused a writing response in fruit fly larvae. But when the temperature was elevated slowly, fewer flies reacted and for those flies that did, the temperature threshold was higher.

To identify the molecular mechanisms behind this phenomenon, the research team identified thermosensory neurons in the brain responsible for sensing the rate of temperature change. When there is a rapid temperature rise, fruit flies would want to protect their brain and so they undergo the writhing response. The response itself was dependent on a transient receptor potential (TRP) channel, TRPA1. The activation of TRPA1 was highly dependent on the rate of temperature change and not the temperature itself. If the temperature change was rapid, TRPA1 turned on quickly to excite the thermosensory brain neurons. And if the temperature change was gradual, TRPA1 was less active. The purpose of this mechanism is to use low-threshold brain sensors to monitor rapid temperature rise as a protective signal to trigger behaviors that would allow quick escape before the brain temperature rises to noxious levels.

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TRPA1 mediates sensation of the rate of temperature change in Drosophila larvae (October 2016)

What feral chickens teach us about evolution

feralisation, domestication, chickens and evolution

Humans know a lot about domesticating animals but not much is known about its reverse process – feralisation. By investigating feral chickens in Hawaii, researchers are attempting to learn what happens during the evolution of a species. Two tropical storms in Hawaii, 3 decades ago, contributed to the release of domesticated chickens to the wild. The domesticated chickens interbred with the existing wild red jungle fowl and produced hybrid offspring with inherited genetic material from both, wild and domesticated parents. Since sexual selection is important for propagation of a species, genes that controlled traits that made a chicken attractive became affected when that chicken returned to the wild.

Domesticated chickens started off with large combs but eventually the combs became smaller in chickens in the wild. During feralisation, the chickens' egg production and brooding behavior were also altered. Researchers determined which regions of the genetic material were altered during feralisation. Then they studied these regions in the hybrid chicken population and correlated the chickens' behavior and appearance to the level of expression of specific genes. In some ways the researchers wanted to see whether the feralisation process is similar to domestication but in the opposite direction. The findings showed that it was not the case. By and large, separate genes were affected when domesticated chickens returned to the wild.

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Feralisation targets different genomic loci to domestication in the chicken (September 2016)

Celebrating self-devouring cells

autophagy, 2016 Nobel prize in physiology or medicine, Yoshinori Oshumi

The 2016 Nobel Prize in Physiology or Medicine has been awarded to Dr. Yoshinori Ohsumi who discovered and elucidated mechanisms underlying autophagy. Autophagy is a crucial process in which cells end up consuming themselves. This process serves multiple functions. During starvation, cells break down proteins and non essential components and reuse them for energy. Cells also use autophagy to eliminate viruses and bacteria and package them for recycling. Disruptions in autophagy are also known to influence aging. And while autophagy was linked to all these processes, little was known about the exact molecular mechanisms of autophagy, what genes were involved or its role in disease development until Dr. Ohsumi began studying this fascinating process in Saccharomyces cerevisiae.

The Nobel Prize for Dr. Ohsumi was well deserved, as acclaimed by prominent experts in the field. The autophagy genes and the metabolic pathways that were discovered by Dr. Ohsumi are present not just in yeast but also in higher organisms, including humans. And mutations in those genes are known to cause disease. Insights provided by the molecular characterization of autophagy have been instrumental in advancing our understanding of this process and have led to a new paradigm in understanding how cells recycle their contents. GenScript congratulates Dr. Ohsumi on this significant achievement and salutes his hard work and curiosity that resulted in this remarkable discovery.

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Autophagy in yeast demonstrated with proteinase-deficient mutants and conditions for its induction (October 1992)

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Isolation and characterization of autophagy-defective mutants of Saccharomyces cerevisiae (October 1993)

Mouse pups born without mothers

parthenogenotes, mitotic reprogramming

Eggs can develop into an embryo without fertilization, a process simply defined as parthenogenesis. Parthenogenesis occurs naturally in many plants, some invertebrate animal species and a few vertebrates. Parthenogenesis has also been induced artificially in a few species including fish and amphibians. The problem with this approach is that the resulting embryos, called parthenogenotes, die after a few days because key developmental processes requiring input from the male gamete (sperm) do not take place.

Researchers have now developed a method of injecting developmentally-incompetent, mouse haploid embryos with sperm which results in healthy offspring with success rate up to 24%. The mouse pups born form this technique seem normal but their DNA started out with different epigenetics marks when compared with mouse pups born as a result of normal fertilization. This finding suggests that different epigenetic pathways or kinetics can establish totipotency. This discovery has ethical implications given the dialog around using human parthenogenotes as a source of embryonic stem cells since they were considered unviable. Other implications on human fertility treatment and breeding of endangered species are possible.

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Mice produced by mitotic reprogramming of sperm injected into haploid parthenogenotes (September 2016)

Aim at fat, shoot at cancer

fatty acid synthesis suppression

Continuous fatty acid synthesis is a common feature of cancer and it is essential in fueling the biosynthetic needs of a growing tumor. This process is regulated by a rate-limiting enzyme called acetyl-CoA carboxylase (ACC). In a recent study, researchers found a way to block this critical process which can help suppress tumor growth. The premise being that, since cancer cells are more dependent on fatty acid synthesis when compared to healthy cells, there might be subsets of cancers sensitive to a drug that could interfere with this metabolic process.

This study describes the ability of a small-molecule allosteric inhibitor called "ND-646" to inhibit ACC enzymes (ACC1 and ACC2) which prevents ACC subunit dimerization to suppress fatty acid synthesis in vitro and in vivo. This finding cements ACC's role in tumor growth and validates the concept of targeting fatty acid synthesis as a novel approach to fight cancer.

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Inhibition of acetyl-CoA carboxylase suppresses fatty acid synthesis and tumor growth of non-small-cell lung cancer in preclinical models (October 2016)

Coffee addiction? Blame the gene, not the bean

caffeine addiction, caffeine metabolism gene, PDSS2 gene

Coffee is one of the most consumed beverages in the world. As per a 2015 Gallup poll, about 64% of American adults drink at least one cup of coffee a day. Despite such popularity, the genetics of caffeine addiction are not fully understood. Using a genome-wide association study, researchers highlight a novel gene involved in caffeine metabolism. They did this by studying two Italian populations using additive, recessive and dominant models for analysis and uncovered a significant association in the PDSS2 gene [Prenyl (Decaprenyl) Diphosphate Synthase, Subunit 2]. This gene has been shown to negatively regulate the expression of caffeine metabolism genes and was thus linked to coffee consumption. The more active that PDSS2 was, the less coffee people drank.

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Non-additive genome-wide association scan reveals a new gene associated with habitual coffee consumption (August 2016)

Vaccine against flesh-eating bacteria possible

Group A streptococcus, GAS, GAS protein hypervariability

Group A Streptococcus (GAS) is a leading cause of worldwide morbidity and mortality yet no vaccine exists against its infection. GAS is known to cause a range of infections ranging from minor illnesses to deadly diseases, that include the toxic shock syndrome and necrotizing fasciitis, also known as the "flesh-eating disease". The biggest bottleneck to vaccine development is the hyper variability of the M protein antigen (major antigen found on the bacterium). There are known to be more than 200 different types of M proteins. While antibodies do recognize M protein hyper variable regions on the bacterium, they do not offer adequate protection.

A recent discovery within the GAS protein hyper variability region has opened up new possibilities for rational therapies and novel vaccine design. Researchers found that the human C4b-binding protein (C4BP), a molecule recruited to the GAS surface, interacts with nearly 90% M protein hyper variable regions. Structure determination revealed four, sequence-diverse M proteins in complex with C4BP with conserved sequence patterns even within the hyper variability. These common sequence patterns are critical in the recruitment of C4BP to the bacterial surface. The idea would be to have antibodies do the same thing as C4BP – recognize many different M protein types for maximum protection.

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Conserved patterns hidden within group A Streptococcus M protein hypervariability recognize human C4b-binding protein (September 2016)

New photosynthesis discovery in wheat

C4 photosynthesis, C3 photosynthesis, photosynthesis in wheat

Photosynthesis is a complex process that involves the synthesis of organic food materials. It takes place in two stages – the light reaction and the dark reaction. In dark reaction, two types of processes can occur – the Calvin cycle or C3 cycle and the Hatch-Slack cycle or C4 cycle. The C4 photosynthetic pathway allows for more efficient CO2 capture by plants where effective carbon supply may be limiting, explaining the high growth rates of C4 plants such as maize. Important crops such as wheat and rice are known to be C3 plants and there has been an ongoing effort to engineer these plants to use the C4 pathway. But it turns out that there maybe no need to "engineer" the C4 pathway in wheat. Nature may have done it already.

Given a recent discovery that turns plant biology on its head, a research team has published a paper showing evidence that C4 photosynthesis occurs in wheat seeds but is absent in the wheat plant leaves. Genes specific for C4 photosynthesis were identified in the wheat genome and found to be preferentially expressed in the photosynthetic pericarp tissue (cross- and tube-cell layers) of the wheat caryopsis.

Wheat crop covers more of the planet than any other crop, so the ramifications of this discovery are enormous. Among other things, this discovery may allow researchers to grow faster-growing, better-yielding wheat crops in areas where wheat currently cannot be grown, leading to additional food security.

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New evidence for grain specific C4 photosynthesis in wheat (August 2016)

Why females usually care more

parental care, female parent, parental investment, sex-role divergence

Across species, females usually tend to be more caring parents. But why exactly is not known. Sex-role evolution theory tries to explain the origin and direction of female-male differences using anisogamy (difference in size of gametes/sex cells), that is, the variation in gamete size leads to large variations in the care offered by the parent. For example, in the case of an egg and sperm, since an egg is a much larger parental investment, the female should be more caring. But there is no propensity for females to care more because of this larger investment. They find that if the only initial difference between sexes is anisogamy, evolution does not favor females becoming more attentive parents.

Using mathematical models, researchers explain this interesting phenomenon. They suggest that individuals benefit less from caring when they face stronger sexual selection and/or a lower certainty of parentage. With more sperms than eggs, it is not certain for a male to be sure that he is the father and that's also why males initially care less than females. The researchers also propose that investment in being sexually attractive might trade off with the ability to provide efficient parental care. In order to balance this, evolution favors more care by the initially more-caring sex. This model confirms that small initial differences in parental investment increase due to positive evolutionary feedback.

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Coevolution of parental investment and sexually selected traits drives sex-role divergence (August 2016)

Why humans are smart

human brain, primate brain, prefrontal cortex, cortical neurons

Human brains are enormous, relatively speaking. An average human brain is 7 times larger than it should be, given the size of our bodies. The human brain uses up 25% of all the energy the body requires each day. In summary, the human brain is awesome. But why exactly is it awesome? For a long time it was believed that the relative size of the prefrontal cortex was the most distinctive feature between human brain and primate brains. But a new study shows that's not the case.

By comparing the brains of primates of varying sizes alongside the human brain, researchers found that the prefrontal region of human and primates holds about 8% cortical neurons. They also found that the volumes of human prefrontal gray and white matter matched the expected volumes for the number of neurons and other cells in the white matter when compared to other primates. And thus the most distinctive feature of the human prefrontal cortex was found, not in its relative volume, but in its absolute number of neurons. Humans have 16 billion compared with 9 billion in gorillas and orangutans and 6-7 billion in chimpanzees.

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No relative expansion of the number of prefrontal neurons in primate and human evolution (August 2016)

Novel finding shows how tumor cells metastasize

Metastasis, Endothelial cell necroptosis, Death Receptor 6, DR6

Metastasis is the leading cause of cancer-related deaths in humans and yet the exact molecular mechanisms of this phenomenon were a mystery. Researchers have now shown for the first time that tumor-cell-induced necroptosis of endothelial cells is what promotes metastasis. The researchers first observed this in cell cultures and were later able to show this effect in mice studies. The team also found that endothelial cells themselves give the signal for their own death. The cells do this by involving a molecule called Death Receptor 6 (DR6). When a cancer cell comes in contact with DR6, Amyloid Precursor Protein (APP) activates it. This event marks the start of the cancer cells' attack on the vascular wall which ultimately culminates in necroptosis of the endothelial cells.

The researchers showed that in genetically modified animals in which DR6 was disabled, less necroptosis and less metastasis occurred. Blocking DR6 or APP also achieved similar outcomes. The discovery of these mechanisms suggest endothelial DR6-mediated necroptotic signaling pathways as promising targets for anti-metastatic therapies.

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Tumour-cell-induced endothelial cell necroptosis via death receptor 6 promotes metastasis (August 2016)

Stunning 3D video representation shows architecture behind neurotransmission

Trans-synaptic nanocolumn, neurotransmitter release, synaptic efficiency

That neurons communicate through synaptic transmission has been known for a long time but how exactly was not clear. Researchers have now shown that a trans-synaptic nanocolumn is critical in alignment of neurotransmitter release to receptors. Key proteins are organized precisely across the gap between neurons. The incredible precision of proteins almost forms a column that stretches between the two neurons. This proximity optimizes neurotransmission efficiency.

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To visualize structures at the synapse level, researchers used single-molecule imaging technology which can locate and track the movement of individual protein molecules within a single synapse. With this approach the scientists identified the precise pattern of neurotransmission in cultured rat hippocampal neurons while revealing the core architectural structure of the synapse. This structure would explain what makes synapses so efficient yet so susceptible to disruption in diseased states. This renewed understanding of synaptic architecture could lead to a better understanding of brain-related conditions such as schizophrenia, Alzheimer's and even depression.

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A trans-synaptic nanocolumn aligns neurotransmitter release to receptors (August 2016)

DNA methylation reveals menopause accelerates aging

epigenetic clock, DNA methylation, menopause, aging

Scientists have debated for decades whether menopause causes aging or vice versa. Using an "epigenetic clock", researchers have now settled the debate once and for all - menopause makes you age faster. To show this, the researchers tracked methylation in DNA samples from more than 3100 women. They carried out an epigenetic clock analysis of blood, saliva and buccal epithelium using data from four large studies. They found that increased epigenetic age acceleration in the blood was significantly associated with early onset of menopause, bilateral oophorectomy (surgical removal of ovaries) and a longer time since menopause.

On the contrary, epigenetic age acceleration in buccal epithelium and saliva did not relate to age at menopause however, a higher epigenetic age in saliva was found in women who underwent bilateral oophorectomy while a lower epigenetic age in buccal epithelium was found in women who underwent menopausal hormone therapy. The younger a woman is when she enters menopause the faster her blood ages. This finding is important because a woman's blood can reflect what's happening in other parts of her body and it could have implications for disease risk and subsequent therapeutic interventions.

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Menopause accelerates biological aging (August 2016)

How poor learners can be converted to good learners

Cinnamon, hippocampal plasticity, memory improvement

Not much is known about the neurological mechanisms that cause someone to be a poor learner. As such, it is not clear how one can improve performance in poor learners. In a startling discovery, researchers successfully used cinnamon to reverse biochemical, cellular and anatomical changes in the brains of mice that were poor learners.

The researchers used a Barnes maze to identify mice with good and bad learning abilities. A Barnes maze is a standard circular maze, consisting of 20 round holes around its circumference, used in psychological laboratory experiments to measure spatial learning and memory. After 2 days of training the mice were examined for their ability to find the target hole. The mice were tested again after a month of cinnamon feeding. The researchers found that the poor-learning mice, after a month of cinnamon consumption, had improved memory and learning at a level found in the good-learning mice.

Researchers found that the hippocampus of poor learners has less cAMP response element-binding protein (CREB, a protein involved in memory and learning) and more GABRA5 (a protein that generates tonic inhibitory conductance in the brain) than good learners. Cinnamon in the body is metabolized into sodium benzoate which is known to activate CREB and reduce GABRA5 and stimulate the plasticity of hippocampal neurons, thereby improving memory and learning. If these results can be replicated in humans, there are enormous implications for learning and development.

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Cinnamon Converts Poor Learning Mice to Good Learners: Implications for Memory Improvement (June 2016)

Startling discovery: immune system dictates behavior

Immune system and behavior, Interferon gamma, neuronal connectivity and social behavior

Immune dysfunction is normally related with a variety of neurological disorders. Some findings have shown that peripheral immunity may influence neuron function although the exact mechanisms were unknown. In a startling discovery that raises fundamental questions about human personality, researchers have now shown that the immune system is in direct control of social behaviors. Mice deficient in adaptive immunity exhibited social deficits and hyper-connectivity of fronto-cortical brain regions. Associations between rodent brain transcriptomes and cellular transcriptomes in response to T-cell derived cytokines indicate a strong interaction between social behavior and Interferon-γ-driven response.

Analysis of the transcriptomes from different organisms also revealed that the Interferon-γ-signaling pathway could mediate an evolutionary link between social behavior and an efficient response against pathogen invasion. In other words, some of our behavior traits may have evolved because of our immune response to pathogens and so our personality may also be dictated by the immune system. Such an arrangement would be evolutionarily crucial because it would allow us to engage in social behaviors that were necessary for survival while developing ways for our immune system to fight diseases that accompanied such behaviors. These findings could have enormous implications in our understanding and the treatment of neurological conditions such as attention deficit hyperactivity disorder (ADHD), autism-spectrum disorders and schizophrenia.

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Unexpected role of interferon-γ in regulating neuronal connectivity and social behaviour (July 2016)

Vaccine protection against Zika virus accomplished

ZIKA vaccine, ZIKV vaccine, Brazilian ZIKV

Zika virus (ZIKV) has been responsible for an unprecedented epidemic in recent times, in Brazil and the Americas. ZIKV has been associated with severe developmental abnormalities such as fetal microcephaly and other birth defects in humans. While the rapid development of a ZIKV vaccine has been a global initiative with high priority, there was no real breakthrough, until now.

In a massive, collaborative effort by researchers at the Harvard Medical School, Walter Reed Army Institute, MGH, MIT and the University of São Paulo, it has been shown that a single immunization of a plasmid DNA vaccine or a purified inactivated virus vaccine provides complete protection in susceptible mice against challenge from ZIKV outbreak Brazilian strain. Four weeks post-vaccination, mice were exposed to the Brazilian strain of ZIKV, which had previously been shown to cause defects in fetal mice similar to those observed in ZIKV infected humans. All vaccinated mice were protected from ZIKV replication. Other mice were vaccinated and exposed to infection eight weeks later and were also protected from infection. The findings indicate that the development of a human vaccine for ZIKV is highly feasible. Clinical trials to test these vaccine candidates are expected to begin later this year.

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Vaccine protection against Zika virus from Brazil (June 2016)

Revolutionizing on-demand diagnosis for malaria and cancer

point-of-care diagnostics, on-demand diagnosis, diagnosis at finger tips

Current analytical methods are insufficient in meeting demands of patient-friendly testing and increased reliability of results. To address this challenge, scientists have successfully demonstrated a two-point, separation on-demand diagnostic strategy for the detection of malaria and cancer antigens, using a paper-based mass spectrometry immunoassay platform. The diagnostic (paper strip) is coated with small synthetic chemical probes that carry a positive charge. These ionic probes allow highly sensitive detection using a handheld mass spectrometer.

The idea is so simple that in theory a patient could apply a drop of blood to a piece of paper at home and mail it to the lab. He/she would have to see the doctor only if a test result comes positive. Besides the convenience factor, another advantage of this approach was that the tests results were accurate even a month after blood sample was collected. This is huge because even people living in remote locations could utilize this testing method in case they needed to ship samples over long distances, which might take several days. This idea has the potential to revolutionize healthcare around the globe. It is a very inexpensive way to get cheap diagnosis for life threatening diseases like malaria in rural Africa and other poor nations where the disease takes thousands of lives each year. Moreover this test can in principle be tailored to detect any diseases for which the body produces antibodies, including cancers of the ovary and large intestine.

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Mass Spectrometry for Paper-Based Immunoassays: Toward On-Demand Diagnosis (May 2016)

The secret behind perfect coffee revealed

perfect coffee, coffee bean, chilling coffee bean

Coffee preparation starts by extracting a complex array of organic molecules from the roasted bean. Scientists have now shown that brewing great coffee starts with simply chilling the bean before the extraction process. The team behind this study looked at the effect of grinding beans at different temperatures. This was done by grinding liquid nitrogen, dry ice, freezer and room temperature coffee respectively. It was discovered that the colder the beans the finer and more uniform the particles were from the grind. This factor is important because a fine and uniform coffee grind allows for better extraction of coffee flavor while causing less variation therein. The cooler temperatures basically allows maximizing the bean surface area and utilize more of the coffee. And thus resulting in a tastier brew in less time and with relatively lesser amount of beans.

These finding have major implications for the coffee industry. Coffee is the second most valuable legally traded commodity (the first being oil). The retail value of the US coffee market alone was estimated to be $48B in 2015. Given this kind of popularity, it is critical for coffee producers to evaluate harvest, storage and shipping temperatures. And for the sellers and consumers, these findings would allow them to brew and taste more flavorful coffee.

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The effect of bean origin and temperature on grinding roasted coffee (Apr 2016)

Why birds are so smart

bird brain, avian intelligence, neurons in bird brain

Birds are remarkably intelligent despite their small brain size. Researchers have found out why by investigating the cellular composition of brains of 28 avian species. Using isotropic fractionator to determine the numbers of neurons in specific brain regions, the researchers showed that the brains of parrots and songbirds contained on average, double the number of neurons as primate brains of the same mass. This indicates that avian brains have higher neuron packing densities than mammalian brains. Additionally, corvids (crow family) and parrots have forebrain neuron counts equal to or greater than primates with much larger brains. These large numbers of neurons in the forebrain, concentrated in high densities, substantially contribute to the neural basis of avian intelligence.

