Y chromosome-linked variation affects locomotor activity in male Drosophila melanogaster and is robust to differences in thermal environment.

Although containing genes important for sex determination, genetic variation within the Y chromosome was traditionally predicted to contribute little to the expression of sexually dimorphic traits. This prediction was shaped by the assumption that the chromosome harbours few protein-coding genes, and that capacity for Y-linked variation to shape adaptation would be hindered by the chromosome's lack of recombination and holandric inheritance. Consequently, most studies exploring the genotypic contributions to sexually dimorphic traits have focused on the autosomes and X chromosome. Yet, several studies have now demonstrated that the Y chromosome harbours variation affecting male fitness, moderating the expression of hundreds of genes across the nuclear genome. Furthermore, emerging results have shown that expression of this Y-linked variation may be sensitive to environmental heterogeneity, leading to the prediction that Y-mediated gene-by-environment interactions will shape the expression of sexually dimorphic phenotypes. We tested this prediction, investigating whether genetic variation across six distinct Y chromosome haplotypes affects the expression of locomotor activity, at each of two temperatures (20 and 28 °C) in male fruit flies (Drosophila melanogaster). Locomotor activity is a sexually dimorphic trait in this species, previously demonstrated to be under intralocus sexual conflict. We demonstrate Y haplotype effects on male locomotor activity, but the rank order and magnitude of these effects were unaltered by differences in temperature. Our study contributes to a growing number of studies demonstrating Y-linked effects moderating expression of traits evolving under sexually antagonistic selection, suggesting a role for the Y chromosome in shaping outcomes of sexual conflict.

G × G × E effect on phenotype expression in a non-conventional model organism, the unicellular slime mould Physarum polycephalum.

In metazoans, the expression of key phenotypic traits is sensitive to two- and three-way interactions between variation in mitochondrial DNA, nuclear DNA and the external environment. Whether gene-by-environment interactions affect phenotypes in single-celled eukaryotes is poorly studied, except in a few species of yeast and fungi. We developed a genetic panel of the unicellular slime mould, Physarum polycephalum containing strains differing in mitochondrial and nuclear DNA haplotypes. The panel also included two strains harbouring a selfishly replicating mitochondrial-fusion (mF) plasmid that could affect phenotype expression. We assayed movement and growth rate differences among the strains across two temperature regimes: 24° and 28°C. We found that the slime mould's growth rate, but not movement, is affected by G × G × E interactions. Predictably, mtDNA × nDNA interactions significantly affected both traits. The inter-trait correlation across the strains in each temperature regime was positive. Surprisingly, the mF plasmid had no negative effects on our chosen traits. Our study is the first to demonstrate genetic regulation of phenotype expression in a unicellular slime mould. The genetic effect on phenotypes manifests via epistatic interactions with the thermal environment, thus shedding new light on the role of G × G × E interactions in trait evolution in protists.

Biomarker panel discriminates diabetics with and without periodontitis pre- and post-therapy.

BACKGROUND AND OBJECTIVE: Biological regulators of periodontal inflammation, collagen degradation, and insulin resistance have not been determined in association with severity of periodontitis and response to periodontal treatment in diabetics. Our objective was to determine whether type 2 diabetes (T2DM) patients with periodontal disease present a distinct salivary biomarker profile compared with T2DM patients without periodontal disease and healthy subjects (without diabetes and periodontitis) pre- and post-nonsurgical therapy. METHODS: Clinical parameters of periodontal health and whole unstimulated saliva were collected from 92 participants (31 Not Periodontitis, NP; 32 T2DM without periodontitis, DWoP; and 29 with T2DM with periodontitis, DWP) at baseline. The T2DM groups received scaling and root planning (SRP) and provided saliva at 6-week follow-up. Salivary concentrations of interleukin (IL)-1ß, IL-6, matrix metalloproteinase-8 (MMP-8), and resistin were measured by immunoassay. RESULTS: The DWP group had significantly more disease and higher salivary concentrations at baseline for IL-1ß, MMP-8, and resistin (p's < .01) compared with DWoP and NP. SRP resulted in significant improvement in periodontal parameters for the T2DM groups; however, more disease persisted (p < .001), and IL-1ß, MMP-8, and resistin concentrations remained significantly higher in the DWP than the DWoP group (p < .01) at 6 weeks post-treatment. Principal component analysis demonstrated the DWoP group appeared more biologically similar to the NP group than the DWP group. Concentrations of these salivary biomarkers increased with increasing periodontal disease severity (p < .05) in this study population. CONCLUSION: Salivary concentrations of IL-1ß, MMP-8, and resistin appear to serve as biomarkers of periodontal status pre- and post-treatment, irrespective of diabetes status.

Field-realistic antidepressant exposure disrupts group foraging dynamics in mosquitofish.

