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Rescooped by Khashayar Farrokhzad from Virology and Bioinformatics from Virology.ca
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Microbial bioinformatics for food safety and production

In the production of fermented foods, microbes play an important role. Optimization of fermentation processes or starter culture production traditionally was a trial-and-error approach inspired by expert knowledge of the fermentation process. Current developments in high-throughput ‘omics’ technologies allow developing more rational approaches to improve fermentation processes both from the food functionality as well as from the food safety perspective. Here, the authors thematically review typical bioinformatics techniques and approaches to improve various aspects of the microbial production of fermented food products and food safety.

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Frontiers | Toxins Secreted by Bacillus Isolated from Lung Adenocarcinomas Favor the Penetration of Toxic Substances | Infectious Diseases

The aim was to explore the eventual role of bacteria in the induction of lung cancer by smoking habits. Viable bacteria closely related to the genus Bacillus were detected at high frequencies in lung-cancer biopsies. Similar, if not identical, microbes were isolated from cigarettes and in smog. Bacteria present in cigarettes could be transferred to a physiological solution via a "smoker" device that mimicked their potential transfer during smoking those bacteria produce exotoxins able to open transmembrane pores. These channels can be used as a way to penetrate cells of benzopyrenes and other toxic substances present in tobacco products. We hypothesize that Bacillaceae present in tobacco play a key role in the development of lung cancer.
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Interesting! A potential microbial connection between smoking and lung cancer. The little buggers are everywhere!

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Gut microbes give anticancer treatments a boost

Gut microbes give anticancer treatments a boost | Microbiology | Scoop.it
Intestinal bacteria increase effectiveness of immune therapy in rodents
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GenoCAD: CAD Software for Synthetic Biology

GenoCAD: CAD Software for Synthetic Biology | Microbiology | Scoop.it
RT @BrainCatalog: GenoCAD: CAD Software for synthetic biology: http://t.co/YTmBQcU3

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How tech billionaires are using money and data to solve for death

How tech billionaires are using money and data to solve for death | Microbiology | Scoop.it
How tech billionaires are using money and data to solve for death. http://wapo.st/humanupgrade

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Comprehensive serological profiling of human populations using a synthetic human virome

Comprehensive serological profiling of human populations using a synthetic human virome | Microbiology | Scoop.it

ABSTRACT

The human virome plays important roles in health and immunity. However, current methods for detecting viral infections and antiviral responses have limited throughput and coverage. Here, we present VirScan, a high-throughput method to comprehensively analyze antiviral antibodies using immunoprecipitation and massively parallel DNA sequencing of a bacteriophage library displaying proteome-wide peptides from all human viruses. We assayed over 108 antibody-peptide interactions in 569 humans across four continents, nearly doubling the number of previously established viral epitopes. We detected antibodies to an average of 10 viral species per person and 84 species in at least two individuals. Although rates of specific virus exposure were heterogeneous across populations, antibody responses targeted strongly conserved “public epitopes” for each virus, suggesting that they may elicit highly similar antibodies. VirScan is a powerful approach for studying interactions between the virome and the immune system.


Via Krishan Maggon
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Science 5 June 2015: 
Vol. 348 no. 6239 
DOI: 10.1126/science.aaa0698RESEARCH ARTICLEComprehensive serological profiling of human populations using a synthetic human viromeGeorge J. Xu1,2,3,4,*, Tomasz Kula3,4,5,*, Qikai Xu3,4, Mamie Z. Li3,4, Suzanne D. Vernon6, Thumbi Ndung’u7,8,9,10,Kiat Ruxrungtham11, Jorge Sanchez12, Christian Brander13, Raymond T. Chung14, Kevin C. O’Connor15,Bruce Walker8,9, H. Benjamin Larman16, Stephen J. Elledge3,4,6,†

