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Ex vivo systems to study host–microbiota interactions in the gastrointestinal tract

Ex vivo systems to study host–microbiota interactions in the gastrointestinal tract | Systems biology and bioinformatics | Scoop.it

It is increasingly apparent that the microbial ecosystems in the mammalian gastrointestinal tract play an intricate role in health and disease. There is a growing interest in the development of targeted strategies for modulating health through the modification of these microbiota.

Ecologists are faced with the challenge of understanding the structure and function of ecosystems, the component parts of which interact with each other in complex and diffuse ways. The human gut microbiota, with its high species richness and diversity (up to 1000 bacterial species per individual) including members of all three domains of life, situated in the dynamic environment of the gastrointestinal tract, is probably among the most complex ecosystems on this planet.

In order to elucidate the mechanistic foundations, and physiological significance, of beneficial or pathogenic relationships between the gut microbiota and their hosts, researchers require tractable model ecosystems that allow to recapitulate and investigate host–microbe and microbe–microbe interactions. This review discusses ex vivo gastrointestinal models systems that can be used to gain mechanistic insights into the emergent properties of the host–microbial superorganism.


Via Guus Roeselers
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Do you think it is ever possible to construct an ex-vivo system for that?

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Systems biology and bioinformatics
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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
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 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.

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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.
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new journal on microbiomes

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PLOS Computational Biology: Ten Simple Rules for Lifelong Learning, According to Hamming

PLOS Computational Biology: Ten Simple Rules for Lifelong Learning, According to Hamming | Systems biology and bioinformatics | Scoop.it
life of trying to achieve excellence in some area is in itself a worthy goal for your life.…[A] life without a struggle…is hardly a life worth living.”
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amazing

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Collective unconscious: how gut microbes shape human behavior

Collective unconscious: how gut microbes shape human behavior | Systems biology and bioinformatics | Scoop.it
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root of uncosciousness

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Protein Complexes in Bacteria

Protein Complexes in Bacteria | Systems biology and bioinformatics | Scoop.it
Author Summary Though more than 20,000 binary protein-protein interactions have been published for a few well-studied bacterial species, the results rarely capture the full extent to which proteins take part in complexes. Here, we use experimentally-observed protein complexes from E . coli or Mycoplasma pneumoniae , as well as gene orthology, to predict protein complexes across many species of bacteria. Surprisingly, the majority of protein complexes is not conserved, demonstrating an une
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conservation of protein complex content is not constant in bacteria - is it because the places of some preitein in complexes were overtaken by other proteins?

how does it correspond to phylogeny and evolution?

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Frontiers | Macromolecular networks and intelligence in microorganisms | Microbiotechnology, Ecotoxicology and Bioremediation

Living organisms persist by virtue of complex interactions among many components organized into dynamic, environment-responsive networks that span multiple scales and dimensions. Biological networks constitute a type of Information and Communication Technology (ICT): they receive information from the outside and inside of cells, integrate and interpret this information, and then activate a response. Biological networks enable molecules within cells, and even cells themselves, to communicate with each other and their environment. We have become accustomed to associating brain activity – particularly activity of the human brain – with a phenomenon we call “intelligence”. Yet, four billion years of evolution could have selected networks with topologies and dynamics that confer traits analogous to this intelligence, even though they were outside the intercellular networks of the brain. Here, we explore how macromolecular networks in microbes confer intelligent characteristics, such as memory, anticipation, adaptation and reflection and we review current understanding of how network organization reflects the type of intelligence required for the environments in which they were selected. We propose that, if we were to leave terms such as “human” and “brain” out of the defining features of “intelligence”, all forms of life – from microbes to humans – exhibit some or all characteristics consistent with “intelligence”. We then review advances in genome-wide data production and analysis, especially in microbes, that provide a lens into microbial intelligence and propose how the insights derived from quantitatively characterizing biomolecular networks may enable synthetic biologists to create intelligent molecular networks for biotechnology, possibly generating new forms of intelligence, first in silico and then in vivo.
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Level of intelligence and computational mechanisms for intracellular calculations

 

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Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome : Nature : Nature Publishing Group

Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome : Nature : Nature Publishing Group | Systems biology and bioinformatics | Scoop.it
The intestinal tract is inhabited by a large and diverse community of microbes collectively referred to as the gut microbiota. While the gut microbiota provides important benefits to its host, especially in metabolism and immune development, disturbance of the microbiota-host relationship is associated with numerous chronic inflammatory diseases, including inflammatory bowel disease and the group of obesity-associated diseases collectively referred to as metabolic syndrome. A primary means by which the intestine is protected from its microbiota is via multi-layered mucus structures that cover the intestinal surface, thereby allowing the vast majority of gut bacteria to be kept at a safe distance from epithelial cells that line the intestine. Thus, agents that disrupt mucus-bacterial interactions might have the potential to promote diseases associated with gut inflammation. Consequently, it has been hypothesized that emulsifiers, detergent-like molecules that are a ubiquitous component of processed foods and that can increase bacterial translocation across epithelia in vitro, might be promoting the increase in inflammatory bowel disease observed since the mid-twentieth century. Here we report that, in mice, relatively low concentrations of two commonly used emulsifiers, namely carboxymethylcellulose and polysorbate-80, induced low-grade inflammation and obesity/metabolic syndrome in wild-type hosts and promoted robust colitis in mice predisposed to this disorder. Emulsifier-induced metabolic syndrome was associated with microbiota encroachment, altered species composition and increased pro-inflammatory potential. Use of germ-free mice and faecal transplants indicated that such changes in microbiota were necessary and sufficient for both low-grade inflammation and metabolic syndrome. These results support the emerging concept that perturbed host-microbiota interactions resulting in low-grade inflammation can promote adiposity and its associated metabolic effects. Moreover, they suggest that the broad use of emulsifying agents might be contributing to an increased societal incidence of obesity/metabolic syndrome and other chronic inflammatory diseases.
Dmitry Alexeev's insight:

should we test the chemicals one by one - or finally have a preassumption of thier influence on gut?

