Tag Archives: storage

General microbiology and science digest, September 16, 2014

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Detection of microbes in tissues, a magnet to pull out bacteria from blood, temperature stability of samples, enriching for rare microbial community members, bioinformatics tools for microbiome research, and Bik’s Picks.
Microbial detection

Metagenomic Assay for Identification of Microbial Pathogens in Tumor Tissues – Don A. Baldwin – mBio

“the PathoChip platform was developed by targeting viral, prokaryotic, and eukaryotic genomes with multiple DNA probes in a microarray format that can be combined with a variety of upstream sample preparation protocols and downstream data analysis. “

More microbes

Review: Physical stress and bacterial colonization – Michael Otto – FEMS Microbiology Reviews

“This review will give an overview over the mechanisms human bacterial colonizers have to withstand physical stresses with a focus on bacterial adhesion.”

Techniques

16S rRNA gene pyrosequencing of reference and clinical samples and investigation of the temperature stability of microbiome profiles – Jun Hang – Microbiome

“Three readily available mock bacterial community materials and two commercial extraction techniques, Qiagen DNeasy and MO BIO PowerSoil DNA purification methods, were used to assess procedures for 16S ribosomal DNA amplification and pyrosequencing-based analysis.”

Improving the genetic representation of rare taxa within complex microbial communities using DNA normalisation methods – Dragana Gagic – Molecular Ecology Resources

“The synthetic metagenome was fractionated and thermally re-natured, allowing the most abundant sequences to hybridise. Double-stranded DNA was removed either by hydroxyapatite chromatography, or by a duplex-specific nuclease (DSN).”

Bioinformatics

A better sequence-read simulator program for metagenomics – Stephen Johnson – BMC Bioinformatics

“We present BEAR (Better Emulation for Artificial Reads), a program that uses a machine-learning approach to generate reads with lengths and quality values that closely match empirically-derived distributions.”

Gene finding in metatranscriptomic sequences – Wazim Mohammed Ismail, Yuzhen Ye and Haixu Tang – BMC Bioinformatics

“In this paper, we present TransGeneScan, a software tool for finding genes in assembled transcripts from metatranscriptomic sequences.”

Data analysis for 16S microbial profiling from different benchtop sequencing platforms
Victor S. Pylro – Journal of Microbiological Methods

“Satisfactory results were obtained in those pipelines that applied a chimera-filtering step.”

Metagenome fragment classification based on multiple motif-occurrence profiles – Naoki Matsushita – PeerJ

“we have updated the Naïve Bayes Classifier method using multiple sets of occurrence profiles for each reference genome by normalizing the genome sizes, dividing each genome sequence into a set of subsequences of similar length and generating profiles for each subsequence.”

Revolutionizing prokaryotic systematics through next-generation sequencing – Vartul Sangal – Methods in Microbiology

“In this chapter, we have provided a brief summary of recent advances in sequencing technologies and easy to use bioinformatic tools to analyse sequence data, with a focus on prokaryotic biology. “

Microbes in the news

A Lesson in Language – McAlarnen, Lindsey A. – Academic Medicine

“while I expected a challenge working with human microbiome expert Dr. Rob Knight, I never expected to be as lost as I was that first morning.”

An extracorporeal blood-cleansing device for sepsis therapy – Joo H Kang – Nature Medicine

“Magnets pull the opsonin-bound pathogens and toxins from the blood; the cleansed blood is then returned back to the individual. “

Science and career

Too Few University Jobs For America’s Young Scientists – Richard Harris – NPR Morning Edition

“Imagine a job where about half of all the work is being done by people who are in training. That’s, in fact, what happens in the world of biological and medical research.”

Diversity in Science: Where Are the Data? – Fred Guterl – Scientific American

“Global figures on diversity in the science and engineering workforce are hard to come by, but what we know is not flattering”

 

Bik’s Picks

Jack the Ripper, more poison at NIH, Rosetta & the comet – Tabitha M. Powledge – PLOS Blogs

“Scientists have greeted with hoots and catcalls the claim that Jack the Ripper, the near-mythical late-19th Century London serial killer, has been identified from DNA as an immigrant Polish baker named Aaron Kosminski.”

Human faces are so variable because we evolved to look unique – ScienceDaily

“The amazing variety of human faces — far greater than that of most other animals — is the result of evolutionary pressure to make each of us unique and easily recognizable”

Joanne Chang Brings the Sweet Science of Sugar to Harvard – Leah Blumenthal – Eater.com

“Harvard University’s annual Science & Cooking public lecture series brings chefs from around the world to lecture on the intersection of science and cooking.”

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Human microbiome, July 17

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Protozoa detection in fecal samples from children, airway microbiome, and Staphylococcus transmission between mother and child.

Oral microbiome

Oral Lihong GuoIntercellular communications in multispecies oral microbial communities – Lihong Guo – Frontiers in Microbiology

“This review will summarize the evidence that oral microbes participate in intercellular communications with co-inhabitants through cell contact-dependent physical interactions, metabolic interdependencies, as well as coordinative signaling systems to establish and maintain balanced microbial communities.”

Respiratory microbiome

Screen Shot 2014-07-17 at 4.58.37 PMAirway Microbiome Dynamics in Exacerbations of Chronic Obstructive Pulmonary Disease – Yvonne J. Huang – Journal of Clinical Microbiology

“In this study, temporal changes in the airway microbiome before, at the onset of, and after an acute exacerbation were examined in 60 sputum samples collected from subjects enrolled in a longitudinal study of bacterial infection in COPD.”