+Author Affiliations

1Program in Biophysics, Harvard University, Cambridge, MA 02115, USA.2Harvard-Massachusetts Institute of Technology (MIT) Division of Health Sciences and Technology, Cambridge, MA 02139, USA.3Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA.4Department of Genetics, Harvard University Medical School, Boston, MA 02115, USA.5Program in Biological and Biomedical Sciences, Harvard University, Cambridge, MA 02115, USA.6Solve ME/CFS Initiative, Los Angeles, CA 90036, USA.7KwaZulu-Natal Research Institute for Tuberculosis and HIV, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.8HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, Durban, South Africa.9Ragon Institute of Massachusetts General Hospital, MIT, and Harvard University, Cambridge, MA 02139, USA.10Max Planck Institute for Infection Biology, Chariteplatz, D-10117 Berlin, Germany.11Vaccine and Cellular Immunology Laboratory, Department of Medicine, Faculty of Medicine; and Chula-Vaccine Research Center, Chulalongkorn University, Bangkok, Thailand.12Asociación Civil IMPACTA Salud y Educación, Lima, Peru.13AIDS Research Institute-IrsiCaixa and AIDS Unit, Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.14Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA.15Department of Neurology, Yale School of Medicine, New Haven, CT 06520, USA.16Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD 21205, USA.↵†Corresponding author. E-mail: selledge@genetics.med.harvard.edu

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Krishan Maggon 's curator insight, June 5, 2015 3:23 PM
Science 5 June 2015: 
Vol. 348 no. 6239 
DOI: 10.1126/science.aaa0698RESEARCH ARTICLEComprehensive serological profiling of human populations using a synthetic human viromeGeorge J. Xu1,2,3,4,*, Tomasz Kula3,4,5,*, Qikai Xu3,4, Mamie Z. Li3,4, Suzanne D. Vernon6, Thumbi Ndung’u7,8,9,10,Kiat Ruxrungtham11, Jorge Sanchez12, Christian Brander13, Raymond T. Chung14, Kevin C. O’Connor15,Bruce Walker8,9, H. Benjamin Larman16, Stephen J. Elledge3,4,6,†

+Author Affiliations

1Program in Biophysics, Harvard University, Cambridge, MA 02115, USA.2Harvard-Massachusetts Institute of Technology (MIT) Division of Health Sciences and Technology, Cambridge, MA 02139, USA.3Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA.4Department of Genetics, Harvard University Medical School, Boston, MA 02115, USA.5Program in Biological and Biomedical Sciences, Harvard University, Cambridge, MA 02115, USA.6Solve ME/CFS Initiative, Los Angeles, CA 90036, USA.7KwaZulu-Natal Research Institute for Tuberculosis and HIV, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.8HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, Durban, South Africa.9Ragon Institute of Massachusetts General Hospital, MIT, and Harvard University, Cambridge, MA 02139, USA.10Max Planck Institute for Infection Biology, Chariteplatz, D-10117 Berlin, Germany.11Vaccine and Cellular Immunology Laboratory, Department of Medicine, Faculty of Medicine; and Chula-Vaccine Research Center, Chulalongkorn University, Bangkok, Thailand.12Asociación Civil IMPACTA Salud y Educación, Lima, Peru.13AIDS Research Institute-IrsiCaixa and AIDS Unit, Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.14Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA.15Department of Neurology, Yale School of Medicine, New Haven, CT 06520, USA.16Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD 21205, USA.↵†Corresponding author. E-mail: selledge@genetics.med.harvard.edu
Krishan Maggon 's curator insight, June 5, 2015 3:24 PM
Science 5 June 2015: 
Vol. 348 no. 6239 
DOI: 10.1126/science.aaa0698RESEARCH ARTICLEComprehensive serological profiling of human populations using a synthetic human viromeGeorge J. Xu1,2,3,4,*, Tomasz Kula3,4,5,*, Qikai Xu3,4, Mamie Z. Li3,4, Suzanne D. Vernon6, Thumbi Ndung’u7,8,9,10,Kiat Ruxrungtham11, Jorge Sanchez12, Christian Brander13, Raymond T. Chung14, Kevin C. O’Connor15,Bruce Walker8,9, H. Benjamin Larman16, Stephen J. Elledge3,4,6,†

