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Abstract Background Mitochondrial genomes differ from the nuclear genome and in humans it is known that mitochondrial variants contribute to genetic disorders. Prior to genomics, some livestock studies assessed the role of the mitochondrial genome but these were limited and inconclusive. Modern genome sequencing provides an opportunity to re-evaluate the potential impact of mitochondrial variation on livestock traits. This study first evaluated the empirical accuracy of mitochondrial sequence imputation and then used real and imputed mitochondrial sequence genotypes to study the role of mitochondrial variants on milk production traits of dairy cattle. Results The empirical accuracy of imputation from Single Nucleotide Polymorphism (SNP) panels to mitochondrial sequence genotypes was assessed in 516 test animals of Holstein, Jersey and Red breeds using Beagle software and a sequence reference of 1883 animals. The overall accuracy estimated as the Pearson’s correlation squared (R2) between all imputed and real genotypes across all animals was 0.454. The low accuracy was attributed partly to the majority of variants having low minor allele frequency (MAF 0.9 (of 954 variants segregating in the test animals) and 138 of these overlapped the sites with DR2 > 0.9. This suggests that the DR2 statistic is a reasonable proxy to select sites that are imputed with higher accuracy for downstream analyses. Accordingly, in the second part of the study mitochondrial sequence variants were imputed from real mitochondrial SNP panel genotypes of 9515 Australian Holstein, Jersey and Red dairy cattle. Then, using only sites with DR2 > 0.900 and real genotypes, we undertook a genome-wide association study (GWAS) for milk, fat and protein yields. The GWAS mitochondrial SNP effects were not significant. Conclusion The accuracy of imputation of mitochondrial genotypes from the SNP panel to sequence was generally low. The Beagle DR2 statistic enabled selection of sites imputed with higher empirical accuracy. We recommend building larger reference populations with mitochondrial sequence to improve the accuracy of imputing less common variants and ensuring that SNP panels include common variants in the D-loop region.

Abstract Background Mastitis is a disease that incurs significant costs in the dairy industry. A promising approach to mitigate its negative effects is to genetically improve the resistance of dairy cattle to mastitis. A meta-analysis of genome-wide association studies (GWAS) across multiple breeds for clinical mastitis (CM) and its indicator trait, somatic cell score (SCS), is a powerful method to identify functional genetic variants that impact mastitis resistance. Results We conducted meta-analyses of eight and fourteen GWAS on CM and SCS, respectively, using 30,689 and 119,438 animals from six dairy cattle breeds. Methods for the meta-analyses were selected to properly account for the multi-breed structure of the GWAS data. Our study revealed 58 lead markers that were associated with mastitis incidence, including 16 loci that did not overlap with previously identified quantitative trait loci (QTL), as curated at the Animal QTLdb. Post-GWAS analysis techniques such as gene-based analysis and genomic feature enrichment analysis enabled prioritization of 31 candidate genes and 14 credible candidate causal variants that affect mastitis. Conclusions Our list of candidate genes can help to elucidate the genetic architecture underlying mastitis resistance and provide better tools for the prevention or treatment of mastitis, ultimately contributing to more sustainable animal production.

Abstract For decades, superfluid helium has attracted the interest of the scientific community as an extremely pure realisation of a quantum liquid, only accessible at temperatures close to absolute zero. Previously, helium films have only been observed directly using X-rays. However, this method is limited to temperatures above 1 K due to the high levels of energy deposition, and it also suffers from an inability to distinguish between helium isotopes. Here we show that a 3He layer on top of a phase separated mixture film at 170 mK gradually dissolves into the 4He with increasing temperature. We also observe an anomaly in film behaviour near 300 mK and unexpected restoration of the layered structure at 1.5 K which is consistent with a re-entrant phase transition leading to the suppression of superfluidity in the film near 300 mK. Our successful application of neutron scattering to study helium films at ultra-low temperatures opens up new possibilities for future research.

Abstract Background The study of ancestral alleles provides insights into the evolutionary history, selection, and genetic structures of a population. In cattle, ancestral alleles are widely used in genetic analyses, including the detection of signatures of selection, determination of breed ancestry, and identification of admixture. Having a comprehensive list of ancestral alleles is expected to improve the accuracy of these genetic analyses. However, the list of ancestral alleles in cattle, especially at the whole genome sequence level, is far from complete. In fact, the current largest list of ancestral alleles (~ 42 million) represents less than 28% of the total number of detected variants in cattle. To address this issue and develop a genomic resource for evolutionary studies, we determined ancestral alleles in cattle by comparing prior derived whole-genome sequence variants to an out-species group using a population-based likelihood ratio test. Results Our study determined and makes available the largest list of ancestral alleles in cattle to date (70.1 million) and includes 2.3 million on the X chromosome. There was high concordance (97.6%) of the determined ancestral alleles with those from previous studies when only high-probability ancestral alleles were considered (29.8 million positions) and another 23.5 million high-confidence ancestral alleles were novel, expanding the available reference list to improve the accuracies of genetic analyses involving ancestral alleles. The high concordance of the results with previous studies implies that our approach using genomic sequence variants and a likelihood ratio test to determine ancestral alleles is appropriate. Conclusions Considering the high concordance of ancestral alleles across studies, the ancestral alleles determined in this study including those not previously listed, particularly those with high-probability estimates, may be used for further genetic analyses with reasonable accuracy. Our approach that used predetermined variants in species and the likelihood ratio test to determine ancestral alleles is applicable to other species for which sequence level genotypes are available.

