Tag Archives: PCR

General microbiology and science, July 22

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Amplifying long PCR products, primer design, metagenomic analysis and ecology, network analysis and the Picks.

Techniques

Long-range PCR in next-generation sequencing: comparison of six enzymes and evaluation on the MiSeq sequencer – Haiying Jia – Nature Scientific Reports

“We evaluated six long-range DNA polymerases to amplify three amplicons, with sizes of 12.9 kb, 9.7 kb, and 5.8 kb, respectively. “

DegePrime, a Program for Degenerate Primer Design for Broad-Taxonomic-Range PCR in Microbial Ecology Studies – Luisa W. Hugerth – Applied and Environmental Microbiology

“Here, we present the computer program DegePrime that, for each position of a multiple sequence alignment, finds a degenerate oligomer of as high coverage as possible and outputs its coverage among taxonomic divisions.”

Metagenomic analysis and ecology

Implications of streamlining theory for microbial ecology – Stephen J Giovannoni – ISME Journal

“The small genomes of obligate insect endosymbionts have been attributed to genetic drift caused by small effective population sizes (Ne). In contrast, streamlining theory attributes small cells and genomes to selection for efficient use of nutrients in populations where Ne is large and nutrients limit growth.”

Parallel Evolution of Streptococcus pneumoniae and Streptococcus mitis to Pathogenic and Mutualistic Lifestyles – Mogens Kilian – mBio

“In a comparative analysis of 35 genomes, including phylogenetic analyses of all predicted genes, we have shown that the pathogenic pneumococcus has evolved into a master of genomic flexibility while lineages that evolved into the nonpathogenic S. mitis secured harmonious coexistence with their host by stabilizing an approximately 15%-reduced genome devoid of many virulence genes.”

Proteomics

Elevated temperature alters proteomic responses of individual organisms within a biofilm community – Annika C Mosier – ISME Journal

“The study is the first application of tandem mass tag (TMT)-based proteomics to a microbial community. We accurately, precisely and reproducibly quantified thousands of proteins in biofilms growing at 40, 43 and 46 °C. “

Bioinformatics

Detecting Communities Based on Network Topology – Wei Liu – Nature Scientific Reports

“We analyzed 16 different types of networks, and compared our partitions with Infomap, LPA, Fastgreedy and Walktrap, which are popular algorithms for community detection. Most of the partitions generated using our approach compare favorably to those generated by these other algorithms. “

Dr. Bik’s Picks

FGF5 is a crucial regulator of hair length in humans – Claire A. Higgins – PNAS

“In this study, we obtained DNA from families segregating excessively long eyelashes consistent with an autosomal recessive trait.”

Science and Culture: Hunting fractals in the music of J. S. Bach – Stephen Ornes – PNAS

“Bach has similarly attracted the attention of other fractal hunters, including Harlan Brothers, a jazz guitarist, composer, and mathematician in Branford, Connecticut. For more than a decade, Brothers has been mapping fractals in music.”

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General microbiology and science, June 16

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It’s late and I got lots for you, so no pictures today. Dengue, phages, ecology, techniques, and lots more.

Antibiotic resistance

Review: Microbiological effects of sublethal levels of antibiotics – Dan I. Andersson & Diarmaid Hughes – Nature Reviews Microbiology

“In this Review, we discuss the ecology of antibiotics and the ability of subinhibitory concentrations to select for bacterial resistance. “

A Bacterial Battle  – Lisa M. Jarvis – Chemical and Engineering News

“The regulatory path to approving new antibiotics has been cleared, but work still remains to rebuild a healthy drug pipeline”

Bacteria are everywhere
How safe is your kitchen? – Lyxan Toledanes – The Daily News Online

“Despite a spacious kitchen, Parker sat on the counter next to Masters’ prep area, where she was chopping vegetables and chicken on separate cutting mats. ”

Adventures in the microbiome (part 2) – Mike Edmund

“There’s an intriguing case report that was just published in Clinical Microbiology and Infection”

Stafford students find bacteria on tainted tablets – Amanda Oglesby

“Four sixth-graders huddled over a table inside All Saints Regional Catholic School as they took turns swabbing bacteria from the surfaces of an iPhone and iPad.”