+Author Affiliations

1Program in Biophysics, Harvard University, Cambridge, MA 02115, USA.2Harvard-Massachusetts Institute of Technology (MIT) Division of Health Sciences and Technology, Cambridge, MA 02139, USA.3Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA.4Department of Genetics, Harvard University Medical School, Boston, MA 02115, USA.5Program in Biological and Biomedical Sciences, Harvard University, Cambridge, MA 02115, USA.6Solve ME/CFS Initiative, Los Angeles, CA 90036, USA.7KwaZulu-Natal Research Institute for Tuberculosis and HIV, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.8HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, Durban, South Africa.9Ragon Institute of Massachusetts General Hospital, MIT, and Harvard University, Cambridge, MA 02139, USA.10Max Planck Institute for Infection Biology, Chariteplatz, D-10117 Berlin, Germany.11Vaccine and Cellular Immunology Laboratory, Department of Medicine, Faculty of Medicine; and Chula-Vaccine Research Center, Chulalongkorn University, Bangkok, Thailand.12Asociación Civil IMPACTA Salud y Educación, Lima, Peru.13AIDS Research Institute-IrsiCaixa and AIDS Unit, Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.14Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA.15Department of Neurology, Yale School of Medicine, New Haven, CT 06520, USA.16Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD 21205, USA.↵†Corresponding author. E-mail: selledge@genetics.med.harvard.edu

 

Systematic viral epitope scanning (VirScan).

This method allows comprehensive analysis of antiviral antibodies in human sera. VirScan combines DNA microarray synthesis and bacteriophage display to create a uniform, synthetic representation of peptide epitopes comprising the human virome. Immunoprecipitation and high-throughput DNA sequencing reveal the peptides recognized by antibodies in the sample. The color of each cell in the heatmap depicts the relative number of antigenic epitopes detected for a virus (rows) in each sample (columns).

Franc Viktor Nekrep's curator insight, August 4, 2015 7:33 AM

Science 5 June 2015: 
Vol. 348 no. 6239 
DOI: 10.1126/science.aaa0698RESEARCH ARTICLEComprehensive serological profiling of human populations using a synthetic human viromeGeorge J. Xu1,2,3,4,*, Tomasz Kula3,4,5,*, Qikai Xu3,4, Mamie Z. Li3,4, Suzanne D. Vernon6, Thumbi Ndung’u7,8,9,10,Kiat Ruxrungtham11, Jorge Sanchez12, Christian Brander13, Raymond T. Chung14, Kevin C. O’Connor15,Bruce Walker8,9, H. Benjamin Larman16, Stephen J. Elledge3,4,6,†

+Author Affiliations

1Program in Biophysics, Harvard University, Cambridge, MA 02115, USA.2Harvard-Massachusetts Institute of Technology (MIT) Division of Health Sciences and Technology, Cambridge, MA 02139, USA.3Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women's Hospital, Boston, MA 02115, USA.4Department of Genetics, Harvard University Medical School, Boston, MA 02115, USA.5Program in Biological and Biomedical Sciences, Harvard University, Cambridge, MA 02115, USA.6Solve ME/CFS Initiative, Los Angeles, CA 90036, USA.7KwaZulu-Natal Research Institute for Tuberculosis and HIV, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa.8HIV Pathogenesis Programme, Doris Duke Medical Research Institute, Nelson R. Mandela School of Medicine, Durban, South Africa.9Ragon Institute of Massachusetts General Hospital, MIT, and Harvard University, Cambridge, MA 02139, USA.10Max Planck Institute for Infection Biology, Chariteplatz, D-10117 Berlin, Germany.11Vaccine and Cellular Immunology Laboratory, Department of Medicine, Faculty of Medicine; and Chula-Vaccine Research Center, Chulalongkorn University, Bangkok, Thailand.12Asociación Civil IMPACTA Salud y Educación, Lima, Peru.13AIDS Research Institute-IrsiCaixa and AIDS Unit, Hospital Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.14Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA.15Department of Neurology, Yale School of Medicine, New Haven, CT 06520, USA.16Division of Immunology, Department of Pathology, Johns Hopkins University, Baltimore, MD 21205, USA.↵†Corresponding author. E-mail: selledge@genetics.med.harvard.edu

