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Abstract Scavenging mammals and vultures can exploit and deplete carcasses much faster than other birds and invertebrates. Vultures are strongly influenced by habitat type, e.g. tree cover, since they rely on their eyesight to detect carcasses. It remains unclear whether and how facultative scavengers – both other birds and mammals – are influenced by tree cover and how that affect carcass decomposition time, which in turn affects biodiversity and ecological processes, including the cycle of energy and nutrients. We studied whether the carcass detection and consumption, hence carcass decomposition speed, by facultative avian and mammalian scavengers varies with tree cover in areas without vultures. Fresh mammal carcasses were placed in different landscapes across the Netherlands at locations that widely varied in tree cover. Camera traps were used to record carcass exploitation by facultative avian and mammalian scavengers and to estimate carcass decomposition time. We found that carcass detection and consumption by birds, wild boar, and other mammals varied between locations. Carcass decomposition speed indeed increased with carcass detection and exploitation by mammals, especially by wild boar. However, this variation was not related to tree cover. We conclude that tree cover is not a major determinant of carcass exploitation by facultative scavengers in areas without obligate scavengers and large carnivores.

Continuous nitrogen deposition threatens ecosystems by acidifying soils, causing a stoichiometric imbalance in the vegetation and ultimately, the disappearance of plant and animal species. There is a gap in knowledge of how decomposers such as oribatid mites cope with the effects of nitrogen deposition. Therefore, we conducted feeding experiments with the herbivorous mite Platynothrus peltifer (C.L. Koch, 1839) to assess its fitness as a measure of its reproductive response towards different nitrogen levels in its diet. Mites were collected from the field, starved, and allowed to lay eggs. We recorded the number of eggs during 60 days of experimental trial. The fecundity of mites varied with different elemental compositions, whereby phosphorus seemed to be a limiting factor. With ongoing nitrogen deposition in the future and concomitant phosphorus limitation, we expect a negative impact on the population dynamics of herbivorous decomposers such as Platynothrus peltifer.

Investigators have recently introduced powerful methods for population genetic inference that rely on supervised machine learning from simulated data. Despite their performance advantages, these methods can fail when the simulated training data does not adequately resemble data from the real world. Here, we show that this "simulation mis-specification" problem can be framed as a "domain adaptation" problem, where a model learned from one data distribution is applied to a dataset drawn from a different distribution. By applying an established domain-adaptation technique based on a gradient reversal layer (GRL), originally introduced for image classification, we show that the effects of simulation mis-specification can be substantially mitigated. We focus our analysis on two state-of-the-art deep-learning population genetic methods-SIA, which infers positive selection from features of the ancestral recombination graph (ARG), and ReLERNN, which infers recombination rates from genotype matrices. In the case of SIA, the domain adaptive framework also compensates for ARG inference error. Using the domain-adaptive SIA (dadaSIA) model, we estimate improved selection coefficients at selected loci in the 1000 Genomes CEU population. We anticipate that domain adaptation will prove to be widely applicable in the growing use of supervised machine learning in population genetics.

The extent to which sequence variation impacts plant fitness is poorly understood. High-resolution maps detailing the constraint acting on the genome, especially in regulatory sites, would be beneficial as functional annotation of noncoding sequences remains sparse. Here, we present a fitness consequence (fitCons) map for rice (Oryza sativa). We inferred fitCons scores (ρ) for 246 inferred genome classes derived from nine functional genomic and epigenomic datasets, including chromatin accessibility, messenger RNA/small RNA transcription, DNA methylation, histone modifications and engaged RNA polymerase activity. These were integrated with genome-wide polymorphism and divergence data from 1,477 rice accessions and 11 reference genome sequences in the Oryzeae. We found ρ to be multimodal, with ~9% of the rice genome falling into classes where more than half of the bases would probably have a fitness consequence if mutated. Around 2% of the rice genome showed evidence of weak negative selection, frequently at candidate regulatory sites, including a novel set of 1,000 potentially active enhancer elements. This fitCons map provides perspective on the evolutionary forces associated with genome diversity, aids in genome annotation and can guide crop breeding programs.