Myocardial infarction (MI) triggers adverse ventricular remodeling (VR), cardiac fibrosis, and subsequent heart failure. Extracellular nicotinamide phosphoribosyltransferase (eNAMPT) is postulated to play a significant role in VR processing via activation of the TLR4 inflammatory pathway. We hypothesized that an eNAMPT specific monoclonal antibody (mAb) could target and neutralize overexpressed eNAMPT post-MI and attenuate chronic cardiac inflammation and fibrosis. We investigated humanized ALT-100 and ALT-300 mAb with high eNAMPT-neutralizing capacity in an infarct rat model to test our hypothesis. ALT-300 was 99mTc-labeled to generate 99mTc-ALT-300 for imaging myocardial eNAMPT expression at 2 hours, 1 week, and 4 weeks post-IRI. The eNAMPT-neutralizing ALT-100 mAb (0.4 mg/kg) or saline was administered intraperitoneally at 1 hour and 24 hours post-reperfusion and twice a week for 4 weeks. Cardiac function changes were determined by echocardiography at 3 days and 4 weeks post-IRI. 99mTc-ALT-300 uptake was initially localized to the ischemic area at risk (IAR) of the left ventricle (LV) and subsequently extended to adjacent non-ischemic areas 2 hours to 4 weeks post-IRI. Radioactive uptake (%ID/g) of 99mTc-ALT-300 in the IAR increased from 1 week to 4 weeks (0.54 ± 0.16 vs. 0.78 ± 0.13, P

Abstract Studies have demonstrated that structural variants (SV) play a substantial role in the evolution of species and have an impact on Mendelian traits in the genome. However, unlike small variants (

Abstract Background Causal variants for complex traits, such as eQTL are often found in non-coding regions of the genome, where they are hypothesised to influence phenotypes by regulating gene expression. Many regulatory regions are marked by histone modifications, which can be assayed by chromatin immunoprecipitation followed by sequencing (ChIP-seq). Sequence reads from ChIP-seq form peaks at putative regulatory regions, which may reflect the amount of regulatory activity at this region. Therefore, eQTL which are also associated with differences in histone modifications are excellent candidate causal variants. Results We assayed the histone modifications H3K4Me3, H3K4Me1 and H3K27ac and mRNA in the mammary gland of up to 400 animals. We identified QTL for peak height (histone QTL), exon expression (eeQTL), allele specific expression (aseQTL) and allele specific binding (asbQTL). By intersecting these results, we identify variants which may influence gene expression by altering regulatory regions of the genome, and may be causal variants for other traits. Lastly, we find that these variants are found in putative transcription factor binding sites, identifying a mechanism for the effect of many eQTL. Conclusions We find that allele specific and traditional QTL analysis often identify the same genetic variants and provide evidence that many eQTL are regulatory variants which alter activity at regulatory regions of the bovine genome. Our work provides methodological and biological updates on how regulatory mechanisms interplay at multi-omics levels.

Land-use conversion and resulting habitat fragmentation can affect the source(s) of primary productivity that fuels food webs and alter their structure in ways that leads to biodiversity loss. We investigated the effects of landscape modification on food webs in the Araguaia River floodplain in central Brazil using the top predator, and indicator species Caiman crocodilus (Crocodilia, Alligatoridae). We measured carbon (δ13C) and nitrogen (δ15N) isotope values of three tissues with different isotopic incorporation rates to evaluate spatial and temporal changes in caiman isotopic niche width with hierarchical Bayesian models that accounted for habitat use, intraspecific trait variation (sex and body size), and landscape attributes (composition and configuration). We also measured δ13C values of essential amino acids to assess if different primary producers are fueling aquatic food webs in natural and anthropogenic areas. Spatial analysis showed that caiman in agricultural areas had larger isotopic niche widths, which likely reflects some use of terrestrial resources in environments dominated by C4 plants. Patterns in δ13C values among essential amino acids were clearly different between natural and anthropogenic habitats. Overall, our findings suggest that caimans can persist in heterogeneous landscapes fueled by natural and agricultural energy sources of energy, which has implications for effectively managing such landscapes to maximize biodiversity.

Abstract Maternal diversity based on a sub-region of mitochondrial genome or variants were commonly used to understand past demographic events in livestock. Additionally, there is growing evidence of direct association of mitochondrial genetic variants with a range of phenotypes. Therefore, this study used complete bovine mitogenomes from a large sequence database to explore the full spectrum of maternal diversity. Mitogenome diversity was evaluated among 1883 animals representing 156 globally important cattle breeds. Overall, the mitogenomes were diverse: presenting 11 major haplogroups, expanding to 1309 unique haplotypes, with nucleotide diversity 0.011 and haplotype diversity 0.999. A small proportion of African taurine (3.5%) and indicine (1.3%) haplogroups were found among the European taurine breeds and composites. The haplogrouping was largely consistent with the population structure derived from alternate clustering methods (e.g. PCA and hierarchical clustering). Further, we present evidence confirming a new indicine subgroup (I1a, 64 animals) mainly consisting of breeds originating from China and characterised by two private mutations within the I1 haplogroup. The total genetic variation was attributed mainly to within-breed variance (96.9%). The accuracy of the imputation of missing genotypes was high (99.8%) except for the relatively rare heteroplasmic genotypes, suggesting the potential for trait association studies within a breed.

