Effects of post-mortem storage conditions of bovine epididymides on sperm characteristics:investigating a tool for preservation of sperm from endangered species

The aim of this study was to establish and validate a reliable and efficient protocol for the recovery and cryopreservation of epididymal spermatozoa used for in vitro fertilization, using bulls of two different age classes. Testicles from 26 (37–51 weeks old, group 1) and 19 (52–115 weeks old, group 2) Danish Holstein bulls were collected after slaughter and stored at 5°C. After 0, 24 or 48 h, epididymides were isolated and spermatozoa collected. Assessments included spermatozoal motility, viability and morphology before and after cryopreservation and in vitro embryo production. Results showed that live spermatozoa can be collected from epididymides of bulls after their death. Storage of the testicles at 5°C for 24 h followed by cryopreservation of recovered epididymal spermatozoa resulted in 21% (group 1) and 31% (group 2) blastocysts produced in vitro. These results illustrate that epididymal spermatozoa recovered from testicles kept in specific conditions can be used to preserve genetic material from endangered and threatened species or populations in nature as well as in domestic and zoo animals

Candidate Genes Detected in Transcriptome Studies Are Strongly Dependent on Genetic Background

Whole genome transcriptomic studies can point to potential candidate genes for organismal traits. However, the importance of potential candidates is rarely followed up through functional studies and/or by comparing results across independent studies. We have analysed the overlap of candidate genes identified from studies of gene expression in Drosophila melanogaster using similar technical platforms. We found little overlap across studies between putative candidate genes for the same traits in the same sex. Instead there was a high degree of overlap between different traits and sexes within the same genetic backgrounds. Putative candidates found using transcriptomics therefore appear very sensitive to genetic background and this can mask or override effects of treatments. The functional importance of putative candidate genes emerging from transcriptome studies needs to be validated through additional experiments and in future studies we suggest a focus on the genes, networks and pathways affecting traits in a consistent manner across backgrounds

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Experimental Approaches for Testing if Tolerance Curves Are Useful for Predicting Fitness in Fluctuating Environments

Most experimental studies on adaptation to stressful environments are performed under conditions that are rather constant and rarely ecologically relevant. Fluctuations in natural environmental conditions are ubiquitous and include for example variation in intensity and duration of temperature, droughts, parasite loads, and availability of nutrients, predators and competitors. The frequency and amplitude of many of these fluctuations are expected to increase with climate change. Tolerance curves are often used to describe fitness components across environmental gradients. Such curves can be obtained by assessing performance in a range of constant environmental conditions. In this perspective we briefly list theoretical and experimental evidence why results obtained under constant environmental conditions might be misleading for processes in nature and therefore may not be suitable for predicting fitness and future species distribution and abundance. We further suggest experimental avenues that can provide a better foundation for forecasts of the distribution of biota

Experimental Approaches for Testing if Tolerance Curves Are Useful for Predicting Fitness in Fluctuating Environments

Most experimental studies on adaptation to stressful environments are performed under conditions that are rather constant and rarely ecologically relevant. Fluctuations in natural environmental conditions are ubiquitous and include for example variation in intensity and duration of temperature, droughts, parasite loads, and availability of nutrients, predators and competitors. The frequency and amplitude of many of these fluctuations are expected to increase with climate change. Tolerance curves are often used to describe fitness components across environmental gradients. Such curves can be obtained by assessing performance in a range of constant environmental conditions. In this perspective we briefly list theoretical and experimental evidence why results obtained under constant environmental conditions might be misleading for processes in nature and therefore may not be suitable for predicting fitness and future species distribution and abundance. We further suggest experimental avenues that can provide a better foundation for forecasts of the distribution of biota.peerReviewe

Raw Wing Data

This file contains the coordinates of each landmark from the wing. See Supplementary information/appendix in paper for the position of landmarks on the wing

Metabolic and functional characterization of effects of developmental temperature in Drosophila melanogaster

