Assay validation and interspecific comparison of salivary glucocorticoids in three amphibian species

Amphibians are one of the most threatened groups of species, facing stressors ranging from habitat degradation and pollution to disease and overexploitation. Stress hormones (glucocorticoids, GCs) provide one quantitative metric of stress,and developing non-invasive methods for measuring GCs in amphibians would clarify how diverse environmental stressors impact individual health in this taxonomic group. Saliva is an advantageous matrix for quantifying GCs, as it is sampled less invasively than plasma while still detecting both baseline and acute elevation of GCs within a short timeframe. Little work has employed this method in amphibian species, and it has never been pharmacologically and biologically validated. Here, we conduct analytical, pharmacological and biological validation experiments for measuring salivary corticosterone in three amphibian species: the American bullfrog (Rana catesbeiana), the green frog (Rana clamitans) and the northern leopard frog (Rana pipiens). These species are faced with a broad range of environmental challenges, and in part of its range R. pipiens populations are currently in decline. In addition to demonstrating that this method can be reliably used in multiple amphibian species, we present an examination of intrinsic biological factors (sex, body condition) that may contribute to GC secretion, and a demonstration that saliva can be collected from free-living animals in the field to quantify corticosterone. Our findings suggest that saliva may be useful for less invasively quantifying GCs in many amphibian species

Maternal steroid levels and the autistic traits of the mother and infant.

BackgroundPrenatal sex steroids have been associated with autism in several clinical and epidemiological studies. It is unclear how this relates to the autistic traits of the mother and how early this can be detected during pregnancy and postnatal development.MethodsMaternal serum was collected from pregnant women (n = 122) before or during their first ultrasound appointment [mean = 12.7 (SD = 0.7) weeks]. Concentrations of the following were measured via immunoassays: testosterone, estradiol, dehydroepiandrosterone sulphate, progesterone; and sex hormone-binding globulin which was used to compute the free fractions of estradiol (FEI) and testosterone (FTI). Standardised human choriogonadotropin (hCG) and pregnancy-associated plasma protein A (PAPP-A) values were obtained from clinical records corresponding to the same serum samples. Mothers completed the Autism Spectrum Quotient (AQ) and for their infants, the Quantitative Checklist for Autism in Toddlers (Q-CHAT) when the infants were between 18 and 20 months old.ResultsFEI was positively associated with maternal autistic traits in univariate (n = 108, Pearson's r = 0.22, p = 0.019) and multiple regression models (semipartial r = 0.19, p = 0.048) controlling for maternal age and a diagnosis of PCOS. Maternal estradiol levels significantly interacted with fetal sex in predicting infant Q-CHAT scores, with a positive relationship in males but not females (n = 100, interaction term: semipartial r = 0.23, p = 0.036) after controlling for maternal AQ and other covariates. The opposite was found for standardised hCG values and Q-CHAT scores, with a positive association in females but not in males (n = 151, interaction term: r = -0.25, p = 0.005).LimitationsSample size of this cohort was small, with potential ascertainment bias given elective recruitment. Clinical covariates were controlled in multiple regression models, but additional research is needed to confirm the statistically significant findings in larger cohorts.ConclusionMaternal steroid factors during pregnancy are associated with autistic traits in mothers and their infants

Genetic and Transcriptional Analysis of Human Host Response to Healthy Gut Microbiota

Many studies have demonstrated the importance of the gut microbiota in healthy and disease states. However, establishing the causality of host-microbiota interactions in humans is still challenging. Here, we describe a novel experimental system to define the transcriptional response induced by the microbiota for human cells and to shed light on the molecular mechanisms underlying host-gut microbiota interactions. In primary human colonic epithelial cells, we identified over 6,000 genes whose expression changed at various time points following coculturing with the gut microbiota of a healthy individual. Among the differentially expressed genes we found a 1.8-fold enrichment of genes associated with diseases that have been previously linked to the microbiome, such as obesity and colorectal cancer. In addition, our experimental system allowed us to identify 87 host single nucleotide polymorphisms (SNPs) that show allele-specific expression in 69 genes. Furthermore, for 12 SNPs in 12 different genes, allele-specific expression is conditional on the exposure to the microbiota. Of these 12 genes, 8 have been associated with diseases linked to the gut microbiota, specifically colorectal cancer, obesity, and type 2 diabetes. Our study demonstrates a scalable approach to study host-gut microbiota interactions and can be used to identify putative mechanisms for the interplay between host genetics and the microbiota in health and disease