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The dangers of default parameters in bioinformatics: lessons from Bowtie and TopHat

The dangers of default parameters in bioinformatics: lessons from Bowtie and TopHat | Microbiology | Scoop.it

Most bioinformatics tools are equipped with a vast array of command-line options which let the user configure the inputs, outputs, and performance of the software. You may not wish to explore every possible option when using a particular piece of software, but you should always try to have a look at the manual. 


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Detection of significant protein coevolution

Motivation: The evolution of proteins cannot be fully understood without taking into account the coevolutionary linkages entangling them. From a practical point of view, coevolution between protein families has been used as a way of detecting protein interactions and functional relationships from genomic information. The most common approach to inferring protein coevolution involves the quantification of phylogenetic tree similarity using a family of methodologies termed mirrortree. In spite of their success, a fundamental problem of these approaches is the lack of an adequate statistical framework to assess the significance of a given coevolutionary score (tree similarity). As a consequence, a number of ad hoc filters and arbitrary thresholds are required in an attempt to obtain a final set of confident coevolutionary signals.


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Electron microscopes are close to imaging individual atoms

Electron microscopes are close to imaging individual atoms | Microbiology | Scoop.it

Today’s digital photos are far more vivid than just a few years ago, thanks to a steady stream of advances in optics, detectors, and software. Similar advances have also improved the ability of machines called cryo-electron microscopes (cryo-EMs) to see the Lilliputian world of atoms and molecules. Now, researchers report that they’ve created the highest ever resolution cryo-EM image, revealing a druglike molecule bound to its protein target at near atomic resolution. The resolution is so sharp that it rivals images produced by x-ray crystallography, long the gold standard for mapping the atomic contours of proteins. This newfound success is likely to dramatically help drugmakers design novel medicines for a wide variety of conditions.


“This represents a new era in imaging of proteins in humans with immense implications for drug design,” says Francis Collins, who heads the U.S. National Institutes of Health in Bethesda, Maryland. Collins may be partial. He’s the boss of the team of researchers from the National Cancer Institute (NCI) and the National Heart, Lung, and Blood Institute that carried out the work. Still, others agree that the new work represents an important milestone. “It’s a major advance in the technology,” says Wah Chiu, a cryo-EM structural biologist at Baylor College of Medicine in Houston, Texas. “It shows [cryo-EM] technology is here.”


Cryo-EM has long seemed behind the times—an old hand tool compared with the modern power tools of structural biology. The two main power tools, x-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy, enable researchers to pin down the position of protein features to less than 0.2 nanometers, good enough to see individual atoms. By contrast, cryo-EM has long been limited to a resolution of 0.5 nm or more.


Cryo-EM has been around for decades. But until recently its resolution hasn’t even been close to crystallography and NMR. “We used to be called the field of blob-ology,” says Sriram Subramaniam, a cryo-EM structural biologist at NCI, who led the current project. But steady improvements to the electron beam generators, detectors, and imaging analysis software have slowly helped cryo-EM inch closer to the powerhouse techniques. Earlier this year, for example, two groups of researchers broke the 0.3-nm-resolution benchmark, enough to get a decent view of the side arms of two proteins’ individual amino acids. Still, plenty of detail in the images remained fuzzy.


