Improving functional annotation for industrial microbes: a case study with Pichia pastoris.

The research communities studying microbial model organisms, such as Escherichia coli or Saccharomyces cerevisiae, are well served by model organism databases that have extensive functional annotation. However, this is not true of many industrial microbes that are used widely in biotechnology. In this Opinion piece, we use Pichia (Komagataella) pastoris to illustrate the limitations of the available annotation. We consider the resources that can be implemented in the short term both to improve Gene Ontology (GO) annotation coverage based on annotation transfer, and to establish curation pipelines for the literature corpus of this organism.We gratefully acknowledge funding from the Wellcome Trust (PomBase and Canto; WT090548MA to SGO), and the EU 7th Framework Programme (BIOLEDGE Contract No: 289126 to SGO).This is the published version distributed under a Creative Commons Attribution License 2.0, which can also be found on the publisher's website at: http://www.sciencedirect.com/science/article/pii/S0167779914001061

Noise exposure potentiates exocytosis from cochlear inner hair cells

Noise-induced hearing loss has gained relevance as one of the most common forms of hearing impairment. The anatomical correlates of hearing loss, principally cell damage and/or death, are relatively well-understood histologically. However, much less is known about the physiological aspects of damaged, surviving cells. Here we addressed the functional consequences of noise exposure on the capacity of inner hair cells (IHCs) to release synaptic vesicles at synapses with spiral ganglion neurons (SGNs). Mice of either sex at postnatal day (P) 15-16 were exposed to 1-12 kHz noise at 120 dB sound pressure level (SPL), for 1 h. Exocytosis was measured by tracking changes in membrane capacitance (ΔCm) from IHCs of the apical cochlea. Upon IHC depolarization to different membrane potentials, Δ

Lake Michigan’s suitability for bigheaded carp: The importance of diet flexibility and subsurface habitat

As bighead (Hypophthalmichthys nobilis) and silver carp (Hypophthalmichthys molitrix)—collectively bigheaded carp (BHC)—arrive at Lake Michigan’s doorstep, questions remain as to whether there is sufficient food to support these invasive filter‐feeding fishes in the upper Laurentian Great Lakes. Previous studies suggest that suitable BHC habitat is limited to a few productive, nearshore areas. However, those studies did not consider the influence of BHC’s diet plasticity or the presence of spatially‐discrete subsurface prey resources. This study aimed to characterise Lake Michigan’s suitability for BHC and evaluate the importance of these considerations in habitat suitability assessments.We used simulated outputs of prey biomass (phytoplankton, zooplankton, and detritus) and water temperature from a three‐dimensional biophysical model of Lake Michigan to evaluate growth rate potential (GRP, quantitative index of habitat suitability) of adult BHC throughout the entire volume of the lake. Our GRP model applied a foraging model and a bioenergetics model to translate prey concentrations and water temperatures into habitat quality indexed by individual fish growth rate. We defined suitable habitat as habitats that can support GRP ≥ 0 g g−1 day−1. We developed six feeding scenarios to evaluate the impact of diet flexibility and subsurface prey resources on suitable habitat quantity. Scenarios were defined by the number of prey types the fish could consume and the depths at which they could feed (surface or whole water column).Consistent with previous studies, we found that habitats with the highest quality were concentrated near river mouths and in eutrophic areas of Green Bay. However, in contrast to previous studies, we found suitable offshore habitat for bighead carp owing to our added considerations of diet plasticity and subsurface prey resources. For silver carp, these considerations extended suitable habitat within Green Bay and in some tributary‐influenced nearshore areas, but offshore areas remained predominantly unsuitable in all feeding scenarios. Differences in simulated habitat suitability between these two species probably reflect differences in energy density and mass of the specific fishes we used in our model. However, reports of these two species in environments where they coexist indicate that bighead carp grow at faster rates than silver carp, as our model simulated.Our vertical analysis at Muskegon, MI, U.S.A. indicates that subsurface temperature and prey biomass are not only sufficient to support bighead carp growth but provide maximum habitat quality during late summer stratification.Overall, our study demonstrates that BHC are capable of surviving and growing in much larger areas of Lake Michigan than predicted by previous studies, and thus suggests that the risk of establishment is not sufficiently reduced by low plankton concentrations. Maps generated by our model identified the potential for cross‐lake migration corridors that may facilitate and accelerate lake‐wide movements. We believe these maps could be used to prioritise surveillance protocols by identifying areas to which BHC might spread upon entering the lake. More broadly, this research demonstrates how the physiology and trophic ecology of BHC contributes to their high invasive capacity and can permit their survival in novel environments.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/151968/1/fwb13382_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/151968/2/fwb13382.pd

PomBase 2015: updates to the fission yeast database.

