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Tuesday, 21 August 2018

Adaptive Evolution Study of MERS-Coronavirus lead to the identification of Spike Attachment mutations that enhanced entry in non-permissive cell line

Middle East Respiratory Syndrome (MERS) – Coronavirus (CoV) has its importance due to its known high mortality rate of about 35% as declared by World Health Organization (WHO). This virus is known to be originated from bats and passed then to humans through zoonotic spill over events. Previously several species that support MERS-CoV infection had been studied but until this paper published in Cell Reports shows the genetic mechanisms underlying cross-species adaptation.

Letko et. al. studied the adaptive evolution of MERS-CoV using broad taxonomic distribution of BAT species. (Source Cell Reports)
The research was lead by Vincent Munster who is a virologist at NIAID, NIH, USA and also Michael Letko, a visiting research fellow at Munster’s lab. Munster is primarily interested in evolutionary dynamics of viruses and also cross species transmission events, and in this current research published recently in August 2018 has shown the impressive study on hoast breadth and adaptability of MERS-CoV.

Letko selected 16 bat species with broad taxonomic distribution to screen in vitro MERS-CoV entry based on transfected DPP4 expression in non-permissive cell line. Among 16 species only one species Desmodus rotundus DPP4 (drDPP4) had shown least permissive to viral replication. Letko carry forward to understand the differences in MERS Spike that is involved in interaction with DPP4 receptor. Homo sapiens DPP4 and drDPP4 was found to have differences in two amino acid locations I295T and R317T respectively. Later when they try to express these mutations in non-permissive cell lines show that these mutations are important to restrict virus entry.

Letko hypothesized that MERS-CoV can adapt to these variation while serially passaging the virus, where try to look into the cytopathic effects of the virus. Serially passaging the virus leading adaptation of the MERS-CoV was observed where they identified two important mutations in Spike which allow the virus to entry into cell lines which was non-permissive for wild type MERS-CoV.
Later team wanted to understand the phenotype of these mutations, which show that the adaptive virus has developed alteration of surface charge of Spike that allowed entry of MERS-CoV.

The team conclude its importance of the study is focused on virus endpoint study where there perform wide selection of specie where assessing host breadth. Although team suggests that during viral adaptation there might be continuous accumulation of other mutations apart from virus spike which remained unclear in their study.

Journal Source:

Letko M, Miazgowicz K, McMinn R, Seifert S, Sola I, Enjuanes L et al. Adaptive Evolution of MERS-CoV to Species Variation in DPP4. Cell Reports. 2018;24(7):1730-1737.
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Friday, 6 July 2018

Aspirin could be a new ray of hope to Alzheimer's disease.




Alzheimer's disease is a neurodegenerative disorder, a type of dementia, that adversely affects memory, thinking, and behavior. It majorly affects elderly of 65 years and above, but there are chances of early onset of the disorder. There are approximately 9.9 million people suffering from the disease, with one new case every 3.2 seconds (source: The Global Voice on Dementia).


Alzheimer's disease is mainly caused by the accumulation of toxic beta-amyloid (plagues) due to its impaired clearance mechanism from the hippocampal region of the brain. Lysosomes are the major cellular degradative machinery that plays a pivotal role in cell homeostasis. Its abnormal functioning leads to a number of neurodegenerative disorders, Alzheimer's being of them.

aspirin
Image source: Google Images
Aspirin has been known to enhance the lysosomal biogenesis in the brain cells by upregulating the transcription factor EB, which is the main regulator of lysosome synthesis. Researchers at the University Medical Centre, Chicago conducted various experiments on mice based on the above findings. They concluded that low-dose of aspirin administered orally can stimulate lysosomal biogenesis and thus, helping in clearance of stored toxic compounds in brain cells in Alzheimer's disease and other storage disorders.

Aspirin, also known as acetylsalicylic acid, is one of the widely used medications around the world for alleviating pain, fever, and inflammation. It is also an anticoagulant that works by inhibiting carboxylase enzyme and reduces both platelet aggregation and the following coagulation. Thus, also used in the long-term to prevent heart attacks, ischemic strokes, and blood clots.

Unleashing the new role of aspirin have helped in design new treatment regimen that could help in unraveling the mysteries of Alzheimer's disease.