Abstract RNA sequencing offers unprecedented access to the transcriptome. Key to this is the identification and quantification of many different species of RNA from the same sample at the same time. In this study we describe a novel protocol for simultaneous detection of coding and non-coding transcripts using modifications to the Ion Total RNA-Seq kit v2 protocol, with integration of QIASeq FastSelect rRNA removal kit. We report highly consistent sequencing libraries can be produced from both frozen high integrity mouse hippocampal tissue and the more challenging post-mortem human tissue. Removal of rRNA using FastSelect was extremely efficient, resulting in less than 1.5% rRNA content in the final library. We identified > 30,000 unique transcripts from all samples, including protein-coding genes and many species of non-coding RNA, in biologically-relevant proportions. Furthermore, the normalized sequencing read count for select genes significantly negatively correlated with Ct values from qRT-PCR analysis from the same samples. These results indicate that this protocol accurately and consistently identifies and quantifies a wide variety of transcripts simultaneously. The highly efficient rRNA depletion, coupled with minimized sample handling and without complicated and high-loss size selection protocols, makes this protocol useful to researchers wishing to investigate whole transcriptomes.

Xiang and colleagues infer mutant alleles in 113,000 cattle to quantify the effect of these mutations on complex traits including body size, fertility and milk production, and compare these mutation sites across 100 species of vertebrates. Some sites show long term selective pressure, are heavily conserved and demonstrate hybrid vigour, whereas sites selected over shorter time periods are biased towards undesirable mutation.

Music is commonly played in the operating rooms and contributes to overall noise level. High noise levels in the operating room, often surpassing the National Institute for Occupational Safety and Health recommendations, affect clinician communication and vigilance. This study's primary aim was to reduce anesthesia provider response time to alarms to improve quality of care to patients undergoing general anesthesia. The aim of this quality improvement project was to reduce anesthesia provider response time to vital sign alarms with the tested intervention of the CanaryBox device to modulate music volume in the OR by August of 2021. Utilizing improvement science methods including the Model of Improvement and tested interventions via the Plan-Do-Study-Act cycles, we utilized the CanaryBox in the pediatric orthopedic operating rooms at Monroe Carell Jr. Children's Hospital at Vanderbilt. This device modulates music volume according to the severity of patient vital sign deviations. Timestamps of onset and response to patient vital sign alarms, recorded by the Philips IntelliVue Information Center system, were collected for 12 control (pre-intervention) and 58 intervention (with the CanaryBox) cases. Median and average response times were calculated for pre- and post-intervention cases. There was an associated decrease (improvement) in average anesthesia provider alarm response times from 30.2 seconds in pre-intervention cases to 23.6 seconds with CanaryBox intervention cases. Improved anesthesia provider response times with implementation of the CanaryBox imply less distraction due to unnecessary noise levels at critical periods. This improved vigilance and decreased response time indicate anesthesia providers deliver higher levels of patient care when the CanaryBox is modulating music volume.

Abstract Background Remission of diabetes can be rewarding for patients and physicians, but there is limited study of how patients perceive the timeline of a disease along the continuum of glycaemic control. Objective To explore how patients perceive the timeline of diabetes along the continuum of glycaemic control and their goals of care and to identify whether family physicians communicate the principles of regression and remission of diabetes. Design Mixed methods approach of qualitative semi‐structured interviews with purposive sampling followed by cross‐sectional survey of physicians. Participants Thirty‐three patients living with prediabetes (preDM) or type 2 diabetes mellitus (T2DM) at medical centres in Georgia and Nevada; and 387 family physicians providing primary care within the same health system. Results Patients described two timelines of diabetes: as a lifelong condition or as a condition that can be cured. Patients who perceived a lifelong condition described five treatment goals: reducing glucose‐related laboratory values, losing weight, reducing medication, preventing treatment intensification and avoiding complications. For patients who perceived diabetes as a disease with an end, the goal of care was to achieve normoglycaemia. In response to patient vignettes that described potential cases of remission and regression, 38.2% of physician respondents would still communicate that a patient has preDM and 94.6% would tell the patient that he still had diabetes. Conclusions Most physicians here exhibited reluctance to communicate remission or regression in patient care. Yet, patients describe two different potential timelines, including a subset who expect their diabetes can be ‘cured’. Physicians should incorporate shared decision making to create a shared mental model of diabetes and its potential outcomes with patients. Patient or Public Contribution In this mixed methods study, as patients participated in the qualitative phase of this study, we asked patients to tell us what additional questions we should ask in subsequent interviews. Data from this qualitative phase informed the design and interpretation of the quantitative phase with physician participants.

