Investigating the Impact of Storage Conditions on Microbial Community Composition in Soil Samples

Recent advances in DNA sequencing technologies have allowed scientists to probe increasingly complex biological systems, including the diversity of bacteria in the environment. However, despite a multitude of recent studies incorporating these methods, many questions regarding how environmental samples should be collected and stored still persist. Here, we assess the impact of different soil storage conditions on microbial community composition using Illumina-based 16S rRNA V4 amplicon sequencing. Both storage time and temperature affected bacterial community composition and structure. Frozen samples maintained the highest alpha diversity and differed least in beta diversity, suggesting the utility of cold storage for maintaining consistent communities. Samples stored for intermediate times (three and seven days) had both the highest alpha diversity and the largest differences in overall beta diversity, showing the degree of community change after sample collection. These divergences notwithstanding, differences in neither storage time nor storage temperature substantially altered overall communities relative to more than 500 previously examined soil samples. These results systematically support previous studies and stress the importance of methodological consistency for accurate characterization and comparison of soil microbiological assemblages.</p

Drug-like antagonists of P2Y receptors — from lead identification to drug development

P2Y receptors are expressed in virtually all cells and tissue types and mediate an astonishing array of biological functions, including platelet aggregation, smooth muscle cell proliferation, and immune regulation. The P2Y receptors belong to the G protein-coupled receptor superfamily and are composed of eight members encoded by distinct genes that can be subdivided into two groups on the basis of their coupling to specific G-proteins. Extensive research has been undertaken to find modulators of P2Y receptors, although to date only a limited number of small-molecule P2Y receptor antagonists have been approved by drug/medicines agencies. This Perspective reviews the known P2Y receptor antagonists, highlighting oral drug-like receptor antagonists, and considers future opportunities for the development of small molecules for clinical evaluation

Influence of particle size on the physicochemical properties and stickiness of dairy powders

peer-reviewedThe compositional and physicochemical properties of different whey permeate (WPP), demineralised whey (DWP) and skim milk powder (SMP) size fractions were investigated. Bulk composition of WPP and DWP was significantly (P < 0.05) influenced by powder particle size; smaller particles had higher protein and lower lactose contents. Microscopic observations showed that WPP and DWP contained both larger lactose crystals and smaller amorphous particles. Bulk composition of SMP did not vary with particle size. Surface composition of the smallest SMP fraction (<75 μm) showed significantly lower protein (−9%) and higher fat (+5%) coverage compared with non-fractionated powders. For all powders, smaller particles were more susceptible to sticking. Hygroscopicity of SMP was not affected by particle size; hygroscopicity of semi-crystalline powders was inversely related to particle size. This study provides insights into differences between size fractions of dairy powders, which can potentially impact the sticking/caking behaviour of fine particles during processing.ACCEPTEDpeer-reviewe

Influence of conjugated linoleic acid (CLA) or tetradecylthioacetic acid (TTA) on growth, lipid composition, fatty acid metabolism and lipid gene expression of rainbow trout (Oncorhynchus mykiss L.)

Our objective was to test the hypotheses that conjugated linoleic acid (CLA) and/or tetradecylthioacetic acid (TTA) would have beneficial effects on the nutritional quality of rainbow trout (Oncorhynchus mykiss) through decreased lipid content of flesh or viscera, and increased levels of beneficial fatty acids including accumulation of CLA or TTA themselves. The specific aims of this study were to determine the effects of CLA and TTA on growth performance, lipid and fatty acid metabolism, and selected gene expression in commercial sized trout grown in seawater. Trout were fed for eight weeks on fish meal and fish oil diets containing either 0.5% or 1% CLA, or 0.5% TTA. The effects of the supplemented fatty acids on growth, feed efficiency, lipid contents, class compositions and fatty acid compositions of flesh and liver were determined, along with liver highly unsaturated fatty acid synthesis, activities of key enzymes of fatty acid oxidation in liver and muscle, and expression of carnitine palmitoyltransferase-I (CPT-I) and fatty acyl desaturase and elongase genes. Neither functional fatty acid had any effect on growth parameters, condition factor, viscero- and hepato-somatic indices or fillet colour, and there were no mortalities in any of the treatments. Dietary CLA, but not TTA, decreased the lipid content of liver, but neither fatty acid had any significant effect on lipid class compositions of liver and flesh. Both CLA and TTA were incorporated into tissue lipids, with higher percentages found in flesh compared to liver. In addition, production of hexaene fatty acid by liver microsomes was increased by dietary CLA or TTA, and both functional fatty acids increased the proportion of n-3 fatty acids in liver mainly due to increased 20:5n-3 and 22:6n-3. However, the expression of fatty acyl Δ6 desaturase was significantly lower in fish fed CLA or TTA, whereas the expression of PUFA elongase was increased, significantly so in fish fed 1% CLA. CPT-I activity was increased by TTA in liver and red muscle, and acyl CoA oxidase activity was increased by TTA in liver and CLA at the higher dietary inclusion level in red muscle. There was a clear trend for CPT-I expression to be increased in fish fed 0.5% CLA or TTA in all tissues although this was only significant in white muscle. The results showed that both CLA and TTA had effects on lipid metabolism that partly support the hypotheses tested. Although CLA or TTA did not enhance growth parameters, feed conversion or potential yield, nutritional quality could be enhanced, and sea-run trout fed CLA or TTA could be beneficial in the human diet through provision of bioactive fatty acids, with no detrimental effects on 20:5n-3 or 22:6n-3 levels

