Oxidative stress and cryoresistance of sturgeon sperm: A review.

Currently, the majority of sturgeons are relict fishes of high economic value yet endangered with extinction. Cryopreservation of sperm has great potential in fish farming and conservation, but the problem of low cryoresistance of sturgeon sperm has not yet been solved. The goal of this work was to review current literature data on the causes of low tolerance of sturgeon sperm to cryodamage. The influence of cryopreservation on the parameters of physiology and metabolism of sturgeon sperm (morphology and fine ultrastructure, mobility and fertilization ability, integrity of the plasma membrane, protein, lipid and metabolite profiles, antioxidant status, DNA damage), as well as on biomarkers of oxidative stress (lipids peroxidation levels and carbonyl derivatives of proteins) is discussed. Since the development of oxidative stress is an important mechanism of sperm cryodamage induction, the review presents the literature on the role of oxygen-derived species in damage of sturgeon reproductive cells caused by cryopreservation. Particular attention is paid to the system of antioxidant protection of sturgeon seminal plasma and spermatozoa, represented by antioxidant enzymes and low molecular weight antioxidants capable of utilizing various reactive forms of oxygen and nitrogen. The review discusses the results of lipidomic and proteomic studies of sturgeon sperm, which made it possible to obtain new data on the lipid composition of cell membranes, to detect proteins involved in the protection of sturgeon spermatozoa from oxidative damage during cryopreservation. This review presents the use of «omics¼ technology to elucidate the mechanism of cryodamage in sturgeon sperm. Additionally, the review summarizes information on the unique anatomical, morphological, biochemical, and physiological features of sturgeon sperm, which may be associated with low cryoresistance of sturgeon, in order to establish prospects for further research on improving the methods of the conservation of sperm of these threatened species.

Investigation of ancestral alleles in the Bovinae subfamily.

BACKGROUND: In evolutionary theory, divergence and speciation can arise from long periods of reproductive isolation, genetic mutation, selection and environmental adaptation. After divergence, alleles can either persist in their initial state (ancestral allele - AA), co-exist or be replaced by a mutated state (derived alleles -DA). In this study, we aligned whole genome sequences of individuals from the Bovinae subfamily to the cattle reference genome (ARS.UCD-1.2) for defining ancestral alleles necessary for selection signatures study. RESULTS: Accommodating independent divergent of each lineage from the initial ancestral state, AA were defined based on fixed alleles on at least two groups of yak, bison and gayal-gaur-banteng resulting in ~ 32.4 million variants. Using non-overlapping scanning windows of 10 Kb, we counted the AA observed within taurine and zebu cattle. We focused on the extreme points, regions with top 0. 1% (high count) and regions without any occurrence of AA (null count). High count regions preserved gene functions from ancestral states that are still beneficial in the current condition, while null counts regions were linked to mutated ones. For both cattle, high count regions were associated with basal lipid metabolism, essential for survival of various environmental pressures. Mutated regions were associated to productive traits in taurine, i.e. higher metabolism, cell development and behaviors and in immune response domain for zebu. CONCLUSIONS: Our findings suggest that retaining and losing AA in some regions are varied and made it species-specific with possibility of overlapping as it depends on the selective pressure they had to experience.

Core functions, knowledge bases and essential services: A proposed prescription for the evolution of the preventive medicine specialty.

The pandemonium from the 2020 pandemic calls for a greater emphasis on prevention, public health and population health. Yet the role of preventive medicine specialists, ideally qualified to lead this charge, remains difficult to situate within the houses of medicine and public health. To overcome this challenge to its identity and evolve to better tackle novel and on-going public health and population health problems, the authors propose that the specialty of preventive medicine should assert 3 core functions within preventive care; expand and modernize its knowledge base; and enhance its residency training accordingly. The authors also propose 10 essential services, not otherwise systematically provided by other specialties, that the preventive medicine specialty can optimally fulfill as its unique contributions within medicine and public health.

Assessing Bos taurus introgression in the UOA Bos indicus assembly.