Abstract Background Variants that regulate transcription, such as expression quantitative trait loci (eQTL), have shown enrichment in genome-wide association studies (GWAS) for mammalian complex traits. However, no study has reported eQTL in sheep, although it is an important agricultural species for which many GWAS of complex meat traits have been conducted. Using RNA sequence data produced from liver and muscle from 149 sheep and imputed whole-genome single nucleotide polymorphisms (SNPs), our aim was to dissect the genetic architecture of the transcriptome by associating sheep genotypes with three major molecular phenotypes including gene expression (geQTL), exon expression (eeQTL) and RNA splicing (sQTL). We also examined these three types of eQTL for their enrichment in GWAS of multi-meat traits and fatty acid profiles. Results Whereas a relatively small number of molecular phenotypes were significantly heritable (h2 > 0, P

Abstract Background Mutations in the mitochondrial genome have been implicated in mitochondrial disease, often characterized by impaired cellular energy metabolism. Cellular energy metabolism in mitochondria involves mitochondrial proteins (MP) from both the nuclear (NuMP) and mitochondrial (MtMP) genomes. The expression of MP genes in tissues may be tissue specific to meet varying specific energy demands across the tissues. Currently, the characteristics of MP gene expression in tissues of dairy cattle are not well understood. In this study, we profile the expression of MP genes in 29 adult and six foetal tissues in dairy cattle using RNA sequencing and gene expression analyses: particularly differential gene expression and co-expression network analyses. Results MP genes were differentially expressed (DE; over-expressed or under-expressed) across tissues in cattle. All 29 tissues showed DE NuMP genes in varying proportions of over-expression and under-expression. On the other hand, DE of MtMP genes was observed in

Abstract Cardiac amyloidosis results in an infiltrative restrictive cardiomyopathy, with a number of characteristic features: biventricular hypertrophy, abnormal myocardial global longitudinal strain with relative apical sparing, biatrial dilation, and small pericardial effusion along with conduction abnormalities. Amyloid deposits leading to hemodynamically significant valvular heart disease are very rare. We describe a rare case of concomitant moderately severe tricuspid and mitral valve stenosis because of ongoing amyloid deposition in a patient with progressive multiple myeloma and fat pad biopsy‐proven light chain amyloidosis. Worsening infiltrative cardiomyopathy and valvulopathy despite evidence‐based chemotherapy and heart failure pharmacotherapy led to end‐stage disease and death. Valvular involvement in cardiac amyloidosis requires early recognition of the underlying disease condition to guide directed medical therapy and prevent its progression. In this instance, valvuloplasty or valve replacement is not a viable option.

Concern about adolescent diets, obesity, and the associated health risks have been growing in the United States. This inspired former First Lady Michelle Obama to spearhead the Healthy Hunger-Free Kids Act (HHFKA), which made changes to the national school lunch program by increasing servings of whole grains, fruits, and vegetables. Our study examined the variability of student carbohydrate sources throughout the day and before and after the implementation of HHFKA using a stable isotope dietary biomarker. This method uses carbon stable isotope values of exhaled CO2 breath (δ13Cbreath) and provides a quantitative, non-invasive measure. δ13Cbreath samples were collected throughout the day from students (n = 31) that attended a public high school in Salt Lake City, UT. δ13Cbreath measurements reflected the short-term carbohydrate inputs from the previous meal. Carbohydrate sources were not consistent throughout the day; most students had their lowest inputs of corn/sugar-based carbohydrates after lunch. We compared our results with an earlier study that had been conducted pre-HHFKA. After-lunch δ13Cbreath values decreased significantly between the two time points, suggesting an increase in whole grain, fruit, and vegetable carbohydrates in the lunch program. Our results demonstrated that δ13Cbreath measurements provide a valuable tool to examine carbohydrate sources in an individual's diet throughout the day. We believe that this tool could be beneficial to studies examining the relationship between sugar sweetened beverages, added sugars, and refined carbohydrates and health outcomes like diabetes and obesity in both adolescent and adult populations.

Background: PDQeX is a novel, single-step DNA extraction method that purifies nucleic acid from sample in under 30 min. Materials & Methods: Six bacterial suspensions from species with different cell morphologies and growth optima were made. DNA from half the suspension was purified using PDQeX and the other half using a conventional column purification method. Sequencing and analyses using Ion PGM were performed, blinded to extraction method and species. Results: Genomes extracted with either method sequenced successfully. No significant sequence distribution biases were evident between PDQeX and column purification. Surveyed community preference suggested comparable performance between the two extraction methods. Conclusion: DNA prepared using the PDQeX performs as well for whole-genome sequencing as DNA purified using a conventional method, albeit much more rapidly.

