General microbiology and science, June 17

How to freeze and preserve communities, host response, standardized metadata for pathogens, primers for fungal detection and more. Check out Dr. Bik’s Picks for coffee in space and sticky tongues.

Infection and host response

The effect of age on the systemic inflammatory response in patients with community-acquired pneumonia – Lonneke A. van Vught – Clinical Microbiology and Infection

“Serum concentrations of pro-inflammatory (interleukin (IL)-6 and IL-8) and anti-inflammatory cytokines (IL-10 and IL-1 receptor antagonist) did not differ between age groups, although admission IL-8 levels tended to be higher in old patients (p = 0.05). “

Clinical Disease Severity of Respiratory Viral Co-Infection versus Single Viral Infection: A Systematic Review and Meta-Analysis – Sandra A. Asner – PLOS ONE

“No differences in clinical disease severity between viral co-infections and single respiratory infections were documented.”

Standardized Metadata for Human Pathogen/Vector Genomic Sequences – Vivien G. Dugan – PLOS ONE

“The standard includes data fields about characteristics of the organism or environmental source of the specimen, spatial-temporal information about the specimen isolation event, phenotypic characteristics of the pathogen/vector isolated, and project leadership and support. “

Discovering Hidden Connections among Diseases, Genes and Drugs Based on Microarray Expression Profiles with Negative-Term Filtering – Jain-Shing Wu – PLOS ONE

“This study proposes a novel means of employing existing GEPs to reveal hidden relationships among diseases, genes, and drugs within a rich biomedical database, PubMed. Unlike the co-occurrence method, which considers only the appearance of keywords, the proposed method also takes into account negative relationships and non-relationships among keywords, the importance of which has been demonstrated in previous studies.”

MS spectrometry and microbiology

A simple, robust and rapid approach to detect carbapenemases in Gram negative isolates by MALDI-TOF mass spectrometry: validation with triple quadripole tandem mass spectrometry, microarray and PCR – Christelle Vogne – Clinical Microbiology and Infection

“Here, we developed a simple, easy and rapid MALDI-TOF-based assay to detect carbapenemases and compared this innovative test with 4 other diagnostic approaches on 47 clinical isolates. “

Source-Identifying Biomarker Ions between Environmental and Clinical Burkholderia pseudomallei Using Whole-Cell Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) – Suthamat Niyompanich – PLOS ONE

“In this present study, we employed a whole-cell MALDI-TOF MS approach for assessing its potency in clustering a total of 11 different B. pseudomallei isolates (consisting of 5 environmental and 6 clinical isolates) with respect to their origins and to further investigate the source-identifying biomarker ions belonging to each bacterial group.”

Phages and viruses

Effectiveness of bacteriophages in the sputum of cystic fibrosis patients – Emilie Saussereau – Clinical Microbiology and Infection

“The demonstration that bacteriophages infect their bacterial hosts in the sputum environment, regardless of the clinical characteristics of the patients, represents a major step towards the development of bacteriophage therapy to treat chronic lung infections.”

Standards for Sequencing Viral Genomes in the Era of High-Throughput Sequencing
Jason T. Ladner – mBio

“Here, we propose five “standard” categories that encompass all stages of viral genome finishing, and we define them using simple criteria that are agnostic to the technology used for sequencing.”

Dengue

Dengue Serosurvey in Sint Eustatius – Teresa Leslie – PLOS ONE

“ Few studies have investigated dengue on Sint Eustatius. Blood samples were collected to determine the prevalence of antibodies against dengue in the Sint Eustatius population.”

General microbiology

Invited Editorial: Bioterrorism: myth or reality? – Gilbert Greub and Martin P. Grobusch – Clinical Microbiology and Infection

“Interestingly, while there are no doubt many features which tell those topics apart from each other, bioterrorism, in its broad sense, in its perception by the public, strikingly shares some features with the human interest in viral hemorrhagic fevers as witnessed during the recent Zaire ebolavirus disease outbreak “

Invited Editorial: New epidemiology of Staphylococcus aureus infections – Jean-Philippe Rasigade – Clinical Microbiology and Infection

“The clinical and molecular epidemiology of S. aureus infections has changed dramatically over the past two decades with the emergence of community-associated methicillin-resistant S. aureus (CA-MRSA).”

Sequencing and data analysis

Summarizing Specific Profiles in Illumina Sequencing from Whole-Genome Amplified DNA – Isheng J. Tsai – DNA Research

“To utilize the full potential of WGA to reveal the real biological interest, this article highlights the importance of recognizing additional sources of errors from amplified sequence reads and discusses the potential implications in downstream analyses.”

The Bias Associated with Amplicon Sequencing Does Not Affect the Quantitative Assessment of Bacterial Community Dynamics – Federico M. Ibarbalz – PLOS ONE

“The performance of two sets of primers targeting variable regions of the 16S rRNA gene V1–V3 and V4 was compared in their ability to describe changes of bacterial diversity and temporal turnover in full-scale activated sludge.”

HIVE-Hexagon: High-Performance, Parallelized Sequence Alignment for Next-Generation Sequencing Data Analysis – Luis Santana-Quintero – PLOS ONE

“High-performance Integrated Virtual Environment (HIVE), a cloud-based environment optimized for storage and analysis of extra-large data, presents an algorithmic solution: the HIVE-hexagon DNA sequence aligner. “

Sample preparation, primers, PCR

Optimized Cryopreservation of Mixed Microbial Communities for Conserved Functionality and Diversity – Frederiek-Maarten Kerckhof – PLOS ONE

“ In summary, we have evaluated a cryopreservation protocol that succeeded in preserving both community structure and functionality of value-added microbiomes. ”

Comparison and Validation of Some ITS Primer Pairs Useful for Fungal Metabarcoding Studies – Michiel Op De Beeck – PLOS ONE

“In the current study, three selected primer pairs were tested for their suitability as fungal metabarcoding primers.”

Chromosome organization

Assessing Diversity of DNA Structure-Related Sequence Features in Prokaryotic Genomes – Yongjie Huang and Jan Mrázek – DNA Research

“Our results show that simple sequence repeats and Z-DNA-promoting patterns are generally suppressed in prokaryotic genomes, whereas palindromes and inverted repeats are over-represented.”

Dr. Bik’s Picks

Tongue adhesion in the horned frog Ceratophrys sp. – Thomas Kleinteich & Stanislav N. Gorb- Scientific Reports

“Here we measured for the first time adhesive forces and tongue contact areas in living individuals of a horned frog (Ceratophrys sp.) against glass. We found that Ceratophrys sp. generates adhesive forces well beyond its own body weight.”

Good news: Espresso machine in SPAAAACE. Bad news: Fuelled by URINE – Simon Sharwood – The Register

“A critical issue standing between humanity and long-term residence in space has been solved after boffins invented an espresso machine they plan to send up to the International Space Station (ISS), groan-inducingly dubbed the ISSpresso.”

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