The Earth Microbiome Project: Meeting report of the "1 EMP meeting on sample selection and acquisition" at Argonne National Laboratory October 6 2010.

This report details the outcome the first meeting of the Earth Microbiome Project to discuss sample selection and acquisition. The meeting, held at the Argonne National Laboratory on Wednesday October 6(th) 2010, focused on discussion of how to prioritize environmental samples for sequencing and metagenomic analysis as part of the global effort of the EMP to systematically determine the functional and phylogenetic diversity of microbial communities across the world

Tougher Laws, Too Few Prosecutions? A Mixed Methods Study of Nurses’ Experiences Regarding the Reporting of Occupational Violence to the Police

ProblemAssaults on nurses by patients are common. To deter occupational violence against nurses, assaults attract penalties of longer imprisonment in many jurisdictions (domestically and internationally). However, the deterrent value of harsher penalties has been questioned when many assaults are underreported.AimTo identify the barriers and enablers to the reporting and prosecution of assaults experienced by nurses.MethodsIn this study participants were recruited using a snowballing technique through health workforce emails, social media channels, and professional organisations. The investigator-developed survey prompted for categorical and open-ended responses. Descriptive and qualitative content analyses were used to analyse the study data.FindingsOf the N = 275 respondents, n = 237 nurses had been assaulted at work. Assaulted nurses were typically female, over 31 years old, had more than five years of nursing experience, and worked in an emergency department. Overwhelmingly, nurses indicated receiving poor support when they wanted to report an assault to the police. Dominant themes (N = 6) identified systemic barriers that hinder criminal reporting, which was found to be a consequence of organisational and policing lapses, and self-limiting nursing culture.DiscussionThis study identified several barriers for nurses to report and prosecute assaultive patients in Australia. The barriers point to a strong imperative for organisations that employ nurses and police to fulfil their responsibilities to enable and support assaulted nurses to prosecute.ConclusionThe study findings led to important recommendations for organisations and police to support, encourage, and empower nurses to prosecute assaultive patients, and ultimately deter violence

Satellite remote sensing data can be used to model marine microbial metabolite turnover

Sampling ecosystems, even at a local scale, at the temporal and spatial resolution necessary to capture natural variability in microbial communities are prohibitively expensive. We extrapolated marine surface microbial community structure and metabolic potential from 72 16S rRNA amplicon and 8 metagenomic observations using remotely sensed environmental parameters to create a system-scale model of marine microbial metabolism for 5904 grid cells (49 km2) in the Western English Chanel, across 3 years of weekly averages. Thirteen environmental variables predicted the relative abundance of 24 bacterial Orders and 1715 unique enzyme-encoding genes that encode turnover of 2893 metabolites. The genes’ predicted relative abundance was highly correlated (Pearson Correlation 0.72, P-value <10−6) with their observed relative abundance in sequenced metagenomes. Predictions of the relative turnover (synthesis or consumption) of CO2 were significantly correlated with observed surface CO2 fugacity. The spatial and temporal variation in the predicted relative abundances of genes coding for cyanase, carbon monoxide and malate dehydrogenase were investigated along with the predicted inter-annual variation in relative consumption or production of ~3000 metabolites forming six significant temporal clusters. These spatiotemporal distributions could possibly be explained by the co-occurrence of anaerobic and aerobic metabolisms associated with localized plankton blooms or sediment resuspension, which facilitate the presence of anaerobic micro-niches. This predictive model provides a general framework for focusing future sampling and experimental design to relate biogeochemical turnover to microbial ecology

Does higher-yielding agriculture mean more environmental harm?

A criticism of the land-sparing approach to preserving biodiversity, by restricting farmland to a smaller, higher-yielding area, is that other impacts are higher in food produced this way. This study aims to investigate the evidence for this based on currently available data and models for greenhouse gas emissions, N, P and soil loss and water use. We asked 25 experts to identify and supply data to plot environmental impact per unit of product against yield for the beef, dairy, wheat and rice sectors. This produced data from modelling and field trials and the lifecycle assessment and field trial literature. The data were modelled statistically to adjust for differences between the studies. Given data limitations, it does not seem that higher yielding agricultural production has higher impacts, often quite the reverse. We ask those conducting field studies to collect data that can definitively answer this question.CCI project code: CCI 06-16-00

Genomic Standards Consortium projects

© The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Standards in Genomic Sciences 9 (2014): 599-601, doi:10.4056/sigs.5559680.The Genomic Standards Consortium (GSC) is an open-membership community working towards the development, implementation and harmonization of standards in the field of genomics. The mission of the GSC is to improve digital descriptions of genomes, metagenomes and gene marker sequences. The GSC started in late 2005 with the defined task of establishing what is now termed the “Minimum Information about any Sequence” (MIxS) standard [1,2]. As an outgrowth of the activities surrounding the creation and implementation of the MixS standard there are now 18 projects within the GSC [3]. These efforts cover an ever widening range of standardization activities. Given the growth of projects and to promote transparency, participation and adoption the GSC has developed a “GSC Project Description Template”. A complete set of GSC Project Descriptions and the template are available on the GSC website. The GSC has an open policy of participation and continues to welcome new efforts. Any projects that facilitate the standard descriptions and exchange of data are potential candidates for inclusion under the GSC umbrella. Areas that expand the scope of the GSC are encouraged. Through these collective activities we hope to help foster the growth of the ‘bioinformatics standards’ community. For more information on the GSC and its range of projects, please see http://gensc.org/

O-Antigen Biosynthesis: Hitting the Sweet Spot for a Q Fever Vaccine

Poster presented at the 2017 Defence and Security Doctoral Symposium.Coxiella burnetii, the causative agent of Q fever, is a pathogen with a worldwide distribution. Biological material shed from ruminant infections contaminates dirt and dust, which can cause infection on inhalation. Humans generally present with flu-like symptoms, however, patients can develop life-changing maladies such as hepatitis, chronic fatigue, and endocarditis. Q fever was initially identified as a military problem when thousands were affected during WWI. More recently, Q fever has been recognised as a problem in UK troops returning from Afghanistan. C. burnetii is classified as a CDC category B bioterrorism agent, the second highest category, yet there is no Q fever vaccine licensed in the UK/EU/US. For C. burnetii, the lipopolysaccharide (LPS) is the main determinant of virulence, and many of the most effective modern vaccines target such sugar structures. Furthermore, the sugars that comprise the C. burnetii LPS are highly unusual, making this the primary target for vaccine development. In order to facilitate production of a subunit vaccine, focus is on elucidating the pathways for biosynthesis of two very rare sugars, virenose and dihydrohydroxystreptose (DHHS). Therefore in addition to providing the basis for a novel Q fever vaccine, for livestock and humans, this project will highlight novel biochemistry