Abstract The experimental evidence of the exchange bias (EB) effect in epitaxial heterostructures of ferromagnetic La0.67Sr0.33MnO3 (LSMO) and paramagnetic LaNiO3 (LNO) grown on MgO(001) substrates is reported. The macroscopic magnetization measurements show a clear indication of EB in LNO/LSMO and LSMO/LNO/LSMO heterostructures. The strength of the exchange coupling rapidly reduces as the temperature is increased and almost vanishes above 50 K. Using spin dependent polarized neutron reflectometry (PNR) detailed depth dependent magnetization profiles of the heterostructures are investigated to understand the role of interface magnetism in the observed EB. PNR results establish the emergence of the interfacial ferromagnetic LNO layer of thickness ≈22–35 Å (≈6–9 unit cell) and magnetization ≈80 emu cc−1 at the LNO/LSMO interface for T

Introduction Most interventions to date regarding breaking bad news focus on late-stage disease or disclosing a cancer diagnosis. Little attention has been given to delivery of chronic metabolic disease diagnoses such as prediabetes/type 2 diabetes. Methods Informed by the American Diabetes Association standards of care and formative research conducted by our research team, we developed this curriculum through the six-step approach to curriculum development. The curriculum consists of a 2- or 3-hour intervention that teaches medical decision-making, interpersonal communication, and clinical documentation in the context of prediabetes and type 2 diabetes followed by role-play and clinical practice. Results Across three cohorts, 53 clinicians completed the curriculum. Across the three iterations, learners rated the curricular intervention as worthwhile and delivered at an appropriate level. In a community hospital setting, learners scored significantly higher on a knowledge check than did a control group of six clinicians (p < .001). Learners in the community hospital also indicated high response efficacy and self-efficacy. At the academic medical center, simulated patients indicated high measures on the Diabetes Health Threat Communication Questionnaire. Discussion The moment of diagnosis presents a key opportunity to affect patients' perceptions of the disease. This curriculum guides clinicians in making the most of diagnosis delivery. Pairing of qualitative, patient-centered research alongside the iterative curriculum design process allows the curriculum to be adaptable and scalable to multiple settings and learner types.

Bangladesh exhibits the second highest rate of smokeless tobacco (SLT) product usage in the world, and this has been associated with the high upper aerodigestive tract cancer incidence in this country. The goal of the present study was to examine the levels of the highly carcinogenic tobacco-specific nitrosamines (TSNAs) in Bangladeshi SLT products and compare these levels to that observed in SLT brands from southeast Asia and the USA. The levels of TSNAs and nicotine were determined by LC-MS/MS in twenty-eight SLT brands and several tobacco additives from Bangladesh, as well as several SLT brands from India, Pakistan and the USA. The levels of N-nitrosonornicotine (NNN), 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK), N-nitrosoanatabine (NAT) and N-nitrosoanabasine (NAB) in Bangladeshi SLT brands ranged from 1.1-59, 0.15-34, 0.79-45, and 0.037-13 μg/g SLT powder, respectively. The mean levels of the highly carcinogenic TSNAs (NNN+NNK) were 7.4-, 2.4-, and 63-fold higher in Bangladeshi SLT products as compared to SLT brands from the USA, India and Pakistan, respectively; these trends were also observed for NAT and NAB. Similar mean levels of nicotine were observed in the Bangladeshi brands (31 mg/g powder) versus brands from the USA (25 mg/g powder) and India (20 mg/g powder); they were 3-fold higher than brands from Pakistan (10 mg/g powder). Gul SLT brands exhibited the highest pH and the highest levels of unprotonated nicotine. The high levels of TSNAs in Bangladeshi SLT brands may be an important factor contributing to the high rates of upper aerodigestive tract cancer in Bangladesh.

Cellular stress response mechanisms normally function to enhance survival and allow for cells to return to homeostasis following an adverse event. Cancer cells often co-opt these same mechanisms as a means to evade apoptosis and mitigate a state of constant cellular stress. Activating transcription factor 5 (ATF5) is upregulated under diverse stress conditions and is overexpressed in a variety of cancers. It was demonstrated ATF5 is a survival factor in transformed, but not normal cells. However, the regulation of ATF5 is not fully understood. The purpose of the present study was to investigate miRNA regulation at the 3' untranslated region (UTR) of ATF5, with the goal of demonstrating a reversal of the upregulation of ATF5 induced under diverse cellular stress in cancer cells. A multifactorial approach using in silico analysis was employed to identify miRNAs 433-3p, 520b-3p, and 129-5p as potential regulators of ATF5, based on their predicted binding sites over the span of the ATF5 3' UTR. Luciferase reporter assay data validated all three miRNA candidates by demonstrating direct binding to the target ATF5 3'. However, functional studies revealed miR-520b-3p as the sole candidate able to reverse the upregulation of ATF5 protein under diverse cellular stress. Additionally, miR-520b-3p levels were inversely related to ATF5 mRNA under endoplasmic reticulum stress and amino acid deprivation. This is the first evidence that regulation at the 3' UTR is involved in modulating ATF5 levels under cellular stress and suggests an important role for miRNA-520b-3p in the regulation of ATF5.