For more interesting reads you can subscribe to my blog Scinergy21. Here is the link
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Thursday, 26 April 2018

NEXTGENPCR: PCR in Under 2 Minutes


As written by Julia Travers; Canon BioMedical and Molecular Biology Systems have announced the upcoming release of the NEXTGENPCR thermocycler, which can carry out polymerase chain reaction within minutes. PCR is a lab technique used to create up to billions of copies of a specific segment of DNA. PCR, which is used in many branches of science and can typically can take hours, can now be completed in as little as two minutes. This thermocycler is described by the companies as representing the first significant advance in this process in 15 years. Dennis Snyder, senior director of global commercial operations for Canon BioMedical said: “Time to result is a constant concern for lab users, and we immediately saw an advantage in incorporating NEXTGENPCR as part of our portfolio. We are, therefore, delighted to secure this collaboration and look forward to rolling out NEXTGENPCR in the U.S. and Canada to both existing and new customers."


A press release explains that NEXTGENPCR achieves these speedy results by approaching the heating and cooling process in a new way; instead of heating and cooling Peltier blocks, it “moves standard format microplates rapidly across three temperature zones already set to the required denaturing, extension and annealing temperatures.” With this advancement in PCR technique, a three-step, 30-cycle protocol that amplifies a 100-base pair fragment can be carried out in less than two minutes. During PCR, temperature changes are implemented to separate strands of DNA, and then an enzyme is used to synthesize new strands that are complementary to the target sequence. Scientists amplify or copy target regions of DNA that they want to analyse or use in a new way. For example, the copies might be used to study gene functions or in forensics, medical diagnostics, ecology, molecular biology or molecular archaeology. PCR has been around since the 80s, when it was developed by Nobel Prize winner Kary Mullis. “MBS shares in our commitment to high-quality products that improve the laboratory experience,” Snyder said, adding that “offering the NEXTGENPCR products to our customers will shorten their protocols without requiring them to change their procedures." Gert de Vos, the inventor of the NEXTGENPCR, In addition to the plate, it was important to achieve high-speed PCR while also considering those things important to a user such as how much space the instrument takes on the bench, how much energy is used, and, in the end, how much the device will cost.

Image Credit: Canon BioMedical

NEXTGENPCR reportedly has an intuitive interface and can be easily integrated into existing lab protocols and routines. It also greatly reduces the power consumption levels of PCR.
NEXTGENPCR will initially be distributed in the U.S. and Canon BioMedical also holds distribution rights in Canada. Canon BioMedical is a wholly owned subsidiary of Canon U.S.A. and MBS is a Dutch biotechnology company. According to these companies, the global life sciences instrumentation market is predicted to reach a value of $85.1 billion by 2022, with the U.S. and Canada accounting for the largest share.

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Wednesday, 7 March 2018

1.6 Billion Years Old breath discovered from India

1.6 million years of old bacteria was found from the pockmarks in rock found from central India. A research that published in the journal Geobiology identified most of the microbes are cyanobacteria. These ancient one of the oldest bacteria identified till now are capable to synthesize photosynthesis like modern plants using sunlight as energy and giving out oxygen as byproduct. This cyanobacteria are the earliest life forms paving away 2.4 billion of years ago started to supply oxygen to earth.

Fossilized bubbles formed by cyanobacteria on 1.6 billion years old fossilized mat obtained from Vindhyan Supergroup, central India. Credit: Stefan Bengtson. (Source PhysOrg)
Cyanobacterial excreted materials harden into several layers to form stromatolites. These stromatolites are found in very few places now. Therese Sallstedt, a biologist from Swedish Museum of Natural History with her colleagues has studied these rocks from Vindhyan Supergroup which might contain oldest fossils on earth.

In rock layers scientists found tiny spherical voids which was not ever found before. Researchers in their paper mentioned that in fossil microbial mats that thrive now are in hydrothermal water.

The bubbles are as small as 50 to 500microns which for comparison human hair is just 50micron in diameter. Some of the spheres were found to be squished which signify that they were once compressed before they formed rock. It is important to note that researchers also found filament structures which are probable remains of cyanobacteria.

The mats were once filled with oxygen as was produced by old cyanobacteria. The stromatolites contain higher concentration of calcium phosphate called phosphorites. Hence the discovery of oxygen bubbles within these phosphorites produced by cyanobacteria is a major discovery of early life.