Related: see 007 crow's remarkable 8-piece-puzzle solving skill

   

This study answers a mystery that has puzzled scientists for a long time now, which is, how can birds with their small brains perform complicated cognitive behaviors? And while the relationship between intelligence, neuron count and neuron density is not yet firmly established from this study, the researchers believe that bird brains with same or greater forebrain neuron counts than primates, can potentially provide the birds with much higher cognitive power per pound, than mammals. Given these new findings, the derisive term "bird brain" should now be considered a compliment!

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Birds have primate-like numbers of neurons in the forebrain (Jun 2016)

Utilizing genetic variants for therapeutic target validation

genomic screening, therapeutic target validation

FDA has indicated that new anti-diabetic medications should not be associated with an unacceptable risk of developing cardiovascular complications. Scientists have reported a novel genomic approach that can address this concern. The approach can systematically demonstrate at an early stage whether a drug will put patient at risk of developing heart disease or cancer. The technique involves identifying genetic variants that mimic a drug's action on its intended target and then examining large patient cohorts to see whether these genetic variants are associated with adverse health risks such as cardiovascular diseases or certain cancers.

The researchers looked at 6 genes that encode targets of various drugs for type 2 diabetes or obesity. They wanted to see if there were any genetic variations that were linked to traits like obesity or high blood glucose levels. Using cohorts totaling >50,000 individuals researchers landed on a gene variant of GLP1R (glucagon-like peptide-1 receptor) which is the target for certain drugs used to treat high blood glucose levels. The researchers then compared this variant against outcomes such as heart disease. Rather than cause any additional risk, in >200,000 individuals the GLP1R variant turned out to confer protection against coronary heart disease. This study will help clinicians determine early whether certain drugs will put patients at risk of developing certain diseases.

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A genomic approach to therapeutic target validation identifies a glucose-lowering GLP1R variant protective for coronary heart disease (Jun 2016)

Microfluidics technology demonstrates how tumor cells metastasize

tumor cell metastasis, microfluidics technology and tumor cells

Metastasis is responsible for 90% cancer-related deaths and is primarily driven by circulating tumor cells in the blood stream. It was long assumed that circulating tumor cell clusters (CTC clusters) were too large to pass through narrow blood vessels to reach distant organs during metastasis. In a recent PNAS publication, scientists report the use of microfluidics devices to demonstrate that CTC clusters rapidly organized into a single file cellular chain in order to slide through capillaries.

   

The researchers reached this assumption by examining CTC in microfluidic devices, computational simulations and through animal studies. The researchers observed that over 90% of CTC containing up to 20 cells successfully traversed 5-10μm constrictions even in whole blood. To do so, clusters rapidly and reversibly reorganized into single-file geometries that reduced their hydrodynamic resistance. These studies demonstrate hitherto unidentified cell behavior and may be crucial in devising new strategies for reducing the incidence of metastasis in cancer patients.

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Clusters of circulating tumor cells traverse capillary-sized vessels (April 2016)

Achilles heel of bacteria discovered

Achilles heel of bacteria discovered

Bacterial biofilms pose a significant medical challenge because they are difficult to treat using standard therapeutic approaches. Given that biofilms shield bacteria from antibiotics, they are a major barrier to antibiotic effectiveness. A recent study published in Science indicates that the very enzymes that Pseudomonas aeruginosa uses to create biofilms can also be used to disrupt biofilm formation. An important component of biofilm formation in P. aeruginosa is the synthesis of exopolysaccharides Pel and Psl which are involved in maintaining the structural integrity of the biofilm and protecting bacteria from antimicrobials. The research behind this finding discovered that the enzymes (glycoside hydrolases) that the bacteria use for biofilm formation can degrade the same polymers that they build. Evaluating these enzymes as potential therapeutics, the team demonstrated that these enzymes selectively target and degrade the exopolysaccharide component of the biofilm matrix.

Synthetic versions of these enzymes applied to P. aeruginosa cultures inhibited biofilm formation and reduced biofilm mass by 58%-94%. Human lung cells cultured in the presence of these enzymes suffered no harm indicating that the enzymes would not damage human tissues. However, animal testing will be required to determine the safety and efficacy of this strategy inside the body. This work illustrates the feasibility and benefit of using bacterial exopolysaccharide biosynthetic glycoside hydrolases to develop novel anti-biofilm therapeutics.

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Exopolysaccharide biosynthetic glycoside hydrolases can be utilized to disrupt and prevent Pseudomonas aeruginosa biofilms (May 2016)

Beyond BPA - This chemical in plastic maybe causing obesity in babies

BBP, Benzyl butyl phthalate, obesity in babies

A new study indicates that a chemical routinely used in the food manufacturing industry can increase fat deposits in the body even before birth. Called Benzyl Butyl Phthalate (BBP), it is a chemical that belongs to the phthalate family. BBP is used in many consumer products but human exposure primarily comes from food consumption. BBP is routinely used in the food manufacturing process, particularly in conveyor belts and plastic fittings on machines used to process various packaged foods. Food becomes contaminated with BBP due to leaching from the plastic.

Using animal stem cells, researchers demonstrated that cell lines exposed to BBP showed higher levels of lipid accumulation and adipogenesis in a dose-dependent manner. And because stem cells are undifferentiated cells that can become highly specialized cell types, the epigenetic changes observed in stem cells could impact not just an adult but also the fetus exposed to BBP. Phthalates are termed "endocrine disruptors" and they have been associated with obesity in other studies. This was the first time that the molecular mechanism by which BBP causes fat accumulation and programs the stem cell to become obese by tipping the epigenetic balance was demonstrated.

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Benzyl butyl phthalate induces epigenetic stress to enhance adipogenesis in mesenchymal stem cells (May 2016)

Bacterial survival strategy - enemy's enemy is a friend

mutualism, bacterial resistance

A new study from MIT suggests that bacteria can form drug-resistant communities based on a dynamic phenomenon called mutualism. The enzymatic deactivation of antibiotics by resistant bacteria is part of this cooperative behavior that allows resistant bacteria to protect sensitive bacteria from antibiotics. Such cooperation between microbes can enable microbial communities to survive in harsh environments.

To demonstrate this experimentally the researchers co-cultured two strains of Escherichia coli in the presence of two antibiotics (ampicillin and chloramphenicol). One strain was resistant to ampicillin and the other resistant to chloramphenicol. Under these conditions, the two strains formed cross-protection mutualism, protecting each other so that the co-culture could survive in the presence of an antibiotic combination that would inhibit growth of either strain alone. The researchers also observed large oscillations in the relative abundance of the two strains upon diluting the coculture. While at lower concentrations this cross-protective mutualism ensured long-term survival, at higher concentrations the oscillations destabilized the population leading to collapse. Understanding how bacterial populations survive antibiotic exposure is important clinically and it may have implications on antibiotic-combination administration in combating multi-drug resistant bacteria.

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Oscillatory dynamics in a bacterial cross-protection mutualism (May 2016)

Chemists discover new method to address food supply challenge

natural fertilizer, novel method to create fertilizer, addressing food supply challenge

Nitrogen is critical for plant growth but currently only two methods exist which can break down nitrogen bonds that allows conversion to ammonia, a form that plants can absorb. One is a natural, bacterial process that mankind has utilized since ages for agriculture. The other is the classical Haber-Bösch process which is an artificial nitrogen fixation process and the main industrial procedure for the production of ammonia.

In a recent Science publication, researchers report a light-driven nanoparticle-protein enzymatic reaction that can generate ammonia to create fertilizer. The study indicates that photochemical energy from sunlight or artificial light, catalyzed by nitrogenase enzyme, can power the reaction to replace ATP hyrdolysis. The reaction is typically used to convert nitrogen found in the air, to ammonia, the key ingredient of commercially produced fertilizers.

This light-driven process has the potential to revolutionize agriculture by reducing dependence on fossil fuels and relieving Haber-Bösch's heavy carbon footprint. Such energy-efficient production of ammonia holds promise not just for food production, but also for development of technologies that enable the use of environmentally friendly fuels.

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Light-driven dinitrogen reduction catalyzed by a CdS:nitrogenase MoFe protein biohybrid (Apr 2016)

Novel Trojan horse strategy to fight asthma and other allergies

PLG, PLG nanoparticles, Trojan horse strategy

In a recent PNAS paper, researchers present a novel technology that has the potential to safely and effectively cure patients with life-threatening allergies. The nanoparticle technology involves coating a FDA-approved biopolymer with disease-triggering allergen and injecting it into a patient's bloodstream to achieve the desired therapeutic effect. Made from a molecule called PLG [poly(lactic-co-glycolic acid)], these nanoparticles can be used to create tolerance in the immune system for the treatment of allergic conditions.

A mouse model of allergy was developed to test this technology. The allergen (egg protein) was administered into the lungs of these mice that were pretreated to be allergic to the egg protein. The mice had circulating antibodies in their blood against the allergen. Upon re-exposure to the egg protein, the mouse immune system triggered an asthma-like response. But after treatment with the nanoparticle, these mice no longer had an allergic response to the egg protein - the rationale was that the immune system saw the egg protein as innocuous debris. At the molecular level, the nanoparticle and its allergen cargo are consumed by a macrophage which presents the allergen to the immune system in a harmless fashion. The immune system then shuts down attack on the antigen.

A second advantage of this approach is that it helps creates a normal, balanced immune system by increasing the number of regulatory T cells - the immune cells that are critical for recognizing the airway allergens as normal. This method turns off the dangerous Th2 T cell that triggers allergy while expanding the population of the good, calming regulatory T cells. In theory, this technology can be used for universal treatment against a variety of allergens. Depending upon the allergy, one can load the nanoparticle with the relevant allergen to achieve the therapeutic effect.

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Biodegradable antigen-associated PLG nanoparticles tolerize Th2-mediated allergic airway inflammation pre- and postsensitization (Mar 2016)

Potent new anti-HIV antibodies identified - a new paradigm for HIV therapy

anti-HIV antibodies, broadly neutralizing antibodies, HCDR3 loops

It has been known for quite some time that human immune system is capable of producing antibodies that can neutralize HIV. However, most patients do not elicit these broadly neutralizing antibodies upon HIV infection and even when they do it takes a long time for full response to kick in and induction of antibodies with unusual features, such as long heavy chain complementarity-determining regions 3 (HCDR3) loops. Researchers now have isolated antibodies with a loop-like structure that binds tightly to HIV and neutralizes it – even in people who were never infected with HIV.

Using a special computer program called "Rosetta", the researchers identified the amino acids that bind to HIV and used that information to optimize those specific residues to simulate a vaccination event. To do this they interrogated the structural properties of long Ab HCDR3 loops in HIV-1-naïve donors, while looking for structured HCDR3s similar to those of the HIV-1 bnAb PG9. They fused these sequences onto an antibody called PG9 which is known to be a broad neutralizer of the HIV. In lab tests these engineered antibodies were found to effectively neutralize HIV. These data suggest that HIV-naïve individuals contain B cells that encode HCDR3 loops that can neutralize HIV when presented on a PG9 antibody. These findings reported in the PNAS present a new paradigm for utilizing structure-based vaccine design efforts.

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Long antibody HCDR3s from HIV-naïve donors presented on a PG9 neutralizing antibody background mediate HIV neutralization (Apr 2016)

How to avoid peanut allergy

peanut allergy, food allergy

Food allergies are on the rise and it isn't clear why. According to a 2013 study by the CDC, food allergies among children increased approximately 50% between 1997 and 2011. Among all food allergies, peanut allergy in children is particularly on the rise and it can be life-threatening, for which prevention and treatment is critical. A report in the New England Journal of Medicine suggests that early introduction of peanuts to infant diet significantly reduced the risk of peanut allergy until age 6, even after a 12-month period of peanut avoidance.

The study was a follow on to the LEAP (Learning Early About Peanut Allergy) study, a clinical trial investigating how to best prevent peanut allergy. The study had found that the majority of infants at high-risk of developing peanut allergy are protected from the allergy at age 5 if they eat peanut frequently and as early as in the first year of life. One of the current study's objectives was to see whether those infants that had consumed peanut in the LEAP study continued to remain protected if they stopped peanut consumption for an extended period of time. The researchers found that infants indeed were protected from peanut allergy even when peanut is not consumed for 12 months. In summary, peanut consumption in the first year of life not only prevents peanut allergy early in life but also prevent its development later on, even after consumption has been stopped for a prolonged period of time and resumed again. The researchers assert that more investigation will have to be carried out to better understand the molecular mechanisms behind the development and prevention of peanut allergies and how these findings could apply to other food-related allergies.

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Effect of Avoidance on Peanut Allergy after Early Peanut Consumption (Mar 2016)

Human genome not entirely human

human genome, HERV insertions, Human Endogenous Retrovirus insertions

A new discovery reported in the PNAS suggests that human DNA is less human than previously thought. By examining >2500 sequenced genomes, scientists discovered 19 previously unidentified Human Endogenous Retrovirus (HERV) insertions. In fact it is suggested that about 8% of what we believe is human DNA was actually handed down from viruses over generations. One stretch of DNA found in 50 out of 2500 sequenced genomes, contains the genetic recipe for an intact provirus. Whether the provirus can replicate or not is not known yet but related studies of ancient virus DNA in human sequences suggests that it can impact humans. The provirus was found on the X chromosome has been dubbed Xq21 and it's only the second intact provirus found in human genome. The provirus seems capable of making infectious virus and it could be remnant of a viral epidemic that took place long ago.

In certain instances the HERV sequences are used by the human body to serve a useful purpose. One example is the role of HERV-W syncytin-1 in maintaining human pregnancy. Syncytin was found to be part of the trophoblast cells that surround fetal cells during pregnancy. This layer of cells around the developing fetus protects it from toxins in the mother's blood. The finding provides important information for understanding how retroviruses and humans have evolved together. The results from the current study provide a basis for future studies of HERV evolution and its implication for disease.

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Discovery of unfixed endogenous retrovirus insertions in diverse human populations (Mar 2016)

Novel technology could revolutionize cancer immunotherapy

Microneedle patch, anti-PD1, cancer immunotherapy

Cancer immunotherapy using anti-PD1 antibody has shown tremendous promise but few challenges remain. Firstly, since the anti-PD1 antibodies are injected directly into the bloodstream, they cannot target the tumor site effectively. Also, the overdose of antibodies can cause side effects including the development of autoimmune conditions. To address some of these challenges a group of researchers developed an innovative, biodegradable microneedle patch for the sustained delivery of anti-PD1 in a physiologically controllable manner.

The microneedle is made from biocompatible hyaluronic acid integrated with pH-sensitive dextran nanoparticles that encapsulate anti-PD1 antibodies and the enzyme glucose oxidase. When the patch is applied to a melanoma, blood enters the microneedles and the glucose in the blood stream reacts with the glucose oxidase to produce gluconic acid. The acidic environment causes degradation of the nanoparticles and release of anti-PD1 antibodies into the tumor. This method creates a localized, steady and sustained release of antibodies directly into the tumor microenvironment. The researchers tested this microneedle patch in a melanoma mouse model and found that a single administration of the patch induced robust immune response compared to microneedle without degradation trigger or intratumoral injection of the anti-PD1 antibody with the same dose. The researchers plan on using this administration strategy with other immunomodulators to achieve combination therapy for enhanced antitumor activity.

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Enhanced Cancer Immunotherapy by Microneedle Patch-Assisted Delivery of Anti-PD1 Antibody (Mar 2016)

Accelerating fat burning by blocking a protein function

Fat burning, Gq signaling, brown fat, combating obesity

An international team of scientists has discovered a protein switch in the fat cells of mice and humans, using which excess fat deposits can be simply melted away. Called Gq protein, it is a family of proteins that links to the GPCRs. Blocking Gq signaling with an inhibitor enhanced the differentiation of human and mouse brown fat cells. In contrast, activation of Gq signaling abrogated brown fat maturation. Since brown fat dissipates nutritional energy as heat and correlates with leanness in human adults, the inhibition of Gq signaling is important and maybe a novel therapeutic approach to combat obesity.

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The Gq signalling pathway inhibits brown and beige adipose tissue (Mar 2016)

Fighting deadly antibiotic resistance with these novel compounds

MRSA, antibiotic resistance, tarocin

The widespread emergence of Methicillin-resistant Staphylococcus aureus (MRSA) has eroded the efficacy of current antibiotics. Researchers reported in Science Translational Medicine that certain pathway-specific inhibitory molecules can make drug-resistant bacteria susceptible to antibiotics again. Using a Staphylococcus aureus phenotypic screening strategy, the researchers identified these early-stage pathway-specific inhibitors called Tarocins. Tarocins are inhibitors of wall teichoic acid biosynthesis and are predicted to be chemically synergistic with β-lactams, a family of antibiotics which includes penicillin and methicillin.

Using genetic and biochemical techniques the researchers demonstrated that tarocins inhibited the first step in wall teichoic acid biosynthesis. And while tarocins, individually did not possess intrinsic bioactivity, they exhibited potent antibacterial property when used in combination with broad spectrum β-lactam antibiotics against MRSA, both, in clinical isolates and in a mouse model of MRSA infection. This discovery could provide new arsenal in the fight against deadly, antibiotic-resistant bacterial infections.

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TarO-specific inhibitors of wall teichoic acid biosynthesis restore β-lactam efficacy against methicillin-resistant staphylococci (Mar 2016)

Watch out dads – new study finds that father's stress may impact son's health

paternal psychological stress, father to son stress

Researchers reported in Cell Metabolism that male mice exposed to repeated psychological stress developed high blood glucose levels. But that was not all. Their unstressed male offspring also developed high blood glucose concentrations and hepatic gluconeogenesis. While these effects were also noticed in female offspring from stressed fathers, they were not as significant as those in male stress offspring.

Mechanistically, alteration in DNA methylation and histone modification, as well as changed expression of small non-coding RNAs has been reported to mediate this effect. The current study suggests that paternal stress modifies an epigenetic signature and downregulates expression of a specific micro RNA that targets the 3'UTR of Phosphoenolpyruvate carboxykinase (PEPCK), to cause this effect. PEPCK is an enzyme involved in the metabolic pathway of gluconeogenesis and hence the effect. Such paternal-stress-induced metabolic effects in offspring could be largely reversed by administering the drug RU486.

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Paternal Psychological Stress Reprograms Hepatic Gluconeogenesis in Offspring (Feb 2016)

Lack of certain gut microbes linked to childhood malnutrition

gut microbes and malnutrition, Lactobacillus plantarum

Malnutrition affects millions of children around the world and it is not always remedied by nutrition improvements. In a recent publication, researchers reported that the reason simply could be certain missing gut microbes. In mice, it was shown that strains of Lactobacillus plantarum in the gut sustained growth hormone activity via signaling pathways in the liver, thus overcoming growth hormone resistance.

The research team fed two types of mice – either normal or germ-free mice – a low-protein diet until young adulthood and measured the mice development. While the germ-free mice were stunted completely, normal mice (with gut microbes) showed healthy signs of development. Human gut microbes can be transplanted effectively into germ-free mice to restore healthy development. Using this model a related report showed that the microbiota of healthy children relieved the harmful effects on growth caused by microbiota of the malnourished children. These studies illustrate that beneficial microbiota could be exploited to address malnutrition issues.

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Lactobacillus plantarum strain maintains growth of infant mice during chronic undernutrition (Feb 2016)

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Gut bacteria that prevent growth impairments transmitted by microbiota from malnourished children (Feb 2016)

Plants trick bacteria with this secret chemical weapon

homoserine lactone mimic, quorum sensing, rosmarinic acid

Plants protect themselves from bacterial attack with a myriad of mysterious compounds. One of those protective compounds has been recently reported in Science Signaling. This compound mimics a molecule that bacteria use for communication. Called Rosmarinic acid, the compound binds to a protein in the bacterial quorum-sensing pathway. This pathway is utilized by bacteria to regulate community interactions such as biofilm formation. In vitro and in vivo analysis showed that rosmarinic acid binds a transcriptional regulator called RhIR and stimulates its activity. RhIR is involved in the quorum-sensing pathway of plant and human pathogen Pseudomonas aeruginosa.

Researchers speculate that using rosmarinic acid to activate bacterial quorum-sensing could be one way to trick the bacteria into invading early, i.e., even before they have gathered enough troops. This strategy could allow a plant to fight off bacteria easily since they haven't fully colonized yet. Such an early defense strategy could be useful for limiting crop damage from bacteria and it could also minimize bacterial infections in humans if used as a therapeutic strategy.

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Rosmarinic acid is a homoserine lactone mimic produced by plants that activates a bacterial quorum-sensing regulator (Feb 2016)

DNA can tell early bird from night owl - see if one is better

early bird, morning person, evening person, genetic variants, GWAS, circadian rhythms

Are you a morning person or a night owl? In a study published in Nature Communications, researchers report that our preference for mornings or evenings is determined by the phase of our circadian rhythms. The researchers identified 15 genetic loci significantly associated with morningness, including 7 near established circadian genes. To arrive at these findings, the researchers conducted a genome-wide association study (GWAS) of self-reported morningness, followed by analyses of biological pathways and related phenotypes, using the 23andMe cohort.

