Rise and fall: increasing temperatures have nonlinear effects on aggression in a tropical fish

Environmental conditions are fundamental drivers of animal behaviour. Aggression in ectotherms is a marked example and is often considered positively correlated with temperature. However, many studies exploring this relationship, and its important consequences, focus on a few temperatures and implicitly assume a linear relationship between the two variables. This may limit our understanding of the influence of temperature on aggression. We measured levels of aggression in Neolamprologus pulcher, a cichlid fish commonly used as a model in studies of aggression-based social hierarchy, across a range of temperatures in a mirror aggression test. We used temperatures expected from their natural range with a 2 °C extension on either end. As predicted by thermal performance curves, rates of aggression increased with temperature at the lower end of the temperature range. After reaching a peak, any further increase in temperature resulted in a considerable drop in rates of aggression. Exploring responses at a finer temporal scale, we found that the influence of high temperatures changed dramatically during the 25 min trials. Early in the trials the frequency of aggression increased linearly with temperature, across all temperatures. The initially high levels of aggression at the higher temperatures were not sustained and dropped with increasing duration of exposure to the mirror at high temperatures. Together these findings provide a more comprehensive understanding of the influence of short-term exposure to different temperatures on aggression, such as acute exposure to increased temperatures caused by global warming and associated rapid thermal fluctuations, in African rift lake fishes and in ectotherms more generally. Moreover, our results highlight the importance of measuring aggression across a range of temperatures or otherwise account for nonlinear changes in thermal performance

Libra: scalable k-mer-based tool for massive all-vs-all metagenome comparisons

Background Shotgun metagenomics provides powerful insights into microbial community biodiversity and function. Yet, inferences from metagenomic studies are often limited by dataset size and complexity and are restricted by the availability and completeness of existing databases. De novo comparative metagenomics enables the comparison of metagenomes based on their total genetic content. Results We developed a tool called Libra that performs an all-vs-all comparison of metagenomes for precise clustering based on their k-mer content. Libra uses a scalable Hadoop framework for massive metagenome comparisons, Cosine Similarity for calculating the distance using sequence composition and abundance while normalizing for sequencing depth, and a web-based implementation in iMicrobe (http://imicrobe.us) that uses the CyVerse advanced cyberinfrastructure to promote broad use of the tool by the scientific community. Conclusions A comparison of Libra to equivalent tools using both simulated and real metagenomic datasets, ranging from 80 million to 4.2 billion reads, reveals that methods commonly implemented to reduce compute time for large datasets, such as data reduction, read count normalization, and presence/absence distance metrics, greatly diminish the resolution of large-scale comparative analyses. In contrast, Libra uses all of the reads to calculate k-mer abundance in a Hadoop architecture that can scale to any size dataset to enable global-scale analyses and link microbial signatures to biological processes.National Science Foundation [1640775]Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Effects of Sex and Whole Life Cycle UVB Irradiation on Performance and Mineral and Vitamin D3 Contents in Feeder Crickets (Gryllus bimaculatus)

Captive insectivore nutrition is challenging due to the differing nutritional profiles of wild and captive diets and an incomplete understanding of both. Ultraviolet B (UVB)-irradiation has recently been explored as a means of improving prey-insect vitamin D3 and Ca content. Although short-term irradiation has been successful in some species, it has been unsuccessful in black field crickets (Gryllus bimaculatus)—a commonly cultured feeder insect. We exposed crickets to UVB irradiation from hatchling to adult stages and measured the vitamin D3 and mineral contents of crickets by sex. We did not detect vitamin D3 (detection limit 0.5 iU/g) or an effect of UVB irradiation on mineral content under either UV+ or UV− conditions. We identified large differences between sexes in Ca, K, Mg and P (females higher) and Cu, Fe, S and Zn (males higher), likely linked to reproductive investment. The differences do not straddle the minimum recommended concentrations of minerals for vertebrate growth and thus may be most relevant to animal nutrition in contexts of particular sensitivity or need. We demonstrate a UV-linked trade-off in cricket performance between individual cricket size and the numbers of crickets produced and characterise the energy costs associated with UVB provision. Our results do not support the use of UVB lighting for G. bimaculatus to improve nutrition but demonstrate previously unreported differences in the nutritional profiles between sexes in this species