Influence of dietary conjugated linoleic acid (CLA) and tetradecylthioacetic acid (TTA) on growth, lipid composition and key enzymes of fatty acid oxidation in liver and muscle of Atlantic cod (Gadus morhua L.)

The aim of the present study was to determine the effects of conjugated linoleic acid (CLA) and tetradecylthioacetic acid (TTA) on growth performance, and lipid and fatty acid metabolism in Atlantic cod. The overall objective being to test the hypotheses that CLA and TTA have beneficial effects in cod culture including decreased liver size and proportion through decreased lipid content, and increased nutritional quality through effects on fatty acid compositions including accumulation of bioactive fatty acids, CLA and TTA, in flesh. Juvenile cod were fed for three months on fish meal and fish oil diets of basically commercial formulation, but containing either 0.5% or 1% CLA, or 0.5% TTA. The effects of the functional fatty acids on growth, feed efficiency, body proximate composition, liver weight and lipid composition, fatty acid compositions of flesh and liver, and key enzymes of fatty acid oxidation were determined. Dietary CLA and TTA had no effect on growth parameters in cod juveniles, but viscero- and hepato-somatic indices were increased in fish fed 0.5% CLA and TTA, respectively. Proximate composition of whole fish was not affected by CLA or TTA, and there were no major effects of either functional fatty acid on lipid contents and compositions of liver and flesh. Dietary CLA and TTA were both incorporated into tissue lipids, with CLA deposited to a greater extent in liver, whereas TTA was deposited to a greater extent in flesh. In liver, acyl CoA oxidase (ACO) activity, but not carnitine palmitoyltransferase-I (CPT-I), was increased by CLA, whereas dietary TTA increased both ACO and CPT-I activities. In contrast, ACO activity was reduced by both CLA and TTA in red and white muscle, whereas CPT-I activity was generally not affected by CLA and TTA in either muscle tissue. Therefore, the results only partially supported the hypotheses tested, as CLA and TTA had few beneficial effects in Atlantic cod and did not enhance growth parameters, or improve feed conversion or potential yield through decreased adiposity or liver lipid deposition. However, nutritional quality could be enhanced, and cod fed CLA and/or TTA could be beneficial in the human diet, through provision of bioactive fatty acids with no detrimental effects on n-3 PUFA levels

The Resource Identification Initiative: A cultural shift in publishing

A central tenet in support of research reproducibility is the ability to uniquely identify research resources, i.e., reagents, tools, and materials that are used to perform experiments. However, current reporting practices for research resources are insufficient to allow humans and algorithms to identify the exact resources that are reported or answer basic questions such as What other studies used resource X? To address this issue, the Resource Identification Initiative was launched as a pilot project to improve the reporting standards for research resources in the methods sections of papers and thereby improve identifiability and reproducibility. The pilot engaged over 25 biomedical journal editors from most major publishers, as well as scientists and funding officials. Authors were asked to include Research Resource Identifiers (RRIDs) in their manuscripts prior to publication for three resource types: antibodies, model organisms, and tools (including software and databases). RRIDs represent accession numbers assigned by an authoritative database, e.g., the model organism databases, for each type of resource. To make it easier for authors to obtain RRIDs, resources were aggregated from the appropriate databases and their RRIDs made available in a central web portal ( www.scicrunch.org/resources). RRIDs meet three key criteria: they are machine readable, free to generate and access, and are consistent across publishers and journals. The pilot was launched in February of 2014 and over 300 papers have appeared that report RRIDs. The number of journals participating has expanded from the original 25 to more than 40. Here, we present an overview of the pilot project and its outcomes to date. We show that authors are generally accurate in performing the task of identifying resources and supportive of the goals of the project. We also show that identifiability of the resources pre- and post-pilot showed a dramatic improvement for all three resource types, suggesting that the project has had a significant impact on reproducibility relating to research resources