Morning people are more likely to be female, and were significantly less likely than evening people to have insomnia or sleep apnea. They are also less likely to require >8 hours of sleep/day, to sleep soundly, to sweat while sleeping and to sleep walk. Morning people were associated with lower prevalence of depression and they are less prevalent in extreme Body Mass Index (BMI) groups such as the underweight and the obese. The findings from this study reinforce current understanding of circadian biology.

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GWAS of 89,283 individuals identifies genetic variants associated with self-reporting of being a morning person (Feb 2016)

Cross-reactive Ebola antibodies identified

cross-reactive Ebola antibodies, Ebolavirus

Researchers have isolated antibodies from survivors of the 2007 Ebola outbreak in Uganda, which can neutralize three different species of Ebolavirus (Zaire ebolavirus, Bundibugyo ebolavirus and Sudan ebolavirus). The researchers started by isolating peripheral B cells from survivors of the B. ebolavirus. From this they identified 90 antibodies that bound the viral outer glycoprotein. Majority of these antibodies bound the glycoprotein of two other Ebola strains, in vitro. Nearly a third of these antibodies neutralized B. ebolavirus in an assay routinely used as surrogate of an in vivo infection.

Finally, 7 antibodies out of the pool neutralized all three viral species by binding to a highly conserved region in the outer glycoprotein. The researchers identified 2 neutralizing antibodies that were used to treat Ebola-infected mice and a single treatment with one of these antibodies successfully rescued Ebola-infected guinea pigs. Combination treatment using these 2 antibodies offered complete protection of guinea pigs infected with the Z. ebolavirus. This study demonstrates that cross-reactive antibodies exist in infection survivors and these antibodies are protective in animal models. The study provides a road map to develop antibody-based treatments effective against multiple ebolavirus infections.

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Cross-Reactive and Potent Neutralizing Antibody Responses in Human Survivors of Natural Ebolavirus Infection (Jan 2016)

Biodiversity critical in boosting crop yield

biodiversity, pollinators, small farms

Researchers estimate that agricultural production would have to double by year 2050 to keep up with the growing demand. And increasing yields is a key part of the solution. To evaluate whether improving pollination could make a difference, an international team of researchers looked at 33 pollinator-dependent crops (raspberries, coffee, apples etc.) on 344 fields across 3 continents. Over a period of time, they monitored pollinator diversity and frequency of pollinator visits and measured crop yields.

The team found that low-yielding farms on an average produced only 47% of the yield of the best farms. At the small scale, the density of pollinators visiting crop plants made a larger difference in crop yield. On large farms, the diversity of pollinators was more important, i.e., large farms with greater pollinator diversity yielded more crops. In summary, improving pollination could help improve crop yield on small and large farms and hence minimize the yield gap. Farmers could consider planting pollinator friendly plants beside crop fields and time pesticide applications such that pollinator exposure to pesticide is minimized. Such an approach may provide a sustainable path toward boosting crop yield while preserving biodiversity and promoting a healthy ecosystem.

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Mutually beneficial pollinator diversity and crop yield outcomes in small and large farms (Jan 2016)

Stunning new video shows the spread of antibiotic resistant bacteria

Antibiotic resistance, Stochastic expression of antibiotic resistance, Transient antibiotic resistance, Transient stochastic resistance

Using a series of time-lapse videos, scientists show that single cells within a bacterial colony randomly use a protein cascade strategy to become more or less antibiotic resistant, even when the colony is not exposed to antibiotic. This kind of transient antibiotic resistance maybe the norm for many bacterial populations.

   

The rationale for this strategy can be explained from a metabolic standpoint. Since it is costly for a cell to express proteins that confer antibiotic resistance, a bacterial colony can hedge its bets by enabling individual cells to acquire high levels of resistance while the other cells avoid this extra metabolic burden. And the existence of these few antibiotic-resistant cells would be enough to keep the infection alive despite antibiotic treatment. The finding has important clinical implications and could potentially guide the frequency and timing of antibiotic administration for serious bacterial infections.

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Stochastic expression of a multiple antibiotic resistance activator confers transient resistance in single cells (Jan 2016)

Why food allergies develop

food allergies, food allergy reasons

Researchers estimate that up to 15 million Americans have food allergies and that some sort of food allergy affects 1 in every 13 children in the US. The economic cost of children's food allergies alone is nearly $25B each year. Despite this rise of food allergies in early childhood it is not clear as to why.

In a recent Science Translational Medicine report scientists explain the immunological basis for the development of food allergies. By analyzing cord blood data of 697 babies at birth and at age 1, scientists found that signs of food allergies may be present at birth and that overactive monocytes are to blame. The scientists found that children who developed food allergies had higher monocyte to CD4+ T cell ratio and a lower proportion of natural regulatory T cells (nTreg). In children that developed food allergies, the cord blood monocytes reacted more strongly to bacterial lipopolysaccharide (LPS) than monocytes from kids who did not develop food allergies. The robustness of monocyte attack on LPS is one measure of immune system activity. While a robust response indicates a healthy immune system, for food-allergic children, these overactive monocytes may indicate that their immune system might start attacking food-related proteins.

Since overactive monocytes make more inflammatory cytokines than normal monocytes, these cytokines might push the T cells into becoming allergy-provoking TH2 cells instead of T regulatory cells which carry out the more moderate immune reactions. These findings provide a mechanistic explanation for the development of food allergy in infants.

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Cord blood monocyte-derived inflammatory cytokines suppress IL-2 and induce nonclassic "TH2-type" immunity associated with development of food allergy (Jan 2016)

Rapid new program identifies antibiotic resistant bacteria with high accuracy

Antibiotic resistance, Rapid program for antibiotic resistance detection

Drug-resistant infections have led to an urgent need for the rapid detection of drug-resistant bacteria. To prevent the spread of drug-resistant bacterial strains, it is critical that patients with an infection are treated quickly using the right antibiotics. But finding out which particular bacterial strain has caused infection and the drugs that it is resistant to, involves susceptibility testing, a process that can take days, and even months in some cases. Scientists have believed that it would be much faster to detect resistant bacteria by looking directly at the bacterial genome to identify mutations that confer resistance. But the interpretation of genetic level information requires massive computing power and expert bioinformaticians.

A study published in Nature Communications presents a new, easy-to-use software that can rapidly analyze bacterial DNA and accurately detect antibiotic resistance in two life-threatening bacterial strains – Staphylococcus aureus (a form of which causes Methicillin-resistant Staphylococcus aureus infection, MRSA) and Mycobacterium tuberculosis. This software package is called "Mykrobe Predictor" and it takes raw sequence data as input parameter. It reads bacterial DNA sequence and cross-checks against previous strains to look for resistance-causing mutations. A clinician-friendly report is generated in under 3 minutes. In case of S. aureus the error rates of Mykrobe Predictor are comparable to the standard methods with sensitivity/specificity of 99.1%/99.6% across 12 antibiotics. For M. tuberculosis, this software predicts resistance with sensitivity/specificity of 82.6%/98.5%.

Another advantage of this software is that it can identify infections which are caused by a mixture of both drug-resistant and drug-susceptible bacteria. Mykrobe Predictor software also allows for a simple upgrade for the detection of new resistance mutations as they evolve.

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Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis (Dec 2015)

Synthetic bacteria that fights round worm infections through probiotics

Innate immunity, RNA virus

Round worm infections are a significant health concern affecting more than a billion people worldwide. And scientists might just have found an easy solution to this global menace. By expressing naturally occurring proteins in food-grade bacteria they were able to inhibit a common laboratory roundworm. To do this, scientists cloned the genes encoding Bacillus thuringiensis crystal proteins Cry5B (140kDa) and tCry5B (79kDa, a truncated version of the same protein) into a high copy vector with a strong promoter. They introduced this vector into Lactococcus lactis bacteria, a safe bacterial strain routinely used in the dairy industry, for fermentation purposes. An important property of this bacterium has to do with a discovery the researchers had made several years ago. Normally, big molecules can escape from a cell either by active transport carried out by cellular machinery or if the microbe breaks open through lysis. The scientists observed that large proteins could be released from the L. lactis bacterium without lysis or an active transport mechanism. It was simply due to a leaky phenomenon, the reasons for which are not fully known.

The investigators found that this genetically modified bacterial strain was able to inhibit the common laboratory roundworm, Caenorhabditis elegans via the expression of Bt proteins. Using this approach, the scientists envision that roundworm-infected individuals could be treated simply by eating dairy products like yogurt, fermented by such modified bacterial strains. By exploiting the leaky nature of L. lactis, the investigators are looking at the possibility of using probiotics to orally deliver biotherapeutics directly to the GI tract.

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Intracellular and extracellular expression of Bacillus thuringiensis crystal protein Cry5B in Lactococcus lactis for use as an anthelminthic (Dec 2015)

Drug-like molecule triggers innate immunity against RNA viruses

nnate immunity, RNA virus

Scientists reported in a recent paper that innate immunity can be activated through a drug-like molecule found in our cells. Called RIG-1, this molecule induces genes to control infection caused by a variety of RNA viruses including Ebola, HCV, FluA, RSV, West Nile and Dengue. RIG-1 (Retinioic Acid Inducible Gene-1) codes for a cellular protein implicated for its role as a pathogen recognition receptor. This receptor is one of several pathogen recognition receptors (PRRs) that engage viral pathogen associated molecular patterns. This process results in induction of downstream signaling pathways that activate the transcription factor IRF3. IRF3 plays a major role in antiviral immunity to drive expression of genes responsible for launching an innate immune response, which is critical to restricting virus replication.

RNA viruses pose a significant public health concern because their high mutation rate allows them to escape the immune response. To make the problem worse, there are no known broad-spectrum antivirals against RNA viruses and very few therapeutic options against RNA virus-infection. This discovery would be of tremendous interest to drug makers for the creation of a broad spectrum antiviral. Triggering innate immunity is of great interest to researchers in this field because some viral infections cannot be treated using traditional antivirals. Having innate immunity fight off the infection would be advantageous in such cases and will also make the virus less likely to resist drug because the therapy will target cells and not the virus itself.

protein news

Targeting innate immunity for antiviral therapy through small molecule agonists of the RLR pathway (Dec 2015)

Will your flu shot work? Scientists can now predict

flu vaccine, flu shot, flu shot efficacy

Using a systems analysis approach, scientists have pinpointed shared molecular signatures driving immunity in response to the influenza vaccination. The study included evaluating immune responses in the young, elderly and diabetic subjects vaccinated with the seasonal influenza vaccine across 5 seasons that helped provide a comprehensive picture of the immune response to vaccination.

In this study scientists vaccinated more than 200 subjects, including several elderly individuals across 5 influenza seasons from 2007-2011. They then analyzed blood samples to look at the molecular pathways associated with antibody response to vaccination. They also analyzed previous data for 218 additional subjects.

Through this process the scientists identified molecular signatures that can predict with 80% accuracy whether a vaccine would elicit immune protection a month after vaccination. Within a week of flu shot administration, young individuals generated high levels of antibody-producing B cells while the elderly subjects showed higher levels of monocytes and other inflammatory molecules. This difference in response to vaccine administration indicated impaired vaccine-induced immune response that was observed in the elderly subjects. Even before vaccination, high baseline levels of B cells and reduced levels of monocytes would mean that the vaccine would confer immune protection approximately 4 weeks later.

This study provides novel evidence of a connection between the baseline state of the immune system and lowered response to vaccine administration in certain patients, including the elderly. By providing a shared, vaccine-induced signature and a concrete picture of how the immune system responds to vaccination, this study can guide the design of next-generation vaccines that offer persistent and greater immunity against influenza, especially for individuals at higher risk of infections. It can also guide supplementary therapeutic approaches such as the use of anti-inflammatory drugs to reduce the inflammatory response in the elderly, upon vaccine administration.

protein news

Systems Analysis of Immunity to Influenza Vaccination across Multiple Years and in Diverse Populations Reveals Shared Molecular Signatures (Dec 2015)

Gut bacteria affected by anti-diabetic drugs

gut bacteria, dysbiosis, anti-diabetic drugs

Gut bacteria produce several types of substances that affect human physiology and health in countless ways. Any change in the composition of this bacterial community [gut microbiome] can have a variety of negative health effects. Called "dysbiosis", it has become a focus area of many disease researchers. However, most studies do not factor the potential effects of drugs on the gut microbiome. In a recent study, scientists tried to disentangle the signatures of gut microbiota in diabetic patients from those of metformin. Using over 700 available human gut metagenomes, the scientists analyzed in detail the effects of the most widely used antidiabetic drug – metformin. Their findings indicated that metformin causes favorable changes in the gut microbiota of type 2 diabetes patients. The drug boosts the capability of the gut bacteria to produce butyric acid and propionic acid. These molecules act to reduce blood glucose levels in diabetics.

Metformin is also known for its adverse effects on the gastrointestinal tract, such as bloating and flatulence. The study provides a possible explanation for these effects. The patients treated with metformin were found to have more coliform bacteria in their gut and it may be one of the reasons for these adverse effects. When looking at type 2 diabetes patients that were not treated with metformin, the researchers discovered that they had fewer bacteria that produced butyric acid and propionic acid. The study underscores the need to disentangle the gut microbiota signatures of human diseases from medication-induced effects.

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Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota (Dec 2015)

Surprising effects of Oxytocin hormone discovered

metabolic syndrome, childhood obesity, sugar consumption, metabolic improvement

Oxytocin is best known for its role in lactation, childbirth and social behaviors. New research suggests that oxytocin triggers different effects in men and women and in certain instances the hormone may trigger anxiety. Using intranasal oxytocin in male and female mice, researchers uncovered surprising findings that could have therapeutic implications ranging from drug discovery to drug administration.

Among the mice tested, some were bullied by an aggressive mouse, an experience that would normally reduce the inclination to socialize with unfamiliar mice. Consistent with prior studies, oxytocin increased the motivation for social interaction among stressed male mice. On the other hand, in stressed female mice, oxytocin had no effect whatsoever. But when non-stressed female mice received oxytocin, the motivation for social interaction was reduced. Since reduced social motivation can be part of a depression-like syndrome, inhibiting oxytocin action might have psychological benefits in women with depression or post-traumatic stress disorder (PTSD). This is because clinical studies have found that women with depression or PTSD have elevated oxytocin levels. The research team also found that environment influenced the effects of oxytocin. When mice were tested in familiar surroundings, when compared to a new environment, oxytocin reduced stress in both male and female mice. This indicated that the manner of oxytocin administration is very important in obtaining the desired effect. These findings have implications for utilizing oxytocin as a therapeutic.

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Sex-Specific Effects of Stress on Oxytocin Neurons Correspond With Responses to Intranasal Oxytocin (Oct 2015)

Analog and digital electronic circuitry created inside living plants for the first time

Electronic plants

Roots, stems, leaves and plant vasculature are responsible for transmitting the signals that regulate plant growth and its complex functions. For the first time, scientists have directly merged plant circuitry with electronics, allowing for the manufacture and fabrication of circuits and devices in plants. To achieve this the scientists tried many attempts of introducing conductive polymers through rose stems. Only one polymer, called PEDOT-S, successfully assembled itself inside the xylem channels as conducting wires, while allowing the transport of water and nutrients. By combining the wires with the electrolyte that surrounds these channels the scientists were able to create an electrochemical transistor, which was able to convert ionic signals to electronic output.

The scientists used vacuum infiltration -- a routine method in plant biology - to infuse another PEDOT variant into the leaves. This polymer formed "pixels" of electrochemical cells partitioned by the veins. When voltage was applied it caused the polymer to interact with ions in the leaf, subsequently changing the color of the PEDOT in a display-like device.

These findings are promising and merge the diverse fields of organic electronics and plant science. The objective of this study is to develop applications for energy and environmental sustainability. This technology can potentially enable us to place sensors in plants and use the energy produced in the chlorophyll, produce green antennas or produce new materials.

protein news

Electronic Plants (Nov 2015)

Health improvement in obese children merely by lowering sugar intake

metabolic syndrome, childhood obesity, sugar consumption, metabolic improvement

Metabolic syndrome is a set of conditions that includes elevated blood pressure and blood glucose levels, excess body fat and high cholesterol levels. Together, these factors contribute to a heightened risk of heart disease, diabetes and fatty liver disease. To look at the harmful effects of sugar in the development of metabolic syndrome in children, researchers regulated the sugar consumption of 43 children aged 9-18 who were obese and had at least one other chronic metabolic disorder such as hypertension and high levels of triglycerides. These children were given 9 days of food that restricted sugar but was instead substituted with starch, to maintain the same level of fat, carbohydrate and calories as their usual diets. Blood work was conducted before study began in order to assess blood glucose, blood pressure and glucose tolerance. The study menu restricted sugar but allowed fruit consumption. Carbohydrates were consumed in the form of bagels, cereal and pasta so that the children still consumed the same number of calories from carbohydrate as before, but total dietary sugar was reduced from 28% to 10% and fructose from 12% to 4% of total calories, respectively.

After just 9 days on the sugar-restricted diet, all aspects of the children's metabolic health improved although there was no weight change. Diastolic blood pressure decreased by 5mm, triglycerides by 33 points, LDL-cholesterol by 10 points, and liver function tests improved. Fasting blood glucose went down by 5 points, and insulin levels were cut by 1/3rd. All measures of metabolic health got better just by substituting sugar with starch in processed foods. And all this without changing the number of calories and without exercise. Among other things, the study clearly demonstrates that not all calories are created equal. The source of calories determines how they are processed in the body. And in this aspect, calories from sugar are bad calories because they turn to fat in the liver, driving insulin resistance and elevating risk of metabolic syndrome. In summary, lowering sugar intake even without reducing calories or losing weight is sufficient to improve health. This study has huge ramifications for the food industry and health care.

protein news

Isocaloric fructose restriction and metabolic improvement in children with obesity and metabolic syndrome (Oct 2015)

TV viewing linked to several leading causes of death including diabetes and influenza

TV and higher mortality

Research indicates that ~80% of American adults watch >3 hours of TV per day and multiple studies have demonstrated a link between excessive TV time and poorer health. A recent study that looked at >200,000 chronic disease-free individuals aged 50-71, has confirmed the association of excessive TV time with higher mortality risk from cancer and heart disease. In addition, they identified higher mortality risk from 6 other causes of disease in the US that included diabetes, chronic obstructive pulmonary disease (COPD), influenza, pneumonia, Parkinson's disease and liver disease. Mortality risk from suicide also went up.

When compared to those who watched <1 hour TV per day, the individuals who reported watching 3-4 hours of TV per day were 15% more likely to die from a cause listed above. And those who watched TV in excess of 7 hours were 47% more likely to die during the study period from one of these causes. Even when controlling for factors such as smoking, alcohol consumption and caloric intake, in statistical models, the association remained. One of the biggest concerns from this observational study was that the harmful effects of TV viewing were applicable to active as well as inactive individuals. Meaning, an individual need not necessarily be a "couch potato" to suffer from the harmful effects of TV watching. Even individuals who led healthier and active lifestyles are subject to the harmful effects of excessive TV watching. The investigators however warned that more research would be required to understand the connection between TV watching and higher mortality risk and whether these same associations are found in other sedentary contexts such as driving or sitting in front of a computer at work. Given this finding, prolonged TV viewing can become an important target for public health intervention than previously recognized.

protein news

Causes of Death Associated With Prolonged TV Viewing: NIH-AARP Diet and Health Study (Dec 2015)

New findings on neutrophil mechanism of action

neutrophil, nutritional immunity

Neutrophils are best known for their ability to fight pathogens by phagocytosis and toxication. Additionally, neutrophils also form Neutrophil Extracellular Traps (NETs) to inhibit extracellular microbes. A recent discovery suggests that neutrophils kill fungal pathogens by slowly starving them to death by withholding crucial trace elements. But why?

Metals occupy an essential niche in biological systems. Their electrostatic properties stabilize substrates or reaction intermediates in an enzyme's active sites. And their reactivity is harnessed for catalysis. Organisms must regulate the levels of these elements to satisfy their physiological needs while avoiding cellular harm. And so the host capitalizes on both the significance and toxicity of metals to defend against pathogenic invaders. And to prevent infection from such pathogens, hosts restrict access to essential metals in a process termed "nutritional immunity". Originally coined to refer to restriction of iron availability by the host, "nutritional immunity" is also applied to mechanisms that withhold other essential transition metals or directing the toxicity of these metals against pathogenic invaders.

In order to identify these mechanisms, researchers used a method called Synchrotron Radiation X-Ray Fluorescence (SR-XRF) to investigate unstimulated and phorbol myristate acetate (PMA)-stimulated neutrophils at the sub-micron spatial resolution level. PMA activated the mechanisms deployed by neutrophils to combat infection. In addition, Inductively Coupled Plasma Mass Spectrometry (ICP-MS) revealed a neutrophil-specific composition of Zn, Fe, Cu and Mn ions in comparison with HeLa cells, indicating a neutrophil-specific metallome complying with their designated functions. The researchers are excited about translating their findings into future drugs to help cure fungal infections that are difficult to treat with the current drugs in the market.

protein news

Trace element landscape of resting and activated human neutrophils on the sub-micrometer level (Jun 2015)

Malaria vaccine may cure cancer

Malaria vaccine may cure cancer

Researchers trying to develop an anti-malaria vaccine in pregnant women have stumbled upon an unexpected discovery that could potentially transform cancer therapy. They revealed that the carbohydrate that the malaria parasite attaches itself to – an oncofetal chondroitin sulfate – which is expressed in the placenta is the same as the one displayed on proteoglycans in cancerous cells.