Failure to improve calcium content of earthworms (Dendrobaena veneta) through three methods of gut-loading

The diets provided to many captive insectivores are deficient in calcium and high in phosphorus, which can lead to nutritional disease. Husbandry professionals may address this imbalance through supplementation, but the efficacy of different methods varies between invertebrate taxa. Earthworms are frequently used for aquatic and fossorial insectivores and this along with their rapidly shed mucus layer makes dusting with supplements ineffective; gut loading is likely the only available route to improving nutritional quality. Moreover, earthworms are often considered a good source of calcium, though data exist only for some taxa and results are mixed with regards to calcium content. The present study analysed the calcium and phosphorus content of Dendrobaena veneta earthworms, a species commonly commercially reared and sold for insectivore food, gut loaded on three diets (fresh vegetables, fortified instant porridge oats and a commercial gut loading diet) and quantified the zinc, copper and magnesium content of fasted worms. Dendrobaena worms contained sufficient zinc, copper and magnesium to meet the general requirements of domestic birds, mammals and other vertebrates for these metals. However, calcium and calcium:phosphorus ratios of worms were deficient and did not improve after being offered fortified diets. Insufficient calcium in the diets, unpalatability of food and habituation effects also potentially contributed to this result. Unless better means of improving calcium content of Dendrobaena can be developed, husbandry professionals should be circumspect in their use of this species in a diet and ensure that dietary items with sufficient calcium are also provided

Trend in CT utilisation and its impact on length of stay, readmission and hospital mortality in Western Australia tertiary hospitals: an analysis of linked administrative data 2003-2015

Objective: High use of CT scanning has raised concern due to the potential ionising radiation exposure. This study examined trends of CT during admission to tertiary hospitals and its associations with length of stay (LOS), readmission and mortality. Design Retrospective observational study from 2003 to 2015. Setting: West Australian linked administrative records at individual level. Participants: 2 375 787 episodes of tertiary hospital admission in adults aged 18+ years. Main outcome measures: LOS, 30-day readmissions and mortality stratified by CT use status (any, multiple (CTs to multiple areas during episode), and repeat (repeated CT to the same area)). Methods: Multivariable regression models were used to calculate adjusted rate of CT use status. The significance of changes since 2003 in the outcomes (LOS, 30-day readmission and mortality) was compared among patients with specific CT imaging status relative to those without. Results: Between 2003 and 2015, while the rate of CT increased 3.4% annually, the rate of repeat CTs significantly decreased −1.8% annually and multiple CT showed no change. Compared with 2003 while LOS had a greater decrease in those with any CT, 30- day readmissions had a greater increase among those with any CT, while the probability of mortality remained unchanged between the any CT/no CT groups. A similar result was observed in patients with multiple and repeat CT scanning, except for a significant increase in mortality in the recent years in the repeat CT group. Conclusion: The observed pattern of increase in CT utilisation is likely to be activity-based funding policydriven based on the discordance between LOS and readmissions. Meanwhile, the repeat CT reduction aligns with a more selective strategy of use based on clinical severity. Future research should incorporate in-hospital and out-of-hospital CT to better understand overall CT trends and potential shifts between settings over time.Thi Ninh Ha, Sviatlana Kamarova, David Youens, Cameron Wright, Donald McRobbie, Jenny Doust, John Slavotinek, Max K Bulsara, Rachael Moori

Computed Tomography Angiography for Detection of Pulmonary Embolism in Western Australia Shows Increasing Use with Decreasing Diagnostic Yield