Minimum message length inference of secondary structure from protein coordinate data

Motivation: Secondary structure underpins the folding pattern and architecture of most proteins. Accurate assignment of the secondary structure elements is therefore an important problem. Although many approximate solutions of the secondary structure assignment problem exist, the statement of the problem has resisted a consistent and mathematically rigorous definition. A variety of comparative studies have highlighted major disagreements in the way the available methods define and assign secondary structure to coordinate data

Stakeholders\u27 views on data sharing in multicenter studies

AIM: To understand stakeholders\u27 views on data sharing in multicenter comparative effectiveness research studies and the value of privacy-protecting methods. MATERIALS and METHODS: Semistructured interviews with five US stakeholder groups. RESULTS: We completed 11 interviews, involving patients (n = 15), researchers (n = 10), Institutional Review Board and regulatory staff (n = 3), multicenter research governance experts (n = 2) and healthcare system leaders (n = 4). Perceptions of the benefits and value of research were the strongest influences toward data sharing; cost and security risks were primary influences against sharing. Privacy-protecting methods that share summary-level data were acknowledged as being appealing, but there were concerns about increased cost and potential loss of research validity. CONCLUSION: Stakeholders were open to data sharing in multicenter studies that offer value and minimize security risks

Tracking the evolution of hospice palliative care in Canada: A comparative case study analysis of seven provinces

<p>Abstract</p> <p>Background</p> <p>An aging population, rise in chronic illnesses, increase in life expectancy and shift towards care being provided at the community level are trends that are collectively creating an urgency to advance hospice palliative care (HPC) planning and provision in Canada. The purpose of this study was to analyze the evolution of HPC in seven provinces in Canada so as to inform such planning and provision elsewhere. We have endeavoured to undertake this research out of awareness that good future planning for health and social care, such as HPC, typically requires us to first look backwards before moving forward.</p> <p>Methods</p> <p>To identify key policy and practice events in HPC in Canada, as well as describe facilitators of and barriers to progress, a qualitative comparative case study design was used. Specifically, the evolution and development of HCP in 7 strategically selected provinces is compared. After choosing the case study provinces, the grey literature was searched to create a preliminary timeline for each that described the evolution of HPC beginning in 1970. Key informants (<it>n </it>= 42) were then interviewed to verify the content of each provincial timeline and to discuss barriers and facilitators to the development of HPC. Upon completion of the primary data collection, a face-to-face meeting of the research team was then held so as to conduct a comparative study analysis that focused on provincial commonalities and differences.</p> <p>Results</p> <p>Findings point to the fact that HPC continues to remain at the margins of the health care system. The development of HPC has encountered structural inheritances that have both sped up progress as well as slowed it down. These structural inheritances are: (1) foundational health policies (e.g., the Canada Health Act); (2) service structures and planning (e.g., the dominance of urban-focused initiatives); and (3) health system decisions (e.g., regionalization). As a response to these inheritances, circumventions of the established system of care were taken, often out of necessity. Three kinds of circumventions were identified from the data: (1) interventions to shift the system (e.g., the role of advocacy); (2) service innovations (e.g., educational initiatives); and (3) new alternative structures (e.g., the establishment of independent hospice organizations). Overall, the evolution of HPC across the case study provinces has been markedly slow, but steady and continuous.</p> <p>Conclusions</p> <p>HPC in Canada remains at the margins of the health care system. Its integration into the primary health care system may ensure dedicated and ongoing funding, enhanced access, quality and service responsiveness. Though demographics are expected to influence HPC demand in Canada, our study confirms that concerned citizens, advocacy organizations and local champions will continue to be the agents of change that make the necessary and lasting impacts on HPC in Canada.</p