Journal Source:

Sallstedt T, Bengtson S, Broman C, Crill P, Canfield D. Evidence of oxygenic phototrophy in ancient phosphatic stromatolites from the Paleoproterozoic Vindhyan and Aravalli Supergroups, India. Geobiology. 2018;16(2):139-159.
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Tuesday, 6 March 2018

Video: How Bacteria Rule Over Your Body


The video here is adopted from the animation house of Kurzegat which is just as short as 8mins to explain how bacteria is associated with our health, feelings and even it allows us to crave for junk food.

Image: DiabetesDaily

Points to follow in the video:
1. Healthy microbiome is directly influence to our healthy immune system.
2. World of different microorganisms in our gut.
3. Know how microbiome can make us happy and sad.
4. Microbiome can influence our diet.
5. How to cure disease by fecal transplants.



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Best Universities in Europe 2018 Rankings

Do you want to study in Europe? Then find out this year's best Universities of Europe as ranked by Times Higher Education.

Image Source: Times Higher Education

When we say Europe now its with and without UK.

Here are the top ten Universities ranked by Times Higher Education including UK:
1. University of Oxford, UK
2. University of Cambridge, UK
3. Imperial College London, UK
4. ETH, Zurich, Switzerland
5. University College London, UK
6. London School of Economics and Political Science, UK
7. University of Edinburgh, UK
8. LMU Munich, Germany
9. King's College London, UK
10. Ecole Polytechnique Federale de Lausanne, Switzerland
10. Karolinska Institute, Sweden

Here are the top ten Universities ranked by Times Higher Education excluding UK:
1. ETH Zurich, Germany
2. LMU Munich, Germany
3. Ecole Polytechnique Federale de Lausanne, Switzerland
4. Karolinska Institute, Sweden
5. Technical University of Munich, Germany
6. Heidelberg University, Germany
7. KU Leuven, Belgium
8. University of Amsterdam, Netherlands
9. Humboldt University of Berlin, Germany
10. Delft University of Technology, Netherlands.

Courtesy: Times Higher Education.
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Thursday, 1 March 2018

How fruit juice affects the gut.


It was previously believed that fructose, which is the sugar found in fruit and fruit juice, is processed by the liver. However, a new study suggests that fructose is mainly processed in the small intestine. The study, which is published in the journal Cell Metabolism, reveals that processed high-sugar food and drink only spills over into the liver for processing when the small intestine becomes overwhelmed.
The recent findings add to the body of scientific knowledge on the effects of too much fructose on the body. We know from previous research that excessive consumption of sugar is harmful to the liver, and that chronic overconsumption causes obesity, increases resistance to insulin, and creates conditions for the onset of diabetes. Sometimes in the past, Medical News Today reported on a study that found that fructose-containing products such as sweetened drinks can increase the risk of non-alcoholic steatohepatitis, a form of non-alcoholic fatty liver disease, "which can lead to cirrhosis or liver cancer.”
OBSERVATION OF FRUCTOSE DIGESTION IN MICE
The researchers, from Princeton University in New Jersey, used mice to study how fructose travels through the digestive system. Their findings suggest that there is a physiological difference in how the body processes different amounts of sugar. Rather than the liver processing all the sugar in the body, the team observed that more than 90 percent of fructose was processed in the small intestines of the mice in the study. The team found that fructose not absorbed into the small intestine is passed through to the colon, where it comes into contact with the microbiome, which is the microbiotic flora that inhabits the large intestine and colon.
The researchers explain that the microbiome is not designed to process sugar. So, while a person could eat a large amount of carbohydrates without exposing their microbiome to any sugar, this changes significantly when high-sugar products — such as soda and juice — are consumed. While the findings do not prove that fructose influences the microbiome, the team believes that "an effect is likely." They suggest that this link should be further investigated in future studies, as it may provide new insights into the adverse effects of high sugar intake.
In the study, the small intestine was found to clear fructose more efficiently after a meal. The team theorizes that during periods of fasting, such as in the morning or mid-afternoon, individuals may be more vulnerable to fructose as the small intestine has reduced ability to process it during these times. As study author Joshua D. Rabinowitz, of the Lewis-Sigler Institute for Integrative Genomics at Princeton University, explains, "We can offer some reassurance — at least from these animal studies — that fructose from moderate amounts of fruits will not reach the liver." "We saw that feeding of the mice prior to the sugar exposure enhanced the small intestine's ability to process fructose," Rabinowitz continues. "And that protected the liver and the microbiome from sugar exposure."
Rabinowitz says that the results support "the most old-fashioned advice in the world," which is to "limit sweets to moderate quantities after meals" and avoid sugary drinks outside of meal times.