(1) Background: Pulmonary embolism (PE) can be fatal. Computed tomography pulmonary angiography (CTPA) can accurately diagnose PE, but it should be used only when reasonable pre-test probability exists. Overtesting with CTPA exposes patients to excess ionizing radiation and contrast media, while PE overdiagnosis leads to the treatment of small emboli unlikely to cause harm. This study assessed trends in CTPA use and diagnostic yield. We also assessed trends in PE hospitalizations and mortality to indicate PE severity. (2) Methods: Analysis of Western Australian linked administrative data for 2003–2015 including hospitalizations, emergency department (ED) attendances, and CTPA performed at hospitals. Age-sex standardized trends were calculated for CTPA use, PE hospitalizations, and mortality (as a proxy for severity). Logistic regression assessed diagnostic yield of CTPA following unplanned ED presentations. (3) Results: CTPA use increased from 3.3 per 10,000 person-years in 2003 (95% CI 3.0–3.6) to 17.1 per 10,000 person-years (16.5–17.7) in 2015. Diagnostic yield of CTPA increased from 12.7% in 2003 to 17.4% in 2005, declining to 12.2% in 2015 (p = 0.049). PE hospitalizations increased from 3.8 per 10,000 (3.5–4.1) in 2003 to 5.2 per 10,000 (4.8–5.5) in 2015. Mortality remained constant at 0.50 per 10,000 (0.39–0.62) in 2003 and 0.42 per 10,000 (0.32–0.51) in 2015. (4) Conclusions: CTPA increased from 2003 to 2015, while diagnostic yield decreased, potentially indicating overtesting. PE mortality remained constant despite increasing hospitalizations, likely indicating a higher proportion of less severe cases. As treatment can be harmful, this could represent overdiagnosis

Gramene QTL database: development, content and applications

Gramene is a comparative information resource for plants that integrates data across diverse data domains. In this article, we describe the development of a quantitative trait loci (QTL) database and illustrate how it can be used to facilitate both the forward and reverse genetics research. The QTL database contains the largest online collection of rice QTL data in the world. Using flanking markers as anchors, QTLs originally reported on individual genetic maps have been systematically aligned to the rice sequence where they can be searched as standard genomic features. Researchers can determine whether a QTL co-localizes with other QTLs detected in independent experiments and can combine data from multiple studies to improve the resolution of a QTL position. Candidate genes falling within a QTL interval can be identified and their relationship to particular phenotypes can be inferred based on functional annotations provided by ontology terms. Mutations identified in functional genomics populations and association mapping panels can be aligned with QTL regions to facilitate fine mapping and validation of gene-phenotype associations. By assembling and integrating diverse types of data and information across species and levels of biological complexity, the QTL database enhances the potential to understand and utilize QTL information in biological research

Gramene 2013: comparative plant genomics resources

Gramene (http://www.gramene.org) is a curated online resource for comparative functional genomics in crops and model plant species, currently hosting 27 fully and 10 partially sequenced reference genomes in its build number 38. Its strength derives from the application of a phylogenetic framework for genome comparison and the use of ontologies to integrate structural and functional annotation data. Whole-genome alignments complemented by phylogenetic gene family trees help infer syntenic and orthologous relationships. Genetic variation data, sequences and genome mappings available for 10 species, including Arabidopsis, rice and maize, help infer putative variant effects on genes and transcripts. The pathways section also hosts 10 species-specific metabolic pathways databases developed in-house or by our collaborators using Pathway Tools software, which facilitates searches for pathway, reaction and metabolite annotations, and allows analyses of user-defined expression datasets. Recently, we released a Plant Reactome portal featuring 133 curated rice pathways. This portal will be expanded for Arabidopsis, maize and other plant species. We continue to provide genetic and QTL maps and marker datasets developed by crop researchers. The project provides a unique community platform to support scientific research in plant genomics including studies in evolution, genetics, plant breeding, molecular biology, biochemistry and systems biology

Gramene: a growing plant comparative genomics resource

Gramene (www.gramene.org) is a curated resource for genetic, genomic and comparative genomics data for the major crop species, including rice, maize, wheat and many other plant (mainly grass) species. Gramene is an open-source project. All data and software are freely downloadable through the ftp site (ftp.gramene.org/pub/gramene) and available for use without restriction. Gramene's core data types include genome assembly and annotations, other DNA/mRNA sequences, genetic and physical maps/markers, genes, quantitative trait loci (QTLs), proteins, ontologies, literature and comparative mappings. Since our last NAR publication 2 years ago, we have updated these data types to include new datasets and new connections among them. Completely new features include rice pathways for functional annotation of rice genes; genetic diversity data from rice, maize and wheat to show genetic variations among different germplasms; large-scale genome comparisons among Oryza sativa and its wild relatives for evolutionary studies; and the creation of orthologous gene sets and phylogenetic trees among rice, Arabidopsis thaliana, maize, poplar and several animal species (for reference purpose). We have significantly improved the web interface in order to provide a more user-friendly browsing experience, including a dropdown navigation menu system, unified web page for markers, genes, QTLs and proteins, and enhanced quick search functions