Previous work has investigated selection in the coding genome, but it is not as well characterized in the non-coding genome. By analyzing rare variants in 70k genome sequences from gnomAD, the authors detect very strong purifying selection ("ultraselection”) across the human genome, finding it in some microRNAs and coding sequences but generally rare in regulatory sequences.

Ammonia accumulation is a major challenge in intensive aquaculture, where fish are fed protein-rich diets in large rations, resulting in increased ammonia production when amino acids are metabolized as energy source. Ammonia is primarily excreted via the gills, which have been found to harbor nitrogen-cycle bacteria that convert ammonia into dinitrogen gas (N2) and therefore present a potential in situ detoxifying mechanism. Here, we determined the impact of feeding strategies (demand-feeding and batch-feeding) with two dietary protein levels on growth, nitrogen excretion, and nitrogen metabolism in common carp (Cyprinus carpio, L.) in a 3-week feeding experiment. Demand-fed fish exhibited significantly higher growth rates, though with lower feed efficiency. When corrected for feed intake, nitrogen excretion was not impacted by feeding strategy or dietary protein, but demand-fed fish had significantly more nitrogen unaccounted for in the nitrogen balance and less retained nitrogen. N2 production of individual fish was measured in all experimental groups, and production rates were in the same order of magnitude as the amount of nitrogen unaccounted for, thus potentially explaining the missing nitrogen in the balance. N2 production by carp was also observed when groups of fish were kept in metabolic chambers. Demand feeding furthermore caused a significant increase in hepatic glutamate dehydrogenase activities, indicating elevated ammonia production. However, branchial ammonia transporter expression levels in these animals were stable or decreased. Together, our results suggest that feeding strategy impacts fish growth and nitrogen metabolism, and that conversion of ammonia to N2 by nitrogen cycle bacteria in the gills may explain the unaccounted nitrogen in the balance.

Highways can fragment habitat and be a significant mortality source for mammals. Wildlife exclusion fencing has been shown to reduce wildlife-vehicle collisions, but can also prevent animals from escaping the highway corridor if they enter at access roads or at fence ends. Earthen escape ramps, or “jumpouts,” have been proposed as a possible solution but remain relatively untested. From 2012-2014, we used wildlife cameras to continuously document wildlife use of four jumpout ramps constructed as part of a 2.5-mile wildlife exclusion fence project along Highway 101 near San Luis Obispo, California. Mule deer occasionally used the jumpouts, but quantifying the rate of utilization was confounded by repeated visits by the same individuals. Male and female deer appeared to have different responses to the jumpouts, which warrants deeper investigation using additional data collected from further monitoring through mid-2017. The longer dataset will also better document how individual deer learn to use the jumpouts. Fenced highways can also reduce connectivity unless there is sufficient use of crossing structures. We documented mountain lion, bobcat, black bear, and mule deer used culverts and underpasses in and adjacent to the wildlife fence zone from 2012-2014. Mule deer used the large underpasses almost exclusively, and rarely if ever used culverts. Bear used a wider variety of structures, and bobcats were detected at almost every site and at a higher rate than the other taxa. Mountain lion detections were quite rare, likely due to lower population density in the study area. We propose a deeper multivariate analysis of the factors influencing these species’ use of culverts including culvert dimensionality, nearby habitat, and proximity to cover, based on an expanded dataset of up to five years of continual monitoring at certain sites. The goal of these analyses is to provide information that will help reduce wildlife-vehicle collisions while facilitating regional wildlife connectivity.

Insular organisms often evolve predictable phenotypes, like flightlessness, extreme body sizes, or increased melanin deposition. The evolutionary forces and molecular targets mediating these patterns remain mostly unknown. Here we study the Chestnut-bellied Monarch (Monarcha castaneiventris) from the Solomon Islands, a complex of closely related subspecies in the early stages of speciation. On the large island of Makira M. c. megarhynchus has a chestnut belly, whereas on the small satellite islands of Ugi, and Santa Ana and Santa Catalina (SA/SC) M. c. ugiensis is entirely iridescent blue-black (i.e., melanic). Melanism has likely evolved twice, as the Ugi and SA/SC populations were established independently. To investigate the genetic basis of melanism on each island we generated whole genome sequence data from all three populations. Non-synonymous mutations at the MC1R pigmentation gene are associated with melanism on SA/SC, while ASIP, an antagonistic ligand of MC1R, is associated with melanism on Ugi. Both genes show evidence of selective sweeps in traditional summary statistics and statistics derived from the ancestral recombination graph (ARG). Using the ARG in combination with machine learning, we inferred selection strength, timing of onset and allele frequency trajectories. MC1R shows evidence of a recent, strong, soft selective sweep. The region including ASIP shows more complex signatures; however, we find evidence for sweeps in mutations near ASIP, which are comparatively older than those on MC1R and have been under relatively strong selection. Overall, our study shows convergent melanism results from selective sweeps at independent molecular targets, evolving in taxa where coloration likely mediates reproductive isolation with the neighboring chestnut-bellied subspecies.