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Parasitic Molecules Mimic Human Proteins & Chew through the Gut

One of the most common gastric diseases in the world is due to a parasitic infection from Giardia parasites. New research has revealed how these pathogens cause gut distress; they appear to mimic human molecules, then break gut cells down and consume them as food. This solves a mystery that has eluded scientists for over 300 years. The findings, by investigators at the University of East Anglia, has been reported in GigaScience. 
The Giardia parasite synthesizes two proteins that enable it to break through the layers of mucosal protection in the gut, cutting a barrier that maintains gastrointestinal health. The process allows the pathogen to get to the nutrients behind the gut barrier easily. Typically, the Giardia parasite gets into people through contaminated drinking water or food, causing the disease giardiasis. Rates may be as high as seven percent in high-income nations and thirty percent in low-income countries.
The researchers were interested in knowing why the parasite causes very serious problems for some people. The team at the National Institute for Health Research Health Protection Research Unit in Gastrointestinal Infections of UEA's Norwich Medical School collaborated with colleagues from the Institute of Infection and Global Health at the University of Liverpool. They found that when giardia infected cells in culture, two protein families were made by the parasite. Further study indicated that one of those families can mimic human proteins called tenascins.
Tenascins are critical for tissue health under normal conditions. They control cell adhesion after wounds and direct tissue remodelling. They aid cells that must break apart, as well as regulating the proteins that hold cells together. The parasite appears to have evolved to make proteins that can behave similarly to human proteins, to interfere with these processes. The tenascins that giardia makes don’t hold cells together, however. Instead, they disrupt the junctions keeping cells together and prevent them from healing. "We've discovered an entirely new model for how this disease develops in the gut - which can also explain why in some people the symptoms can be more severe. Because the giardia have broken down the cell barriers and made all these nutrients available, other, opportunistic bacteria can move in to take advantage of these 'ready meals' which can make giardiasis even more severe for some,” said the senior author of the work, Dr. Kevin Tyler of the Norwich Medical School at UEA. "Giardia was one of the very first disease-causing microbes to be visualized - scientists have known of its existence since 1681. But this is the first time we have been able to properly understand why this parasite is so successful," he continued.

The team plans to pursue the research further; next, they want to see if these proteins can be neutralized as a therapeutic for the illness. They are wondering if differences in those molecules might indicate which strains are causing more severe illnesses, something not currently known.

Written by Carmen Leitch.
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Memory can be boosted by Prebiotics.


By adding prebiotics to infant formula, a group of researchers have enhanced the cognitive performance of piglets. The findings back up earlier work and suggest an important role for prebiotics in brain development. Anyone who has had children will have heard the phrase "breast is best." This is a given, but, for a wide range of reasons, not every mother can breast-feed their baby. For this reason, it is important that infant formula provides the best start in life and mimics the incredible capabilities of breast milk as closely as possible. Already, infant formula is a good substitute, but there is always room for improvement when you are competing against Mother Nature.

Breast milk naturally contains prebiotics, which are small, indigestible fiber molecules; they provide a welcoming environment for gut bacteria. Having the gut colonized by bacteria early in life is important for the developing immune system and helps prevent infections. Also, studies have shown that adding prebiotics to infant formula can help improve intestinal function and reduce allergies. A recent study from the University of Illinois' Piglet Nutrition and Cognition Lab investigated what effects adding prebiotics to infant formula might have on pigs. Specifically, they wanted to know whether it would enhance memory and exploratory behavior.