By conjugating diphtheria toxin to recombinant malaria protein VAR2CSA (rVAR2), the researchers were able to inhibit in vivo tumor growth and metastasis. The study demonstrates how a parasite-derived protein can be exploited to target a common but complex, cancer-associated modification. The researchers have already tested thousands of samples from brain tumors to leukemia and found that the malaria protein is able to inhibit more than 90% of all types of tumors. While this approach seems very promising a major drawback is that this treatment cannot be applied to pregnant women. Since the rVAR2-conjugated toxin cannot distinguish placenta from tumor, it would inhibit placenta growth as well. The research team wants to conduct human testing but the earliest possible scenario they predict would be in 4 years.

protein news

Targeting Human Cancer by a Glycosaminoglycan Binding Malaria Protein (Oct 2015)

How plants fight salt stress

salt stress, cellulose synthesis, cellulose synthase, CC proteins

High salt content in soil dramatically stresses plant biology and lowers crop yield. Estimates indicate that salinity impacts nearly 33% of the agricultural lands worldwide. By 2050, we will need to increase our food production by 70% to feed the burgeoning population. Salinity will come in the way of this goal as more than 50% of the agricultural land may be impacted due to high salinity. Hence, there is an urgent need to find mechanisms that can improve plant growth even in saline conditions.

Researchers have now identified specific proteins that help plants fight salt stress and outlined a mechanism for how these proteins assist the plant in producing biomass under salt-stress conditions. Called "Companions of Cellulose Synthase (CC)", the cytoplasmic tails of these membrane proteins were found to bind microtubules and promote microtubule dynamics. To prove their hypothesis, the researchers deleted multiple genes of the CC gene family in Arabidopsis thaliana and grew the plants on saline media. The mutated plants performed much worse than their wild-type cousins. Researchers also showed that plants lacking CC gene activity were unable to keep their microtubules intact. The interaction between CC proteins and microtubules is critical for the shape and stability of plant cells. It supports microtubule organization, cellulose synthase localization at the plasma membrane and renders seedlings less sensitive to stress - thereby aiding plant biomass production during salt stress.

protein news

A Mechanism for Sustained Cellulose Synthesis during Salt Stress (Sep 2015)

Sniffing to detect cancer using electronic nose

electronic nose, nanoparticle-based sensor, exhaled breath, volatile organic compounds, ovarian cancer

Detecting cancer usually involves imaging techniques and invasive procedures. In order to develop safer and less invasive ways of cancer detection, scientists have long explored ways to detect cancer in a patient's breath. In a recent development, researchers reported inventing an "electronic nose" to achieve this goal. The device consists of a small diagnostic flexible array, based on gold-nanoparticle [GNP] sensors which can accurately detect compounds in breath samples that are specific to ovarian cancer.

Each bending state of the GNP-based sensor gives unique nanoparticle spatial organization, altering the interaction between GNP ligands and volatile organic compounds [VOCs], which increases the data obtained from each sensor. These sensors could detect parts per billion [ppb] level VOCs linked to ovarian cancers and detectable in patient-exhaled breath, while distinguishing them from environmental VOCs that exist in breath samples from normal individuals. The device tested on breath samples from 43 volunteers had an accuracy of 82%. This method provides hope of achieving a simple, cost-effective, mobile and noninvasive diagnostic procedure not just for ovarian cancer but for other cancers as well as other diseases.

protein news

Dynamic Nanoparticle-Based Flexible Sensors: Diagnosis of Ovarian Carcinoma from Exhaled Breath (Sep 2015)

Natural defense protein against HIV discovered

HIV-1, ERManI, antiretroviral, defense protein

Earlier research had shown that it was possible to interfere with HIV spread but the exact molecular mechanisms had not been identified. For the first time, scientists have identified ERManI (Endoplasmic Reticulum Class I α-Mannosidase) as the essential host protein that slows the spread of HIV-1. Scientists investigated how the four ER-associated glycoside hydrolase family 47 (GH47) α-mannosidases, ERManI, and ER-degradation enhancing α-mannosidase-like (EDEM) proteins 1, 2, and 3, are involved in the HIV-1 envelope (Env) degradation process. Ectopic expression of these four α-mannosidases uncovered that only ERManI inhibited HIV-1 Env expression in a dose-dependent manner. Basically, ERManI is a host enzyme that adds sugars to proteins. The Env glycoprotein is targeted to the endoplasmic reticulum-associated protein degradation pathway for degradation after infecting cells. And ERManI was found to interact with the Env and initiate this degradation pathway.

With this discovery, ERManI has the potential as a new antiretroviral treatment option. Currently there is no cure for HIV-1 and once patients are infected, they have it for life. Current antiretroviral therapies can prolong life but cannot fully cure a patient. ERManI is different from current treatments in the sense that it can help the body protect itself.

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ERManI (Endoplasmic Reticulum Class I α-Mannosidase) Is Required for HIV-1 Envelope Glycoprotein Degradation via Endoplasmic Reticulum-associated Protein Degradation Pathway (Sep 2015)

Bats contribute millions of dollars in savings in corn field protection

bats, corn-protection, biodiversity conservation

Bats are voracious predators of crop pests, but their ecological impacts in agroecosystems haven't been truly measured. For the first time, through a unique field experiment, scientists assessed the ecological and economic impact of bats in corn agriculture. Researchers studied 12 corn plots in Illinois State during the crop seasons of 2013 & 2014. In 6 plots, researchers erected large, netted exclosures to keep the bats away. The other 6 plots had no exclosures so the bats could access them as usual. At the end of their study, the researchers observed that bats initiated strong and surprising ecological interactions in corn fields. They found that corn plots inaccessible to bats had nearly 60% more corn earworm larvae and more pest-associated fungal growth when compared to the bat-accessible plots.

Studies indicate that corn is grown on more than 150 million hectares worldwide. Based on the current study it is estimated that corn-protection offered by bats by pest suppression alone, could be worth more than a billion dollars globally. Additionally, bats can further benefit farmers by indirectly suppressing pest-associated fungal growth and toxic compound accumulation on the crop. As nocturnal insectivores, bats provide unique ecological services and the current study underscores the importance of conserving biodiversity.

protein news

ERManI (Endoplasmic Reticulum Class I α-Mannosidase) Is Required for HIV-1 Envelope Glycoprotein Degradation via Endoplasmic Reticulum-associated Protein Degradation Pathway (Sep 2015)


Mystery behind flu virus transmission solved

lu virus, influenza virus, soft palate

The epidemiological success of flu viruses relies on successful airborne transmission from person to person. But the viral properties governing the airborne transmission of flu viruses are complex. A new study reveals that the soft palate at the back of the roof of the mouth plays a key role in the flu viruses' ability to transmit through air. Previous research had shown that airborne transmissibility is dependent on the viral surface hemagluttinin (HA) glycoprotein's ability to bind to receptors on human respiratory cells. Some viral strains bind better to alfa 2-6 glycan receptors found primarily in humans and other mammals while others are better suited to bind alfa 2-3 glycan receptors found in birds.

In the current study, researchers made 4 mutations in the HA protein of the flu virus which made it better suited to bind the bird receptors than the human receptors. They then used this strain to infect ferrets that are often used as models of human influenza infection. In theory the mutated virus should not have spread but it traveled through the air just as well as the wild type virus strain. Upon sequencing the virus genome, the scientists found that it had undergone a genetic reversion that allowed its HA protein to bind to the bird as well as human receptors. This experiment validated that gain of binding to the human receptor is critical for aerosol transmission. On examining the different parts of the respiratory tract, scientists discovered that viruses that genetically reverted were most abundantly found in the soft palate. The researchers are next trying to figure out how this genetic reversion takes place and why particularly in the soft palate. They hypothesize that the viruses outcompete each other in the soft palate from which they can spread by packaging themselves into mucus droplets produced by cells in the soft palate.

From a pandemic point of view, this study enables the systematic evaluation of highly transmissible viruses. The findings published in Nature will enable scientists better understand how the flu virus develops airborne transmissibility while helping monitor strains that acquire the potential to cause Influenza outbreaks.

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The soft palate is an important site of adaptation for transmissible influenza viruses (Sep 2015)


Obesity preventable by transplanting gut microbiome

WAT inflammation, TLR signaling, obesity and gut microbiome

A new study reports that the type of fatty diet consumed, affects composition of the gut microbiome in mice. This in turn determines whether the animals develop obesity. Investigators fed mice, diets with the same total number of calories but some mice received nearly all their fat from fish oil whereas others received fats in the form of lard. Mice fed lard developed signs of metabolic disease, including insulin sensitivity and high fasting-blood glucose levels. On the other hand, mice fed fish oil remained relatively healthy. When researchers transplanted gut microbes from the fish oil-fed mice into antibiotic-treated, germ-free mice and subsequently fed the mice lard, they were protected from the unhealthy impact of the saturated fat. At the molecular level, the metabolic disease in lard-fed mice is associated with overactive innate immunity leading to inflammation in the fat cells. This response includes activation of toll like receptors (TLRs), in particular TLR4.

The study demonstrates that the type of fat is important in shaping microbial community and its functional dynamics in our body, which in turn impacts our overall health and wellbeing. Previous studies had shown that switching to a high-fat diet rapidly altered the gut microbiome but the current study goes further to show that the kind of fat consumed, shapes the composition of gut microbiome. It is not clear from this study whether these findings apply to humans. Long-term dietary interventions in humans will have to be monitored carefully along with metabolic and immune profiling, before arriving at that answer.

protein news

Crosstalk between Gut Microbiota and Dietary Lipids Aggravates WAT Inflammation through TLR Signaling (Aug 2015)


Tissue Velcro for the repair of damaged hearts

tissue velcro, biocompatible scaffold, POMaC, 3D tissue constructs

Engineers have made assembling functional heart tissue really easy. They created a biocompatible scaffold that allows sheets of heart cells to snap together just like Velcro. To accomplish this feat, the engineers used a special polymer called POMaC to create a 2D mesh around which the heart cells could grow. POMaC, created by a different team, is a soft, biodegradable elastomeric platform biomaterial created from citric acid, maleic anhydride, and 1,8-octanediol, poly(octamethylene maleate (anhydride) citrate). POMaC is able to closely mimic the mechanical properties of a wide range of soft biological tissues.

The 2D mesh resembles an asymmetric honeycomb, providing a template that causes the heart cells to line up and click in place like Velcro. Upon current stimulation, the heart muscle cells contract together, causing POMaC to bend. The team then stacked sheets of these heart cells on top of each other. And amazingly, the assembled sheets started to function almost instantaneously, beating in synchrony. The engineers hope to create artificial tissue that can be used to repair damaged hearts. The idea is to be able to build and use larger tissue structures immediately before they are required. Conceptually, this technology can be applied to different cell types. Such artificial tissues can be used for in vitro drug testing in a more realistic environment. As the next step, the engineers want to test the functionality of these tissues in vivo, in medical implantation experiments.

protein news

Platform technology for scalable assembly of instantaneously functional mosaic tissues (Aug 2015)


Cell phone data used to track infectious disease spread

disease surveillance, disease monitoring, cell phone data for disease tracking, rubella transmission

Tracking mobile phone data is a controversial matter that often triggers privacy concerns. In a recent publication, scientists reported using anonymous mobile phone data of >15 million subscribers to track the spread of rubella in Kenya. Scientists wanted to see whether cell phone users' travel patterns could predict the seasonal spread of rubella. The team analyzed massive data that contained billions of communications involving people-movement between June 2008 and June 2009. Using the location of the routing tower and the timing of each call and/or text message, the team was able to determine a daily location for each user along with the number of trips the user made each day.

The team then compared the cell phone data with a dataset of rubella incidence in Kenya. These two findings coincided – the cell phone movement pattern lined up with rubella incidence figures. In both their analyses, rubella spike occurred thrice within the 12 month period: September, February and May. This indicated that cell phone movement can be a predictor of infectious-disease spread. Rubella spreads most when children interact at the start of school season and right after holiday breaks. The transmission reduces throughout the rest of the school-term months. This work shows that mobile phone data can be effectively used to capture seasonal human movement patterns that are relevant for understanding infectious diseases. The scientists believe that such data can help policymakers guide healthcare interventions like the timing of immunizations and school closings. This methodology could apply to other seasonally transmitted diseases such as influenza and measles as well.

protein news

Quantifying seasonal population fluxes driving rubella transmission dynamics using mobile phone data (Sep 2015)


Breastfeeding exposes infants to toxic chemicals

breastfeeding and toxicity, PFAS, perfluorinated alkylate substances

Scientists report that a class of industrial chemicals linked to cancer and immune dysfunction builds up in infants when they are breastfed. The chemical – perfluorinated alkylate substance (PFAS) – is used to make water- and stain-resistant products. They have been in use for several decades for the manufacture of products such as rain coats, paints, lubricants and food packaging. They enter our bloodstream through consumption of contaminated water. PFAS is known to contaminate water in the US near various manufacturing facilities.

The scientists conducted this study in 81 children by quantifying the concentrations of this chemical in their blood, at birth and over time. They also looked at the level of this chemical in the mothers' blood before childbirth. The scientists observed that in children that were exclusively breastfed, PFAS concentrations in the blood increased by up to 30% for each month they were breastfed. Lower increases were seen in children who were breastfed partially. In some cases, the child's serum concentration of PFAS had exceeded that of their mothers'. The good news was that PFAS accumulation was reversible and the concentrations had dropped after cessation of breastfeeding.

These results indicate that breastmilk is a major source of PFAS exposure in infants. However, the scientists believe there is no reason to discourage breastfeeding. Hopefully studies like these will motivate governments to take legislative action for testing substances like PFAS for water contamination and monitoring its adverse effects on the population.

protein news

Breastfeeding as an Exposure Pathway for Perfluorinated Alkylates (Aug 2015)


New artificial blood vessels that remain clot-free

artificial blood vessels, clot free, vascular biology, drug entrapped vascular grafts

Surgery related to cardiovascular conditions such as ischemia, often requires vascular graft implantation. Such a graft comprises of artificial blood vessels which can restore blood flow to the affected part. A major issue with such artificial grafts is that they frequently get obstructed due to blood clot formation. Hence, such interventions require that patients take anticoagulants for the rest of their lives. Sometimes, additional surgical procedures are necessitated to fix these clots.

Now, for the first time, scientists have developed artificial blood vessels that are not prone to blood clot formation. The team behind this invention synthesized a thin film composed of densely packed aluminum oxide nanorods mixed with urokinase-type plasminogen activator. The film is essentially a porous matrix that can selectively let in plasminogen [proenzyme naturally occurring in blood plasma]. When plasminogen interacts with the plasminogen activator inside the graft, plasmin is formed which dissolves blood clots. To test how this graft worked, the scientific team grew artificial clots inside the graft. Soon after, the clot started to dissolve and percolated through the graft. The team believes that this drug-entrapment concept will have applications beyond just artificial blood vessels. It can be applied to any suitable medical implant as long as the right kind of drug is available.

protein news

Synthesis of Thrombolytic Sol-Gel Coatings: Toward Drug-Entrapped Vascular Grafts (Aug 2015)


Hypoxia response crystal clear

hypoxia response, hypoxia inducible factors, HIF, ARNT, HIF complex

Hypoxia Inducible Factors (HIFs) coordinate cellular adaptations to low oxygen stress by regulating genes involved in angiogenesis, erythropoiesis and metabolism. Since these programs are involved in the growth and progression of many tumors, HIFs are considered attractive anti-cancer targets. There are ongoing efforts to find drugs that inhibit HIF pathways but thus far there are no drug candidates that bind to HIF directly. Existing candidates bind to a class of enzymes called prolyl hydroxylases (PHDs) that regulate HIF activity.

Now, for the first time, scientists have solved the crystal structure of hypoxia inducible factors (HIFs) in complex with the aryl hydrocarbon receptor nuclear translocator (ARNT) subunit. The scientists identified five different pockets in the HIF complex, all of which can be used for targeting by potential drug candidates, to inhibit HIF function. This new discovery offers novel, HIF-functionality insights while presenting opportunities for rational drug design. Especially to develop drugs that could be useful in treating solid tumors. Since HIF is implicated in several different transcriptional programs, this finding opens up new and exciting possibilities for the treatment of a variety of diseases besides cancer.

protein news

Structural integration in hypoxia-inducible factors (Aug 2015)


Evolutionary selection pressures play role in cancer progression

new model of oncogenesis, evolutionary selection pressure in cancer progression, cancer and evolution

Is accumulation of mutations the real cause of cancer? In a recent PNAS publication, scientists argue otherwise. They propose a new model of oncogenesis that underscores the importance of evolutionary pressures on cell populations. Their theory states that the ecosystem of a healthy tissue allows healthy cells to outcompete cells with cancerous mutations. When an imbalance occurs in this ecosystem, cells with cancerous mutations begin to thrive. For example, many cancerous cells can survive in hypoxic conditions found in the center of developing tumors. This adaptation is advantageous only in oxygen-deprived tissues. In healthy, oxygen-rich tissues, having such a mutation is useless. And so, in healthy tissues, cells that possess this mutation are evolutionarily less competitive than the healthy cells. Thus they die or their population is kept in check by the healthy cells.

This model suggests that people should adopt lifestyle choices that promote the fitness of healthy cells in order to suppress the growth of cancerous cells. This concept is simplified with analogy to a lawn. The health of a lawn is its best defense against unwanted weeds. And supporting the fitness of a healthy lawn requires applying fertilizer to the lawn rather than herbicide to the weeds. This model of oncogenesis has significant implications for cancer therapy and drug design. By concentrating on making drugs that target cancerous mutations, we may be currently focusing on weed removal. Maybe it's time to think differently.

protein news

Toward an evolutionary model of cancer: Considering the mechanisms that govern the fate of somatic mutations (Jul 2015)


How plants defend themselves underground

plant defense mechanisms, plant defense hormones, soil microbiome, plant immune system

How can a plant distinguish friends from foes in a complex soil microbial ecosystem? To explore the interactions between a plant's immune system with its soil bacteria, scientists used Arabidopsis thaliana mutants with altered immune systems. These mutants were deficient in either the biosynthesis or signaling detection of key plant defense hormones, including salicylic acid, jasmonic acid and ethylene.

Using DNA sequencing they profiled soil microbiome colonizing in and around the wild type and mutant plants' roots. They found a significant difference in the soil microbiome community in and around the roots of the wild type and mutant plants. In case of the mutants; such microbes were found that shouldn't have been there in the first place. This was especially in mutants lacking the ability to produce or respond to salicylic acid. These findings show that salicylic acid influences the growth of useful soil microbiome in and around plant roots.

It has been long known that salicylic acid helps the plant ward off pathogens by triggering a broad range of immune responses, including the production of antimicrobial compounds. In the root however, salicylic acid plays a dual role; gatekeeping and recruiting; by increasing the abundance of useful microbes while eliminating others.

protein news

Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa (Jul 2015)


Why men don't live as long as women

placebo research, fake drug discovery, placebo pills

Women now live longer than men in all countries. Scientists have used demographic information from 13 countries to find out why. Using data from 1,763 birth cohorts between years 1800-1935, scientists showed that excess adult male mortality is rooted in the age group 50-70 and that this gender-specific mortality bias emerged in cohorts born in the late 1800s.

As infectious disease prevention, improvements in diet and other health behaviors were adopted by people during late 1800s and early 1900s, death rates dropped drastically. But women started to outlive men after this time point. The scientists observed that, among individuals born after 1880, female death rates decreased 70% faster than male death rates. Data revealed that heart disease was the number one culprit of excessive deaths in men. Smoking-related illnesses contributed for 30% mortality difference between men and women.

protein news

Twentieth century surge of excess adult male mortality (Jul 2015)


Fake-drug discovery: transforming placebos into therapies

placebo research, fake drug discovery, placebo pills

Placebo research sounds more like an oxymoron but remarkably, it seems to work. Apparently, for some clinical conditions, in up to 50% of clinical trials, the placebo works just as well as the drug under investigation. When this was first observed researchers assumed that the drug was no good. But further studies have shown that there is more than meets the eye. In a famous 2010 experiment on 80 irritable bowel syndrome (IBS) patients, one group of participants got no treatment whereas the other group was given placebo pills. Shockingly, the placebo group reported twice as much improvement in their condition as the untreated group. And the real surprise was that the placebo group knew they were taking fake pills! Based on this encouraging finding, scientists are now taking placebo research into cancer survivors.

The 7-week trial will involve cancer survivors who have completed treatments for at least 6 months and are experiencing at least moderate levels of cancer-related fatigue. The idea is to see if placebos can alleviate their symptom severity. For this study, participants will be divided into 2 groups – one receiving placebo while the other will serve as control. After a weeklong wash-out period, they will switch places. The researchers will be looking at intra-group and inter-group differences. They will also analyze saliva samples for evidence of potential genetic biomarker responses.