Psychoactive pollutants, such as antidepressants, are increasingly detected in the environment. Mounting evidence suggests that such pollutants can disrupt the behaviour of non-target species. Despite this, few studies have considered how the response of exposed organisms might be mediated by social context. To redress this, we investigated the impacts of two environmentally realistic concentrations of a pervasive antidepressant pollutant, fluoxetine, on foraging behaviour in fish (Gambusia holbrooki), tested individually or in a group. Fluoxetine did not alter behaviour of solitary fish. However, in a group setting, fluoxetine exposure disrupted the frequency of aggressive interactions and food consumption, with observed effects being contingent on both the mean weight of group members and the level of within-group variation in weight. Our results suggest that behavioural tests in social isolation may not accurately predict the environmental risk of chemical pollutants for group-living species and highlight the potential for social context to mediate the effects of psychoactive pollutants in exposed wildlife.

Enabling the clinical application of artificial intelligence in genomics: a perspective of the AMIA Genomics and Translational Bioinformatics Workgroup.

OBJECTIVE: Given the importance AI in genomics and its potential impact on human health, the American Medical Informatics Association-Genomics and Translational Biomedical Informatics (GenTBI) Workgroup developed this assessment of factors that can further enable the clinical application of AI in this space. PROCESS: A list of relevant factors was developed through GenTBI workgroup discussions in multiple in-person and online meetings, along with review of pertinent publications. This list was then summarized and reviewed to achieve consensus among the group members. CONCLUSIONS: Substantial informatics research and development are needed to fully realize the clinical potential of such technologies. The development of larger datasets is crucial to emulating the success AI is achieving in other domains. It is important that AI methods do not exacerbate existing socio-economic, racial, and ethnic disparities. Genomic data standards are critical to effectively scale such technologies across institutions. With so much uncertainty, complexity and novelty in genomics and medicine, and with an evolving regulatory environment, the current focus should be on using these technologies in an interface with clinicians that emphasizes the value each brings to clinical decision-making.

Diet and mitonuclear haplotype interactions affect growth rate in a slime mould.

Trait expression in metazoans is strongly influenced by the balance of macronutrients (i.e. protein, carbohydrate and fat) in the diet. At the same time, an individual's genetic background seems to regulate the magnitude of phenotypic response to a particular diet. It needs to be better understood whether interactions between diet, genetic background and trait expression are found in unicellular eukaryotes. A protist-the slime mould, Physarum polycephalum can choose diets based on protein-to-carbohydrate (P:C) content to support optimal growth rate. Yet, the role of genetic background (variation in the mitochondrial and nuclear DNAs) in mediating growth rate response to dietary P:C ratios in the slime mould is unknown. Here, we studied the effects of interactions between mitochondrial and nuclear DNA haplotypes and diet (i.e. G × G × E interactions) on the growth rate of P. polycephalum. A genetic panel of six distinct strains of P. polycephalum that differ in their mitochondrial and nuclear DNA haplotypes was used to measure growth rate across five diets that varied in their P:C ratio and total calories. We first determined the strains' growth rate (total biomass and surface area) when grown on a set menu with access to a particular diet. We then assessed whether the growth rate of strains increased on a buffet menu with access to all diets. Our findings show that the growth rate of P. polycephalum is generally higher on diets containing more carbohydrates than protein and that total calories negatively affect the growth rate. Three-way interactions between mitochondrial, nuclear haplotypes and dietary P:C ratios affected the strains' surface area of growth but not biomass. Intriguingly, strains did not increase their surface area and biomass when they had access to all diets on the buffet menu. Our findings have broad implications for our understanding of the effect of mitonuclear interactions on trait expression across diverse eukaryotic lineages.

Multisite evaluation of prediction models for emergency department crowding before and during the COVID-19 pandemic.

OBJECTIVE: To develop a machine learning framework to forecast emergency department (ED) crowding and to evaluate model performance under spatial and temporal data drift. MATERIALS AND METHODS: We obtained 4 datasets, identified by the location: 1-large academic hospital and 2-rural hospital, and time period: pre-coronavirus disease (COVID) (January 1, 2019-February 1, 2020) and COVID-era (May 15, 2020-February 1, 2021). Our primary target was a binary outcome that is equal to 1 if the number of patients with acute respiratory illness that were ED boarding for more than 4 h was above a prescribed historical percentile. We trained a random forest and used the area under the curve (AUC) to evaluate out-of-sample performance for 2 experiments: (1) we evaluated the impact of sudden temporal drift by training models using pre-COVID data and testing them during the COVID-era, (2) we evaluated the impact of spatial drift by testing models trained at location 1 on data from location 2, and vice versa. RESULTS: The baseline AUC values for ED boarding ranged from 0.54 (pre-COVID at location 2) to 0.81 (COVID-era at location 1). Models trained with pre-COVID data performed similarly to COVID-era models (0.82 vs 0.78 at location 1). Models that were transferred from location 2 to location 1 performed worse than models trained at location 1 (0.51 vs 0.78). DISCUSSION AND CONCLUSION: Our results demonstrate that ED boarding is a predictable metric for ED crowding, models were not significantly impacted by temporal data drift, and any attempts at implementation must consider spatial data drift.