REASONS FOR USING PIGS

Using rats and mice to investigate drugs or biological mechanisms is a well-known and incredibly useful method. However, piglets are more similar to baby humans than rodents are. Their behavior, their digestive systems, and even the way their brain develops re much more similar to us than we are to rats. Although adding fiber to a piglet's diet to alter the workings of the brain might seem strange, evidence is already mounting that our gut bacteria play an influential role on our mind and mood.
One of the researchers, Stephen Fleming, says, "There hasn't been a lot of work looking at the gut-brain axis in humans, but a lot of rodent work is showing those connections." For instance, in one study, rodents fed prebiotics shortly after birth displayed increased positive social interactions and improved memory. For the new research, 2-day-old piglets were fed infant formula based on cow's milk supplemented with galactooligosaccharide (GOS), a naturally occurring prebiotic, and polydextrose (PDX), a synthetic carbohydrates with prebiotic activity. When the piglets were 25 days old, they were put through their paces in a range of learning, memory, and stress tests. After 33 days, blood, brain, and intestinal tissue were collected for examination.
To find out whether the prebiotics were having an effect on gut flora, the researchers tested for volatile fatty acids (VFA). Bacteria excrete VFA's as they digest prebiotics, so increased levels indicate increased numbers of bacteria. As expected, in the pigs that were fed PDX and GOS, VFAs were increased in the blood, brain, and colon. It is possible that VFAs could be involved in gut bacteria's influence on our brain and behavior. However, in the current study, the expected change in stress-related behavior was not found; despite measuring changes in VFAs, no connection was seen in behavior.
The researchers were also surprised to find that, in the pigs fed the prebiotic, Serotonin levels in the hippocampus went down. "When you hear less serotonin, there's an immediate reaction to say, 'Well, that's bad,'" Fleming says. But that's not necessarily the case; the pigs didn't display any greater anxiety during stress tests, for instance. This drop in serotonin may have been because of reduced levels of tryptophan, the precursor of serotonin. More research is needed to explore this further. Although the study could not find an alteration in behavior, they did show that the pig's memory was improved by prebiotics. As part of the growing evidence of gut bacteria's impact on brain function, the results make an interesting read. "There are so many ways we can alter the composition of the microbiota and they can have very strong benefits. Promoting good 'gut health' remains a strong focus in the field of nutrition" says study co-author Ryan Dilger, associate professor in the Department of Animal Sciences at the University of Illinois in Chicago. As Dilger says, there is a great deal of interest in gut bacteria's influence on the brain. More work is sure to follow in hot pursuit.

Adapted from Tim Newman


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Monday, 26 February 2018

Pathogen identified that was known to have caused 1545 epidemic in Mexico

Archeologists have provided us several clues for several early human history and the massive epidemics that were caused by some of the pathogens. Researchers use several techniques to analyze DNA and provide with enormous information about the causes of epidemics that happened over 500years ago.

Image: Obtained from Pixabay
Similarly from corpse excavated from a cemetery Teposcolula-Yucundaa located at Oaxaca in southern Mexico, traces of ancient DNA of Salmonella enterica subspecies serovar Paratyphi C was identified. A recent paper published in the journal Nature Ecology and Evolution led by equal contributors Åshild J. Vågene and Alexander Herbig suggest that this bacteria which caused enteric fever might be the same pathogen that was known to have caused 1545 epidemic in this community.
Researchers used a new metagenomic analysis tool called MEGAN alignment tool orMALT to identify this pathogen traces. Modernization of sophisticated techniques of DNA extraction and sequencing has provided easy identification of microbes and phylogenetic analysis from their DNA obtained from remnants of teeth and bones.

Tooth samples which were obtained from the corpse were used to identify both pre-contact and post-contact with the pathogen. The DNA were extracted and were sequenced which then was compared with the bacterial genome database available from NCBI. Additionally researchers with the help of archaeologists took soil samples to assess the background DNA.

The MALT was used to perform alignment and analysis of DNA sequence data. MALT has similar function like BLAST tool used to compute alignment of highly conserved sequence but unlike BLAST, MALT make these computations faster.

Results show that all the samples obtained from individuals from post-contact burial site aligns DNA with S. Paratyphi C DNA and unlikely there are no matches found with pre-contact burial site.

As the study compared only DNA samples from individuals excluding the RNA genomes, hence scientists consider themselves quite far from seeing the whole epidemic picture. Researchers now consider studying the multiple pathogens circulating at that time to have the synergistic effect on the population. This research thus provide insights about the presence of certain pathogens at that time and place of the epidemic but still further understanding is required to analyze the full story.