Screen Shot 2014-07-17 at 4.59.26 PMTime between Collection and Storage Significantly Influences Bacterial Sequence Composition in Sputum Samples from Cystic Fibrosis Respiratory Infections – Leah Cuthbertson – Journal of Clinical Microbiology

“Samples were treated with propidium monoazide to distinguish live from dead cells prior to DNA extraction, and 16S rRNA gene pyrosequencing was used to characterize their bacterial compositions.”

Gut microbiome

Screen Shot 2014-07-17 at 4.58.09 PMThe devil lies in the details: How variations in polysaccharide fine-structure impact the physiology and evolution of gut microbes – Eric C. Martens – Journal of Molecular Biology

“Here, we review the recent literature on this topic and posit that numerous, subtle variations in polysaccharides diversify the spectrum of available nutrient niches, each of which may be best filled by a subset of microorganisms that possess the corresponding proteins to recognize and degrade different carbohydrates”

Pregnancy and birth

Protozoa pediatricDetection of intestinal protozoa in paediatric patients with gastrointestinal symptoms by multiplex real-time PCR – L. Maas – Clinical Microbiology and Infection

“The performance of a multiplex real-time PCR for the detection of Blastocystis, Dientamoeba fragilis, Giardia lamblia, Cryptosporidium species and Entamoeba species in faecal samples was evaluated in an observational prospective study.”

Staph transmTransmission of Staphylococcus aureus between mothers and infants in an African setting – F. Schaumburg – Clinical Microbiology and Infection

“We aimed to investigate the transmission of S. aureus between mothers and their newborns during the first year after delivery in an African setting. In a longitudinal cohort study, colonization of Gabonese mother–infant pairs was assessed at delivery and after 1, 9 and 12 months.”

Commentary: Travelling within the fetal gut: simple rules for an arduous journey
Qiling Xu – BMC Microbiology

“A recent paper in BMC Biology addresses this issue with live imaging of gut explants from mouse embryos.”

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General microbiology and science, June 19

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How to store your sputum samples, how LPS gets inserted into the outer membrane, and why pigs have an even number of toes.

Techniques in microbiome research

Screen Shot 2014-06-19 at 11.16.59 PMTime between sputum sample collection and storage significantly influences bacterial sequence composition from Cystic Fibrosis respiratory infections – Leah Cuthbertson – Journal of Clinical Microbiology

“Aliquots were stored at room temperature before freezing at -80°C for increasing intervals up to 72 hour period. Samples were treated with propidium monoazide, to distinguish live from dead cells, prior to DNA extraction, and 16S rRNA gene pyrosequencing was used to characterise the bacterial composition.”

General microbiology

Screen Shot 2014-06-19 at 11.26.58 PMStructural basis for outer membrane lipopolysaccharide insertion – Haohao Dong – Nature

“Here we report the first crystal structure of the unique integral membrane LPS translocon LptD–LptE complex….These findings not only help us to understand important aspects of bacterial outer membrane biogenesis, but also have significant potential for the development of novel drugs against multi-drug resistant pathogenic bacteria.”

Immunology

Screen Shot 2014-06-19 at 11.13.17 PMTeaching the immune system “self” respect and tolerance – Lucienne Chatenoud – Science

“Tolerance is what we would like to restore to cure such disabling diseases. Kasagi et al. (2) indicate that it may be possible to teach the immune system to tolerate “self” again.”

Screen Shot 2014-06-19 at 11.15.42 PMIn Vivo–Generated Antigen-Specific Regulatory T Cells Treat Autoimmunity Without Compromising Antibacterial Immune Response – Shimpei Kasagi – Science

“These antigen-specific Treg cells specifically ameliorated autoimmunity without compromising immune responses to bacterial antigen. We have thus successfully generated antigen-specific Treg cells with therapeutic activity toward autoimmunity”

Phages, viruses, CRISPRs

Screen Shot 2014-06-19 at 11.18.44 PMHaloarcula hispanica CRISPR authenticates PAM of a target sequence to prime discriminative adaptation – Ming Li – Nucleic Acids Research

Science and ethics

Cheating common, say Brazil’s students – Jack Grove – Times Higher Education

“Of a sample of 47 papers published last year, 29 showed signs of word-by-word plagiarism, seven contained self-plagiarism, three had “mosaic plagiarism” (otherwise known as “synonym substitution”) and one exhibited signs of collusion.”

Dr. Bik’s Picks

Screen Shot 2014-06-19 at 11.23.10 PMThe Dangers Of Data Mining – Tommaso Dorigo – Science 2.0

“On my first day at the Erice School of Science Journalism this past week I attended a lecture by Alessio Cimarelli, who discussed “When Data Journalism meets Science: a “Hackathon””.”

Screen Shot 2014-06-19 at 11.32.23 PMEvolutionary biology: Why cattle, pigs are even-toed – Science Daily

“During their evolution, the basic limb skeletal structure was significantly modified such that today’s hippopotami have four toes, while the second and fifth toe face backwards in pigs.”

 

U.S. Says 75 Government Scientists Possibly Exposed To Live Anthrax – Reuters – Huffington Post

“The potential exposure occurred after researchers working in a high-level biosecurity laboratory at the agency’s Atlanta campus failed to follow proper procedures to inactivate the bacteria.”

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