But how does a placebo produce a therapeutic effect? The scientists believe there could be classical conditioning and/or non-conscious mechanisms at play that could engage the imagination to simulate a therapeutic effect. It could be analogous to watching a horror movie and feeling scared despite knowing the fact that it's fake.

protein news

Placebos without deception: a randomized controlled trial in irritable bowel syndrome (Dec 2010)


Proteins responsible for initiating labor identified

parturition, labor initiation, steroid receptor coactivators

The precise molecular mechanisms that initiate labor have remained a mystery, until now. Researchers have now identified 2 proteins in fetal lungs that are responsible for initiating labor. The 2 proteins are steroid receptor coactivators (SRC) 1 & 2. The researchers found that these 2 proteins activate genes inside the fetal lungs near full term, resulting in the production of surfactant protein molecules - surfactant protein A (SP-A) and platelet-activating factor (PAF). These surfactants are then secreted by the fetal lungs into the amniotic fluid, triggering an inflammatory response that initiates labor. This study provides strong evidence that the fetus is able to regulate the timing of its birth through these mechanisms.

There are significant implications of this study. By understanding the molecular processes that initiate normal-term (40 weeks) labor, scientists can gain insights on the prevention of preterm labor (earlier than 37 weeks). As per CDC estimates, preterm birth affects 1 in 9 infants in the US. Preterm babies are at high risk for serious medical conditions like respiratory distress and neurological disabilities. Therapeutic interventions that could target SRC-1 & SRC-2 function to promote proper surfactant production, could help in triggering normal labor and alleviate the suffering of thousands of infants and their families.

protein news

Steroid receptor coactivators 1 and 2 mediate fetal-to-maternal signaling that initiates parturition (June 2015)


Obesity in teens linked to TV food commercials

teenage obesity, food commercials, overweight adolescents

Adolescent obesity has increased dramatically over the last 3 decades. Research shows that the number of TV shows viewed during childhood is associated with greater risk for obesity. In a recent study, scientists examined neural responses to food commercials and non-food commercials in overweight and healthy-weight adolescents, using functional magnetic resonance imaging (MRI). The commercials were embedded within an age-appropriate show so the participants were unaware of the study's purpose.

The results showed that in all adolescents, the brain regions involved in attention, focus and reward-processing were strongly active while viewing food commercials than non-food commercials. Adolescents who had higher body fat showed a greater reward-related activity than healthy-weight adolescents. One of the most surprising findings in this study was that the food commercials also activated overweight adolescent brain regions that controlled their mouths. This finding suggests the possibility that overweight adolescents mentally simulate eating as they watch food commercials. Such brain responses may indicate that unhealthy eating behaviors are picked up by observation, during adolescence, and they are reinforced during the person's life - potentially hindering an individual's ability to lose weight as they grow older.

Since diet intervention strategies largely focus on fighting food temptation, the current study offers an alternative point of view. An intervention that minimizes the simulation of unhealthy eating or rather, encourages the simulation of healthy eating may prove more beneficial than merely a suppression of desire to eat more. In other words, one could picture themselves eating a healthy meal or salad rather than a fat-loaded burger with a side of French fries.

protein news

Individual Differences in Reward and Somatosensory-Motor Brain Regions Correlate with Adiposity in Adolescents. (May 2015)


Remarkable structural forces that make teeth crack resistant

structural forces in teeth, crack resistance of teeth, compressed strain in teeth, mineral nanoparticles in teeth

Despite being subjected to massive, crushing forces the high crack resistance in teeth makes them so durable. The bulk of teeth are made of dentin, a bone-like material consisting of mineral nanoparticles, embedded in tightly connected collagen protein fibers. And while these connections make teeth strong, they alone cannot stop cracks from propagating in the teeth. A cross functional team of scientists analyzed the complex structure of dentin and investigated what gives teeth their high crack resistance.

They performed micro-beam in-situ stress experiments and analyzed the local orientation of the mineral nanoparticles. They found that when the collagen fibers shrink the attached mineral nanoparticles become increasingly compressed. This compressed state prevents cracks from developing and reaching the inner parts of the tooth, thus ensuring that the sensitive inner pulp is secure. The balance of stress between the nanoparticles and protein molecules is important for maintaining integrity of the tooth. If this link is destroyed by heating, dentin becomes weaker and vulnerable to cracks. These natural compressive forces cannot be mimicked in artificial tooth replacements and hence they do not usually work as well as natural teeth do.

protein news

Compressive Residual Strains in Mineral Nanoparticles as a Possible Origin of Enhanced Crack Resistance in Human Tooth Dentin (May 2015)


Problems with research antibodies and the solutions

research antibodies, reproducibility crisis

Antibodies are the most widely used class of protein-binding reagents yet there are alarming flaws in the reliability of research antibodies. In recent reports, they have been deemed the major driver of a reproducibility crisis – a growing awareness that the results of many biological experiments cannot be replicated and that the conclusions based on these results may be baseless.

Problem: In a controversial 2012 study, it was shown that results in nearly 89% of landmark cancer research papers could not be reproduced. In a separate analysis using 49 commercially available antibodies against 19 signaling receptors, most bound to more than one protein, indicating the fact that they could not distinguish between the receptors. It is believed that poorly characterized and ill-defined antibodies are in large part to be blamed for this irreproducibility and non-specificity.

Solutions: Scientists who have had negative experiences with antibodies are now beginning to speak up. They have been calling for the creation of standards by which antibodies should be generated, used and described. Nearly half a dozen grass-roots efforts have sprung up to provide better ways of assessing antibody quality. Solutions proposed include:

The idea is that, as more and more scientists switch to recombinant expression, uncharacterized and unsequenced research antibody will become obsolete.

GenScript is proud to be a leader in this movement. With a robust portfolio of recombinant antibody services, GenScript delivers high quality antibodies produced using proprietary transient and stable expression technologies. View our recombinant antibody selection guide to identify the right service for your applications.

protein news

Reproducibility crisis: Blame it on the antibodies (May 2015)

protein news

Reproducibility: Standardize antibodies used in research (February 2015)


Engineered probiotics for cancer detection

engineered probiotics, cancer detection, cancer diagnosis

Scientists have used synthetic biology in an ingenious way to detect cancer in the urine. They took a harmless strain of E. coli that colonizes the liver and programmed it into an orally administered diagnostic device that can non-invasively indicate the presence of liver metastasis by producing a luminescent signal, detectable using simple urine test.

To turn this probiotic E. coli (Nissle 1917) into a diagnostic device, the scientists engineered the cells to express the LacZ reporter gene that cleaves lactose into glucose and galactose. They then fed mice these probiotic bacteria. Within 24 hours the probiotic translocated across the gastrointestinal tract and reached the metastatic tumors present in the liver. They then injected the mice with a substrate molecule that is broken down by the LacZ gene product. LacZ breaks down the substrate molecule, consisting of galactose linked to luciferin. Upon cleavage, luciferin is excreted in the urine where it is easily detected by a simple test.

But why didn't orally delivered bacteria accumulate in tumors all over the body – why liver specifically? Because the hepatic portal vein carries them from the digestive tract directly to the liver. The liver is also an ideal organ to target using oral delivery because it is the primary site of metastasis for several types of tumors including colorectal, breast and pancreatic tumors. The bacteria can selectively grow in tumors without adversely affecting host health due to suppressed immune surveillance within the tumor and increased availability of nutrients in the tumor core. This targeted ability of bacteria to selectively home to tumors also raises the possibility of using them as programmable drug delivery vehicles in the future.

protein news

Programmable probiotics for detection of cancer in urine (May 2015)


Antibiotics prescribed during infancy linked to diseases in adult life: gut microbiome implicated

Antibiotic use, infancy, gut microbiome imbalance

Antibiotics are the most common prescription drugs given to children but nearly a third of the prescriptions are considered unnecessary. By analyzing recent epidemiological data, researchers at the University of Minnesota identified a 3-way link among antibiotic use in infants, gut microbiome and diseases in adult life. They observed that antibiotic use during infancy induces imbalances in the gut microbiome – a condition called dysbiosis. And dysbiosis is associated with infectious diseases, allergies, autoimmune disorders and even obesity in later stages of life.

Previous studies have shown links between antibiotic use and dysbiosis. Studies have also shown links between dysbiosis and disease but in this study, for the first time, a direct correlation has been shown between these 3 different aspects. The scientists used their findings to propose a framework for studying antibiotic-related dysbiosis in children. The scientists' recommendations include future investigation into four types of dysbiosis: loss of keystone taxa, loss of diversity, shifts in metabolic capacity and blooms of pathogens. Findings from this study will also help provide recommendations for antibiotic administration in infants.

protein news

Antibiotics, Pediatric Dysbiosis, and Disease (May 2015)


Measles vaccine protects against other infections too

measles vaccine, immunosuppression, vaccination

Immunosuppression after a measles attack is a hallmark of the disease and is known to predispose people to opportunistic infections for up to months at a time. Earlier studies have shown that measles virus attacks and destroys T lymphocytes that protects against diseases by remembering foreign molecules that it encountered before. The research showed that while T lymphocytes return in a month or so, they can only fight off the measles virus but not the other pathogens that they had encountered before. A recent study shows that measles has a much longer effect on the host immune system than was previously thought, extending over 2-3 years.

By conducting detailed analysis of population data from several countries scientists identified a strong correlation between measles incidence and deaths from other diseases. In other words what this meant was reducing measles incidence by vaccination appeared to cause a drop in deaths from other infectious diseases. This study makes for a strong case for vaccinating children with the measles vaccine for the wide protection that it offers. And the benefits of measles vaccination extend beyond just infectious disease prevention. In terms of cost, measles can be a really “expensive disease” with huge economic costs and it consumes public health resources that can be applied to address other important problems in society. As per a CDC report, in 2011 the economic burden of 107 cases spread across 16 outbreaks in the US cost local and state health departments an estimated $2.7 million-$5.3 million.

protein news

Long-term measles-induced immunomodulation increases overall childhood infectious disease mortality (May 2015)


New implantable device for in vivo drug efficacy testing in tumors

implantable device for in vivo drug testing, in vivo drug testing, HTP in vivo drug testing, targeted cancer therapy, personalized medicine

More than 100 drugs have been approved to treat cancer but identifying the right drug for a patient is not easy. That's about to change. MIT chemical engineers have designed an implantable device that will revolutionize cancer treatment. This device can be used to perform drug sensitivity testing of several anticancer agents simultaneously inside the living tumor. The grain-sized device has reservoirs that can carry micro doses of single drugs and drug combinations into spatially distinct regions of a tumor. A physician can test a patient for a range of available drugs to identify the one that works best.

Made from a stiff, crystalline polymer, this device can be implanted into a patient's tumor using a biopsy needle. After implantation, each drug seeps 200-300 microns into the tumor without overlapping with each other. A variety of drug types can be fitted into these reservoirs and local drug concentrations can be chosen to be representative of concentrations achieved during systemic treatment. After a day of drug exposure, the implant is removed along with a sample of the surrounding tumor tissue. Scientists then analyze drug efficacy by using antibodies to stain and detect markers of cell death or proliferation. To test the device the researchers implanted it in mice that were grafted with human prostate, breast and melanoma tumors. These tumors were known to have variable sensitivity to different cancer drugs and the implantable device's results corresponded with the sensitivity profiles seen earlier. The researchers are now working to make the device easier to read while still inside the patient, allowing for a quicker diagnosis.

protein news

An implantable microdevice to perform high-throughput in vivo drug sensitivity testing in tumors (April 2015)


New findings on the relationship between diet, gut bacteria and colon cancer

diet-swap, gut microbiome, gut bacteria, colon cancer

Colon cancer rates are much higher in the US than in Africa yet in the US, African Americans have a high incidence of this disease. To investigate whether diet played any role in this effect, an international team of scientists carried out this study with 2 different groups of 20 volunteers each. One was an African American group while the other group was comprised entirely of volunteers from rural Africa. The groups swapped diets for 2 weeks under tightly controlled conditions. All volunteers had colonoscopy examination before and after the diet swap. Before the experiment began the American-diet group had polyps in their bowel lining that may be harmless but can progress to cancer. None of the African volunteers had these polyps. After 2 weeks on the African diet the Americans showed significantly less inflammation in the colon and reduced biomarkers of cancer risk. The African group's colon cancer risk dramatically increased on the other hand.

The American diet had higher animal protein and fat content while being low in fiber. The African diet on the other hand was high in fiber but low in fat. The major reason for changes in cancer risk was the way in which gut bacteria altered their metabolism to adapt to the new diet. The fiber-rich African diet led to increased saccharolytic fermentation and production of butyric acid and suppressed secondary bile acid synthesis. Butyric acid is an important byproduct of fiber metabolism that is known to have anti-cancer effects.

These findings raise serious concerns about the progressive westernization of African communities and its related health impact. But it's also surprising to note how quickly diet change can lower cancer risk emphasizing the fact that it's never too late to start eating healthy.

protein news

Fat, fibre and cancer risk in African Americans and rural Africans (April 2015)

Major clue on the origin of multicellular life discovered

Loki, Lokiarchaeota, multicellular life, origin of multicellular life

The debate around the origin of eukaryotic cells remains one of the most controversial in modern biology. Genomic research has shown that mitochondria in eukaryotic cells stems from an early bacterial symbiont. Recent studies have also suggested that a primordial archaeon might have engulfed a bacterium and in the process transformed into a complex eukaryotic cell. But the identity and nature of this archaeal ancestor remained unknown, until now.

Scientists have now discovered a new, single-celled microorganism that could end this debate once and for all. Either that or it could add a whole new perspective to existing theories. Named "Lokiarchaeota" or "Loki" for short, this microbe was discovered 1.5 miles under the Atlantic Ocean near hydrothermal vents. Loki looks more like a multicellular organism than any found before. It forms a monophyletic group alongside eukaryotes in phylogenomic analyses and whose genomes encode an expanded repertoire of eukaryotic signature proteins. This observation points to the fact that Loki had complex membrane remodeling capabilities.

These findings provide support for hypotheses in which the eukaryotic cell evolved from Loki and that many components of a eukaryotic cell were already present in Loki. This provided the early cell with a rich genomic tool kit that would support the cellular complexity that came along with evolution and is characteristic of eukaryotic cells.

protein news

Complex archaea that bridge the gap between prokaryotes and eukaryotes (May 2015)

Novel form of ice with unusual structure discovered

square ice, graphene, novel ice, unusual ice, room temperature ice

Scientists recently discovered a form of ice that's never been seen before – its square and can be formed at room temperature. The scientists achieved this by flattening a droplet of water between two sheets of graphene. Graphene is an allotrope of carbon arranged as a 2-dimensional hexagonal lattice in which each atom forms a vertex. It is known to be the basic structural element of other allotropes including graphite and charcoal. Graphene has unusual physicochemical properties in that it is not only stiff, strong and conductive but it can also exert immense pressure on molecules trapped between its layers.

Interesting fact: This study comes from the lab of Andre Geim, well-known for levitating a frog in a magnetic field, for which he was awarded the Ig Nobel prize in 2000. Andre Geim also won the 2010 Nobel Prize in physics (shared with Konstantin Novoselov) for their groundbreaking experiments with graphene.

 

Square ice is strikingly different from normal ice. In normal ice the bonds between oxygen and hydrogen are usually arranged in a tetrahedral manner. But in a layer of square ice, all the atoms lie in a flat plane with a right angle between each oxygen-hydrogen bond. The scientists calculated that the graphene sheets must be exerting more than 10,000 times atmospheric pressure in order to flatten water in this way. It is unclear what the practical applications of this phenomenon are but it seems like this could have use in water filtration and microfluidics technologies. From a geology stand point this observation points to the fact that there could be water even in the driest of places in forms and capillaries that we wouldn't normally think of.

protein news

Square ice in graphene nanocapillaries (Mar 2015)

Surprising finding - plant finds full moon romantic

plant biology, insect pollination, full moon, pollen release

Full moons have ignited passion in humans for centuries, often regarded as a catalyst for romance. A recent study suggests that a shrub found on cliffs and rocks, from Italy to Yemen, may also find the full moon romantic! This mysterious shrub is the Ephedra foeminea, a pine-like gymnosperm. Most gymnosperms are wind-pollinated but some are insect-pollinated and in Ephedra both kinds of pollination occur. No one really knew though how insect pollination took place in this species. In a eureka moment, botanists discovered that this shrub took the full moon's help for insect pollination.

The Ephedra does this by secreting sugary droplets laden with pollen for insects to find. These sugary droplets glint like diamonds under the bright gleam of the full moon. This peculiar adaptation may serve a dual purpose. Many nocturnal insects navigate using the moon and the spectacular reflection of the full moon light in the pollen droplets might be the only apparent means of nocturnal attraction of insects in this shrub. But exactly how the Ephedra determines a full moon remains a mystery. Researchers speculate that the moon's gravitational pull has a role to play or that the plant has a high sensitivity to the amount of moonlight shining on it, which in turn causes pollen release.

protein news

Moonlight pollination in the gymnosperm Ephedra (Gnetales) (Apr 2015)

Are gut bacteria a predictor of obesity?

gut bacteria, microbiome, microbiota, obesity, probiotics

A new study forces us to think – what roles do our gut microbes play in shaping our fat? By creating experimentally-induced obesity in beagles, a team of scientists showed that the guts of obese dogs look similar to those of obese people. In their experiment, researchers fed 7 beagles unrestricted amount of food for 6 months. They fed another 7 beagles controlled food portions during this period. At the end of the 6 months, each dog in the unrestricted-diet group gained an average weight of 4.9 kilos while the controlled-food group did not gain any additional weight.

When researchers examined the fecal samples collected from both groups at the end of 6 months, they found that, like in humans, the guts of beagles that gained weight (obese dogs) contained a smaller diversity of bacteria than those of normal beagles (lean dogs). Microbes from the phylum firmicutes were the predominant (85%) bacteria in the lean dogs whereas proteobacteria were prevalent (76%) in the obese group. The researchers speculate that an abundance of proteobacteria may lead to an increase in lipopolysaccharides which might be contributing to weight gain and chronic inflammation. Gut microbes are known to be critical players in determining susceptibility to depression, anxiety, and other psychiatric disorders and now this latest study might make a stronger case for the importance of "gut-friendly", probiotic foods.

protein news

Association of obesity with serum leptin, adiponectin, and serotonin and gut microflora in beagle dogs (Jan 2015)

New finding on collagen provides fresh perspectives on aging research

Collagen, aging, longevity, insulin-like growth factor, IGF-1, IIS pathway, dauer

It has been demonstrated in invertebrates that the insulin and insulin-like growth factor (IGF) signaling (IIS) pathway plays a major role in the control of longevity. In the roundworm Caenorhabditis elegans, single mutations that diminish insulin/IGF-1 signaling cause the worm to remain active and youthful much longer than usual. This disruption normally sends worms into a hibernation-like state, called dauer, which increases life span by inserting a pause into the life cycle. A team of scientists wondered if blocking the insulin/IGF1 pathway could increase lifespan without this pause. In a Nature publication, they reported that disrupting the insulin/IGF1 pathway at temperatures that block entry into the dauer state, also caused the worms to live longer. Increase in the worm lifespan coincided with a striking up regulation of collagen gene expression.

Collagens are most familiar as the proteins whose age-related dysfunction causes wrinkles and facial lines. Through this study, for the first time it has been shown that collagens are associated with not just external cosmetic usefulness but with overall improved health. The study also suggests a new role in aging for the extracellular matrix where collagens are found. Anti-aging treatments typically work by protecting and repairing cellular components. The importance of collagen production in diverse anti-aging treatments implies that extracellular matrix remodeling is an essential component of longevity. And agents that enhance external youthfulness may also be providing overall health benefits.

protein news

Dauer-independent insulin/IGF-1-signalling implicates collagen remodelling in longevity. (March 2015)

Protein that repairs injured kidney cells identified

Acute kidney injury, chronic kidney disease, kidney repair, MG53

Acute kidney injury (AKI) is a common condition resulting from stress on the kidneys, caused by various medical conditions and treatments. If not treated in time, AKI can lead to chronic kidney disease (CKD) which affects more than 20 million Americans. People with early CKD do not feel ill or notice any symptoms and the only way to find out for sure if a person has CKD is through specific blood and urine tests. Without treatment, a CKD patient could suffer from kidney failure, necessitating either dialysis or a kidney transplant.

In a recent Science Translational Medicine publication, researchers identified "MG53" protein as a vital component of kidney protection. They found that MG53 is not only present in kidney cells but necessary for kidney to repair itself after AKI. A key component of cellular self-repair, MG53 was previously shown to repair heart, lung and skeletal muscle cells as well. The researchers in their study compared normal renal cells to those lacking MG53 protein. While cells with MG53 survived mechanical injury, cells lacking MG53 quickly died. MG53 restoration increased cell survival with no negative side effects, illustrating the protein's role in cell membrane repair. The research team also demonstrated that intravenous application of MG53 protected kidneys from ischemia reperfusion, the tissue damage that occurs when blood supply is restored after lack of oxygen. With its newly discovered reno-protective functions, MG53 could lead to novel preventive or therapeutic treatments for millions of AKI patients.

protein news

MG53-mediated cell membrane repair protects against acute kidney injury. (March 2015)

New benefits of dieting and fasting discovered – it's not just about losing weight

NLRP3, BHB, beta hydroxy butyrate, Deiting, fasting

Scientists have recently reported that a metabolite produced in the body during periods of dieting and fasting can block a part of the immune system involved in inflammatory disorders such as type 2 diabetes, atherosclerosis and Alzheimer's. The compound, β-hydroxybutyrate (BHB) is produced by the body in response to fasting, high-intensity exercise or consumption of a low-carbohydrate ketogenic diet. BHB is known to support mammalian survival during energy-deficit states, by serving as an alternative source of ATP.