Journal Source:

Vågene Å, Herbig A, Campana M, Robles García N, Warinner C, Sabin S et al. Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico. Nature Ecology & Evolution. 2018;2(3):520-528.
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Friday, 26 January 2018

CHANGING MICROBIOTA MIGHT PROMOTE HEALTH

"The aim is to bring novel microbiome diagnostic systems to populations, then use food and probiotics to try and improve biomarkers of health," says study co-author Gregor Reid, a professor at Western University's Schulich School of Medicine & Dentistry and a scientist at Lawson Health Research Institute. However, the study cannot explain causality. As Prof. Reid explains, "It begs the question "if you can stay active and eat well, will you age better, or is healthy aging predicated by the bacteria in your gut?" Either way, there remains a strong and undeniable correlation between a healthy gut and healthy aging.

"The main conclusion is that if you are ridiculously healthy and 90 years old, your gut microbiota is not that different from a healthy 30-year-old in the same population." – Prof. Grg Gloor 

"Whether this is cause or effect is unknown," write the authors. However, Prof. Gloor explains, "This demonstrates that maintaining [the] diversity of your gut as you age is a biomarker of healthy aging, just like low-cholesterol is a biomarker of a healthy circulatory system." "By studying healthy people, we hope to know what we are striving for when people get sick," notes Prof. Reid.

The results of the study, the authors write, "[suggest] that resetting an elderly microbiota to that of a 30-year-old might help promote health."
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THE KEY TO AUTISM – CAN IT BE FOUND IN THE GUT?

At present, the Centers for Disease Control (CDC) estimate that 1 in 68 children will be diagnosed with an autism spectrum disorder. There is no known cause for autism. Autism encompasses a range of conditions and disorders, from mild to severe, so there is likely more than one cause, depending on the child. Research is ongoing in many labs to find as much information as possible. Whether there is a genetic link, an environmental cause, or an immune system factor, finding out about the biology behind autism remains a goal for many in the scientific community.

Recent research by scientists from the University of Massachusetts and MIT suggests that an infection during pregnancy could be connected to an increased risk of giving birth to a child who will develop autism. Knowing how this infection presents could help in the understanding of how autism behaviours in offspring develop and whether or not the infection changes the brains of babies in utero. There are two papers that were published recently, and both papers had the same two scientists as lead authors. They are Gloria Choi, who is an Assistant Professor of Brain and Cognitive Sciences at MIT and a member of the McGovern Institute for Brain Research and Jun Huh, a former assistant professor at UMass Medical School and currently a faculty member at Harvard Medical School. Together, they have published research that looked strains of bacteria in the gut of pregnant women.

The connection between gut bacteria and autism was investigated in a 2010 Danish study that found a correlation between certain viral infections during early pregnancy and a nearly three-fold increased risk of having a child with autism. Choi and Huh published research in 2016 on immune cells, known as Th17 cells and the molecule that activates them (the IL-17 molecule.) In mouse models it was found that inflammation in these cells causes a reaction in the developing brain receptors of a foetus in specific parts of the cortex. Their published work investigated further how “patches” of these receptors in the brains of babies in utero might be a factor in behavioural abnormalities common in autism, such as self-stimming behaviours, repetitive motions, and social difficulties.

One of the papers detailed the role of a protein expressed in the somatosensory cortex and autism behaviours. This is where the brain handles proprioception, the ability to know where one’s body is in the environmental space around it. Intraneurons in this region express a protein called parvalbumin, but in mice that were found to have irregularities in this area, due to inflammation, there were less of these intraneurons and areas of the somatosensory cortex were overexcited in the expression of this protein.

When the researchers were able to normalize the balance in this brain area, behavioral abnormalities in the mice were reversed. Inducing the overstimulation of these neurons resulting in behavioural abnormalities in normal mice. Being able to manipulate the process is key to finding a treatment.


Adapted from Brenda Kelley Kim who is a writer living in the Boston area with interest in cancer research, cardiology and neuroscience. 
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Rare Microbes Make a Critical Contribution to the Environment.

New work published in Applied Environmental Microbiology suggests that bacteria present at very small levels in the environment actually make a vital contribution to the health and stability of that environment. This research concerns microbes that don’t usually account for more than a tenth of a percent of the bacteria in the whole population. "The work aims to provide a fundamental understanding of how biodiversity contributes to ecosystem functioning," said the corresponding author of the work, Kostas Konstantinidis, PhD.