PomBase (http://www.pombase.org) is the model organism database for the fission yeast Schizosaccharomyces pombe. PomBase provides a central hub for the fission yeast community, supporting both exploratory and hypothesis-driven research. It provides users easy access to data ranging from the sequence level, to molecular and phenotypic annotations, through to the display of genome-wide high-throughput studies. Recent improvements to the site extend annotation specificity, improve usability and allow for monthly data updates. Both in-house curators and community researchers provide manually curated data to PomBase. The genome browser provides access to published high-throughput data sets and the genomes of three additional Schizosaccharomyces species (Schizosaccharomyces cryophilus, Schizosaccharomyces japonicus and Schizosaccharomyces octosporus)

A Randomized Controlled Trial of the Effect of Allopurinol on Left Ventricular Mass Index in Hemodialysis Patients

Introduction: Increased left ventricular mass index (LVMI) is associated with mortality in end-stage renal disease. LVMI regression may improve outcomes. Allopurinol has reduced LVMI in randomized controlled trials in chronic kidney disease, diabetes, and ischemic heart disease. This study investigated whether allopurinol would regress LVMI in hemodialysis patients. Methods: This was a randomized placebo-controlled double-blind multicenter trial. A total of 80 patients undergoing regular maintenance hemodialysis were recruited from NHS Tayside, NHS Greater Glasgow and Clyde and NHS Ayrshire and Arran in Scotland, UK. Participants were randomly assigned on a 1:1 ratio to 12 months of therapy with allopurinol 300 mg or placebo after each dialysis session. The primary outcome was change in LVMI, as assessed by cardiac magnetic resonance imaging (MRI) at baseline and 12 months. Secondary outcomes were change in BP, flow-mediated dilation (FMD), augmentation indices (AIx), and pulse wave velocity (PWV). Results: A total of 53 patients, with a mean age of 58 years, completed the study and had MRI follow-up data for analysis. Allopurinol did not regress LVMI (change in LVMI: placebo +3.6 ± 10.4 g/m2; allopurinol: +1.6 ± 11 g/m2; P = 0.49). Allopurinol had no demonstrable effect on BP, FMD, AIx, or PWV. Conclusion: Compared with placebo, treatment with allopurinol did not regress LVMI in this trial

PomBase: a comprehensive online resource for fission yeast.

PomBase (www.pombase.org) is a new model organism database established to provide access to comprehensive, accurate, and up-to-date molecular data and biological information for the fission yeast Schizosaccharomyces pombe to effectively support both exploratory and hypothesis-driven research. PomBase encompasses annotation of genomic sequence and features, comprehensive manual literature curation and genome-wide data sets, and supports sophisticated user-defined queries. The implementation of PomBase integrates a Chado relational database that houses manually curated data with Ensembl software that supports sequence-based annotation and web access. PomBase will provide user-friendly tools to promote curation by experts within the fission yeast community. This will make a key contribution to shaping its content and ensuring its comprehensiveness and long-term relevance

Towards facial expression recognition for on-farm welfare assessment in pigs

Animal welfare is not only an ethically important consideration in good animal husbandry but can also have a significant effect on an animal’s productivity. The aim of this paper was to show that a reduction in animal welfare, in the form of increased stress, can be identified in pigs from frontal images of the animals. We trained a convolutional neural network (CNN) using a leave-one-out design and showed that it is able to discriminate between stressed and unstressed pigs with an accuracy of >90% in unseen animals. Grad-CAM was used to identify the animal regions used, and these supported those used in manual assessments such as the Pig Grimace Scale. This innovative work paves the way for further work examining both positive and negative welfare states with the aim of developing an automated system that can be used in precision livestock farming to improve animal welfare

Research cardiac magnetic resonance imaging in end stage renal disease - incidence, significance and implications of unexpected incidental findings

Objectives: Left ventricular mass (LVM) at cardiac magnetic resonance imaging (CMR) is a frequent end point in clinical trials in nephrology. Trial participants with end stage renal disease (ESRD) may have a greater frequency of incidental findings (IF). We retrospectively investigated prevalence of IF in previous research CMR and reviewed their subsequent impact on participants. Methods: Between 2002 and 2006, 161 ESRD patients underwent CMR in a transplant assessment study. Images were used to assess LV mass and function. In the current study a radiologist reviewed the scans for IF. Review of patient records determined the subsequent clinical significance of IF. Results: There were 150 IF in 95 study participants. Eighty-four (56 %) were new diagnoses. One hundred and two were non-cardiac. Fifteen were suspicious of malignancy. There was a clinically significant IF for 14.9 % of the participants. In six cases earlier identification of an IF may have improved quality of life or survival. Conclusions: Without radiology support clinically important IF may be missed on CMR. Patients undergoing CMR in trials should be counselled about the frequency and implications of IF. Patients with ESRD have a higher prevalence of IF than reported in other populations. Nephrology studies require mechanisms for radiologist reporting and strategies for dealing with IF