Bioslime: new sensor to detect harmful bacteria on food industry surfaces – BarfBlog

“The Biolisme project is using research from the University to develop a sensor capable of collecting and detecting Listeria monocytogenes on food industry surfaces, thereby preventing contaminated products from entering the market.”

Viruses and phages

Functional long-range RNA–RNA interactions in positive-strand RNA viruses – Beth L. Nicholson & K. Andrew White – Nature Reviews Microbiology

“In this Review, we discuss recent insights into the structure and function of these intriguing genomic features and highlight their diverse roles in the gene expression and genome replication of positive-strand RNA viruses.”

Unravelling the structural and mechanistic basis of CRISPR–Cas systems – John van der Oost – Nature Reviews Microbiology

“In this Review, we summarize the recent structural and biochemical insights that have been gained for the three major types of CRISPR–Cas systems, which together provide a detailed molecular understanding of the unique and conserved mechanisms of RNA-guided adaptive immunity in bacteria and archaea.”

The elemental composition of virus particles: implications for marine biogeochemical cycles – Luis F. Jover – Nature Reviews Microbiology

“In this Analysis article, we use a biophysical scaling model of intact virus particles that has been validated using sequence and structural information to quantify differences in the elemental stoichiometry of marine viruses compared with their microbial hosts. “

Phage therapies for plants and people – Michael Gross – Current Biology

Dengue

NEA to explore biological control methods to tackle dengue

“One of the techniques involves the use of Aedes aegypti mosquitoes, which are infected with a certain bacteria, to control their population.”

Techniques general

Storage of Human Biospecimens: Selection of the Optimal Storage Temperature – Allison Hubel – Biopreservation and Biobanking

“The overall objective of this article is to describe the scientific basis for selecting a storage temperature for a biospecimen based on current scientific understanding. To that end, this article reviews some physical basics of the temperature, nucleation, and ice crystal growth present in biological samples stored at low temperatures (−20°C to −196°C), and our current understanding of the role of temperature on the activity of degradative molecules present in biospecimens.”

DNA polymerase hybrids derived from the family-B enzymes of Pyrococcus furiosus and Thermococcus kodakarensis: improving performance in the polymerase chain reaction – Ashraf M. Elshawadfy – Frontiers Microbiology

“The significance of this work is the observation that improvements in PCR performance are easily attainable by blending elements from closely related archaeal polymerases, an approach that may, in future, be extended by using more polymerases from these organisms.”

Metabolomics, Proteomics, Mass spectrometry

Bruker Announces Powerful New Mass Spectrometry Systems and Solutions for Life-Science Research, Clinical Research, Biopharma and Applied Markets – Wall Street Journal

“At the 62(nd) ASMS Conference on Mass Spectrometry and Allied Topics today, Bruker Corporation (NASDAQ:BRKR) today announced mass spectrometry-based product introductions for life-science research and proteomics, for clinical research, for pharma/biopharma/CRO customers, as well as for applied and industrial markets. “

Medically, Proteomics Advances Will Rival the Genetics Advances of the Last Ten Years – Genetic Engineering and Biotechnology News

“..in explaining why proteomics is likely to have such a major impact, Dr. Anderson starts with a major difference between the genetic testing common today, and the proteomic testing that is fast coming on the scene. “

Metagenomics and informatics

Detecting concerted demographic response across community assemblages using hierarchical approximate Bayesian computation – Yvonne L. Chan – Molecular Biology and Evolution

“Here we present a statistical framework for such an analysis based on hierarchical approximate Bayesian computation (hABC) with the goal of detecting concerted demographic histories across an ecological assemblage.”

An Experimentally Determined Evolutionary Model Dramatically Improves Phylogenetic Fit – Jesse D. Bloom – Molecular Biology and Evolution

“Experimental determination of a parameter-free evolutionary model via mutagenesis, functional selection, and deep sequencing.”

Ecology

Trait-based approaches for understanding microbial biodiversity and ecosystem functioning – Sascha Krause – Frontiers in Microbiology

“We argue that combining eco-physiological studies with contemporary molecular tools in a trait-based framework can reinforce our ability to link microbial diversity to ecosystem processes. “

The importance of the viable but non-culturable state in human bacterial pathogens – Laam Li – Frontiers in Microbiology

“The conditions that trigger the induction of the VBNC state and resuscitation from it are summarized and the mechanisms underlying these two processes are discussed. “

Deciphering microbial interactions and detecting keystone species with co-occurrence networks – David Berry – Frontiers in Microbiology

“Here, we simulate multi-species microbial communities with known interaction patterns using generalized Lotka-Volterra dynamics. We then construct co-occurrence networks and evaluate how well networks reveal the underlying interactions and how experimental and ecological parameters can affect network inference and interpretation.”