Abstract High-throughput CRISPR-Cas9 knockout screens are widely used to evaluate gene essentiality in cancer research. Here we introduce a probabilistic modeling framework, Analysis of CRISPR-based Essentiality (ACE), that accounts for multiple sources of variation in CRISPR-Cas9 screens and enables new statistical tests for essentiality. We show using simulations that ACE is effective at predicting both absolute and differential essentiality. When applied to publicly available data, ACE identifies known and novel candidates for genotype-specific essentiality, including RNA m6-A methyltransferases that exhibit enhanced essentiality in the presence of inactivating TP53 mutations. ACE provides a robust framework for identifying genes responsive to subtype-specific therapeutic targeting.

Two new mite species belonging to the genus Stereotydeus Berlese, 1901 were discovered from locations along the coast of Victoria Land, continental Antarctica. Previous records of this genus in the area under study only reported the presence of S. belli and S. mollis. Although those studies included no morphological analyses, it has since been assumed that only these species were present within the area. Specimens of S. ineffabilis sp. nov. and S. nunatakis sp. nov. were obtained, sometimes in sympatry, from four different localities in Central and South Victoria Land and are here described and illustrated using optical and scanning electron microscopy (SEM) techniques. Features useful for identification of the two new Stereotydeus species include the size of the specimens, the length of the apical segment of pedipalps, the presence/absence of division of the femora, the position of solenidia, the shape and disposition of the rhagidiform organs on the tarsi, the shape of the apical setae of the tarsi, the numbers of aggenital setae and the position of the anal opening. A key to 14 of the 15 currently described Antarctic and sub-Antarctic Stereotydeus species is provided.

Abstract Alignments of multiple genomes are a cornerstone of comparative genomics, but generating these alignments remains technically challenging and often impractical. We developed the msa_pipeline workflow (https://bitbucket.org/bucklerlab/msa_pipeline) to allow practical and sensitive multiple alignment of diverged plant genomes and calculation of conservation scores with minimal user inputs. As high repeat content and genomic divergence are substantial challenges in plant genome alignment, we also explored the effect of different masking approaches and parameters of the LAST aligner using genome assemblies of 33 grass species. Compared with conventional masking with RepeatMasker, a masking approach based on k‐mers (nucleotide sequences of k length) increased the alignment rate of coding sequence and noncoding functional regions by 25 and 14%, respectively. We further found that default alignment parameters generally perform well, but parameter tuning can increase the alignment rate for noncoding functional regions by over 52% compared with default LAST settings. Finally, by increasing alignment sensitivity from the default baseline, parameter tuning can increase the number of noncoding sites that can be scored for conservation by over 76%. Overall, tuning of masking and alignment parameters can generate optimized multiple alignments to drive biological discovery in plants.

