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No Evidence of a Common DNA Variant Profile Specific to World Class Endurance Athletes

No Evidence of a Common DNA Variant Profile Specific to World Class Endurance Athletes | Systems biology and bioinformatics | Scoop.it
There are strong genetic components to cardiorespiratory fitness and its response to exercise training. It would be useful to understand the differences in the genomic profile of highly trained endurance athletes of world class caliber and sedentary controls. An international consortium (GAMES) was established in order to compare elite endurance athletes and ethnicity-matched controls in a case-control study design. Genome-wide association studies were undertaken on two cohorts of elite endurance athletes and controls (GENATHLETE and Japanese endurance runners), from which a panel of 45 promising markers was identified. These markers were tested for replication in seven additional cohorts of endurance athletes and controls: from Australia, Ethiopia, Japan, Kenya, Poland, Russia and Spain. The study is based on a total of 1520 endurance athletes (835 who took part in endurance events in World Championships and/or Olympic Games) and 2760 controls. We hypothesized that world-class athletes are likely to be characterized by an even higher concentration of endurance performance alleles and we performed separate analyses on this subsample. The meta-analysis of all available studies revealed one statistically significant marker (rs558129 at GALNTL6 locus, p = 0.0002), even after correcting for multiple testing. As shown by the low heterogeneity index (I 2 = 0), all eight cohorts showed the same direction of association with rs558129, even though p-values varied across the individual studies. In summary, this study did not identify a panel of genomic variants common to these elite endurance athlete groups. Since GAMES was underpowered to identify alleles with small effect sizes, some of the suggestive leads identified should be explored in expanded comparisons of world-class endurance athletes and sedentary controls and in tightly controlled exercise training studies. Such studies have the potential to illuminate the biology not only of world class endurance performance but also of compromised cardiac functions and cardiometabolic diseases.
Dmitry Alexeev's insight:

Largest study so far - we had no chances to have power enough for that - it is just because eilte athletes are elite)

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Yurii Aulchenko's curator insight, February 5, 12:23 PM

Taking trait into account, the sample size is impressive. No genome-wide significant results are found, which is probably no surprise given complexity of the trait. Would be interesting to look at SNP-heritability and guess the architecture, possibly estimating the sample size needed to get to GW-significance. The data/results should in principle allow to do this. 

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The physics of life

The physics of life | Systems biology and bioinformatics | Scoop.it
From flocking birds to swarming molecules, physicists are seeking to understand 'active matter' — and looking for a fundamental theory of the living world.
Dmitry Alexeev's insight:

In my mind this is the direction of science for the next generations - complexity science

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The Brain-Gut Axis, Part 3 – The Gut Microbiota In Disease - Brain Blogger (blog)

The Brain-Gut Axis, Part 3 – The Gut Microbiota In Disease - Brain Blogger (blog) | Systems biology and bioinformatics | Scoop.it
Brain Blogger (blog)
The Brain-Gut Axis, Part 3 – The Gut Microbiota In Disease
Brain Blogger (blog)
In Part 2 of the brain-gut axis article series, I explained how the brain and the gut microbiota communicate.
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Microbial endocrinology: the interplay between the microbiota and the endocrine system

Microbial endocrinology: the interplay between the microbiota and the endocrine system | Systems biology and bioinformatics | Scoop.it
RT @FEMSTweets: Review on the interplay between #microbiota and the #endocrine system http://t.co/jPrm9d8fIz #hormones #microbiome http://t…
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The human gut microbiome as a transporter of antibiotic resistance genes between continents

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Gut microbiota mediate caffeine detoxification in the primary insect pest of coffee : Nature Communications : Nature Publishing Group

Gut microbiota mediate caffeine detoxification in the primary insect pest of coffee : Nature Communications : Nature Publishing Group | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

should we look for coffee degrading bugs in starbucks customers?)

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PLOS Pathogens: Risks of Antibiotic Exposures Early in Life on the Developing Microbiome

PLOS Pathogens: Risks of Antibiotic Exposures Early in Life on the Developing Microbiome | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

altered microbiome and tissue development in infants

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Conducting a Microbiome Study

Conducting a Microbiome Study | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

Starting a micorbiome study?