Scientific writing and publishing

Sources of error in the retracted scientific literature – Arturo Casadevall, R. Grant Steen and Ferric C. Fang – The FASEB Journal

“Analysis of the retraction notices for 423 articles indexed in PubMed revealed that the most common causes of error-related retraction are laboratory errors, analytical errors, and irreproducible results.”

Dr. Bik’s Picks

Magnets: Artificial Magnetic Bacteria: Living Magnets at Room Temperature – Miguel Martín – Adv. Funct. Mater

“After grafting the magnetic nanoparticles, the artificial magnetic bacteria remain alive. In fact they are converted into living magnets at room temperature.”

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More Microbiology and Science, June 5

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Today we’ll learn why koalas hug trees, how to grow plants taller using blood and bacteria, and how to (not) get sick in a veterinary hospital.

Infection, host response, sepsis

Screen Shot 2014-06-05 at 8.35.13 PMGene Expression Profiles of Human Dendritic Cells Interacting with Aspergillus fumigatus in a Bilayer Model of the Alveolar Epithelium/Endothelium Interface – Charles Oliver Morton – PLOS ONE

“Two distinct sub-groups of dendritic cells (DC), monocyte-derived DC (moDC) and myeloid DC (mDC), were included in the model to examine immune responses to fungal infection at the alveolar surface”

Screen Shot 2014-06-05 at 8.52.36 PMDusp3 and Psme3 Are Associated with Murine Susceptibility to Staphylococcus aureus Infection and Human Sepsis – Qin Yan – PLOS Pathogens

“One QTL region on chromosome 11 containing 422 genes was found to be significantly associated with susceptibility to S. aureus infection. “

Screen Shot 2014-06-05 at 8.36.06 PMAn Individual-Based Model of Transmission of Resistant Bacteria in a Veterinary Teaching Hospital – Neeraj Suthar – PLOS ONE

“The model suggested that transmission resulting from contact with healthcare workers was common, and that certain transmission points (housing wards, diagnostics room, and the intensive care unit) presented higher risk for transmission than others (lobby and surgery). “

Dengue

Screen Shot 2014-06-05 at 8.36.42 PMInduction of Neutralizing Antibody Response against Four Dengue Viruses in Mice by Intramuscular Electroporation of Tetravalent DNA Vaccines – Eakachai Prompetchara – PLOS ONE

“This study evaluated neutralizing antibody (NAb) induction of a dengue tetravalent DNA (TDNA) vaccine candidate administered by intramuscular-electroporation (IM-EP) and the benefit of homologous TDNA boosting in mice.”

Circulating Levels of Soluble MICB in Infants with Symptomatic Primary Dengue Virus Infections – Daniel H. Libraty – PLOS ONE

“We found that serum levels of sMICB increased between pre-infection and acute illness among infants with symptomatic primary dengue virus infections”

Screen Shot 2014-06-05 at 8.37.27 PMImmature Dengue Virus Is Infectious in Human Immature Dendritic Cells via Interaction with the Receptor Molecule DC-SIGN – Mareike K. S. Richter – PLOS ONE

“We show that immature DENV is infectious in cells expressing DC-SIGN. Furthermore, we demonstrate that immature dendritic cells, in contrast to macrophage-like cells, do not support antibody-dependent enhancement of immature DENV.”

Viruses and Phages

Screen Shot 2014-06-05 at 8.39.02 PMThe distribution and impact of viral lineages in domains of life – Arshan Nasir

“the distribution of viral lineages follows an ancient, highly dynamic and ongoing process that impacts the evolution of organisms. New viral lineages often arise from existing ones and may cross species barriers to infect new hosts”

Alternative invention for shrimp bacterial pathogens wins patent – Times of India

“Dr Indrani Karunasagar, director, UNESCO Centre for marine Biotechnology and Associate Director of Research, has received the patent for “the process of preparing a consortium of bacteriophages for controlling luminous bacterial disease in shrimp larvae.” Like a virus, a lytic bacteriophage is a virus that infects and replicates within the bacteria and kills it. “

Microbial Ecology

Screen Shot 2014-06-05 at 8.53.35 PMThe microbial contribution to macroecology – Albert Barberán – Frontiers in Microbiology

“We highlight two idiosyncrasies of microorganisms that are fundamental to understanding macroecological patterns and their mechanistic drivers. First, high dispersal rates provide novel opportunities to test the relative importance of niche, stochastic, and historical processes in structuring biological communities. Second, high speciation rates potentially lead to the convergence of ecological and evolutionary time scales.”