An Anglo-Saxon execution cemetery at Walkington Wold, Yorkshire

This paper presents a re-evaluation of a cemetery excavated over 30 years ago at Walkington Wold in east Yorkshire. The cemetery is characterized by careless burial on diverse alignments, and by the fact that most of the skeletons did not have associated crania. The cemetery has been variously described as being the result of an early post-Roman massacre, as providing evidence for a ‘Celtic’ head cult or as an Anglo-Saxon execution cemetery. In order to resolve the matter, radiocarbon dates were acquired and a re-examination of the skeletal remains was undertaken. It was confirmed that the cemetery was an Anglo-Saxon execution cemetery, the only known example from northern England, and the site is set into its wider context in the paper

A multi-jurisdictional outbreak of Salmonella Typhimurium infections linked to backyard poultry—Australia, 2020

Zoonotic salmonellosis can occur either through direct contact with an infected animal or through indirect contact, such as exposure to an infected animal's contaminated environment. Between May and August 2020, a multi-jurisdictional outbreak of Salmonella Typhimurium (STm) infection due to zoonotic transmission was investigated in Australia. In total, 38 outbreak cases of STm with a median age of 5 years were reported. Epidemiological investigation showed contact with live poultry to be a common risk factor with most cases recently purchasing one-week old chicks from produce/pet stores. Traceback investigation of cases identified 25 product/pet stores of which 18 were linked to a single poultry breeder farm. On farm environmental sampling identified the same STm genotype as identified in cases. Whole genome sequencing of both environmental and human outbreak isolates found them to be highly related by phylogenetic analysis. This investigation describes the first documented widespread zoonotic salmonellosis outbreak in Australia attributed to backyard poultry exposure and identified potential risk factors and prevention and control measures for future outbreaks. Prevention of future outbreaks will require an integrated One Health approach involving the poultry industry, produce/pet store owners, animal healthcare providers, public health and veterinary health agencies and the public

High-throughput allele-specific expression across 250 environmental conditions

Gene-by-environment (GxE) interactions determine common disease risk factors and biomedically relevant complex traits. However, quantifying how the environment modulates genetic effects on human quantitative phenotypes presents unique challenges. Environmental covariates are complex and difficult to measure and control at the organismal level, as found in GWAS and epidemiological studies. An alternative approach focuses on the cellular environment using in vitro treatments as a proxy for the organismal environment. These cellular environments simplify the organism-level environmental exposures to provide a tractable influence on subcellular phenotypes, such as gene expression. Expression quantitative trait loci (eQTL) mapping studies identified GxE interactions in response to drug treatment and pathogen exposure. However, eQTL mapping approaches are infeasible for large-scale analysis of multiple cellular environments. Recently, allele-specific expression (ASE) analysis emerged as a powerful tool to identify GxE interactions in gene expression patterns by exploiting naturally occurring environmental exposures. Here we characterized genetic effects on the transcriptional response to 50 treatments in five cell types. We discovered 1455 genes with ASE (FDR \u3c 10%) and 215 genes with GxE interactions. We demonstrated a major role for GxE interactions in complex traits. Genes with a transcriptional response to environmental perturbations showed sevenfold higher odds of being found in GWAS. Additionally, 105 genes that indicated GxE interactions (49%) were identified by GWAS as associated with complex traits. Examples include GIPR–caffeine interaction and obesity and include LAMP3–selenium interaction and Parkinson disease. Our results demonstrate that comprehensive catalogs of GxE interactions are indispensable to thoroughly annotate genes and bridge epidemiological and genome-wide association studies

Functional dynamic genetic effects on gene regulation are specific to particular cell types and environmental conditions

Genetic effects on gene expression and splicing can be modulated by cellular and environmental factors; yet interactions between genotypes, cell type and treatment have not been comprehensively studied together. We used an induced pluripotent stem cell system to study multiple cell types derived from the same individuals and exposed them to a large panel of treatments. Cellular responses involved different genes and pathways for gene expression and splicing, and were highly variable across contexts. For thousands of genes, we identified variable allelic expression across contexts and characterized different types of gene-environment interactions, many of which are associated with complex traits. Promoter functional and evolutionary features distinguished genes with elevated allelic imbalance mean and variance. On average half of the genes with dynamic regulatory interactions were missed by large eQTL mapping studies, indicating the importance of exploring multiple treatments to reveal previously unrecognized regulatory loci that may be important for disease