Abstract Background The concentrations of distinct types of RNA in cells result from a dynamic equilibrium between RNA synthesis and decay. Despite the critical importance of RNA decay rates, current approaches for measuring them are generally labor-intensive, limited in sensitivity, and/or disruptive to normal cellular processes. Here, we introduce a simple method for estimating relative RNA half-lives that is based on two standard and widely available high-throughput assays: Precision Run-On sequencing (PRO-seq) and RNA sequencing (RNA-seq). Results Our method treats PRO-seq as a measure of transcription rate and RNA-seq as a measure of RNA concentration, and estimates the rate of RNA decay required for a steady-state equilibrium. We show that this approach can be used to assay relative RNA half-lives genome-wide, with good accuracy and sensitivity for both coding and noncoding transcription units. Using a structural equation model (SEM), we test several features of transcription units, nearby DNA sequences, and nearby epigenomic marks for associations with RNA stability after controlling for their effects on transcription. We find that RNA splicing-related features are positively correlated with RNA stability, whereas features related to miRNA binding and DNA methylation are negatively correlated with RNA stability. Furthermore, we find that a measure based on U1 binding and polyadenylation sites distinguishes between unstable noncoding and stable coding transcripts but is not predictive of relative stability within the mRNA or lincRNA classes. We also identify several histone modifications that are associated with RNA stability. Conclusion We introduce an approach for estimating the relative half-lives of individual RNAs. Together, our estimation method and systematic analysis shed light on the pervasive impacts of RNA stability on cellular RNA concentrations.

Continuous nitrogen deposition threatens ecosystems by acidifying soils, causing a stoichiometric imbalance in the vegetation and ultimately, the disappearance of plant and animal species. There is a gap in knowledge of how decomposers such as oribatid mites cope with the effects of nitrogen deposition. Therefore, we conducted feeding experiments with the herbivorous mite Platynothrus peltifer (C.L. Koch, 1839) to assess its fitness as a measure of its reproductive response towards different nitrogen levels in its diet. Mites were collected from the field, starved, and allowed to lay eggs. We recorded the number of eggs during 60 days of experimental trial. The fecundity of mites varied with different elemental compositions, whereby phosphorus seemed to be a limiting factor. With ongoing nitrogen deposition in the future and concomitant phosphorus limitation, we expect a negative impact on the population dynamics of herbivorous decomposers such as Platynothrus peltifer. [ABSTRACT FROM AUTHOR]

Common carp (Cyprinus carpio) were fed food with different protein concentrations following different feeding regimes, which were previously shown to affect growth, nitrogen excretion and amino acid catabolism. 16S rRNA gene amplicon sequencing was performed to investigate the gut microbiota of these fish. Lower dietary protein content increased microbial richness, while the combination of demand feeding and dietary protein content affected the composition of the gut microbiota. Hepatic glutamate dehydrogenase (GDH) activity was correlated to the composition of the gut microbiota in all dietary treatments. We found that demand‐fed carp fed a diet containing 39% protein had a significantly higher abundance of Beijerinckiaceae compared to other dietary groups. Network analysis identified this family and two Rhizobiales families as hubs in the microbial association network. In demand‐fed carp, the microbial association network had significantly fewer connections than in batch‐fed carp. In contrast to the large effects of the feeding regime and protein content of the food on growth and nitrogen metabolism, it had only limited effects on gut microbiota composition. However, correlations between gut microbiota composition and liver GDH activity showed that host physiology and gut microbiota are connected, which warrants functional studies into the role of the gut microbiota in fish physiology. [ABSTRACT FROM AUTHOR]

Many ectotherms species grow faster but attain a smaller body size when reared under warmer conditions, a phenomenon known as the Temperature-Size Rule (TSR). This rule appears to be stronger in aquatic ectotherms than in terrestrial ectotherms. The difference could be related to difficulties for oxygen uptake in water, whereas on land, adaptive responses in body size may relate to seasonal time constraints. To assess the role of seasonal time constraints in temperature size response of terrestrial ectotherms, we reared the small copper Lycaena phlaeas at three temperatures (18 ˚C, 23˚C and 28˚C) and two photoperiods (16L: 8D and 12L: 12D). We examined whether differences in body size across treatments was related to (1) differences in growth and development, (2) differences in breakpoints during growth trajectories, or (3) differences in ommatidia size (as a proxy for cell size). We found a weak inverse relationship between developmental temperature and the body size of adult butterflies; adult size decreased by approximately 1% for every degree warmer. Under warmer temperatures, caterpillars developed more quickly and had higher growth rates but reached a smaller body size. Under a short photoperiod, both growth and development were slower, especially at the two lower temperatures, but the body size resulting from slow growth over a longer developmental period did not vary with photoperiod. Breakpoints in growth trajectories occurred when larvae reached ∼40% of their maximum mass and these breakpoints were strongly correlated with the size of the resulting adults, suggesting that adult size is predetermined at an early stage. Temperature did not appear to cause reductions in body size through reductions in cell size. Butterflies were largely able to buffer their body size by modulating larval growth and development in tandem. They appear to use photoperiod as a cue to gauge the availability of time (with 12L: 12D indicating less time available) while temperature speeds up growth and development and as such governs the amount of time they need to complete a developmental cycle. Temperature and photoperiod thus induce changes in voltinism to fit a discrete number of generations into a growing season.