Abstract Background The mutations changing the expression level of a gene, or expression quantitative trait loci (eQTL), can be identified by testing the association between genetic variants and gene expression in multiple individuals (eQTL mapping), or by comparing the expression of the alleles in a heterozygous individual (allele specific expression or ASE analysis). The aims of the study were to find and compare ASE and local eQTL in 4 bovine RNA-sequencing (RNA-Seq) datasets, validate them in an independent ASE study and investigate if they are associated with complex trait variation. Results We present a novel method for distinguishing between ASE driven by polymorphisms in cis and parent of origin effects. We found that single nucleotide polymorphisms (SNPs) driving ASE are also often local eQTL and therefore presumably cis eQTL. These SNPs often, but not always, affect gene expression in multiple tissues and, when they do, the allele increasing expression is usually the same. However, there were systematic differences between ASE and local eQTL and between tissues and breeds. We also found that SNPs significantly associated with gene expression (p

Abstract Background Mammalian phenotypes are shaped by numerous genome variants, many of which may regulate gene transcription or RNA splicing. To identify variants with regulatory functions in cattle, an important economic and model species, we used sequence variants to map a type of expression quantitative trait loci (expression QTLs) that are associated with variations in the RNA splicing, i.e., sQTLs. To further the understanding of regulatory variants, sQTLs were compare with other two types of expression QTLs, 1) variants associated with variations in gene expression, i.e., geQTLs and 2) variants associated with variations in exon expression, i.e., eeQTLs, in different tissues. Results Using whole genome and RNA sequence data from four tissues of over 200 cattle, sQTLs identified using exon inclusion ratios were verified by matching their effects on adjacent intron excision ratios. sQTLs contained the highest percentage of variants that are within the intronic region of genes and contained the lowest percentage of variants that are within intergenic regions, compared to eeQTLs and geQTLs. Many geQTLs and sQTLs are also detected as eeQTLs. Many expression QTLs, including sQTLs, were significant in all four tissues and had a similar effect in each tissue. To verify such expression QTL sharing between tissues, variants surrounding (±1 Mb) the exon or gene were used to build local genomic relationship matrices (LGRM) and estimated genetic correlations between tissues. For many exons, the splicing and expression level was determined by the same cis additive genetic variance in different tissues. Thus, an effective but simple-to-implement meta-analysis combining information from three tissues is introduced to increase power to detect and validate sQTLs. sQTLs and eeQTLs together were more enriched for variants associated with cattle complex traits, compared to geQTLs. Several putative causal mutations were identified, including an sQTL at Chr6:87392580 within the 5th exon of kappa casein (CSN3) associated with milk production traits. Conclusions Using novel analytical approaches, we report the first identification of numerous bovine sQTLs which are extensively shared between multiple tissue types. The significant overlaps between bovine sQTLs and complex traits QTL highlight the contribution of regulatory mutations to phenotypic variations.

Abstract Background Topological association domains (TADs) are chromosomal domains characterised by frequent internal DNA-DNA interactions. The transcription factor CTCF binds to conserved DNA sequence patterns called CTCF binding motifs to either prohibit or facilitate chromosomal interactions. TADs and CTCF binding motifs control gene expression, but they are not yet well defined in the bovine genome. In this paper, we sought to improve the annotation of bovine TADs and CTCF binding motifs, and assess whether the new annotation can reduce the search space for cis-regulatory variants. Results We used genomic synteny to map TADs and CTCF binding motifs from humans, mice, dogs and macaques to the bovine genome. We found that our mapped TADs exhibited the same hallmark properties of those sourced from experimental data, such as housekeeping genes, transfer RNA genes, CTCF binding motifs, short interspersed elements, H3K4me3 and H3K27ac. We showed that runs of genes with the same pattern of allele-specific expression (ASE) (either favouring paternal or maternal allele) were often located in the same TAD or between the same conserved CTCF binding motifs. Analyses of variance showed that when averaged across all bovine tissues tested, TADs explained 14% of ASE variation (standard deviation, SD: 0.056), while CTCF explained 27% (SD: 0.078). Furthermore, we showed that the quantitative trait loci (QTLs) associated with gene expression variation (eQTLs) or ASE variation (aseQTLs), which were identified from mRNA transcripts from 141 lactating cows’ white blood and milk cells, were highly enriched at putative bovine CTCF binding motifs. The linearly-furthermost, and most-significant aseQTL and eQTL for each genic target were located within the same TAD as the gene more often than expected (Chi-Squared test P-value

In the United States, African Americans (AAs) have been disproportionately affected by COVID-19 mortality. However, AAs are more likely to be hesitant in receiving COVID-19 vaccinations when compared to non-Hispanic Whites. We examined factors associated with vaccine hesitancy among a predominant AA community sample. We performed a cross-sectional analysis on data collected from a convenience sample of 257 community-dwelling participants in the Central Savannah River Area from 5 December 2020, through 17 April 2021. Vaccine hesitancy was categorized as resistant, hesitant, and acceptant. We estimated relative odds of vaccine resistance and vaccine hesitancy using polytomous logistic regression models. Nearly one-third of the participants were either hesitant (n = 40, 15.6%) or resistant (n = 42, 16.3%) to receiving a COVID-19 vaccination. Vaccine-resistant participants were more likely to be younger and were more likely to have experienced housing insecurity due to COVID-19 when compared to both acceptant and hesitant participants, respectively. Age accounted for nearly 25% of the variation in vaccine resistance, with 21-fold increased odds (OR: 21.93, 95% CI: 8.97–5.26–91.43) of vaccine resistance in participants aged 18 to 29 compared to 50 and older adults. Housing insecurity accounted for 8% of the variation in vaccine resistance and was associated with 7-fold increased odds of vaccine resistance (AOR: 7.35, 95% CI: 1.99–27.10). In this sample, AAs under the age of 30 and those experiencing housing insecurity because of the COVID-19 pandemic were more likely to be resistant to receiving a free COVID-19 vaccination.