BACKGROUND: Reference genomes are essential in the analysis of genomic data. As the cost of sequencing decreases, multiple reference genomes are being produced within species to alleviate problems such as low mapping accuracy and reference allele bias in variant calling that can be associated with the alignment of divergent samples to a single reference individual. The latest reference sequence adopted by the scientific community for the analysis of cattle data is ARS_UCD1.2, built from the DNA of a Hereford cow (Bos taurus taurus-B. taurus). A complementary genome assembly, UOA_Brahman_1, was recently built to represent the other cattle subspecies (Bos taurus indicus-B. indicus) from a Brahman cow haplotype to further support analysis of B. indicus data. In this study, we aligned the sequence data of 15 B. taurus and B. indicus breeds to each of these references. RESULTS: The alignment of B. taurus individuals against UOA_Brahman_1 detected up to five million more single-nucleotide variants (SNVs) compared to that against ARS_UCD1.2. Similarly, the alignment of B. indicus individuals against ARS_UCD1.2 resulted in one and a half million more SNVs than that against UOA_Brahman_1. The number of SNVs with nearly fixed alternative alleles also increased in the alignments with cross-subspecies. Interestingly, the alignment of B. taurus cattle against UOA_Brahman_1 revealed regions with a smaller than expected number of counts of SNVs with nearly fixed alternative alleles. Since B. taurus introgression represents on average 10% of the genome of Brahman cattle, we suggest that these regions comprise taurine DNA as opposed to indicine DNA in the UOA_Brahman_1 reference genome. Principal component and admixture analyses using genotypes inferred from this region support these taurine-introgressed loci. Overall, the flagged taurine segments represent 13.7% of the UOA_Brahman_1 assembly. The genes located within these segments were previously reported to be under positive selection in Brahman cattle, and include functional candidate genes implicated in feed efficiency, development and immunity. CONCLUSIONS: We report a list of taurine segments that are in the UOA_Brahman_1 assembly, which will be useful for the interpretation of interesting genomic features (e.g., signatures of selection, runs of homozygosity, increased mutation rate, etc.) that could appear in future re-sequencing analysis of indicine cattle.

Variants at the ASIP locus contribute to coat color darkening in Nellore cattle.

BACKGROUND: Nellore cattle (Bos indicus) are well-known for their adaptation to warm and humid environments. Hair length and coat color may impact heat tolerance. The Nellore breed has been strongly selected for white coat, but bulls generally exhibit darker hair ranging from light grey to black on the head, neck, hump, and knees. Given the potential contribution of coat color variation to the adaptation of cattle populations to tropical and sub-tropical environments, our aim was to map positional and functional candidate genetic variants associated with darkness of hair coat (DHC) in Nellore bulls. RESULTS: We performed a genome-wide association study (GWAS) for DHC using data from 432 Nellore bulls that were genotyped for more than 777 k single nucleotide polymorphism (SNP) markers. A single major association signal was detected in the vicinity of the agouti signaling protein gene (ASIP). The analysis of whole-genome sequence (WGS) data from 21 bulls revealed functional variants that are associated with DHC, including a structural rearrangement involving ASIP (ASIP-SV1). We further characterized this structural variant using Oxford Nanopore sequencing data from 13 Australian Brahman heifers, which share ancestry with Nellore cattle; we found that this variant originates from a 1155-bp deletion followed by an insertion of a transposable element of more than 150 bp that may impact the recruitment of ASIP non-coding exons. CONCLUSIONS: Our results indicate that the variant ASIP sequence causes darker coat pigmentation on specific parts of the body, most likely through a decreased expression of ASIP and consequently an increased production of eumelanin.

Population Health Rounds: A Novel Vehicle for Training in Population Medicine and Clinical Preventive Medicine.

CONTEXT: Preventive medicine residents must train in population medicine (including analytics and population health) and clinical preventive medicine (including screening, behavioral counseling, and chemoprophylaxis). Yet, opportunities to perform both functions concurrently for the same population are scarce. Residents must also master the art of preventive medicine, but they often lack an established community of practice that provides a continuous forum to do so. This project explored Population Health Rounds as a novel vehicle to optimize preventive medicine residency training. PROGRAM DESCRIPTION: Modeled after traditional medical rounds, Population Health Rounds consist of a 1-hour weekly meeting engaging preventive medicine residents and supervising attendings at Stony Brook Medicine in both population medicine and clinical preventive medicine concurrently, including patient case discussions and targeted population health analytics. EVALUATION AND RESULTS: Because of the pandemic, the rounds have predominantly focused on COVID-19 and its effects on the hospital employee population. In addition to providing direct patient care to COVID-19-positive and exposed employees, residents have analyzed data on this population and made recommendations to hospital leadership based on COVID-19's institutional epidemiology, including incidence, prevalence, and predictive factors. A formative qualitative survey of resident perceptions offers insights on the value and learning outcomes of this new model. DISCUSSION AND CONCLUSION: Factors that may impact the implementation, sustainability, and feasibility of this model are discussed. The preventive medicine residency program is commissioned to address gaps in clinical preventive services for the patient-centered medical home tied to the sponsoring institution's family medicine practice. Additional plans are underway to expand the rounds to other clinical contexts, such as lifestyle medicine in the occupational setting, and for targeted populations, such as the underserved. Replication of the Population Health Rounds model is recommended to determine its effectiveness.

Reproducibility and validity of food group intake in a short food frequency questionnaire for the middle-aged Japanese population.