BHB directly inhibits NLRP3 which is part of a protein complex [inflammasome] driving the inflammatory responses in several disorders. In their study, the scientists focused on macrophage response because of their involvement in inflammation. The team introduced BHB to mouse models of inflammatory disease caused by NLP3. They found that exposure to BHB reduced inflammation. Inflammation was also reduced when mice were fed a ketogenic diet, which elevated the levels of BHB in the bloodstream. Mechanistically, BHB inhibits the NLRP3 inflammasome by preventing K+ efflux and reducing ASC oligomerization and speck formation.

protein news

The ketone metabolite β-hydroxybutyrate blocks NLRP3 inflammasome-mediated inflammatory disease (March 2015)

Breakthrough in diabetes control – "smart insulin"

Smart insulin

Diabetes patients that follow an insulin regimen are prone to serious complications resulting from hyperglycemic and hypoglycemic states. To develop a more autonomous therapy with improved blood glucose control, scientists have engineered a chemically modified form of insulin that's long-lasting and glucose-responsive. Two modifications were made to create this glucose-responsive insulin. One was the addition of an aliphatic domain to facilitate hydrophobic interactions. This helped the insulin circulate in the bloodstream longer.

The other modification was the attachment of a chemical group called phenylboronic acid (PBA), a molecule that can reversibly bind glucose. When blood glucose levels are high, sugar binds to insulin and activates it, allowing the insulin to stimulate cells to absorb the excess sugar. In a mice study, this modified insulin derivative enabled the rapid reversal of blood glucose following glucose challenge, while responding rapidly to changes in blood sugar levels. Continuous glucose monitoring also revealed responsiveness matching that of a healthy pancreas. The engineered, responsive insulin represents a major conceptual advance in diabetes management. The researchers next plan on testing this insulin in other animal models while continuing to work on its chemical composition, in order to make it more responsive to blood glucose levels.

protein news

Glucose-responsive insulin activity by covalent modification with aliphatic phenylboronic acid conjugates (February 2015)

Novel technology developed to recover more recombinant protein from yeast

Yeast protein production

Saccharomyces cerevisiae has been a popular choice for the production of recombinant biopharmaceuticals because of its ability to secrete proteins to the culture medium. For a long time scientists were trying to improve the secretory pathway in S. cerevisiae in order to increase recombinant protein yields in the media. But they failed to take account of an important fact – S. cerevisiae reabsorbs more than half the protein that it secretes, through the process of endocytosis.

Researchers found the proteins in yeast responsible for endocytosis and trafficking to the vacuole. Using a modified TEV Protease-Mediated Induction of Protein Instability (mTIPI) system, they were able to disrupt the endocytotic and vacuolar complexes which prevented uptake functions. The knockdown of genes (Rvs161 and End3) involved in endocytosis, improved the concentration of recombinant protein in S. cerevisiae cultures when compared to cultures from the wild type strain. The research team behind this study harvested 2-3 fold more protein from the mutated yeast since it was unable to reabsorb the secreted protein. Being able to recover more protein from yeast could add tremendous value to the biotechnology industry. It would be worth investigating if such knockdown experiments can be done with other eukaryotic hosts used for recombinant protein and antibody production.

protein news

Blocking endocytotic mechanisms to improve heterologous protein titers in Saccharomyces cerevisiae (February 2015)

GPCR signaling molecule responsible for alcohol addiction identified

Alcohol addiction, GPCR signaling molecule, RGS6

Despite the prevalence of alcohol abuse worldwide with 17 million adults in the US alone suffering from an alcohol use disorder, the molecular mechanisms of alcohol effects have been difficult to identify. In a recent publication, scientists have identified the regulator of G protein signaling 6 (RGS6) as a novel target with potential utility in the treatment of alcoholism and its resultant toxicity.

Researchers showed that RGS6-/- mice drank less alcohol than wild type mice even when alcohol was abundant, suggesting they were immune to its habit-forming properties. And when forced to drink alcohol, RGS6-/- mice were largely protected from the toxic side effects of excessive consumption, including alcohol-induced cardiomyopathy, hepatic steatosis, gastrointestinal barrier dysfunction and endotoxemia. And although RGS6 plays a role both in alcohol craving and the consequences of excessive consumption, it does not necessarily mean that the best way to target this molecule is to develop a single drug. That's because the dual-protective function resulting from RGS6 knockout is mediated by 2 different pathways. RGS6's protective effects on organs are mediated by the regulation of reactive oxygen species-dependent apoptosis. The effects on craving on the other hand are linked to RGS6's function as a G-protein regulator.

protein news

Regulator of G protein signaling 6 is a critical mediator of both reward-related behavioral and pathological responses to alcohol (February 2015)

Synthetic biology making GMOs safer

Synthetic biology making GMOs safer

Genetically modified organisms (GMOs) are widely used at large scales and in open environments, but their use continues to generate safety concerns. Although genetic safeguards for biocontainment are in place, they are not fail-safe, being susceptible to leaky gene expression and mutations. Scientists have now devised a way to ensure that GMOs can be safely confined in the open environment by demonstrating proof of concept in a bacterial strain. They essentially rewrote the DNA of an E. coli strain which made it dependent on a special synthetic amino acid not found in nature. Termed genomically recoded organism (GRO), it's a subset of GMO with built-in safety switches making it 10,000 times better than the NIH's recommendation for escape rate for GMOs.

While GMOs are susceptible to mutations, what makes this GRO safe is the fact that it has multiple genes that depend on the synthetic amino acid. The odds of independent mutations in each of those genes are on the order of 1 in a trillion. Using a similar approach, scientists can possibly create safer GMOs for use in open systems, for applications like food production, designer probiotics to combat diseases, and specialized microorganisms that can clean up oil spills and landfills.

protein news

Biocontainment of genetically modified organisms by synthetic protein design (February 2015)

protein news

Recoded organisms engineered to depend on synthetic amino acids (February 2015)

protein news

Multilayered genetic safeguards limit growth of microorganisms to defined environments (February 2015)

What does Myc have to do with longer and healthier life?

Myc and longevity

Myc is a transcription factor that plays a major role in gene expression. Some estimates indicate that nearly 15%-20% of all genes in the human body are directly regulated by Myc expression. Mutations in the Myc gene are either known or suspected drivers in a variety of cancers. While there are ongoing attempts to develop Myc inhibitors, a recent study indicates that such inhibitors could have potential implications beyond cancer treatment. Scientists discovered that reducing the expression of Myc significantly increased longevity and healthspan of laboratory mice. They showed that mice with only one copy of Myc lived an average of 15% longer than those with both copies. These experimental mice also showed many signs of better health as they grew older, as measured by a broad range of indicators.

The only noticeable trade-off to Myc down regulation was that the mice were about 15% smaller than the wild-type mice. There were no other tradeoffs that would classically go with an increased life span though. If these findings could be reproduced in humans, there could be significant health advantages such has having healthier lipid and cholesterol metabolism, stronger bones, reduced cancer progression, higher metabolic rate, improved motor control and reduced immunosenescence.

protein news

Reduced Expression of MYC Increases Longevity and Enhances Healthspan (January 2015)

Proteomics in drug discovery - see how it helped identify 4 psoriasis targets

Proteomics in drug discovery

Out of the estimated 50,000 proteins in the human body, scientists have zeroed in on 4 proteins that appear most likely to contribute to psoriasis. Using a proteomics screening approach, the scientists studied protein expression changes in KC-Tie2, a psoriasis mouse model, before validating these changes in human psoriasis patient samples.

5482 peptides mapping to 1281 proteins were identified and quantitated, to identify proteins that showed differential regulation in psoriasis mouse skin samples. From this pool they focused on 4 that stood out due to their high prevalence in human psoriasis. The mouse proteins and the equivalent human protein names along with the protein expression fold-increase are listed in the table below.

Protein in psoriasis mouse skin Equivalent protein name
in humans
Protein expression fold-increase in mouse
stefin A1
cystatin A
342.4
slc25a5
slc25a5
46.2
serpinb3b
serpinB1
35.6
KLK6
KLK6
4.7

Using parallel LC/MS/MS analyses, the investigators also analyzed samples from a separate cohort of animals and verified protein level increases of 1.3 fold (slc25a5), 29,000 fold (stefin A1) and 322 fold (KLK6) between the psoriasis mouse samples and the control mouse samples. Investigators then confirmed the increased presence of the 4 proteins in human lesional psoriasis skin samples compared with normal skin. This study highlights the usefulness of proteomic approaches in identifying novel peptides/proteins that are differentially regulated in disease states, for the discovery of novel therapeutic targets.

protein news

Proteomics of skin proteins in psoriasis: from discovery and verification in a mouse model to confirmation in humans (January 2015)

New way of protein synthesis discovered: surprising twist in the central dogma of biology

New way of protein synthesis

When something goes wrong during protein synthesis, a ribosome quality control complex is summoned to disassemble the ribosome and recycle the partly made protein. Scientists have now reported an unexpected mechanism of protein synthesis in eukaryotes with a surprising role for a member of the ribosome quality control complex - Rqc2.

They found that, before the partly made protein is recycled, Rqc2 recruits alanine- and threonine-charged tRNAs to the ribosome and directs the elongation of nascent chain, independent of mRNA. The result is a truncated protein with randomly added alanines and threonines – a seemingly nonsensical sequence which likely serves specific purposes. This sequence could be a signal to destroy the protein or a quality check mechanism to ensure that the ribosome is functioning normally. Evidence suggests that this quality check mechanism could be faulty in neurodegenerative diseases such as Alzheimer's and ALS and this discovery could provide fresh insights into research in these areas.

protein news

Rqc2p and 60S ribosomal subunits mediate mRNA-independent elongation of nascent chains (January 2015)

Surprising finding of high calorie diet on cancer progression

High calorie diet and cancer progression

Scientists have identified the molecular chaperone FKBP10, as a potential new therapeutic target for lung cancer. Tests conducted using human lung cancer cell lines showed that FKBP10 is needed for the growth of cells bearing a common oncogenic mutation and in mouse models of this cancer, genetically knocking down FKBP10 expression slowed down tumor growth.

The scientists conducting this study also investigated the relationship between increased calorie intake and cancer. Given the high incidence and aggressive nature of lung cancers driven by KRAS mutations, the scientists used KRAS-tumor mouse models for their study. They used 3 groups of mice in which they could activate the KRAS-driven tumors using a chemical switch. Their results demonstrate how, high calorie diet could alter the growth of lung tumors depending on when the high calorie diet intake began. The results are summarized in the table below:

Mice type High calorie diet started at Tumor initiated at Lungs examined at Result
Mice fed standard diet
-
18 weeks
29 weeks
Normal tumors
Mice fed high
calorie diet
22 weeks
18 weeks
29 weeks
Big and widespread tumors of advanced grade
Mice fed high
calorie diet
6 weeks
18 weeks
29 weeks
Fewer and smaller tumors than mice on standard diet

It is well known that high calorie diet is linked to diabetes and obesity, both associated with a higher risk of cancer. And while these findings may not have direct implications for human diets, they help explain why some people with obesity are more likely to develop certain cancers while providing new insights to therapeutic intervention.

protein news

Diet-Induced Unresolved ER Stress Hinders KRAS-Driven Lung Tumorigenesis (January 2015)

Novel strategy for soluble recombinant protein and antibody fragment production

Novel strategy for recombinant protein and antibody fragment production

Researchers have reported the use of Antarctic bacterium Pseudoalteromonas haloplanktis to address the solubility and activity challenges in recombinant protein and antibody production. Combining the use of a regulated psychrophilic gene expression system with an optimized fermentation protocol, they obtained recombinant VHH in fully soluble form and correctly translocated into the periplasmic space.

Using a cold-adapted bacterium for recombinant protein production is advantageous because it displays useful metabolic and physiological traits that make it a suitable host for protein production, especially when conventional systems fail. Because of its adaptation, this strain is able to grow optimally even at reduced temperatures, where hydrophobic interactions are significantly minimized and a rich arsenal of folding factors and catalysts support high quality protein folding. As reported by the researchers, such a system allowed the soluble, bioactive production of several difficult-to-express proteins and antibody fragments.

protein news

Soluble Recombinant Protein Production in Pseudoalteromonas haloplanktis TAC125(January 2015)

First successful vaccination against prion-related disease reported

Vaccine against prion disease

Prions are infectious proteins that propagate by converting otherwise healthy proteins (PrPC - cellular) into a disease state (PrpSc - scrapie). In a landmark study, scientists have reported the first successful vaccination of deer against chronic wasting disease (CWD), a fatal brain disorder caused by prions. CWD is the deer-equivalent of Creutzfeldt-Jakob disease in humans, scrapie in sheep and mad cow disease in cattle.

Using attenuated Salmonella for mucosal immunization, scientists vaccinated 5 white-tailed deer while another 6 deer were given a placebo. All of the deer were exposed to prion-infected brain tissue. The animals receiving vaccine were given eight boosters over 11 months until the key antibodies were detectable in blood, saliva, and feces. The deer also were monitored daily for signs of illness, and investigators performed biopsies of the animals' tonsils and gut tissue every three months to search for signs of CWD infection. Within two years, all of the deer given the placebo developed CWD. Four deer given the real vaccine took significantly longer to develop infection -- and the fifth one remained infection free.

This deer study has widespread implications from beef import bans to Alzheimer's research. This vaccination method could become a widespread technique not only for preventing but potentially treating many prion-related diseases, while providing valuable insights into how to make a vaccine against human neurodegenerative diseases like Alzheimer's.

protein news

Mucosal immunization with an attenuated Salmonella vaccine partially protects white-tailed deer from chronic wasting disease (January 2015)

Sparks literally fly when egg meets sperm

Zinc sparks during fertilization

Mammalian fertilization triggers the release of zinc ions in waves called zinc sparks. These sparks are necessary for inducing the transition from egg to embryo. Despite the importance of these zinc-efflux events little was known about their origin, until now. Using live-cell imaging and elemental mapping, scientists have determined that these zinc sparks originate from zinc-filled vesicles near the egg's outer membrane.

   

X-ray fluorescence and electron microscopy techniques were used to map and quantify the zinc distribution inside the mouse eggs. Data revealed ~8000 zinc-filled vesicles near the egg's outer membrane on one side of the cell, each vesicle containing nearly a million zinc atoms. These vesicles undergo dynamic movement during oocyte maturation and exocytosis at the time of fertilization. This is a really important finding because it provides a framework for understanding how zinc fluxes regulate other cellular processes.

protein news

Quantitative mapping of zinc fluxes in the mammalian egg reveals the origin of fertilization-induced zinc sparks (December 2014)


Cancer prevented by repurposed osteoporosis drug

Repurposed osteoporosis drug prevents cancer

Bisphosphonates are a class of drugs that prevent the loss of bone mass and they are the most commonly prescribed drugs for osteoporosis and skeletal metastases. They have also been shown to reduce cancer progression but only in certain patient subgroups. Nobody knew though as to why certain groups of cancers were more responsive than others. Using connectivity mapping, computational modeling and biological assays scientists have identified the kinase domain of human epidermal growth factor receptors (hEFGR or HER) as the potential new molecular target for bisphosphonate action. In a related mice study the scientists provided proof of concept in xenografted mice showing that bisphosphonates killed lung, breast and colon cancer cells that were driven by HER overexpression while also halting the growth of EGFR-driven tumors.

This study has significant clinical implications for HER-driven cancer patients because the study suggests that bisphosphonates can be repurposed for the prevention and treatment of HER-driven cancers. These drugs could prevent cancers, they could be used in combination with EGFR blockers and anti-HER2 therapies and they could be used to treat patients that have developed resistance to existing EGFR-targeting drugs.

protein news

Bisphosphonates inactivate human EGFRs to exert antitumor actions (December 2014)

protein news

Repurposing of bisphosphonates for the prevention and therapy of nonsmall cell lung and breast cancer (December 2014)

Crystal structure of Influenza polymerase revealed

Crystal structure of influenza polymerase

Researchers recently solved the crystal structure of full length Influenza polymerase. This is the first time that a polymerase structure of a negative-strand virus has been solved. Other members in this family include pathogens such as the Ebola virus, rabies virus, respiratory syncytial virus etc.

In 2 related papers the researchers published the crystal structures of Influenza A and B polymerases and detailed their cap-snatching and RNA replication mechanisms. In the first paper the researchers determined the atomic structure of bat FluA polymerase bound to viral genomic RNA preceding RNA replication and in the second paper the team solved the atomic structure of human FluB and compared structures of these two polymerases to deduce exactly how the enzymes worked.

Within the polymerase the researchers found 3 subunits that comprised a large and complex structure full of crevices, tunnels, channels and cavities into which RNA entered, bound and moved along before exiting.

These two strains are important because Influenza A is the fast-evolving strain that affects humans and birds and Influenza B is a strain that causes seasonal flu in humans. And while there are drugs and vaccines to treat the flu there is a great need to identify new flu targets for drug discovery. That's because the evolution of this virus is so unpredictable that there's no way to tell the location and severity of the next pandemic. This finding presents new opportunities for anti-influenza drug design.

protein news Structure of influenza A polymerase bound to the viral RNA promoter (December 2014)
protein news Structural insight into cap-snatching and RNA synthesis by influenza polymerase (December 2014)

New finding – Cure neonatal cardiomyopathy using gene therapy

Gene therapy cures neonatal cardiomyopathy

Hypertrophic cardiomyopathy (HCM) is the second most common form of heart muscle disease comprising ~35-40% of cardiomyopathies in children. In this condition the heart appears normal at birth but heart failure develops quickly resulting in the death of affected children within the first year of life. It was long known that frameshift mutations in the cardiac-type Myosin-binding protein C (cMyBP-C) cause neonatal HCM - cMyBP-C plays a key role in the structure and function of heart muscle sarcomeres.

Scientists recently reported using gene therapy to prevent neonatal HCM in mice. To do this mouse models were created that were genetically engineered to carry 2 copies of a mutant Mybpc3 gene that encoded mutations similar to the ones found in human infants with this condition. The hearts of these mice appear healthy at birth but soon afterward the animals develop cardiac HCM. Using non-pathogenic adeno-associated virus as vector, the scientists then delivered DNA encoding healthy version of Mybpc3 along with cardiac-specific proteins and promoter to the mice cardiomyocytes. As a result, healthy cMyBP-C produced by the virus replaced the mutant protein, preventing disease phenotype long-term.

This is a significant finding that can prevent systolic heart failure followed by premature death in infants with this mutation but it is a big step to go from mice to humans that requires the necessary authorization. Further validation in large-animal models will have to be done which will necessitate the development of a suitable transgenic animal.

protein news Mybpc3 gene therapy for neonatal cardiomyopathy enables long-term disease prevention in mice (December 2014)

Protein responsible for sense of touch in mammals identified

Piezo2, touch protein

The identity of molecules involved in the sensation of touch has now been revealed. Scientists have identified "Piezo2" ion-channel protein as the molecule responsible. Mice that lack the Piezo2 ion-channel protein in their skin cells and nerve endings lose nearly all sensitivity to light touch but retain mostly normal sensitivity to painful mechanical stimuli.

Using advanced genomics techniques the scientists first identified two mechanically activated ion-channel proteins in mouse cells – Piezo1 & Piezo2. Out of the 2 ion-channel proteins, Piezo2 was expressed at higher levels in the touch-sensing neurons based in the spinal dorsal root ganglia which extend nerve processes into the skin. The scientists demonstrated that conditional knockout mice lacking Piezo2 showed a clear behavioral difference from normal mice in that they observed a dramatic reduction in their responsiveness to ordinary light touch stimuli. Remarkably, these touch-insensitive mice remained responsive to skin-applied stimuli that are normally painful, such as heat, cold and pinching.

The finding suggests that the detection of light touch is mediated principally by one set of nerve ends using piezo2 ion channels. Stronger, pain-causing touch sensations appear to be mediated by a less force-sensitive set of nerve ends with their own ion channel proteins, yet to be discovered. The team behind this finding plans to investigate if any interaction exists between these two nerve systems. It is well known that chronic pain conditions can make even light touch stimuli feel painful due to the prominent role of CNS factors in chronic pain states. This latest discovery will help dissect the relationship between touch and pain, potentially leading to new therapies for chronic pain conditions.

protein news Piezo2 is the major transducer of mechanical forces for touch sensation in mice (December 2014)

SIRT1 and metabolic dysfunction

SIRT1, metabolic dysfunction

SIRT1 also known as Sirtuin 1 or "silent mating type information regulation 2 homolog - 1" is a protein that deacetylates proteins that contribute to cellular regulation. Scientists showed more than a decade ago that sirtuins coordinate a variety of hormonal networks, regulatory proteins and other genes that are involved in keeping cells healthy. In a later study, scientists showed that SIRT1 protects against the harmful effects of a high fat diet, including diabetes.

In their experiment, scientists wanted to see what would happen to mice that lacked SIRT1 protein in their fat cells. When put on a high-fat diet, mice lacking the protein started to develop metabolic disorders such as diabetes, much sooner than normal mice given a high fat diet because of the cleavage of SIRT1 protein by caspase-1, an event that was triggered by inflammation.