Sex differences in postprandial blood glucose and body surface temperature are contingent on flight in the fruit bat, Cynopterus sphinx.

The postprandial blood glucose level is very high for the body size in frugivorous bats. Like other homeotherms, bats release heat during digestion of dietary macronutrients. Despite males and females of the same species exhibiting different foraging behaviour, empirical support for sex differences in blood glucose and body surface temperature in fruit bats is poor. Moreover, while flight affects postprandial metabolism, whether such effects are different in each sex of fruit bats is unclear. Here, we studied these questions in the fruit bat, Cynopterus sphinx We first assessed whether there are sex differences in the postprandial level of blood glucose and body surface temperature over time in rested bats. We then assessed whether flight affects outcomes of sex differences in both traits. We found that the estimated marginal means of both traits were generally higher in females than males, in rested bats. Notably, the sex difference in both traits was only significant at specific sampling time of the assay. Further, the trait means significantly differed between the sexes only in the rested, but not active, bats, meaning that signals of sex difference in metabolic traits eroded when bats were active. Taken together, our findings suggest that in C. sphinx, the sex specificity in the expression of metabolic traits is significantly dependent on physical activity.

Low mammalian species richness is associated with Kyasanur Forest disease outbreak risk in deforested landscapes in the Western Ghats, India.

Kyasanur forest disease virus (KFDV) is a rapidly expanding tick-borne zoonotic virus with natural foci in the forested region of the Western Ghats of South India. The Western Ghats is one of the world's most important biodiversity hotspots and, like many such areas of high biodiversity, is under significant pressure from anthropogenic landscape change. The current study sought to quantify mammalian species richness using ensemble models of the distributions of a sample of species extant in the Western Ghats and to explore its association with KFDV outbreaks, as well as the modifying effects of deforestation on this association. Species richness was quantified as a composite of individual species' distributions, as derived from ensembles of boosted regression tree, random forest, and generalised additive models. Species richness was further adjusted for the potential biotic constraints of sympatric species. Both species richness and forest loss demonstrated strong positive associations with KFDV outbreaks, however forest loss substantially modified the association between species richness and outbreaks. High species richness was associated with increased KFDV risk but only in areas of low forest loss. In contrast, lower species richness was associated with increased KFDV risk in areas of greater forest loss. This relationship persisted when species richness was adjusted for biotic constraints at the taluk-level. In addition, the taluk-level species abundances of three monkey species (Macaca radiata, Semnopithecus hypoleucus, and Semnopithecus priam) were also associated with outbreaks. These results suggest that increased monitoring of wildlife in areas of significant habitat fragmentation may add considerably to critical knowledge gaps in KFDV epidemiology and infection ecology and should be incorporated into novel One Health surveillance development for the region. In addition, the inclusion of some primate species as sentinels of KFDV circulation into general wildlife surveillance architecture may add further value.

Prescribing patterns of opioid analgesics in a dental setting: 2013-2018.

OBJECTIVE: Analgesic prescribing patterns are influenced by internal and external factors. Understanding these factors could help improve prescribing practices. STUDY DESIGN: We conducted a retrospective analysis of electronic health records with regard to analgesic prescriptions written from 2013 through 2018 at the University of Kentucky College of Dentistry. Deidentified information (age, gender, dental procedures, analgesic drug, quantity, and refills) were recorded and studied with respect to national guidelines and recent state legislation using the χ2 test, analysis of variance, logistic regression, and multiple linear regression. RESULTS: Opioids comprised 74.9% of the 17,099 analgesic prescriptions written. Extractions were most commonly associated with opioid prescriptions. Multivariate analysis showed that (1) older patients were more likely to receive an opioid prescription (P < .01) but with fewer pills (P < .01); (2) surgical extractions were associated with a lower opioid prescription rate (P < .01) but more opioid pills per prescription compared with nonsurgical extractions (P < .01); and (3) the odds of receiving an opioid prescription and the number of opioid pills prescribed decreased over year after release of the national guideline (P < .01) and after enactment of state legislation (P < .01). CONCLUSIONS: Regulations and guidelines were associated with reduction in opioid prescriptions.

Sex-specific effects of mitochondrial haplotype on metabolic rate in Drosophila melanogaster support predictions of the Mother's Curse hypothesis.