BackgroundNitrogen (NOx, NHy) and acidifying (NOx, NHy, SOx) deposition has reduced the biodiversity of European dry heathlands. Restoration efforts such as sod-cutting (removal of vegetation, litter and humus layer) often shifted these systems from N to P limitation and have had limited success in restoring the invertebrate community. Possible reasons for this include the unresolved acidification and a change in food plant stoichiometry. Here, we investigate how liming and P addition change food nutritional quality and their consequences for invertebrate performance.MethodsWe performed feeding experiments with field crickets (Gryllus campestris), using plant material collected from a full factorial field experiment with liming and P addition. We related female reproduction as measure of individual fitness to elemental ratios of plants fed to the crickets.ResultsP addition stimulated cricket daily reproduction and shortened their reproductive period, resulting in no difference in total reproduction. Liming greatly reduced both daily and total reproduction and resulted in more females cannibalizing on their male mates. Females that did so could partly offset the liming induced reduction in reproduction, suggesting dietary deficiency. P-addition improved food quality (lower N:P ratios) while liming led to skewed Mn:Mg and Fe:Mg ratios that compare unfavorably to ratios found in terrestrial invertebrates.ConclusionIncreased plant N:P ratio following sod-cutting constrains the reproductive potential in Gryllus campestris in a non-linear way. Liming reduced nutritional quality, likely by inducing deficiencies in Fe or Mn.Management ImplicationsHigh-impact restoration management practices such as sod cutting and liming cause new problems for invertebrates rooted in ecological stoichiometry. Since P-addition only partially offsets these negative effects, we instead advocate the use of less intensive N removal management and weaker buffering agents to reduce soil acidification. Furthermore, a reduction in N emission is paramount as it will remove the need for disruptive interventions.

INTRODUCTION: The Ultrasound Screening Exam for Underlying Lesions (USEFUL) was developed in an attempt to establish a role for bedside ultrasound in the primary and preventive care setting. It is the purpose of our pilot study to determine if students were first capable of performing all of the various scans required of our USEFUL while defining such an ultrasound-assisted physical exam that would supplement the standard hands-on physical exam in the same head-to-toe structure. We also aimed to assess the time needed for an adequate exam and analyze if times improved with repetition and previous ultrasound training. METHODS: Medical students with ranging levels of ultrasound training received a 25-minute presentation on our USEFUL followed by a 30-minute hands-on session. Following the hands-on session, the students were asked to perform a timed USEFUL on 2-3 standardized subjects. All images were documented as normal or abnormal with the understanding that an official detailed exam would be performed if an abnormality were to be found. All images were read and deemed adequate by board eligible emergency medicine ultrasound fellows. RESULTS: Twenty-six exams were performed by 9 students. The average time spent by all students per USEFUL was 11 minutes and 19 seconds. Students who had received the University of California, Irvine School of Medicines integrated ultrasound curriculum performed the USEFUL significantly faster (p< 0.0025). The time it took to complete the USEFUL ranged from 6 minutes and 32 seconds to 17 minutes, and improvement was seen with each USEFUL performed. The average time to complete the USEFUL on the first standardized patient was 13 minutes and 20 seconds, while 11 minutes and 2 seconds, and 9 minutes and 20 seconds were spent performing the exam on the second and third patient, respectively. CONCLUSION: Students were able to effectively complete all scans required by the USEFUL in a timely manner. Students who have been a part of the integrated ultrasound in medicine curriculum performed the USEFUL significantly faster than students who had not. Students were able to significantly improve upon the time it took them to complete the USEFUL with successive attempts. Future endpoints are aimed at assessing the feasibility and outcomes of an ultrasound-assisted physical exam in a primary care setting and the exams effect on doctor-patient satisfaction. [West J Emerg Med. 2014;15(3):260-266.].