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A novel algorithm for detecting multiple covariance and clustering of biological sequences

A novel algorithm for detecting multiple covariance and clustering of biological sequences | microbiology | Scoop.it
Single genetic mutations are always followed by a set of compensatory mutations. Thus, multiple changes commonly occur in biological sequences and play crucial roles in maintaining conformational and functional stability.
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Fast and powerful multiple covariance detector
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PLOS Pathogens: Battling Phages: How Bacteria Defend against Viral Attack

PLOS Pathogens: Battling Phages: How Bacteria Defend against Viral Attack | microbiology | Scoop.it
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A guide for running large projects

A guide for running large projects | microbiology | Scoop.it
As I hope most of you know, I have two jobs: I run a research group at The Roslin Institute, and I am also Head of Bioinformatics at Edinburgh Genomics, an academic genomics facility at the Univers...
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Howard Fox's curator insight, December 23, 2014 7:51 PM

Who knew Microbiology could be so interesting

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Contaminomics: Why Some Microbiome Studies May Be Wrong – Phenomena: Not Exactly Rocket Science

Contaminomics: Why Some Microbiome Studies May Be Wrong – Phenomena: Not Exactly Rocket Science | microbiology | Scoop.it
You’ve got a group of people with a mysterious disease, and you suspect that some microbe might be responsible. You collect blood and tissue samples, you extract the DNA from them using a commonly ...
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Microbiology: Microbiome science needs a healthy dose of scepticism

Microbiology: Microbiome science needs a healthy dose of scepticism | microbiology | Scoop.it
To guard against hype, those interpreting research on the body's microscopic communities should ask five questions, says William P. Hanage.
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The Phylogeny of Everything, the Origin of Eukaryotes, and the Rules of Taxonomy: Death to Archaea, Bacteria, and Eucarya! Long live Archaebacteria, Eubacteria, Eukaryota, and Prokaryota!

The Phylogeny of Everything, the Origin of Eukaryotes, and the Rules of Taxonomy: Death to Archaea, Bacteria, and Eucarya! Long live Archaebacteria, Eubacteria, Eukaryota, and Prokaryota! | microbiology | Scoop.it
The Phylogeny of Everything, the Origin of Eukaryotes, and the Rules of Taxonomy: Death to Archaea, Bacteria, and Eucarya! Long live Archaebacteria, Eubacteria, Eukaryota, and Prokaryota!
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New software aims to improve sorting the microbiome - thecherrycreeknews.com

New software aims to improve sorting the microbiome - thecherrycreeknews.com | microbiology | Scoop.it
Software from Joint BioEnergy Institute facilitates analysis of uncultivated microbial populations  IMAGE: MaxBin, an automated software program for binning the genomes of individual microbial species from metagenomic sequences is available online through JBEI. Click here for more information. Microbes – the… Continue Reading →
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Frontiers | Soil bacterial community composition altered by increased nutrient availability in Arctic tundra soils | Terrestrial Microbiology

The pool of soil organic carbon (SOC) in the Arctic is disproportionally large compared to those in other biomes. This large quantity of SOC accumulated over millennia due to slow rates of decomposition relative to net primary productivity. Decomposition is constrained by low temperatures and nutrient concentrations, which limit soil microbial activity. We investigated how nutrients limit bacterial and fungal biomass and community composition in organic and mineral soils within moist acidic tussock tundra ecosystems. We sampled two experimental arrays of moist acidic tussock tundra that included fertilized and non-fertilized control plots. One array included plots that had been fertilized annually since 1989 and the other since 2006. Fertilization significantly altered overall bacterial community composition and reduced evenness, to a greater degree in organic than mineral soils, and in the 1989 compared to the 2006 site. The relative abundance of copiotrophic α-proteobacteria and β-proteobacteria was higher in fertilized than control soils, and oligotrophic Acidobacteria were less abundant in fertilized than control soils at the 1989 site. Fungal community composition was less sensitive to increased nutrient availability, and fungal responses to fertilization were not consistent between soil horizons and sites. We detected two ectomycorrhizal genera, Russula and Cortinarius spp., associated with shrubs. Their relative abundance was not affected by fertilization despite increased dominance of their host plants in the fertilized plots. Our results indicate that fertilization, which has been commonly used to simulate warming in Arctic tundra, has limited applicability for investigating fungal dynamics under warming.
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Protocols for metagenomic DNA extraction and Illumina amplicon library preparation for faecal and swab samples - Vo - 2014 - Molecular Ecology Resources - Wiley Online Library

Protocols for metagenomic DNA extraction and Illumina amplicon library preparation for faecal and swab samples - Vo - 2014 - Molecular Ecology Resources - Wiley Online Library | microbiology | Scoop.it
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Conserved and host-specific features of influenza virion architecture : Nature Communications : Nature Publishing Group

Viruses use virions to spread between hosts, and virion composition is therefore the primary determinant of viral transmissibility and immunogenicity. However, the virions of many viruses are complex and pleomorphic, making them difficult to analyse in detail. Here we address this by identifying and quantifying virion proteins with mass spectrometry, producing a complete and quantified model of the hundreds of host-encoded and viral proteins that make up the pleomorphic virions of influenza viruses. We show that a conserved influenza virion architecture is maintained across diverse combinations of virus and host. This ‘core’ architecture, which includes substantial quantities of host proteins as well as the viral protein NS1, is elaborated with abundant host-dependent features. As a result, influenza virions produced by mammalian and avian hosts have distinct protein compositions. Finally, we note that influenza virions share an underlying protein composition with exosomes, suggesting that influenza virions form by subverting microvesicle production.