For their current study, Subramaniam and his colleagues sought to refine their images of β-galactosidase, a protein they imaged last year at a resolution of 0.33 nm. The protein serves as a good test case, Subramaniam says, because researchers can compare their images to existing x-ray structures to check their accuracy. Subramaniam adds that the current advance was more a product of painstaking refinements to a variety of techniques—including protein purification procedures that ensure each protein copy is identical and software improvements that allow researchers to better align their images. Subramaniam and his colleagues used some 40,000 separate images to piece together the final shape of their molecule. They report online today in Science that these refinements allowed them to produce a cryo-EM image of β-galactosidase at a resolution of 0.22 nm, not quite sharp enough to see individual atoms, but clear enough to see water molecules that bind to the protein in spots critical to the function of the molecule.


The above composite image of the protein β-galactosidase shows the progression of cryo-EM’s ability to resolve a protein’s features from mere blobs (left) a few years ago to the ultrafine 0.22-nanometer resolution today (right).


Via Dr. Stefan Gruenwald
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SageRave of Get Custom Content's curator insight, June 12, 2015 5:03 PM

My deeply geeky heart skipped a beat when I saw this.

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Targeted diversity generation by intraterrestrial archaea and archaeal viruses

Targeted diversity generation by intraterrestrial archaea and archaeal viruses | Microbiology | Scoop.it

In the evolutionary arms race between microbes, their parasites, and their neighbours, the capacity for rapid protein diversification is a potent weapon. Diversity-generating retroelements (DGRs) use mutagenic reverse transcription and retrohoming to generate myriad variants of a target gene. Originally discovered in pathogens, these retroelements have been identified in bacteria and their viruses, but never in archaea. Here we report the discovery of intact DGRs in two distinct intraterrestrial archaeal systems: a novel virus that appears to infect archaea in the marine subsurface, and, separately, two uncultivated nanoarchaea from the terrestrial subsurface. The viral DGR system targets putative tail fibre ligand-binding domains, potentially generating >1018 protein variants. The two single-cell nanoarchaeal genomes each possess ≥4 distinct DGRs. Against an expected background of low genome-wide mutation rates, these results demonstrate a previously unsuspected potential for rapid, targeted sequence diversification in intraterrestrial archaea and their viruses.

  


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Enzyme Improves CRISPR | The Scientist Magazine®

Enzyme Improves CRISPR | The Scientist Magazine® | Microbiology | Scoop.it
A smaller Cas9 protein enables in vivo genome engineering via viral vectors.
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Breathing in Bacteria | The Scientist Magazine®

Breathing in Bacteria | The Scientist Magazine® | Microbiology | Scoop.it
The healthy lung receives microbes from the mouth, a new model suggests.
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BioTechniques - DNA Extraction: Overcoming Obstacles in Microbial Studies

BioTechniques - DNA Extraction: Overcoming Obstacles in Microbial Studies | Microbiology | Scoop.it
What are the most efficient methods to extract microbial DNA that accurately represents the community it is isolated from? Janelle Weaver reports on efforts to identify the best methods for DNA extraction from unknown frontiers in the...
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Unraveling the Web of Viroinformatics: Computational Tools and Databases in Virus Research

Unraveling the Web of Viroinformatics: Computational Tools and Databases in Virus Research | Microbiology | Scoop.it

The beginning of the second century of research in the field of virology (the first virus was discovered in 1898) was marked by its amalgamation with bioinformatics, resulting in the birth of a new domain—viroinformatics. 


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Mining the microbial dark matter

Mining the microbial dark matter | Microbiology | Scoop.it
Microbiologists are finding new ways to explore the vast universe of unknown microbes in the hunt for antibiotics.

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NatProdChem's curator insight, June 25, 2015 3:43 AM

Must read paper !

Greg "Stock Shaman "Shafransky's curator insight, July 10, 2015 6:49 PM

microbe mining

malik matwi's comment, December 13, 2015 3:01 PM
neither dark matter nor energy http://iiste.org/Journals/index.php/APTA/article/view/26837
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WORLD'S LARGEST NATURAL SOUND LIBRARY NOW ONLINE - Video & Filmmaker magazine

WORLD'S LARGEST NATURAL SOUND LIBRARY NOW ONLINE - Video & Filmmaker magazine | Microbiology | Scoop.it

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Scientists find smallest life forms on Earth

Scientists find smallest life forms on Earth | Microbiology | Scoop.it
Over the last two decades, scientists have argued back and forth on whether or not ultra-small bacteria exist.