Objectives: The present study takes a culture-centered approach to better understand how the experiences of culture affect patient’s perception of type 2 diabetes mellitus (T2DM). This study explores personal models of T2DM and compares personal models across regional and race/ethnicity differences. Methods: In a practice-based research network, a cross-sectional survey was distributed to patients diagnosed with T2DM at medical centers in Nevada and Georgia. In analyses of covariance, controlling for age, health literacy, and patient activation, geographic location, and race/ethnicity were tested onto 5 dimensions of illness representation. Results: Among 685 patients, race/ethnicity was significantly associated with lower reported understanding diabetes ( P < .01) and less perceived longevity of diabetes ( P < .001). Geographic location was significantly associated with seriousness of the disease ( P < .005) and impact of diabetes ( P < .001). Conclusion: Non-Hispanic White Americans report greater understanding and perceive a longer disease course than non-Hispanic Black Americans and Asian Americans. Regionally, patients in Nevada perceive T2DM as more serious and having more impact on their lives than patients living in Georgia. Primary care physicians should elicit patient perceptions of diabetes within the context of the patient’s ethnic and geographic culture group to improve discussions about diabetes self-management. Specifically, primary care physicians should address the seriousness of a diabetes diagnosis and the chronic nature of the disease with patients who belong to communities with a higher prevalence of the disease.

Asexual Epichloë fungi are strictly seed-transmitted endophytic symbionts of cool-season grasses and spend their entire life cycle within the host plant. Endophyte infection can confer protective benefits to its host through the production of bioprotective compounds. Inversely, plants provide nourishment and shelter to the resident endophyte in return. Current understanding of the changes in global gene expression of asexual Epichloë endophytes during the early stages of host-endophyte symbiotum is limited. A time-course study using a deep RNA-sequencing approach was performed at six stages of germination, using seeds infected with one of three endophyte strains belonging to different representative taxa. Analysis of the most abundantly expressed endophyte genes identified that most were predicted to have a role in stress and defence responses. The number of differentially expressed genes observed at early time points was greater than those detected at later time points, suggesting an active transcriptional reprogramming of endophytes at the onset of seed germination. Gene ontology enrichment analysis revealed dynamic changes in global gene expression consistent with the developmental processes of symbiotic relationships. Expression of pathway genes for biosynthesis of key secondary metabolites was studied comprehensively and fuzzy clustering identified some unique expression patterns. Furthermore, comparisons of the transcriptomes from three endophyte strains in planta identified genes unique to each strain, including genes predicted to be associated with secondary metabolism. Findings from this study highlight the importance of better understanding the unique properties of individual endophyte strains and will serve as an excellent resource for future studies of host-endophyte interactions.

Osteogenesis imperfecta (OI) is a rare genetic connective-tissue disorder with bone fragility. To avoid iatrogenic fractures, healthcare providers have traditionally avoided using non-invasive blood pressure (NIBP) cuffs and extremity tourniquets in the OI population in the perioperative setting. Here, we hypothesize that these procedures do not lead to iatrogenic fractures or other complications in patients with OI. A retrospective study of all children with OI who underwent surgery at a single tertiary care children’s hospital from 1998 to 2018 was performed. Patient positioning and the use of NIBP cuffs, arterial lines, and extremity tourniquets were documented. Fractures and other complications were recorded. Forty-nine patients with a median age of 7.9 years (range: 0.2–17.7) were identified. These patients underwent 273 procedures, of which 229 were orthopaedic operations. A total of 246 (90.1%) procedures included the use of an NIBP cuff, 61 (22.3%) an extremity tourniquet, and 40 (14.7%) an arterial line. Pediatric patients with OI did not experience any iatrogenic fractures related to hemodynamic monitoring or extremity tourniquet use during the 20-year period of this study. Given the benefits of continuous intra-operative hemodynamic monitoring and extremity tourniquets, we recommend that NIBP cuffs, arterial lines, and tourniquets be selectively considered for use in children with OI.

Anesthesiology is one of the leading medical specialties in patient safety. Pediatric anesthesiology is inherently higher risk than adult anesthesia due to differences in the physiology in children. In this review, we aimed to describe the highest yield safety topics for pediatric anesthesia and efforts to ameliorate risk. Conclusions: Pediatric anesthesiology has made great strides in patient perioperative safety with initiatives including the creation of a specialty society, quality and safety committees, large multi-institutional research efforts, and quality improvement initiatives. Common pediatric peri-operative events are now monitored with multi-institution and organization collaborative efforts, such as Wake Up Safe.

Pediatric anesthesiology is a subspecialty of anesthesiology that deals with the high-risk pediatric population. The specialty has made significant advancement in large collaborative efforts to study and increase patient safety, including the creation of international societies, a dedicated journal, special committees and interest groups, and multi-institution databases for research and quality improvement. Readily available resources were created to help with the education of future pediatric anesthesiologists as well as continuing medical education. Conclusions: Specialty societies and collaborations in pediatric anesthesia are crucial for continuous improvement in the care of children. They promote research, education, quality improvement, and advocacy at the local, national, and international level.