The ability of ectotherms to respond to changes in their thermal environment through plastic mechanisms is central to their adaptive capability. However, we still lack knowledge on the physiological and functional responses by which ectotherms acclimate to temperatures during development, and in particular, how physiological stress at extreme temperatures may counteract beneficial acclimation responses at benign temperatures. We exposed Drosophila melanogaster to 10 developmental temperatures covering their entire permissible temperature range. We obtained metabolic profiles and reaction norms for several functional traits: egg-to-adult viability, developmental time, and heat and cold tolerance. Females were more heat tolerant than males, whereas no sexual dimorphism was found in cold tolerance. A group of metabolites, mainly free amino acids, had linear reaction norms. Several energy-carrying molecules, as well as some sugars, showed distinct inverted U-shaped norms of reaction across the thermal range, resulting in a positive correlation between metabolite intensities and egg-to-adult viability. At extreme temperatures, low levels of these metabolites were interpreted as a response characteristic of costs of homeostatic perturbations. Our results provide novel insights into a range of metabolites reported to be central for the acclimation response and suggest several new candidate metabolites. Low and high temperatures result in different adaptive physiological responses, but they also have commonalities likely to be a result of the failure to compensate for the physiological stress. We suggest that the regulation of metabolites that are tightly connected to the performance curve is important for the ability of ectotherms to cope with variation in temperature

Data from: Humidity affects genetic architecture of heat resistance in Drosophila melanogaster

Laboratory experiments on Drosophila have often demonstrated increased heritability for morphological and life-history traits under environmental stress. We used parent-offspring comparisons to examine the impact of humidity levels on the heritability of a physiological trait, resistance to heat, measured as knockdown time at constant temperature. Drosophila melanogaster were reared under standard non-stressful conditions and heat-shocked as adults at extreme high or low humidity. Mean knockdown time was decreased in the stressful dry environment but there was a significant sex-by-treatment interaction: at low humidity females were more heat resistant than males, whereas at high humidity the situation was reversed. Phenotypic variability of knockdown time was also lower in the dry environment. The magnitude of genetic correlation between the sexes at high humidity indicated genetic variation for sexual dimorphism in heat resistance. Heritability estimates based on one-parent – offspring regressions tended to be higher under desiccation stress and this could be explained by decreased environmental variance of heat resistance at low humidity. There was no indication that the additive genetic variance and evolvability of heat resistance differed between the environments. The pattern of heritability estimates suggests that populations of D. melanogaster may have a greater potential for evolving higher thermal tolerance under arid conditions

Data from: Effects of photoperiod on life-history and thermal stress resistance traits across populations of Drosophila subobscura

Intro: Organisms use environmental cues to match their phenotype with the future availability of resources and environmental conditions. Changes in the magnitude and frequency of environmental cues such as photoperiod and temperature along latitudes can be used by organisms to predict seasonal changes. While the role of temperature variation on the induction of plastic and seasonal responses is well established, the importance of photoperiod for predicting seasonal changes is less explored. M&M: Here we studied changes in life-history and thermal stress resistance traits in Drosophila subobscura in response to variation in photoperiod (6:18, 12:12 and 18:6 light:dark cycles) mimicking seasonal variations in daylength. Populations of D. subobscura were collected from five locations along a latitudinal gradient (from North Africa and Europe). These populations were exposed to different photoperiods for two generations, whereafter egg-to-adult viability, productivity, dry body weight, thermal tolerance, and starvation resistance were assessed. Results: We found strong effects of photoperiod, origin of populations, and their interactions on life-history and stress resistance traits. Thermal resistance varied between the populations and the effect of photoperiod depended on the trait and the method applied for the assessment of thermal resistance. Perspectives: Our results show a strong effect of the origin of population and photoperiod on a range of fitness related traits and provide evidence for local adaptation to environmental cues (photoperiod by population interaction). The findings emphasize an important and often neglected role of photoperiod in studies on thermal resistance and suggest that cues induced by photoperiod may provide some buffer enabling populations to cope with a more variable and unpredictable future climate