 

The researchers found several kinds of bacteria from three microbial phyla that are poorly understood. The bacteria were in groundwater and are thought to be quite common. But what surprised Luef and her colleagues was that the bacteria were  close to and in some cases smaller than what many scientists have long considered the lower size limit of life. They reported the findings in the spring in the journal Nature Communications.

The cells had an average volume 0.009 ± 0.002 cubic microns, meaning 150 of the bacteria would fit inside a single cell of Escherichia coli.


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Ed Rybicki's comment, October 8, 2015 4:25 AM
And of course, AGAIN they ignore the fact that viruses are alive...but it's nice that FINALLY someone seems to have nailed the nanobacteria we kept hearing about.
Ed Rybicki's curator insight, October 8, 2015 4:27 AM

Cell-based: because circoviruses are the smallest organisms at 1.9 - 2 Kb of DNA B-)

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Get With the Program | The Scientist Magazine®

Get With the Program | The Scientist Magazine® | Microbiology | Scoop.it
DIY tips for adding coding to your analysis arsenal
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The Elements of Bioinformatics

The Elements of Bioinformatics | Microbiology | Scoop.it
An interactive periodic table of common bioinformatics tools and their alternatives.

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Nature News: Plant denizens get the big-science treatment (2015)

Nature News: Plant denizens get the big-science treatment (2015) | Microbiology | Scoop.it

A plant may be rooted in place, but it is never lonely. There are bacteria in, on and near it, munching away on their host, on each other, on compounds in the soil. Amoebae dine on bacteria, nematodes feast on roots, insects devour fruit — with consequences for the chemistry of the soil, the taste of a leaf or the productivity of a crop.

 

From 30 June to 2 July, more than 200 researchers gathered in Washington DC for the first meeting of the Phytobiomes Initiative, an ambitious proposal to catalogue and characterize a plant’s most intimate associates and their impact on agriculture. By the end of the year, attendees hope to carve out a project that will apply this knowledge in ways that will appeal to funders in industry and government.

 

“We want to get more money,” says plant pathologist Linda Kinkel at the University of Minnesota in St Paul. “But beyond that, let’s just all try to talk the same language and come up with some shared goals.”

 

Leach coined the term phytobiome in 2013,at a retreat about food security. She defines the phytobiome broadly, to encompass microbes, insects, nematodes and plants as well as the abiotic factors that influence all these.

 

Since then, she has visited companies, funding agencies and universities to call for a unifying phytobiomes initiative. She has teamed up with Kellye Eversole, a consultant based in Bethesda, Maryland, and the co-owner of a small family farm in Oklahoma, who has experience working on large agricultural genomics projects, including the US National Plant Genome Initiative. That initiative was launched in 1998 and continues to crank out databases and other tools for analysing plant genomes.

 

Leach hopes that the Phytobiomes Initiative will leave a similar legacy, but she is mindful that federal funding has tightened considerably since 1998. Still, she notes that the project can build on several emerging trends in agriculture. Industry has shown renewed interest in boosting plant growth by manipulating associated microbes (Nature 504, 199; 2013). Companies and farmers are also investing in ‘precision agriculture’, which uses high-tech monitors to track conditions in a field or even around individual plants, allowing farmers to water and fertilize in exactly the right places.

 

High-tech future

 

Eversole foresees a day when tractors will carry dipstick-like gauges that provide a snapshot of the microbial community in the soil. Data from the Phytobiomes Initiative would then help farmers to manipulate that community to their advantage, she says.

 

But first, the initiative needs to standardize protocols and metrics, the meeting’s attendees determined. Kinkel says that efforts are likely to focus initially on cataloguing microbes and insects and their interactions with different crops and habitats. “We’re where plant biologists were 150 years ago,” she says. “We’re still trying to inventory things.”