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My No-Soap, No-Shampoo, Bacteria-Rich Hygiene Experiment

My No-Soap, No-Shampoo, Bacteria-Rich Hygiene Experiment | Systems biology and bioinformatics | Scoop.it
What happens when you leave cleanliness up to your microbiome?
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I never heard it before on AObiome+ pructs

restoring innate ability to prouce fine fragrance is great

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Huang and Boushey provide their... - Journal of Allergy and Clinical Immunology | Facebook

Huang and Boushey provide their perspective on the findings of studies of differences in the airway microbiome in patients with asthma vs. healthy...
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Microbiomes of lungs
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Rescooped by Dmitry Alexeev from Amazing Science
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Squid uses luminescent bacteria to match moonlight welling down from above to cancel out its own shadow

Squid uses luminescent bacteria to match moonlight welling down from above to cancel out its own shadow | Systems biology and bioinformatics | Scoop.it

The aquarium looks empty, but there is something in it. A pair of eyes stick out from the sandy floor, and their owner is easily scooped up into a glass bowl. At first, the creature looks like a hazelnut truffle — small, round and covered in tiny flecks. But with a gentle shake, the flecks of sand fall off to reveal a female Hawaiian bobtail squid (Euprymna scolopes), about the size of a thumb. As she jets furiously around the bowl, discs of pigment bloom and fade over her skin like a living pointillist painting.


There are no other animals in the bowl, but the squid is not alone. Its undersides contain a two-chambered light organ that is full of glowing bacteria called Vibrio fischeri. In the wild, their luminescence is thought to match the moonlight welling down from above and cancel out the squid's shadow, hiding the animal from predators. From below, the squid is invisible. From above, it is adorable. “They're just so beautiful,” says Margaret McFall-Ngai, a zoologist at the University of Wisconsin–Madison. “They're phenomenal lab animals.”


Few things excite McFall-Ngai more than the partnership between the bobtail squid and V. fischeri — and that is after studying it for more than 26 years. Over that time, she has shown that this symbiotic relationship is more intimate than anyone had imagined. She has found that the bacterium out-competes other microbes to establish an entirely faithful relationship with one host. It interacts with the squid's immune system, guides its body clock and shapes its early development by transforming its body.




Via Dr. Stefan Gruenwald
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cast no shadow

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Blood Work: Scientists Uncover Surprising New Tools to Rejuvenate the Brain | ucsf.edu

Blood Work: Scientists Uncover Surprising New Tools to Rejuvenate the Brain | ucsf.edu | Systems biology and bioinformatics | Scoop.it
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its none systems biology non bioinformatics... yet)

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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.
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miRNA peptides found active in plants

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New drug for Crohn's disease targets RNA

New drug for Crohn's disease targets RNA | Systems biology and bioinformatics | Scoop.it
If eventually approved, treatment would be among a handful of its kind
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Improving microbial fitness in the mammalian gut by in vivo temporal functional metagenomics

Improving microbial fitness in the mammalian gut by in vivo temporal functional metagenomics | Systems biology and bioinformatics | Scoop.it
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ribust genetic engeneering platform for gene function elucidation in vivo

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Restriction-Modification Systems as Mobile Epigenetic Elements - Madame Curie Bioscience Database - NCBI Bookshelf

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RM systems review 

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An Integrated Approach to Reconstructing Genome-Scale Transcriptional Regulatory Networks

An Integrated Approach to Reconstructing Genome-Scale Transcriptional Regulatory Networks | Systems biology and bioinformatics | Scoop.it
Author Summary The ever growing amount of genomic data enables the assembly of large-scale network models that can provide important new insights into living systems. However, assembly and validation of such large-scale models can be challenging, since we often lack sufficient information to make accurate predictions. This work describes a new approach for constructing large-scale transcriptional regulatory networks of individual cells. We show that the reconstructed network captures a signif
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guide for trn reconstruction in bacteria

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Separating the microbiome from the hyperbolome

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comprehensive point of view on translation in microbiome - nothing has been ever translated so quickly - indeed

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A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples

A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples | Systems biology and bioinformatics | Scoop.it
An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms
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very very very fast tool)

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Voluntary and forced exercise differentially alter the gut microbiome in C57BL/6J mice

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taking excercises voluntarily is spmething different)

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A disease module in the interactome explains disease heterogeneity, drug response and captures novel pathways and genes

A disease module in the interactome explains disease heterogeneity, drug response and captures novel pathways and genes | Systems biology and bioinformatics | Scoop.it
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network science allows for new approaches to disease analysis

 

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Studies on Modulation of Gut Microbiota by Wine Polyphenols: From Isolated Cultures to Omic Approaches

Studies on Modulation of Gut Microbiota by Wine Polyphenols: From Isolated Cultures to Omic Approaches | Systems biology and bioinformatics | Scoop.it
Moderate consumption of wine seems to produce positive health effects derived from the occurrence of bioactive polyphenols. The gut microbiota is involved in the metabolism of phenolic compounds, and these compounds and/or their metabolites may modulate gut microbiota through the stimulation of the growth of beneficial bacteria and the inhibition of pathogenic bacteria. The characterization of bacterial metabolites derived from polyphenols is essential in order to understand their effects, inclu
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we just like wine and microbiota)

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