Multisite Comparison of MRI Defacing Software Across Multiple Cohorts

With improvements to both scan quality and facial recognition software, there is an increased risk of participants being identified by a 3D render of their structural neuroimaging scans, even when all other personal information has been removed. To prevent this, facial features should be removed before data are shared or openly released, but while there are several publicly available software algorithms to do this, there has been no comprehensive review of their accuracy within the general population. To address this, we tested multiple algorithms on 300 scans from three neuroscience research projects, funded in part by the Ontario Brain Institute, to cover a wide range of ages (3–85 years) and multiple patient cohorts. While skull stripping is more thorough at removing identifiable features, we focused mainly on defacing software, as skull stripping also removes potentially useful information, which may be required for future analyses. We tested six publicly available algorithms (afni_refacer, deepdefacer, mri_deface, mridefacer, pydeface, quickshear), with one skull stripper (FreeSurfer) included for comparison. Accuracy was measured through a pass/fail system with two criteria; one, that all facial features had been removed and two, that no brain tissue was removed in the process. A subset of defaced scans were also run through several preprocessing pipelines to ensure that none of the algorithms would alter the resulting outputs. We found that the success rates varied strongly between defacers, with afni_refacer (89%) and pydeface (83%) having the highest rates, overall. In both cases, the primary source of failure came from a single dataset that the defacer appeared to struggle with - the youngest cohort (3–20 years) for afni_refacer and the oldest (44–85 years) for pydeface, demonstrating that defacer performance not only depends on the data provided, but that this effect varies between algorithms. While there were some very minor differences between the preprocessing results for defaced and original scans, none of these were significant and were within the range of variation between using different NIfTI converters, or using raw DICOM files

Development and application of an electronic treatment register: a system for enumerating populations and monitoring treatment during mass drug administration.

We developed an electronic treatment register for the DeWorm3 Project, a cluster-randomised, controlled trial in Benin, India, and Malawi testing the feasibility of interrupting transmission of soil-transmitted helminths through community-wide mass drug administration. The electronic treatment register was designed in xlsform, deployed via the SurveyCTO mobile data collection platform, and implemented on smartphones running the Android operating system. The versatile system enables collection of census and treatment status information, facilitates data aggregation and visualisation, and permits real-time feedback loops during implementation of mass drug administration. Here we describe the system's design and use within the DeWorm3 Project and key features, and by sharing the register here, we hope our readers will further explore its use within their research and disease-control activities

A HIF-LIMD1 negative feedback mechanism mitigates the pro-tumorigenic effects of hypoxia

The adaptive cellular response to low oxygen tensions is mediated by the hypoxia inducible factors (HIFs), a family of heterodimeric transcription factors composed of HIF-α and β subunits. Prolonged HIF expression is a key contributor to cellular transformation, tumourigenesis and metastasis. As such, HIF degradation under hypoxic conditions is an essential homeostatic and tumour suppressive mechanism. LIMD1 complexes with PHD2 and VHL in physiological oxygen levels (normoxia) to facilitate proteasomal degradation of the HIF-α subunit. Here, we identify LIMD1 as a HIF-1 target gene, which mediates a previously uncharacterised, negative regulatory feedback mechanism for hypoxic HIF-α degradation by modulating PHD2-LIMD1- VHL complex formation. Hypoxic induction of LIMD1 expression results in increased HIF-α protein degradation, inhibiting HIF-1 target-gene expression, tumour growth and vascularisation. Furthermore, we report that copy number variation at the LIMD1 locus occurs in 47.1% of lung adenocarcinoma patients, correlates with enhanced expression of a HIF target gene signature and is a negative prognostic indicator. Taken together, our data open a new field of research into the aetiology, diagnosis and prognosis of LIMD1-negative lung cancers