In the environment at large, these are low levels, but in individual communities there may be hundreds of them, actually therefore, composing 20 to 30 percent of specific bacteria in an aquatic group.Termed the rare biosphere, these uncommon species were found to harbor large amounts of genes capable of allowing for organic pollutant degredation. The abilities conferred by those microbes may be helping the entire microbial population remain stable in the face of environmental pressures and alterations. The investigators, a team from Georgia Institute of Technology, Atlanta, wanted to test this idea, so they created mesocosms, or laboratory environments, made up of 20 liters of water. These reservoirs were then inoculated with water samples taken from a local freshwater source, Lake Lanier. An illustrative example of a mesocosm is shown in the video above.

Three common organic chemicals, not present in the samples they took from the lake, were then dribbled into the mesocosms. The scientists wanted ot ensure that the microbes had not be acclimated to the presence of those pollutants in order to reveal as much as possible about the microbes’ abilities. "Also, the important environmental pollutants are generally at low concentration in most natural environments, similar to the organic compounds used here--except during major events such as oil spills" said Konstantinidis, the Carlton S. Wilder Associate Professor in the School of Civil & Environmental Engineering at Georgia Tech.

The pollutants used included 2,4-dichlorophenoxyacetic acid (2,4-D), a common herbicide that is a known endocrine disrupter and may be a carcinogen, according to the International Agency for Research on Cancer. The other compounds were caffeine (1,3,7-trimethyluric acid) and 4-nitrophenol (4-NP), used in fungicide production and one byproduct of pesticide breakdown."We chose these compounds because their biodegradation pathways and the underlying genes are known, which facilitated tracking which microbial populations encoded the proteins for the biodegradation of these organic compounds," explained Konstantinidis. The researchers repeatedly assayed the bacterial levels in the mseocosms to find which ones grew more or grew less. "The results allowed us to rigorously test the hypothesis that low abundance species, as opposed to common species, provided the metabolic diversity that enabled the community to respond to the added compounds and the changing conditions," said Konstantinidis.

The goal of the work was to improve our predictions of how microbial communities might react to future disruptions from stuff like oil, pesticides, or climate change, said Konstantinidis. We may learn a lot more about how microbes contribute to the function and resilience of our ecosystem, and the possible consequences microbes face due to contaminant spills or climate change. In a Tedx talk, speaker Duccio Cavalieri, Ph.D. explains why maintaining diversity among microbes is to everyone’s benefit.

Sources: AAAS/Eurekalert!, American Society for Microbiology, Applied Environmental Microbiology 

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DEPRESSION SHOWN TO BE REVERSED IN MICE USING PROBIOTICS.

Is it true that you are what you eat? Well, have some bacteria then and get happy. Actually it’s much more complex than that. New research from the University of Virginia School of Medicine (UVA) has shown that depressive symptoms and behaviours in mice were reversed when the mice were given food containing lactobacillus, which is a probiotic bacteria found in yogurt that is made with live cultures. The research was even able to uncover the specific process for how these probiotics impacted mood. Finding a link that makes such a close connection between the gut microbiome and mental health is a major step forward in learning more about depression and how it can be treated.

Depression isn’t just feeling sad for a while, it’s a very real neurobiological illness. Major depressive disorder affects approximately 14.8 million American adults, or about 6.7 percent of the U.S. population age 18 and older, in any given year. As many as one in 33 children and one in eight adolescents have clinical depression. Depression also puts those who suffer with it at a higher risk for heart attacks, even if they have no other cardiovascular risk factors. Since depression can seriously hinder things like a person’s ability to have a rewarding career and a stable family life, research into treatments and causes are crucial.

Lead researcher on the study at UVA, Alban Gaultier, stated, “The big hope for this kind of research is that we won’t need to bother with complex drugs and side-effects when we can just play with the microbiome. It would be magical just to change your diet, to change the bacteria you take, and fix your health – and your mood. It’s a huge problem and the treatments are not very good, because they come with huge side-effects.”