This finding raised the possibility that drugs that would enhance SIRT1 activity may also help protect against obesity-linked diabetes. Through their studies the scientists showed that development of metabolic disorders is a 2-step process. In step-1 inactivation of SIRT1 would take place because of a high-fat diet and in step-2 metabolic dysfunction would follow.

protein news

High-fat diet triggers inflammation-induced cleavage of SIRT1 in adipose tissue to promote metabolic dysfunction

New ALS finding

SOD, superoxide dismutase, ALS finding

Amyotrophic lateral sclerosis (ALS), often referred to as "Lou Gehrig's Disease", is a progressive neurodegenerative disease that affects nerve cells in the brain and the spinal cord. While the cause of ALS was not completely understood, a lot has been learned about the physiology of this disease over the years. In a recent finding, scientists have suggested instability of the superoxide dismutase (SOD) protein as the likely cause of Amyotrophic lateral sclerosis.

A defining feature of SOD-linked ALS is the accumulation of SOD protein clusters in the affected motor neurons and support cells. Even in ALS cases not linked to SOD, SOD aggregates are found in the affected cells. In this study the scientists propose a framework destabilization theory in which they propose that mutant SOD1 genes that are linked with ALS, all code for structurally unstable variants of the SOD protein. Since unstable SOD proteins are unable to fold properly they begin to aggregate quickly and overwhelm the neuronal cleanup systems thereby triggering ALS.

The scientists also found a difference in the shape of SOD aggregates. SOD mutations caused long, rod-shaped aggregates whereas aggregates not linked to SOD mutation were more compact and folded in their structure. The unstable nature of mutant SOD proteins was also linked to their inability to take up copper ions normally. The impaired ability to retain copper and the longer aggregates correlated with mutations found in more severe cases of ALS.

protein news

Aggregation propensities of superoxide dismutase G93 hotspot mutants mirror ALS clinical phenotypes (October 2014)

A method to produce high amounts of recombinant, fused bioactive cytokines in E. coli

Fusokines, recombinant bioactive cytokines

Recombinant human cytokines are routinely used as biopharmaceuticals and combination cytokine therapies have been tried as potential cancer treatments. Such combination cytokines or "fusokines" are produced by the fusion of different cytokines to form one large polypeptide. Usually fusokines are produced in mammalian cells but the system can be inefficient for the production of GMP-compliant fusokines.

A group of researchers reported soluble expression of bioactive recombinant GIFT15 (GM-CSF + IL15) in E. coli. Since rGIFT15 was unstable in the E. coli cytoplasm it was tethered to 3 different fusion partners – Thioredoxin, GST and MBP to attempt stable, soluble expression. Out of the 3, soluble protein was observed only with the addition of MBP at the N-terminus. The activity of rGIFT15 derived using this approach was comparable to the activity of rGIFT15 derived from a mammalian source.

Learn more about the MBP tag and why it is so effective at producing soluble protein.

protein news Maltose-Binding Protein Fusion Allows for High Level Bacterial Expression and Purification of Bioactive Mammalian Cytokine Derivatives (September2014)

Elusive HIV spike protein molecular details revealed

HIV spike protein

AIDS has been a global health concern largely because the Human Immunodeficiency Virus (HIV) has been adept at evading the host immune response. In recent, related discoveries, scientists have provided high resolution images of the surface spike protein of the HIV-1 and monitored how it constantly changes shape. This envelope spike protein consists of three gp120 (glycoprotein) and three gp41 subunits. Using this spike protein the virus binds to host cells and enters it. As the only viral antigen on the HIV-1 surface, the spike is both a target of neutralizing antibodies and a focus of vaccine research.

In this study, the researchers found that the spike protein has to be in an open state in order to bind and infect cells. In a closed state, the HIV-1 is less accessible to antibodies. Since the spike protein stays longer in the closed state, attacking the virus becomes difficult. This partly explains how some HIV positive individuals are able to fight off the disease – they have broadly neutralizing antibodies in circulation that keeps the spike protein closed, thereby preventing the spread of the virus. Together, the discovery by these two groups provides information that would help in developing ways to attack the virus using novel drug and vaccine approaches.

protein news Structure and immune recognition of trimeric pre-fusion HIV-1 Env (October 2014)

protein news Conformational dynamics of single HIV-1 envelope trimers on the surface of native virions (October 2014)

How bacteria breach the blood-brain barrier

Breaching the blood-brain barrier

The blood–brain barrier (BBB) is a highly selective, permeability barrier that plays a protective role by separating the circulating blood from the brain extracellular fluid in the central nervous system. In a recent study, researchers identified molecules on the surface of human cells to which Neisseria meningitidis (meningitis causing bacteria) binds, thus allowing it to penetrate the BBB.

The researchers found a complex 3-way interaction between non-integrin laminin receptor and galectin-3 on human cell surface with molecules on the bacterial cell surface. The bacterial cell surface molecules implicated in this process were PilQ, PilE and PorA. PilQ specifically interacted with a 37kDa laminin receptor precursor (37LRP) along with galectin-3. PilE was found to interact with only galectin-3 and PorA interacted only with 37LRP.

The researchers report that such binding and the subsequent interaction specifically led to the internalization of the bacterium by the human cell and that it was a vital step that allowed the bacterium to evade the human immune system and breach the BBB. The findings from this study can be applied to improve our understanding of other host-pathogen interactions which would ultimately lead to novel therapeutic interventions against deadly infections.

protein news Deciphering the complex three-way interaction between the non-integrin laminin receptor, galectin-3 and Neisseria meningitidis. (October 2014)

Evolved protein with a potential to stop metastasis

Axl protein, metastasis

Cancers turn deadly when cancer cells metastasize i.e., break away from their origin and travel through the bloodstream to start new, aggressive cancers elsewhere in the body. A team of scientists at Stanford has developed a novel, protein therapy approach for the inhibition of metastasis.

The interaction between two cell surface proteins is key for metastasis to occur. Axl, a cancer cell surface protein interacts with Gas6, found on healthy human cells in the blood stream. When 2 Axl proteins bind 2 Gas6 proteins, the biochemical signals that are generated, enable cancer cells to break away and form new cancer nodules in a different part of the body.

To inhibit this interaction the scientists used a protein engineering approach to create a harmless version of Axl protein that acted like a decoy and bound to Gas6, thus preventing it from interacting with the "harmful Axl" [the ones present on cancer cells]. To create the decoy Axl, the scientists used a directed evolution approach to generate millions of Axl variants that they evaluated using High-throughput screening, to identify the one variant that bound Gas6 100-fold more tightly than the wild-type protein.

Intravenous injection of this bioengineered decoy protein in mice with aggressive breast and ovarian cancers yielded remarkable results. Breast cancer mice showed 78% fewer metastatic nodules post-treatment when compared to the untreated mice and mice with ovarian cancer had a 90% reduction in metastatic nodules when compared to the control group. This can be a very promising alternative to current cancer treatment options.

protein news An engineered Axl 'decoy receptor' effectively silences the Gas6-Axl signaling axis (August 2014)

2014 Lasker Award for Basic Medical Research

Lasker award for basic medical research

Instituted in 1945, the Lasker Awards are among the most respected science awards in the world. They are also known as “America’s Nobels” because 86 Lasker laureates have gone on to win the Nobel Prize, including 47 in the last 3 decades. There are 4 categories of Lasker awards and each year, the awards are given to recognize the contributions of scientists, physicians, and public servants who have made major advances in the understanding, diagnosis, treatment, cure, and prevention of human disease.

This year, the Lasker award for basic medical research went to Kazutoshi Mori (Kyoto University) and Peter Walter (University of California, San Francisco) for their “discoveries concerning the unfolded protein response (UPR) — an intracellular quality control system that detects harmful misfolded proteins in the endoplasmic reticulum and signals the nucleus to carry out corrective measures.”

About UPR: Approximately a third of cellular proteins pass through the Endoplasmic Reticulum (ER) which performs stringent quality control of these proteins. All proteins need to assume the proper 3-dimensional shape in order to function properly in the harsh cellular environment. Related to this is the fact that cells are under constant stress and have to make rapid, real time decisions about survival or death.

A major indicator of stress is the accumulation of unfolded proteins within the Endoplasmic Reticulum (ER), which triggers a transcriptional cascade in order to increase the folding capacity of the ER. If the metabolic burden is too great and homeostasis cannot be achieved, the response shifts from damage control to the induction of pro-apoptotic pathways that would ultimately cause cell death. This response to unfolded proteins or the UPR is conserved among all eukaryotes, and dysfunction in this pathway underlies many human diseases, including Alzheimer's, Parkinson's, Diabetes and Cancer.

protein news Read more about the award, the winners and their work

Steering the Immune system

Steering the immune system

In autoimmune diseases like Multiple Sclerosis (MS), cells of the immune system start attacking self-antigens that are found on the surface of neurons, in turn causing inflammation that damages myelin (the protective insulation around nerve fibers), resulting in neurological problems.

In a recent study, scientists reported that it is possible to program T-cells that trigger this attack into a less aggressive mode, without losing their ability to protect the body from disease. The scientists accomplished this in mice by injecting them with very tiny amounts of a self-antigen and then gradually increasing the dose – a strategy known as escalating dose immunotherapy.

Gene expression profiles at each stage of the immunotherapy showed that T-cells were gradually changing from pro-inflammatory activated cells to less-responsive cells that were more tolerant to these neurological antigens. The study provides valuable insight into how autoimmune disease-causing cells can be switched off in a targeted fashion by using immunotherapeutic approaches.

protein news Sequential transcriptional changes dictate safe and effective antigen-specific immunotherapy. (September 2014)

Tumor-fighting super bacteria

Clostridium novyi, Tumor fighting bacteria

Scientists recently reported the creation and microscopic application of an attenuated strain of Clostridium novyi [C. novyi], to generate a localized, anti-tumor response after intra-tumoral injection. The experiments were first performed in rats and since a rat response may not accurately predict the response of human patients, studies were conducted using canine tumors. Canine tumors serve as a translational bridge to human trials because of their semblance to human tumors, in that they occur in animals with heterogeneous genetic backgrounds, are of host origin and are due to spontaneous rather than engineered mutations. On the basis of encouraging animal studies, a human patient with an advanced leiomyosarcoma was treated using this method and showed an effective response.

C. novyi is a naturally occurring soil bacterium that thrives in oxygen-deficient environments which makes it a targeted means of destroying hypoxic tumor cells that are difficult to treat with chemotherapy and radiation. The origins of this research are in century-old accounts of an early immunotherapy using Coley toxins, named after the first proponent of this technique, Dr. William B. Coley. Use of Coley toxins is an early form of immunotherapy, a method of treatment in which a person receives substances designed to boost the immune system and help the body fight diseases such as cancer. Side effects from the use of Coley toxins are typical of a bacterial infection, such as fever, sepsis and inflammation.

protein news Intratumoral injection of Clostridium novyi-NT spores induces antitumor responses (August 2014)

The surprising link between diabetes and obesity

Link between diabetes and obesity

A new study by scientists at Amgen Inc. and Washington State University, offers new and surprising insights into the relationship between diabetes and obesity – the two metabolic evils that often accompany each other in human beings. While studying grizzly bears at the only captive grizzly facility in the world [Washington State University], the researchers discovered a natural, reversible state of diabetes that serves a real biological purpose – to cope with the long term fasting associated with hibernation.

Investigators found that grizzlies become obese but not diabetic in the fall, become diabetic [insulin resistant] during winter hibernation and then become normal again in spring, when they wake up from their slumber. All this while, the animal's insulin levels remain constant. The team also showed that grizzlies are most obese when they are least diabetic [most insulin sensitive] At the molecular level, obesity, in preparation for hibernation is coupled to insulin sensitivity via a modified PTEN/AKT signaling wherein a kinase shuts down the activity of PTEN protein specifically in the fat cells.

Finding out more about how animals cope with conditions that would normally cause disease in human beings can possibly lead to the design of better therapeutic interventions.

protein news Grizzly bears exhibit augmented insulin sensitivity while obese prior to a reversible insulin resistance during hibernation (August 2014)

Functional protein recovery from Inclusion bodies

Functional proteins, Inclusion bodies

Many recombinant proteins when produced in E. coli, aggregate as insoluble protein clusters called inclusion bodies (IBs). Typically, IBs are either discarded from further processing or are eventually used for In vitro denaturation and refolding purposes. To do this, upon recombinant protein overexpression, cells are lysed and the IBs are isolated, washed and solubilized and the right set of conditions are identified for refolding [and re-oxidation if disulfide bond formation is required]. Although usually considered as an unnecessary evil in protein production, recent insights into the molecular architecture of IBs have revealed that they can yield functionally pure and active proteins.

Bacterial IBs were shown to have high biological activity, penetrability in mammalian cells and mechanical and biological stability that allows their use as naturally immobilized enzymes or nanostructured materials for tissue engineering. However, since all these applications require that the bacterial protein product be free from endotoxin, a group of researchers showed that IBs produced in an endotoxin-free E. coli strain yielded superior, functional protein for a variety of downstream applications.

protein news Production of functional inclusion bodies in endotoxin-free Escherichia coli (August 2014)

Muscle maintenance and regeneration – key player identified

Oxytocin, muscle maintenance and regeneration

Muscle tissue suffers from atrophy with age and its regenerative capacity also declines over time. Most molecules discovered thus far to boost tissue regeneration are also implicated in cancers. During a quest to find safer alternatives that can regenerate tissue, scientists reported that the hormone Oxytocin is required for proper muscle tissue regeneration and homeostasis and that its levels decline with age.

To investigate Oxytocin's role in muscle repair, the researchers injected it in old mice intradermally, for four days first and then for five more days after muscle injury. Following the nine-day treatment, they found that the muscles of mice that received hormone treatment healed much better than the muscles of the control group that did not receive Oxytocin. Also, extra Oxytocin administered into young mice did not cause a significant change in muscle regeneration and a genetic lack of Oxytocin did not cause a developmental defect but instead precipitated the loss of muscle tissue.

Oxytocin could be an alternative to hormone replacement therapy as a way to combat aging and other organ related degeneration.

protein news Oxytocin is an age-specific circulating hormone that is necessary for muscle maintenance and regeneration (June 2014)

Why the color of fat tissue is important

WAT browning, uncoupling protein 1, UCP1

White adipose tissue (WAT) or white fat normally stores calories while Brown adipose tissue (BAT) or brown fat expends them and generates heat in the process. Hence the transition of WAT to BAT, a phenomenon called WAT browning, can help with weight loss. A group of scientists recently reported that WAT browning is the precursor to cachexia; a wasting syndrome characterized by excessive weight loss and is known to cause a significant number of deaths in cancer patients.

WAT browning is associated with increased expression of uncoupling protein 1 (UCP1) which is known to uncouple mitochondrial respiration towards heat generation instead of ATP synthesis leading to increased lipid mobilization and energy expenditure in cachectic mice. This transformation leads to increased energy consumption and organ wasting. Inflammation was found to play an important role in WAT browning and during cancer-associated cachexia and thus, anti-inflammatory compounds that can inhibit WAT browning can help ameliorate this life-threatening condition.

protein news A Switch from White to Brown Fat Increases Energy Expenditure in Cancer-Associated Cachexia (July 2014)

The discovery of a new class of human proteins with previously unidentified activities

aminoacyl tRNA synthetase gene family, new class of human proteins discovered

In a landmark study conducted by scientists at the Scripps Research Institute, The Hong Kong University of Science and Technology, aTyr Pharma and their collaborators, a new class of human proteins has been discovered. These proteins [nearly 250], called Physiocrines belong to the aminoacyl tRNA synthetase gene family and carry out novel, diverse and distinct biological functions.

The aminoacyl tRNA synthetase gene family codes for a group of 20 ubiquitous enzymes almost all of which are part of the protein synthesis machinery. Using recombinant protein purification, deep sequencing technique, mass spectroscopy and cell based assays, the team made this discovery. The finding is significant, also because it highlights the alternate use of a gene family whose protein product normally performs catalytic activities for non-catalytic regulation of basic and complex physiological processes spanning metabolism, vascularization, stem cell biology and immunology.

These proteins are viewed as therapeutically relevant with a potentially wide range of implications in human disease.

protein news Human tRNA synthetase catalytic nulls with diverse functions (July 2014)

Tweaking transcriptional programming for high quality recombinant protein production

Tweaking transcriptional programming for recombinant protein production

Since overexpression of recombinant proteins in E. coli often leads to the formation of inclusion bodies, producing properly folded, soluble proteins is undoubtedly the most important end goal in a protein expression campaign. Various approaches have been devised to bypass the insolubility issues during E. coli expression and in a recent report a group of researchers discuss reprogramming the E. coli proteostasis [protein homeostasis] network to achieve high yields of soluble, functional protein. The premise of their studies is that the basal E. coli proteostasis network is insufficient, and often unable, to fold overexpressed proteins, thus clogging the folding machinery.

By overexpressing a mutant, negative-feedback deficient heat shock transcription factor [s32 I54N] before and during overexpression of the protein of interest, reprogramming can be achieved, resulting in high yields of soluble and functional recombinant target protein. The authors explain that this method is better than simply co-expressing/over-expressing chaperones, co-chaperones, foldases or other components of the proteostasis network because reprogramming readies the folding machinery and up regulates the essential folding components beforehand thus maintaining system capability of the folding machinery.

protein news The Heat-Shock Response Transcriptional Program Enables High-Yield and High-Quality Recombinant Protein Production in Escherichia coli (July 2014)

Mutation that prevents from getting drunk

BK potassium channel, SLO-1, mutation that prevents from getting drunk

BK potassium channel is a neuronal target that, along with other functions, is known to alter behaviors in a wide range of species. In the nematode worm Caenorhabditis elegans, mutations that eliminate the BK channel [SLO-1] convey dramatic resistance to intoxication by ethanol. One important aspect of this modified alcohol target is that the mutation only affects its response to alcohol while all other functions remain intact.

The authors hypothesized that certain conserved amino acids are critical for ethanol modulation, but not for basal channel function. To identify such residues, they screened C. elegans strains with different missense mutations in the SLO-1 channel and found a strain with the SLO-1 missense mutation T381I in the RCK1 domain that was highly resistant to intoxication but did not interfere with other BK channel-dependent behaviors. The worms were a good model for intoxication. Alcohol slowed their crawling and wriggling movements and they also stopped laying eggs. This landmark study could lead to the development of new drugs to treat alcohol withdrawal symptoms.

protein news Conserved Single Residue in the BK Potassium Channel Required for Activation by Alcohol and Intoxication in C. elegans.
(July 2014)

Recombinant Immune protein promotes complement activation and protects against serious bacterial infections

Properdin, recombinant protein prevents sepsis

Bacterial infections such as Septicemia are serious health concerns that can prove fatal if left untreated promptly. They happen when disease-causing bacteria enter the bloodstream and multiply rapidly while releasing deadly toxins into the bloodstream. While such infections are often treated using intravenous antibiotics, the mortality rate from such cases remains high. That is because antibiotics aren't always effective.

To circumvent such problems and to address this major medical problem, in a landmark study, a group of scientists reported the therapeutic application of recombinant Properdin for the successful treatment of serious bacterial infections. Using mouse models for infection, they found that low doses of recombinant Properdin administered before infection with N. meningitidis activated the immune complement system that helped the body fight infection, thereby causing a 90% survival, while control mice that did not receive treatment, died. For S. pneumoniae infected mice, recombinant Properdin application significantly prolonged survival rates and decreased bacterial load in the blood. The authors also demonstrated that recombinant Properdin was a more effective therapeutic agent than native Properdin.

Since this approach does not target a particular microbe but triggers the body's self-defense mechanism, these findings could open up new avenues for fighting infections caused by multi-drug resistant bacteria and possibly other deadly pathogens.

protein news Low-dose recombinant properdin provides substantial protection against Streptococcus pneumoniae and Neisseria meningitidis infection (April 2014)

Necroptosis, MLKL proteins, PIP

Necroptosis is implicated in many diseases and understanding this process is essential in the search for new therapies. While mixed lineage kinase domain-like (MLKL) protein has been known to be a critical component of necroptosis induction, how MLKL transduces the death signal was not clear. In a recent finding, scientists demonstrated that the full four-helical bundle domain (4HBD) in the N-terminal region of MLKL is required and sufficient to induce its oligomerization and trigger cell death.

They also found a patch of positively charged amino acids on the surface of the 4HBD that bound to phosphatidylinositol phosphates (PIPs) and allowed the recruitment of MLKL to the plasma membrane that resulted in the formation of pores consisting of MLKL proteins, due to which cells absorbed excess water causing them to explode. Detailed knowledge about how MLKL proteins create pores offers possibilities for the development of new therapeutic interventions for tolerating or preventing cell death.

protein news MLKL compromises plasma membrane integrity by binding to phosphatidylinositol phosphates (May 2014)

A novel approach for the soluble production of aggregation-prone recombinant proteins in E. coli

HI18, novel approach for soluble production of aggregation-proine proteins

Protein aggregation is a common problem during Recombinant protein production in E. coli. This happens for a variety of reasons but most commonly when overexpression of a heterologous gene results in the formation of insoluble aggregates called inclusion bodies. While various strategies have been developed to bypass aggregation issues, none of them guarantee soluble protein. A group of researchers recently reported a fusion-partner based approach, where in, using an aggregation inhibiting protein tag [HI18]; they were able to produce recombinant soluble Human Islet Amyloid Polypeptide [IAPP], a major component of pancreatic amyloid deposits in type 2 diabetes.