Evolutionary theory proposes that maternal inheritance of mitochondria will facilitate the accumulation of mitochondrial DNA (mtDNA) mutations that are harmful to males but benign or beneficial to females. Furthermore, mtDNA haplotypes sampled from across a given species distribution are expected to differ in the number and identity of these 'male-harming' mutations they accumulate. Consequently, it is predicted that the genetic variation which delineates distinct mtDNA haplotypes of a given species should confer larger phenotypic effects on males than females (reflecting mtDNA mutations that are male-harming, but female-benign), or sexually antagonistic effects (reflecting mutations that are male-harming, but female-benefitting). These predictions have received support from recent work examining mitochondrial haplotypic effects on adult life-history traits in Drosophila melanogaster. Here, we explore whether similar signatures of male-bias or sexual antagonism extend to a key physiological trait-metabolic rate. We measured the effects of mitochondrial haplotypes on the amount of carbon dioxide produced by individual flies, controlling for mass and activity, across 13 strains of D. melanogaster that differed only in their mtDNA haplotype. The effects of mtDNA haplotype on metabolic rate were larger in males than females. Furthermore, we observed a negative intersexual correlation across the haplotypes for metabolic rate. Finally, we uncovered a male-specific negative correlation, across haplotypes, between metabolic rate and longevity. These results are consistent with the hypothesis that maternal mitochondrial inheritance has led to the accumulation of a sex-specific genetic load within the mitochondrial genome, which affects metabolic rate and that may have consequences for the evolution of sex differences in life history. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.

Interactions Between Mitochondrial Haplotype and Dietary Macronutrient Ratios Confer Sex-Specific Effects on Longevity in Drosophila melanogaster.

Recent studies have demonstrated that modifications to the ratio of dietary macronutrients affect longevity in a diverse range of species. However, the degree to which levels of natural genotypic variation shape these dietary effects on longevity remains unclear. The mitochondria have long been linked to the aging process. The mitochondria possess their own genome, and previous studies have shown that mitochondrial genetic variation affects longevity in insects. Furthermore, the mitochondria are the sites in which dietary nutrients are oxidized to produce adenosine triphosphate, suggesting a capacity for dietary quality to mediate the link between mitochondrial genotype and longevity. Here, we measured longevity of male and female fruit flies, across a panel of genetic strains of Drosophila melanogaster, which vary only in their mitochondrial haplotype, when fed one of the two isocaloric diets that differed in their protein-to-carbohydrate ratio. The mitochondrial haplotype affected the longevity of flies, but the pattern of these effects differed across the two diets in males, but not in females. We discuss the implications of these results in relation to an evolutionary theory linking maternal inheritance of mitochondria to the accumulation of male-harming mitochondrial mutations, and to the theory exploring the evolution of phenotypic plasticity to novel environments.

Dim artificial light at night affects mating, reproductive output, and reactive oxygen species in Drosophila melanogaster.

Humans are lighting the night-time environment with ever increasing extent and intensity, resulting in a variety of negative ecological effects in individuals and populations. Effects of light at night on reproductive fitness traits are demonstrated across taxa however, the mechanisms underlying these effects are largely untested. One possible mechanism is that light at night may result in perturbed reactive oxygen species (ROS) and oxidative stress levels. Here, we reared Drosophila melanogaster under either dim (10 lx) light or no light (0 lx) at night for three generations and then compared mating and lifetime oviposition patterns. In a second experiment, we explored whether exposure to light at night treatments resulted in variation in ROS levels in the heads and ovaries of six, 23- and 36-day-old females. We demonstrate that dim light at night affects mating and reproductive output: 10 lx flies courted for longer prior to mating, and female oviposition patterns differed to 0 lx females. ROS levels were lower in the ovaries but not heads, of 10 lx compared with 0 lx females. We suggest that reduced ROS levels may reflect changes in ovarian physiology and cell signaling, which may be related to the differences observed in oviposition patterns. Taken together, our results indicate negative consequences for invertebrates under more stressful, urban, lit conditions and further investigation into the mechanisms driving these changes is warranted to manage invertebrate communities in a brighter future.

Gene expression during the first 28 days of axolotl limb regeneration I: Experimental design and global analysis of gene expression.

While it is appreciated that global gene expression analyses can provide novel insights about complex biological processes, experiments are generally insufficiently powered to achieve this goal. Here we report the results of a robust microarray experiment of axolotl forelimb regeneration. At each of 20 post-amputation time points, we estimated gene expression for 10 replicate RNA samples that were isolated from 1 mm of heterogeneous tissue collected from the distal limb tip. We show that the limb transcription program diverges progressively with time from the non-injured state, and divergence among time adjacent samples is mostly gradual. However, punctuated episodes of transcription were identified for five intervals of time, with four of these coinciding with well-described stages of limb regeneration-amputation, early bud, late bud, and pallet. The results suggest that regeneration is highly temporally structured and regulated by mechanisms that function within narrow windows of time to coordinate transcription within and across cell types of the regenerating limb. Our results provide an integrative framework for hypothesis generation using this complex and highly informative data set.