So what exactly is the “gut microbiome?” It’s the living bacteria inside the intestinal tract that is responsible for, among other things, keeping the body in balance. It’s a popular target of researchers looking into all kinds of illnesses. Connecting it to mental illness or other neurological conditions has been difficult. However, since the mouse model is used in research because of its similarity to humans, Galtier’s team looked at mice that were subjected to stress since stress can cause depression. Of course in mice, it was more about observing how they acted and looking for “depressive like behaviors” and “despair behavior” since there is obviously no other way to judge mood in animals.

When the gut microbiome composition was examined in the mice, both before and after a period of stress there was one major change that stood out. The bacteria lactobacillus was reduced in correlation to the onset of depressive behaviors in the mice. When the researchers added lactobacillus cultures back to the food of the depressed mice, the behaviors stopped and they began to behave as they had before the stress was induced.


The research at UVA took it a step further and also investigated how exactly this mechanism of lactobacillus fluctuation worked. Their study revealed that amounts of Lactobacillus in the gut will impact levels of a metabolite in the blood called kynurenine which is known to fuel depression. When lactobacillus went down, kynurenine went up and the despair behaviors of the mice began. The team hopes that they can translate these results in humans. Graduate student Ioana Marin, a researcher on the study said, “There has been some work in humans and quite a bit in animal models talking about how this metabolite, kynurenine, can influence behavior. It’s something produced with inflammation that we know is connected with depression. But the question still remains: How? How does this molecule affect the brain? What are the processes?” This are the begging questions scientist are looking answer for. 
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IN GUT BACTERIA , HOW DOES THE IMMUNE SYSTEM KNOWS FRIEND FROM FOE?

Our guts are home to a complex community of more than 100 trillion microbial cells that play an important role in health and disease.
These gut-resident microbes, or gut microbiota - which with their genetic material are known as the gut microbiome - influence metabolism, nutrition, and immune function.
Scientists are discovering that disruption in the gut microbiota is linked to obesity, inflammatory bowel disease, and other gastrointestinal disorders. It has also been suggested that obesity’s effect on the gut microbiome may explain its strong link with type 2 diabetes. Others have likened the uniqueness of a person's gut microbiota to that of a "DNA fingerprint," raising potential privacy concerns for participants of human microbiome research projects.
In this particular study the cell called dendritic cells (DCs) that have evolved two distinctive - and what may appear to be opposite - roles in the human body, in that they can both promote and inhibit immune response. DCs help to activate the immune system in response to infection, but they are also involved in actively suppressing it in certain situations.They suppress immunity by triggering induced regulatory T cells (iTregs), a type of cell that controls the development of immune tolerance.
As immunity inhibitors in the gut, DCs help to train the immune system to treat gut microbiota as friend rather than foe. They do this by internalizing proteins from the microbiota and migrating to lymph nodes associated with the gut. As they travel to the lymph nodes, the DCs break down the internalized friendly bacteria proteins into smaller pieces that become similar to “identity badges” that they wear on their cell surfaces.
These identity badges are displayed with specific binding proteins that iTregs recognize, with the effect that the iTregs do not promote immune responses against proteins wearing the identity badges. Prof. Brocker says: "We believe that these iTregs are specific for the proteins produced by natural gut bacteria." The team explains that the migration to lymph cells by the DCs - particularly those whose cell surfaces display a protein called CD103+ - is an important part of keeping the immune system updated on the composition of the gut microbiota. However, what the researchers wanted to discover was how this tolerance mechanism might be switched off in an emergency. Their investigation led them to another molecule that DCs display on their cell surfaces - known as CD40 - that behaves in a similar way to an alarm button. When activated, CD40 binds to a partner molecule on the surface of another type of T cell effector T cells, which turns DCs from inhibitors of immune response to promoters. In tests on mice, the researchers showed that animals whose CD40 signalling was permanently switched on developed severe colitis, but no other symptoms.
They found that the affected dendritic cells still migrate to the lymph nodes from the gut lining, but when they get there they commit cell suicide (apoptosis) and thus deny the regulatory T cells the opportunity to sense the identity badges of the microbiota proteins that would normally protect them from immune attack. This results in a generalized immune response in which T lymphocytes travel to the gut lining and cause inflammation. The team found that giving the mice antibiotics that killed their gut microbiota also reduced the inflammation, and the animals survived. The researchers now want to find out whether particular regulatory T cells are programmed for specific gut bacteria, as this study might suggest.
Culled from Catherine paddock (PhD) write up
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