Via burkesquires, Mel Melendrez-Vallard
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Frontiers | Phage–host interplay: examples from tailed phages and Gram-negative bacterial pathogens | Terrestrial Microbiology

Complex interactions between bacteriophages and their bacterial hosts play significant roles in shaping the structure of environmental microbial communities, not only by genetic transduction but also by modification of bacterial gene expression patterns. Survival of phages solely depends on their ability to infect their bacterial hosts, most importantly during phage entry. Successful dynamic adaptation of bacteriophages when facing selective pressures, such as host adaptation and resistance, dictates their abundance and diversification. Co-evolution of the phage tail fibers and bacterial receptors determine bacterial host ranges, mechanisms of phage entry and other infection parameters. This review summarizes the current knowledge about the physical interactions between tailed bacteriophages and bacterial pathogens (e.g., Salmonella enterica and Pseudomonas aeruginosa) and the influences of the phage on host gene expression. Understanding these interactions can offer insights into phage-host dynamics and suggest novel strategies for the design of bacterial pathogen biological controls.
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Using the common cold to kill cancer

Using the common cold to kill cancer | microbiology | Scoop.it
In 2013, Barbara Williams was diagnosed with stage four pancreatic cancer. She was given less than a year to live.
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Access : Metagenomic reconstructions of bacterial CRISPR loci constrain population histories : The ISME Journal

The ISME Journal: Multidisciplinary Journal of Microbial Ecology is the official Journal of the International Society for Microbial Ecology, publishing high-quality, original research papers, short communications, commentary articles and reviews in the rapidly expanding and diverse discipline of microbial ecology.
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Who are the contaminants in your sequencing project?

Who are the contaminants in your sequencing project? | microbiology | Scoop.it
Well, been having many discussions recently about PCR amplification happening from "negative" controls where no sample DNA was added. Such amplification is alas pretty common - due to contamination...
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BMC Biology | Full text | Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

BMC Biology | Full text | Reagent and laboratory contamination can critically impact sequence-based microbiome analyses | microbiology | Scoop.it
The study of microbial communities has been revolutionised in recent years by the widespread adoption of culture independent analytical techniques such as 16S rRNA gene sequencing and metagenomics. One potential confounder of these sequence-based approaches is the presence of contamination in DNA extraction kits and other laboratory reagents.
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Artificial sweeteners induce glucose intolerance by altering the gut microbiota : Nature : Nature Publishing Group

Artificial sweeteners induce glucose intolerance by altering the gut microbiota : Nature : Nature Publishing Group | microbiology | Scoop.it
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Validating generalized incremental joint variant calling with GATK HaplotypeCaller, FreeBayes, Platypus and samtools

Validating generalized incremental joint variant calling with GATK HaplotypeCaller, FreeBayes, Platypus and samtools | microbiology | Scoop.it
Incremental joint variant calling Variant calling in large populations is challenging due to the difficulty in providing a consistent set of calls at all possible variable positions. A finalized se...
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Methods for Rapid Virus Identification and Quantification

Methods for Rapid Virus Identification and Quantification | microbiology | Scoop.it

Via Mel Melendrez-Vallard
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DNA extraction protocols cause differences in 16S rRNA amplicon sequencing efficiency but not in community profile composition or structure - Rubin - 2014 - MicrobiologyOpen - Wiley Online Library

DNA extraction protocols cause differences in 16S rRNA amplicon sequencing efficiency but not in community profile composition or structure - Rubin - 2014 - MicrobiologyOpen - Wiley Online Library | microbiology | Scoop.it
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Metagenomic epidemiology: a new frontier -- Francis and Riley -- Journal of Epidemiology & Community Health

Metagenomic epidemiology: a new frontier -- Francis and Riley -- Journal of Epidemiology & Community Health | microbiology | Scoop.it
20th century view that viruses, bacteria and fungi operated independently to cause disease. Now, we are beginning to view a more complex and nuanced interpretation with increased recognition of the importance of commensalism, synergy and balance of microbiota in human health.1 In this commentary we hope to briefly summarise studies into the bacterial and viral microbiome and how this shifting paradigm affects epidemiology.
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BigDataScript: A scripting language for data pipelines

BigDataScript: A scripting language for data pipelines | microbiology | Scoop.it
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Seems cool!

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Microbiology: Microbiome science needs a healthy dose of scepticism

Microbiology: Microbiome science needs a healthy dose of scepticism | microbiology | Scoop.it
To guard against hype, those interpreting research on the body's microscopic communities should ask five questions, says William P. Hanage.
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Rescooped by Wei Shen from Viruses, Immunology & Bioinformatics from Virology.uvic.ca
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Quantitative Temporal Viromics: An Approach to Investigate Host-Pathogen Interaction

Quantitative Temporal Viromics: An Approach to Investigate Host-Pathogen Interaction | microbiology | Scoop.it

A systematic quantitative analysis of temporal changes in host and viral proteins throughout the course of a productive infection could provide dynamic insights into virus-host interaction. We developed a proteomic technique called “quantitative temporal viromics” (QTV), which employs multiplexed tandem-mass-tag-based mass spectrometry. Human cytomegalovirus (HCMV) is not only an important pathogen but a paradigm of viral immune evasion. QTV detailed how HCMV orchestrates the expression of >8,000 cellular proteins, including 1,200 cell-surface proteins to manipulate signaling pathways and counterintrinsic, innate, and adaptive immune defenses. QTV predicted natural killer and T cell ligands, as well as 29 viral proteins present at the cell surface, potential therapeutic targets. Temporal profiles of >80% of HCMV canonical genes and 14 noncanonical HCMV open reading frames were defined. QTV is a powerful method that can yield important insights into viral infection and is applicable to any virus with a robust in vitro model.


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