HI18 sequestered IAPP monomers and shielded its hydrophobic patches during expression and purification, thereby preventing its aggregation. The researchers were able to cleave IAPP from the fusion construct and purify it to homogeneity. The results demonstrate the viability of this approach and its applicability to other aggregation-prone proteins.

protein news Engineered aggregation inhibitor fusion for production of highly amyloidogenic human islet amyloid polypeptide (June 2014)

Why exercise is good for you – molecular mechanisms identified

PGC1-alfa, Metrnl, why exercise is good

It has long been known that exercise provides several health benefits and guards against metabolic disorders like obesity and diabetes. However, the exact molecular mechanisms of fat breakdown were not clear. In a recent study, researchers used an isoform of the Peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PGC1-a) as a discovery tool to identify meteorin-like (Metrnl), a circulating factor that is induced in muscle after exercise, and in fat tissue upon cold exposure.

Metrnl stimulated energy expenditure and improved glucose tolerance and the expression of genes that were associated with beige fat breakdown (UCP-1, DIO2, PGC-1 a and ERR- a) and anti-inflammatory cytokines (IL-10 and TGF-ß). These findings bring to light, the hitherto unknown relationship between an immune pathway and fat breakdown and pave the way for new, anti-obesity treatments.

protein news Meteorin-like is a hormone that regulates immune-adipose interactions to increase beige fat thermogenesis (June 2014)

Fatty liver disease in mice prevented by blocking delivery of fructose to the liver

NAFLD, GLUT8, blocking delivery of fructose to liver

Non Alcoholic Fatty Liver Disease (NAFLD) is considered the most common cause of liver cirrhosis worldwide. NAFLD often accompanies obesity, high blood sugar and blood pressure. Scientists have long studied this disease and have known that fructose is processed in the liver and stored there as triglycerides but the molecular mechanisms of fructose uptake were not clear. In a recent study, researchers demonstrated that GLUT8, a facilitative glucose and fructose cell surface transporter protein was involved in transporting fructose into the liver and that blocking or eliminating GLUT8 reduced the amount of fructose that entered the liver, thereby preventing the development of fatty livers.

Mice lacking GLUT8 were also shown to metabolize liver fat faster than control mice. This study paves the way for future therapeutics that might target GLUT8 and block fructose uptake by the liver but until we get there, lowering fructose intake and increasing physical activity are still regarded healthier alternatives to fight NAFLD.

protein news Glucose transporter 8 (GLUT8) mediates fructose-induced de novo lipogenesis and macrosteatosis. (April 2014)

Mitochondrial and ER proteins implicated in dementia

VAPB, PTPIP51, TDP-43, proteins implicated in dementia

Mitochondria and the endoplasmic reticulum (ER) form tight structural associations that facilitate a number of cellular functions. However, the molecular mechanisms of these interactions aren't properly understood.

A group of researchers showed that the ER protein VAPB interacted with mitochondrial protein PTPIP51 to regulate ER-mitochondria associations and that TDP-43, a protein implicated in dementia, disturbs this interaction to regulate cellular Ca2+ homeostasis. These studies point to a new pathogenic mechanism for TDP-43 and may also provide a potential new target for the development of new treatments for devastating neurological conditions like dementia.

protein news ER-mitochondria associations are regulated by the VAPB-PTPIP51 interaction and are disrupted by ALS/FTD-associated TDP-43. Nature (June 2014)

Bacterial secretion system for high yield, soluble scFv production

scFv, bacterial secretion system for scFv production

Single-chain variable fragments (scFvs) serve a variety of research purposes including in therapeutic and diagnostic applications. They are good alternatives to Monoclonal antibodies (Mabs) and unlike Mabs which are often produced in mammalian cells; scFvs can be produced in E. coli.

Given the challenges involved in scFv overexpression in E. coli, a group of scientists developed an efficient scFv secretion system using a bacterial secretory carrier protein called osmY. By fusing osmY and a periplasmic leader sequence (pelB) to anti-EGFR scFv (Epidermal growth factor receptor), they were able to generate high yields of soluble, functional and secreted scFv.

protein news Functional production of a soluble and secreted single-chain antibody by a bacterial secretion system. PLOS (May 2014)

Crystal structure of key blood clotting factors solved

P2Y receptors, crystal structures of blood clotting factors

P2Y receptors are a family of purinergic G protein-coupled receptors that are involved in various, critical biological functions like memory, movement, sleep etc. At the molecular level, they are also implicated in cellular functions like apoptosis, cellular proliferation and cytokine secretion.

In a study published recently, scientists mapped the detailed structure of the P2Y12 receptor in complex with a non-nucleotide reversible antagonist called AZD1283. The receptor structures were mapped using advanced X-ray crystallographic techniques coupled with sophisticated computational analysis.

While the agonist-antagonist function of the P2Y12 receptor has been poorly understood thus far, it has significant bearing from a clinical perspective as a target for the inhibition of platelet aggregation, since improper activation of blood platelets can result in life-threatening conditions like stroke and heart attack. This research has great potential for the development of future drugs targeting the P2Y12 receptor.

protein news Structure of the human P2Y12 receptor in complex with an antithrombotic drug. Nature (March 2014)

Dystrophin found to have tumor suppressing and anti-metastatic properties

Dystrophin, DMD, tumor-suppression, anti-metastatic

A recent study published in Nature Genetics showed that, in certain cancers that arose from muscle cells, loss of the dystrophin protein appeared to be the last in a series of steps in which tumors turned metastatic. This study established dystrophin as a protein with tumor-suppressing and anti-metastatic properties. The researchers involved in this study identified dystrophin during a genetic screen aimed at finding similarities between different myogenic tumors. During this study they found deletions in the dystrophin gene in more than 60 percent of 40 high-grade tumors that were sequenced.

Dystrophin gene is one of the largest known genes in the human genome and the biological role of its protein product is to connect muscle fibers to the extracellular matrix. Mutations in the gene for dystrophin lead to a set of disorders marked by progressive muscle weakness, the best studied condition being "Duchenne Muscular Dystrophy".

The new findings show that, in cancer cells, the same loss also made it easier for cells to metastasize. This discovery can have practical implications for the use of muscular dystrophy therapeutics to treat myogenic tumors. Read More...

Breakthrough finding on Non-steroidal anti-inflammatory drugs (NSAIDs)

NSAIDs, COX

Researchers recently found that inhibiting one step of prostaglandin synthesis in macrophages seemed to confer cardiovascular benefits in mice. This finding provides a refreshing new perspective on the relationship between NSAIDs and the cardiovascular system.

NSAIDs work by preventing the cyclooxygenase (COX) enzyme from producing prostaglandins, a class of molecules that induce swelling, pain and fever. However, while most painkillers are specific to COX-2, they are found to raise the risk of heart attack and stroke in patients taking them, due to the inhibition of heart-protective proteins called prostacyclins.

An alternative approach focused on inhibiting the enzyme prostaglandin E synthase-1, which is the last enzyme in the production chain that leads to prostaglandin E2. It was reported that in both male and female mice fed a high-fat diet, knocking out prostaglandin E synthase-1 specifically in macrophages could protect the animals from heart disease. This discovery could point the way to new cardiovascular drugs as well as safer NSAIDs. Read More...

High level E. coli expression without the use of chemical inducer

E. coli expression without chemical inducer, SoxRS, dissolved oxygen

A recent study showed that the induction of recombinant protein expression by increasing dissolved oxygen concentration was found to be an easy and efficient expression strategy that excluded the use of chemical, nutrient or thermal inducers that might potentially have negative effects on recombinant protein production.

The researchers that conducted this study exploited the SoxRS regulon in E. coli which is activated in response to elevated dissolved oxygen concentration. This is a function that likely protects bacteria from possible oxygen damage. It was found that SoxS expression could be elevated up to 16 fold, making it a possible candidate for recombinant protein expression. Read More...

Auxeticity reported in stem cells during differentiation and reprogramming

Auxeticity, Stem cell differentiation and reprogramming

Auxetic materials when stretched become thicker, perpendicular to the applied force. This is an unusual property that occurs due to the hinge-like structures of these materials. Typically, auxeticity has been demonstrated in manmade materials but is very rare in nature. A team of researchers that include biologists, engineers and physicists, have reported auxeticity in the nuclei of embryonic stem cells during differentiation.

Many questions about differentiation remain as scientists try to unravel the molecular mechanisms that occur inside a cell during this phase. It was recently discovered that when the stem cell is in the process of transforming into a specialized cell, its nucleus takes on an auxetic property, allowing it to absorb essential materials from its surroundings, hinting at the importance of this property as a possible prerequisite to differentiation. The auxetic properties only appear in the stem cell's nucleus when it is in the transition stage, changing from an embryonic, non-specific stem cell into a differentiated, tissue-specific cell.

Studying how auxeticity has evolved in nature will guide research into new ways to produce auxetic materials, which might have many diverse applications in our daily lives. Since such materials are expected to have mechanical properties such as high energy absorption and fracture resistance, Auxetics may be useful in applications such as body armor, packing material, shoulder pads etc. Read More…

Egg and Sperm hookup – Molecular mechanisms identified

Fertilization, Izumo1, Juno, Folr4, ICSI, IVF

Scientists have finally revealed the mystery behind mammalian fertilization. In 2005, the discovery of “Izumo1” (named after a Japanese marriage shrine), on the sperm surface, propelled researchers into looking for its counterpart on the egg. After years of research, scientists have identified folate receptor 4 (Folr4) as the receptor for Izumo1 on the mouse egg. They call it “Juno” (after the Roman goddess of fertility) and they demonstrate that Izumo1-Juno interaction is conserved within several mammalian species and it is a prerequisite for fertilization to proceed naturally - if either molecule is absent, fertilization cannot occur.

It was found that post-fertilization, Juno sheds rapidly from the oolemma and this hints towards a mechanism for the membrane block to polyspermy which ensures that eggs normally fuse with just a single sperm. Knockout female mice lacking Juno are shown to be completely infertile.

Among other things, these findings could help guide the development of new contraceptives for sterilizing domestic and wild animals and for guiding new infertility treatments. For example, if a woman has a mutation in the gene encoding for Juno, her eggs cannot be fertilized the normal way. Even In Vitro Fertilization (IVF) procedures wouldn’t work for her. But a method called Intra Cytoplasmic Sperm Injection (ICSI) can. ICSI involves injecting the sperm directly into the egg with the help of a needle. In the future, it may be possible to offer women seeking infertility treatment a genetic test to screen for defects in the Juno gene, and those affected could be offered ICSI directly instead of going through IVF. Read More…

Test tube baby – Lesley and John Brown came to the clinic of Robert Edwards and Patrick Steptoe after 9 years of failed attempts to have a child. IVF treatment was carried out and the fertilized egg that had developed into an embryo with 8 cells was returned to Mrs. Brown. Louise Brown, a healthy baby was born after a full-term pregnancy on July 25, 1978. A new era in medicine had begun. Read More…

Reliable predictor of Alzheimer's disease identified

Predictor of Alzheimer's disease, REST protein, NRSF

Alzheimer's disease is a devastating, progressive brain disease that gradually destroys memory and cognitive skills and eventually the ability to carry out even the most basic tasks of daily life. Symptoms are associated with aging and they typically show after age 60. The disease is named after German psychiatrist Dr. Alois Alzheimer, who first identified this disease in the brain tissue of a woman who died of a mysterious mental illness.

For a long time researchers linked Alzheimer's disease to the plaques and tangles that formed in the brain, along with a loss of connections between neurons. However, while the formation of plaques has been associated with Alzheimer's, they are not necessarily predictive of the disease i.e., the formation of plaques does not necessarily mean that a person would develop the disease.

A group of Harvard researchers have identified a neuro-protective protein called REST, (also known as neuron-restrictive silencer factor, NRSF) a transcription factor that switches genes on and off and it naturally increases during aging. Using techniques like Chromatin immunoprecipitation, deep sequencing and expression analysis, the researchers showed that REST was found to repress genes involved in Alzheimer's disease while inducing genes that protected the brain against oxidative stress and toxic effects of the beta-amyloid plaques. Based on this new discovery, the levels and activity of REST protein may be a key indicator whether a person develops this disease or not. Read More…

Plasmid titration for protein expression optimization

Plasmid titration for expression optimization

Nod-like receptors (NLRs) or “Nucleotide-binding oligomerization domain receptors” are innate immune sensors involved in a variety of cell signaling functions, especially during cell invasion by pathogens. Transient expression of NLRs is often sub-optimal because while NLR expression as such is high, the protein is usually poorly soluble due to aggregation problems. A group of scientists at the Crystal and Structural Chemistry Department at the Utrecht University in Netherlands, hypothesized, that for NLRs that aggregated, the expression rates achieved at standard transfection conditions were too high, causing an overburden on the protein folding machinery.

Using NLRs as a case study, they demonstrated that titrating plasmid concentration was an efficient method to control expression rates and would ultimately allow for the optimization of soluble protein expression. Using plasmid titration technique the authors demonstrated that 50-fold plasmid dilution increased the amount of soluble NOD1 protein approximately 5-fold. Read More...

A novel strategy to improve membrane protein expression in Yeast

Novel strategy to improve membrane protein expression in yeast, PAH1 gene

Membrane proteins play indispensable roles in the physiology of an organism. However, recombinant production of membrane proteins is one of the biggest hurdles facing protein biochemists today. A group of scientists in Belgium showed that, by increasing the intracellular membrane production by interfering with a key enzymatic step of lipid synthesis, enhanced expression of recombinant membrane proteins in yeast is achieved. Specifically, they engineered the oleotrophic yeast, Yarrowia lipolytica, by deleting the phosphatidic acid phosphatase, PAH1 gene, which led to massive proliferation of endoplasmic reticulum (ER) membranes. For all 8 tested representatives of different integral membrane protein families, they obtained enhanced protein accumulation. Read More...

Transient transfection for faster recombinant protein production

Transient transfection for faster recombinant protein production

The Baculovirus Expression Vector System (BEVS) is a powerful and versatile system for expression and production of high quality recombinant proteins. There are several advantages of this system, such as improved protein solubility, ability to incorporate post-translational modifications, and higher yields for secreted proteins. A recent study discussed the advantages of transient transfection as an alternative to the BEVS, for faster production of recombinant proteins in Sf9 cells. Through their study, the scientists demonstrated that transient transfection provided an alternative to the BEVS for the rapid production of recombinant proteins in Sf9 cells. Read More...

Overcoming recombinant protein production hurdles using a classical, award-winning approach

Chemical protein synthesis, solid phase peptide synthesis

Recombinant protein production is an essential technique to generate the desired amount of protein for downstream purposes. However, it is not always easy to do so, with the most encountered problems being, no expression or insoluble expression. Unfortunately, the Molecular Weight [MW] of a protein is never an indicator of its expression profile. Often times, even low MW proteins can be extremely challenging to produce, in the desired conformation and with sufficient purity.

To address this issue, GenScript scientists adopted a classical technique to provide low MW, target proteins [20-22kDa, up to 200 amino acids] by using a technique called chemical protein synthesis. This technique is based on GenScript's proprietary segment condensation and advanced peptide synthesis technologies. Among others applications, this technique would be extremely useful for the delivery of low MW, disease targets in a high purity, soluble form, for drug discovery research. In fact, the technology used by our scientists is based on the ground breaking work done by Bruce Merrifield over three decades ago. For his "development of methodology for chemical synthesis on a solid matrix", Dr. Merrifield was awarded the Nobel Prize in Chemistry, in 1984. Read More ...

The impact of a popular affinity tag on protein activity

His tag impact on protein activity

The (His)6 is a stretch of 6 Histidine residues and it is one of the most common tags used for the purification and detection of recombinant proteins, which can be placed either at the N or the C termini. However, in a recent study, a group of researchers in France underscored the importance of using this tag more judiciously. Using an enzyme "YedY", found in Gram-negative bacteria, they demonstrated that a (His)6 fused to the C-terminus of this enzyme was detrimental to its activity and resulted in an 8-fold decrease in its catalytic efficiency as opposed to an N-terminally placed tag. Read More ...

A brief history of the (His)6 tag

Did you know that the use of a (His)6 tag was first reported in 1988 by scientists at Roche, in Basel, Switzerland. Their landmark Nature Biotechnology publication titled "Genetic Approach to Facilitate Purification of Recombinant Proteins with a Novel Metal Chelate Adsorbent" was instrumental in the production of thousands of recombinant proteins ever since. Read More ...

An unconventional method to boost recombinant protein levels

Unconventional method to boost recombinant protein levels, MazF, mRNA interferase

MazF is an mRNA interferase enzyme in E.coli that functions as and degrades cellular mRNA in a targeted fashion, at the "ACA" sequence. This degradation of cellular mRNA causes a precipitous drop in cellular protein synthesis. A group of scientists at the Robert Wood Johnson Medical School in New Jersey, exploited the degeneracy of the genetic code to modify all "ACA" triplets within their gene of interest in a way that the corresponding amino acid (Threonine) remained unchanged. Consequently, induction of MazF toxin caused degradation of E.coli cellular mRNA but the recombinant gene transcription and protein synthesis continued, causing significant accumulation of high quality target protein. This expression system enables unparalleled signal to noise ratios that could dramatically simplify structural and functional studies of difficult-to-purify, biologically important proteins. Read More ...

Low temperature induction results in high levels of protein

Low temperature induction, E. coli expression

Producing recombinant proteins in E.coli, in soluble form, can be a challenging task. Often times, overexpression causes protein to accumulate as insoluble aggregates within the cytoplasm. To overcome issues of insoluble protein production, a group of scientists in Spain evaluated the impact of culture density, temperature and expression duration on the production of eukaryotic enzymes in E.coli. They found that soluble protein yields were 3-fold higher than usual when early log phase cultures were induced at 4°C for 48-72 hours. Read More ...

Promoter placement and its impact on expression

Promoter placement and impact on expression, mammalian expression

Mammalian cell expression is largely dependent on the nature and properties of the target gene and the host cell. In a recent study, a group of scientists in Japan developed a potent promoter system that enabled high expression of target genes. They found that engineering an additional promoter downstream of their target gene, in a mammalian expression vector, caused its enhanced expression in a variety of cell types. This novel method will prove valuable in the production of recombinant proteins in mammalian cells. Read More...

Tandem fusions and bacterial strain evolution for enhanced functional membrane protein production

Tandem fusions, bacterial strain evolution, functional membrane protein production

Membrane protein production remains a significant challenge in its characterization and structure determination. Despite the fact that there are a variety of host cell types, E.coli remains the popular choice for producing recombinant membrane proteins. A group of scientists in Netherlands devised a robust strategy to increase the probability of functional membrane protein overexpression in E.coli.

By fusing Green Fluorescent Protein (GFP) and the Erythromycin Resistance protein (ErmC) to the C-terminus of a target membrane protein they wer e able to track the folding state of their target protein while using Erythromycin to select for increased expression. By increasing erythromycin concentration in the growth media and testing different membrane targets, they were able to identify four evolved E.coli strains, all of which carried a mutation in the hns gene, whose product is implicated in genome organization and transcriptional silencing. Through their experiments the group showed that partial removal of the transcriptional silencing mechanism was related to production of proteins that were essential for functional overexpression of membrane proteins. Read More…

About GPCRs

G-protein-coupled receptors (GPCRs) are a class of membrane proteins that allow the transmission of a wide variety of signals over the cell membrane, between different cells and over long distances inside the body. The molecular mechanisms of action of GPCRs were worked in great detail by Brian Kobilka and Robert Lefkowitz for which they were jointly awarded the Nobel Prize in Chemistry for 2012. Read More…

The role of an anti-apoptotic factor in recombinant protein production

Bcl-xL, anti-apoptotic factor

Transient gene expression is becoming a popular alternative to stable cell line development, for the production of recombinant proteins in mammalian cells. Improvements to transient expression protocols range from the optimization of transfection media and culturing conditions to developments that include using cell lines engineered for apoptosis resistance. In a recent study, scientists at the Johns Hopkins University and Frederick National Laboratory for Cancer Research examined an alternative method of utilizing the benefits of anti-apoptotic gene expression to enhance the transient expression of biotherapeutics, specifically, through the co-transfection of Bcl-xL along with the product-coding target gene.

Chinese Hamster Ovary(CHO) cells were co-transfected with the product-coding gene and a vector containing Bcl-xL, using Polyethylenimine (PEI) reagent. They found that the cells co-transfected with Bcl-xL demonstrated reduced apoptosis, increased specific productivity, and an overall increase in product yield. Similar results were also found by the use of other anti-apoptotic factors in CHO and HEK cells. Read More…

About Bcl-xL

B-cell lymphoma-extra-large (Bcl-xL) is a mitochondrial transmembrane protein and a member of the Bcl-2 family of proteins which are known to act as either pro- or anti-apoptotic proteins. Bcl-xL itself acts as an anti-apoptotic molecule by preventing the release of mitochondrial contents such as cytochrome c, which would lead to caspase activation. Higher levels of Bcl-xL push a cell toward survival mode by making the membranes pores less permeable and leaky. Read More…

A simple trick to improve full length recombinant protein purity

Trick to improve full length recombinant protein purity

It is important to set goals for purity and quantity before embarking on a protein purification project. A good purification protocol should be simple to perform while being efficient and cost-effective.

The key to successful and efficient protein purification is to arrange steps in a logical way to maximize yield and minimize the number of steps required to achieve the desired result. In a recent scientific video journal, a group of scientists demonstrated a double-tagging affinity purification technique that allowed the recovery of highly purified, full length target protein. By adding an N-terminal GST and a C-terminal 10x His tag to their target protein, they eliminated degraded protein and were able to purify enriched, full length target protein successfully. Read More…

 
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