Don't forget to do read through

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Metagenome Sequencing of the Hadza Hunter-Gatherer Gut Microbiota

Metagenome Sequencing of the Hadza Hunter-Gatherer Gut Microbiota | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

before mismatch diseases we were like this)

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Rescooped by Dmitry Alexeev from Papers
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Ranking in interconnected multilayer networks reveals versatile nodes

Ranking in interconnected multilayer networks reveals versatile nodes | Systems biology and bioinformatics | Scoop.it

The determination of the most central agents in complex networks is important because they are responsible for a faster propagation of information, epidemics, failures and congestion, among others. A challenging problem is to identify them in networked systems characterized by different types of interactions, forming interconnected multilayer networks. Here we describe a mathematical framework that allows us to calculate centrality in such networks and rank nodes accordingly, finding the ones that play the most central roles in the cohesion of the whole structure, bridging together different types of relations. These nodes are the most versatile in the multilayer network. We investigate empirical interconnected multilayer networks and show that the approaches based on aggregating—or neglecting—the multilayer structure lead to a wrong identification of the most versatile nodes, overestimating the importance of more marginal agents and demonstrating the power of versatility in predicting their role in diffusive and congestion processes.

 

Ranking in interconnected multilayer networks reveals versatile nodes
Manlio De Domenico, Albert Solé-Ribalta, Elisa Omodei, Sergio Gómez & Alex Arenas

Nature Communications 6, Article number: 6868 http://dx.doi.org/10.1038/ncomms7868 ;


Via Complexity Digest
Dmitry Alexeev's insight:

 insight on the networks

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Stability and phylogenetic correlation in gut microbiota: lessons from ants and apes - Sanders - 2014 - Molecular Ecology - Wiley Online Library

Stability and phylogenetic correlation in gut microbiota: lessons from ants and apes - Sanders - 2014 - Molecular Ecology - Wiley Online Library | Systems biology and bioinformatics | Scoop.it
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RNA chaperones buffer deleterious mutations in E. coli

RNA chaperones buffer deleterious mutations in E. coli | Systems biology and bioinformatics | Scoop.it

тумукBoth proteins and RNAs can misfold into non-functional conformations. Protein chaperones promote native folding of nascent polypeptides and re-folding of misfolded species, thereby buffering mutations that compromise protein structure and function. Here we show that RNA chaperones can also act as mutation buffers that enhance organismal fitness. Using competition assays, we demonstrate that overexpression of select RNA chaperones, including three DEAD box RNA helicases (CsdA, SrmB, RhlB) and the cold shock protein CspA, improves fitness of two independently evolved E. coli mutator strains that have accumulated deleterious mutations during short- and long-term laboratory evolution. We identify strain-specific mutations that are deleterious and subject to buffering when introduced individually into the ancestral genotype. For DEAD box RNA helicases we show that buffering requires helicase activity, implicating RNA structural remodelling in the buffering process. Our results suggest that RNA chaperones might play a fundamental role in RNA evolution and evolvability.

Dmitry Alexeev's insight:

never heard it before - RNA chaperones - they buffer the mutations

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Home : npj Biofilms and Microbiomes

Home : npj Biofilms and Microbiomes | Systems biology and bioinformatics | Scoop.it
npj Biofilms and Microbiomes is a new open-access, online only multi- and interdisciplinary journal dedicated to publishing the finest research on microbial biofilms and microbiomes.
Dmitry Alexeev's insight:

new journal on microbiomes

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BMC Bioinformatics

BMC Bioinformatics | Systems biology and bioinformatics | Scoop.it
BMC Bioinformatics is an open access journal publishing original peer-reviewed research articles in all aspects of the development, testing and novel application of computational and statistical methods for the modeling and analysis of all kinds of biological data, as well as other areas of computational biology. 
BMC Bioinformatics is part of the BMC series which publishes subject-specific journals focused on the needs of individual research communities across all areas of biology and medicine. We offer an efficient, fair and friendly peer review service, and are committed to publishing all sound science, provided that there is some advance in knowledge presented by the work.
BMC series - open, inclusive and trusted.
Dmitry Alexeev's insight:

We published a good research in BMC - next aim is Oxford BI

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Microbiota-Dependent Sequelae of Acute Infection Compromise Tissue-Specific Immunity: Cell

Microbiota-Dependent Sequelae of Acute Infection Compromise Tissue-Specific Immunity: Cell | Systems biology and bioinformatics | Scoop.it
Dmitry Alexeev's insight:

watch video abstract

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Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes

Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes | Systems biology and bioinformatics | Scoop.it
This Essay lays out ten principles that advance a unified theory of the evolution and ecology of host-associated microbiomes.
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HealthMap | Flu Map | Contagious Disease Surveillance | Virus Awareness

HealthMap | Flu Map | Contagious Disease Surveillance | Virus Awareness | Systems biology and bioinformatics | Scoop.it
HealthMap brings together disparate data sources to achieve a unified and comprehensive view of the current global state of infectious diseases.
Dmitry Alexeev's insight:

cool heatmap of infectious outbreaks

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At Tiny Scales, a Giant Burst on Tree of Life

At Tiny Scales, a Giant Burst on Tree of Life | Systems biology and bioinformatics | Scoop.it

A new technique for finding and characterizing microbes has boosted the number of known bacteria by almost 50 percent, revealing a hidden world all around us.


Via Integrated DNA Technologies
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Obesity: Medicinal mushroom reduces obesity by modulating microbiota : Nature Reviews Endocrinology : Nature Publishing Group

Obesity: Medicinal mushroom reduces obesity by modulating microbiota : Nature Reviews Endocrinology : Nature Publishing Group | Systems biology and bioinformatics | Scoop.it
Ganoderma lucidum
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i've just ordered one )

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Genome Biology | Full text | Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome

Average genome size is an important, yet often overlooked, property of microbial communities. We developed MicrobeCensus to rapidly and accurately estimate average genome size from shotgun metagenomic data and applied our tool to 1,352 human microbiome samples. We found that average genome size differs significantly within and between body sites and tracks with major functional and taxonomic differences. In the gut, average genome size is positively correlated with the abundance of Bacteroides and genes related to carbohydrate metabolism. Importantly, we found that average genome size variation can bias comparative analyses, and that normalization improves detection of differentially abundant genes.
Dmitry Alexeev's insight:

well size matters isn't it?

i enjoyed the difference in genome sizes between body habitats

 

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Frontiers | The Intestinal Microbiome in Early Life: Health and Disease | Immunotherapies and Vaccines

Frontiers | The Intestinal Microbiome in Early Life: Health and Disease | Immunotherapies and Vaccines | Systems biology and bioinformatics | Scoop.it
Human microbial colonization begins at birth and continues to develop and modulate in species abundance for about three years, until the microbiota becomes adult-like. During the same time period, ...
Dmitry Alexeev's insight:

i just like the infographics)

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Enterotoxigenic Bacteroides fragilis induces oncogenic regulatory T cells (TUM9P.1000)

Dmitry Alexeev's insight:

it is seen well because toxin is stromg, but what about other less strong toxins? from other gut bacteria

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Sanders: Disentangling the coevolutionary histories of animal gut microbiota - YouTube

Jon Sanders
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Manipulative Microbiomes | The Scientist Magazine®

Manipulative Microbiomes | The Scientist Magazine® | Systems biology and bioinformatics | Scoop.it
Cancer Cell
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one more idea on micorbial command center

 

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Primary transcripts of microRNAs encode regulatory peptides : Nature : Nature Publishing Group

Primary transcripts of microRNAs encode regulatory peptides : Nature : Nature Publishing Group | Systems biology and bioinformatics | Scoop.it
MicroRNAs (miRNAs) are small regulatory RNA molecules that inhibit the expression of specific target genes by binding to and cleaving their messenger RNAs or otherwise inhibiting their translation into proteins. miRNAs are transcribed as much larger primary transcripts (pri-miRNAs), the function of which is not fully understood. Here we show that plant pri-miRNAs contain short open reading frame sequences that encode regulatory peptides. The pri-miR171b of Medicago truncatula and the pri-miR165a of Arabidopsis thaliana produce peptides, which we term miPEP171b and miPEP165a, respectively, that enhance the accumulation of their corresponding mature miRNAs, resulting in downregulation of target genes involved in root development. The mechanism of miRNA-encoded peptide (miPEP) action involves increasing transcription of the pri-miRNA. Five other pri-miRNAs of A. thaliana and M. truncatula encode active miPEPs, suggesting that miPEPs are widespread throughout the plant kingdom. Synthetic miPEP171b and miPEP165a peptides applied to plants specifically trigger the accumulation of miR171b and miR165a, leading to reduction of lateral root development and stimulation of main root growth, respectively, suggesting that miPEPs might have agronomical applications.
Dmitry Alexeev's insight:

miRNA peptides found active in plants

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