The balance and distribution of epithelial cell types is required to maintain tissue homeostasis. A hallmark of airway diseases is epithelial remodeling, leading to increased goblet cell numbers and an overproduction of mucus. In the conducting airway, basal cells act as progenitors for both secretory and ciliated cells. To identify mechanisms regulating basal cell fate, we developed a screenable 3D culture system of airway epithelial morphogenesis. We performed a high-throughput screen using a collection of secreted proteins and identified inflammatory cytokines that specifically biased basal cell differentiation toward a goblet cell fate, culminating in enhanced mucus production. We also demonstrate a specific requirement for Notch2 in cytokine-induced goblet cell metaplasia in vitro and in vivo. We conclude that inhibition of Notch2 prevents goblet cell metaplasia induced by a broad range of stimuli and propose Notch2 neutralization as a therapeutic strategy for preventing goblet cell metaplasia in airway diseases.

Botrytis species are generally considered to be aggressive, necrotrophic plant pathogens. By contrast to this general perception, however, Botrytis species could frequently be isolated from the interior of multiple tissues in apparently healthy hosts of many species. Infection frequencies reached 50% of samples or more, but were commonly less, and cryptic infections were rare or absent in some plant species. Prevalence varied substantially from year to year and from tissue to tissue, but some host species routinely had high prevalence. The same genotype was found to occur throughout a host, representing mycelial spread. B. cinerea and B. pseudocinerea are the species that most commonly occur as cryptic infections, but phylogenetically distant isolates of Botrytis were also detected, one of which does not correspond to previously described species. Sporulation and visible damage occurred only when infected tissues were stressed, or became mature or senescent. There was no evidence of cryptic infection having a deleterious effect on growth of the host, and prevalence was probably greater in plants grown in high light conditions. Isolates from cryptic infections were often capable of causing disease (to varying extents) when spore suspensions were inoculated onto their own host as well as on distinct host species, arguing against co-adaptation between cryptic isolates and their hosts. These data collectively suggest that several Botrytis species, including the most notorious pathogenic species, exist frequently in cryptic form to an extent that has thus far largely been neglected, and do not need to cause disease on healthy hosts in order to complete their life-cycles.

Environmental factors play a key role in the etiology of depression. The rodent forced swim test (FST) is commonly used as a preclinical model of depression, with increases in escape-directed behavior reflecting antidepressant effects, and increases in immobility reflecting behavioral despair. Environmental enrichment leads to serotonergic alterations in rats, but it is unknown whether these alterations may influence the efficacy of common antidepressants. Male Sprague-Dawley rats were reared in enriched (EC), standard (SC), or isolated (IC) conditions. Following the rearing period, fluoxetine (10 or 20 mg/kg, i.p.) was administered 23.5 hrs, 5 hrs, and 1 hr before locomotor and FST measures. Following locomotor testing and FST exposure, rats were weighed to assess fluoxetine-, FST-, and environmental condition-induced moderations in weight gain. Results revealed an antidepressant effect of environmental enrichment and a depressant effect of isolation. Regardless of significant fluoxetine effects on locomotor activity, fluoxetine generally decreased swimming and increased immobility in all three environmental conditions, with IC-fluoxetine (10 mg/kg) rats and EC-fluoxetine (20 mg/kg) rats swimming less than vehicle counterparts. Subchronic 20 mg/kg fluoxetine also induced significant weight loss, and differential rearing appeared to moderate weight gain following FST stress. These results suggest that differential rearing has the ability to alter FST behaviors, fluoxetine efficacy, and post-stressor well-being. Moreover, 20 mg/kg fluoxetine, administered subchronically, may lead to atypical effects of those commonly observed in the FST, highlighting the importance and impact of both environmental condition and dosing regimen in common animal models of depression.

Religious and spiritual (R/S) conversations at the end-of-life function to help patients and their families find comfort in difficult circumstances. Physicians who feel uncertain about how to discuss topics related to religious beliefs may seek to avoid R/S conversations with their patients. This study utilized a two-group objective structured clinical examination with a standardized patient to explore differences in physicians’ use of R/S topic avoidance tactics during a clinical interaction. Results indicated that physicians used more topic avoidance tactics in response to patients’ R/S inquiries than patients’ R/S disclosures; however, the use of topic avoidance tactics did not eliminate the need to engage in patient-initiated R/S interactions.

The Coronavirus disease (COVID-19) pandemic has increased anxiety and stress among teacher education managers and has given rise to the question of whether they have the competencies to execute their operational responsibilities productively. The theories of resilience and transformational leadership underpin this study in which teacher education managers' resilience and their responsiveness to the well-being of staff executing their operational practices in an open distance e-learning context were explored. A qualitative approach was adopted and virtual video conferencing interviews with teacher education managers were used to explore how they mitigated their strategic and operational roles and their managerial functions to ensure the well-being and organisational performance of staff working from home. Results revealed the experiences of distance managers to have been positive in that they implemented organisational strategies to mitigate the challenges faced to ensure wellness and performance among staff working from a distance. Further research applying a mixed-method design should be undertaken to determine how resilient managers and staff working from home are. That may yield different results.