More microbiology

Screen Shot 2014-06-05 at 8.40.05 PMInteractions between Bacillus anthracis and Plants May Promote Anthrax Transmission
Holly H. Ganz – PLOS Neglected Tropical Diseases

“We found that B. anthracis increased the rate of establishment of a native grass (Enneapogon desvauxii) by 50% and that grass seeds exposed to blood reached heights that were 45% taller than controls.”

Screen Shot 2014-06-05 at 8.54.21 PMTo be or not to be associated: power study of four statistical modeling approaches to identify parasite associations in cross-sectional studies – Elise Vaumourin – Frontiers in Cellular and Infection Microbiology

“We applied these four approaches to detect associations within two populations of multi-infected hosts: (1) rodents infected with Bartonella sp., Babesia microti and Anaplasma phagocytophilum and (2) bovine population infected with Theileria sp. and Babesia sp”

Screen Shot 2014-06-05 at 8.47.24 PMPCR performance of a thermostable heterodimeric archaeal DNA polymerase – Tom Killelea – Frontiers in Microbiology, Evolutionary and Genomic Microbiology

“Here we looked at the PCR performances of the proof-reading D-type DNA polymerase from P. abyssi, Pab-polD. Fragments, 3 kilobases in length, were specifically PCR-amplified in its optimized reaction buffer. Pab-polD showed not only a greater resistance to high denaturation temperatures than Taq during cycling, but also a superior tolerance to the presence of potential inhibitors. “

Arsenic metabolism

Screen Shot 2014-06-05 at 8.50.18 PMArsenic and old toenails – University of British Columbia

“We successfully recruited 35,000 Atlantic Canadians whose health will be tracked over the next 25 years, and the project will be a major resource for cancer prevention research. More than 22,000 participants provided blood and toenail clippings, which ended up being an official Guinness World Record.”

Marine Mammals (and turtles)

Screen Shot 2014-06-05 at 8.51.14 PMSatellite Tracking of Sympatric Marine Megafauna Can Inform the Biological Basis for Species Co-Management – Christian Gredzens – PLOS ONE

“Fast-acquisition satellite telemetry was used to track eleven dugongs and ten green turtles at two geographically distinct foraging locations in Queensland, Australia to evaluate the inter- and intra-species spatial relationships and assess the efficacy of existing protection zones. “

Dr. Bik’s Picks

Screen Shot 2014-06-05 at 8.48.40 PMThe sheep genome illuminates biology of the rumen and lipid metabolism – Yu Jiang- Science

“We have developed and analyzed a high-quality reference sheep genome and transcriptomes from 40 different tissues. We identified highly expressed genes encoding keratin cross-linking proteins associated with rumen evolution.”

Screen Shot 2014-06-05 at 8.55.17 PMMapping the Global Distribution of Livestock – Timothy P. Robinson – PLOS ONE

“This paper describes the current approach in detail and presents new global distribution maps at 1 km resolution for cattle, pigs and chickens, and a partial distribution map for ducks. These digital layers are made publically available via the Livestock Geo-Wiki (http://www.livestock.geo-wiki.org), as will be the maps of other livestock types as they are produced.”

Screen Shot 2014-06-05 at 9.02.51 PMCatfish ‘See’ Their Next Meal with Acid-Sensing Whiskers – Charles Q. Choi – LiveScience

“Catfish have evolved sensors on their whiskers that can help the animals hunt in the dark by detecting slight changes in water acidity, the first time such sensors have been seen in fish, researchers say.”

Screen Shot 2014-06-05 at 8.56.34 PMWhy Koalas Hug Trees – Tia Ghose – LiveScience

“Now, scientists have figured out why the iconic Australian marsupials hug trees: The trunks help the koala bears keep cool, according to a new study.”

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