 

Work has already begun along these lines: for example, a group at the International Rice Research Institute in Los Baños in the Philippines is fishing for microbial DNA in data discarded from an effort to sequence the rice genome. The goal is to determine which microbes prefer which strains of the crop.

 

Kinkel, meanwhile, has begun experimenting with manipulating carbon levels in the soil to alter the microbial population, with the aim of improving plant productivity. “If we can understand better who lives on and within plants, we have the potential to manage them to have healthier, more resilient plants,” she says.

 

Projects such as these would move faster under an organized, cohesive framework, says Sarah Lebeis, a microbiologist at the University of Tennessee in Knoxville who is studying how plants manipulate microbial communities by secreting antibiotics into the soil. “Right now we’re working as individuals,” she says. “Having an initiative will give us focus and hopefully we’ll progress further, faster, better.”


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Broad Institute, Google Genomics combine bioinformatics and computing expertise

Broad Institute, Google Genomics combine bioinformatics and computing expertise | Microbiology | Scoop.it

Broad Institute of MIT and Harvard is teaming up with Google Genomics to explore how to break down major technical barriers that increasingly hinder biomedical research by addressing the need for computing infrastructure to store and process enormous datasets, and by creating tools to analyze such data and unravel long-standing mysteries about human health.

As a first step, Broad Institute’s Genome Analysis Toolkit, or GATK, will be offered as a service on the Google Cloud Platform, as part of Google Genomics. The goal is to enable any genomic researcher to upload, store, and analyze data in a cloud-based environment that combines the Broad Institute’s best-in-class genomic analysis tools with the scale and computing power of Google.

GATK is a software package developed at the Broad Institute to analyze high-throughput genomic sequencing data. GATK offers a wide variety of analysis tools, with a primary focus on genetic variant discovery and genotyping as well as a strong emphasis on data quality assurance. Its robust architecture, powerful processing engine, and high-performance computing features make it capable of taking on projects of any size.

GATK is already available for download at no cost to academic and non-profit users. In addition, business users can license GATK from the Broad. To date, more than 20,000 users have processed genomic data using GATK.

The Google Genomics service will provide researchers with a powerful, additional way to use GATK. Researchers will be able to upload genetic data and run GATK-powered analyses on Google Cloud Platform, and may use GATK to analyze genetic data already available for research via Google Genomics. GATK as a service will make best-practice genomic analysis readily available to researchers who don’t have access to the dedicated compute infrastructure and engineering teams required for analyzing genomic data at scale. An initial alpha release of the GATK service will be made available to a limited set of users.

“Large-scale genomic information is accelerating scientific progress in cancer, diabetes, psychiatric disorders, and many other diseases,” said Eric Lander, President and Director of Broad Institute. “Storing, analyzing, and managing these data is becoming a critical challenge for biomedical researchers. We are excited to work with Google’s talented and experienced engineers to develop ways to empower researchers around the world by making it easier to access and use genomic information.”


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Factors to Consider When Choosing a Lab for PhD Training

Factors to Consider When Choosing a Lab for PhD Training | Microbiology | Scoop.it
A life-long career in scientific research depends alot on your PhD training as the primary “developmental” phase followed by the “pay-off” phase of postdoctoral training and beyond. Accruing the mu...

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A Virus In Your Mouth Helps Fight The Flu

A Virus In Your Mouth Helps Fight The Flu | Microbiology | Scoop.it
It's related to herpes. And it infects most of the world — about half of Americans, nearly all the developing world. But don't go out and get infected. The virus has a dark side, too.

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Protection Without a Vaccine

Protection Without a Vaccine | Microbiology | Scoop.it
With a new type of gene therapy, scientists hope to engineer the body to resist infections.

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Kathleen McLeod's curator insight, August 6, 2015 2:30 PM

What do you think? Could this be effective? Can you think of any better viral vectors for incorporation of the antibody DNA?