PURPOSE: The purpose of this study was to evaluate the reproducibility and validity of a short food frequency questionnaire (FFQ) for food group intake in Japan, the reproducibility and partial validity of which were previously confirmed for nutrients. METHODS: A total of 288 middle-aged healthy volunteers from 11 different areas of Japan provided nonconsecutive 3-day weighed dietary records (DRs) at 3-month intervals over four seasons. We evaluated reproducibility based on the first (FFQ1) and second (FFQ2) questionnaires and their validity against the DRs by comparing the intake of 20 food groups. Spearman's rank correlation coefficients (SRs) were calculated between energy-adjusted intake from the FFQs and that from the DRs. RESULTS: The intake of 20 food groups estimated from the two FFQs was mostly equivalent. The median energy-adjusted SRs between the FFQ1 and FFQ2 were 0.61 (range 0.38-0.86) for men and 0.66 (0.45-0.84) for women. For validity, the median de-attenuated SRs between DRs and the FFQ1 were 0.51 (0.17-0.76) for men and 0.47 (0.23-0.77) for women. Compared with the DRs, the proportion of cross-classification into exact plus adjacent quintiles with the FFQ1 ranged from 58 to 86% in men and from 57 to 86% in women. According to the robust Z scores and the Bland-Altman plot graphs, the underestimation errors in the FFQ1 tended to be greater in individuals with high mean levels of consumption for meat for men and for other vegetables for both men and women. CONCLUSION: The FFQ demonstrated high reproducibility and reasonable validity for food group intake. This questionnaire is short and remains appropriate for identifying associations between diet and health/disease among adults in Japan.

Hygiene and emollient interventions for maintaining skin integrity in older people in hospital and residential care settings.

BACKGROUND: Ageing has a degenerative effect on the skin, leaving it more vulnerable to damage. Hygiene and emollient interventions may help maintain skin integrity in older people in hospital and residential care settings; however, at present, most care is based on "tried and tested" practice, rather than on evidence. OBJECTIVES: To assess the effects of hygiene and emollient interventions for maintaining skin integrity in older people in hospital and residential care settings. SEARCH METHODS: We searched the Cochrane Skin Specialised Register, CENTRAL, MEDLINE, Embase, and CINAHL, up to January 2019. We also searched five trials registers. SELECTION CRITERIA: Randomised controlled trials comparing hygiene and emollient interventions versus placebo, no intervention, or standard practices for older people aged ≥ 60 years in hospital or residential care settings. DATA COLLECTION AND ANALYSIS: We used standard methodological procedures as expected by Cochrane. Primary outcomes were frequency of skin damage, for example, complete loss of integrity (tears or ulceration) or partial loss of integrity (fissuring), and side effects. Secondary outcomes included transepidermal water loss (TEWL), stratum corneum hydration (SCH), erythema, and clinical scores of dryness or itch. We used GRADE to assess the quality of evidence. MAIN RESULTS: We included six trials involving 1598 residential care home residents; no included trial had a hospital setting. Most participants had a mean age of 80+ years; when specified, more women were recruited than men. Two studies included only people with diagnosed dry skin. Studies were conducted in Asia, Australasia, Europe, and North America. A range of hygiene and emollient interventions were assessed: a moisturising soap bar; combinations of water soak, oil soak, and lotion; regular application of a commercially available moisturiser; use of two different standardised skin care regimens comprising a body wash and leave-on body lotion; bed bath with "wash gloves" containing numerous ingredients; and application of a hot towel after usual care bed bath. In five studies, treatment duration ranged from five days to six months; only one study had post-treatment follow-up (one to eight days from end of treatment). Outcomes in the hot towel study were measured 15 minutes after the skin was wiped with a dry towel. Three studies each had high risk of attrition, detection, and performance bias. Only one trial (n = 984) assessed frequency of skin damage via average monthly incidence of skin tears during six months of treatment. The emollient group (usual care plus twice-daily application of moisturiser) had 5.76 tears per month per 1000 occupied bed-days compared with 10.57 tears in the usual care only group (ad hoc or no standardised skin-moisturising regimen) (P = 0.004), but this is based on very low-quality evidence, so we are uncertain of this result. Only one trial (n = 133) reported measuring side effects. At 56 ± 4 days from baseline, there were three undesirable effects (itch (mild), redness (mild/moderate), and irritation (severe)) in intervention group 1 (regimen consisting of a moisturising body wash and a moisturising leave-on lotion) and one event (mild skin dryness) in intervention group 2 (regimen consisting of body wash and a water-in-oil emulsion containing emollients and 4% urea). In both groups, the body wash was used daily and the emollient twice daily for eight weeks. There were zero adverse events in the usual care group. This result is based on very low-quality evidence. This same study also measured TEWL at 56 ± 4 days in the mid-volar forearm (n = 106) and the lower leg (n = 105). Compared to usual care, there may be no difference in TEWL between intervention groups, but evidence quality is low. One study, which compared application of a hot towel for 10 seconds after a usual care bed bath versus usual care bed bath only, also measured TEWL at 15 minutes after the skin was wiped with a dry towel for one second. The mean TEWL was 8.6 g/m²/h (standard deviation (SD) 3.2) in the hot towel group compared with 8.9 g/m²/h (SD 4.1) in the usual care group (low-quality evidence; n = 42), showing there may be little or no difference between groups. A lower score is more favourable. Three studies (266 participants) measured SCH, but all evidence is of very low quality; we did not combine these studies due to differences in treatments (different skin care regimens for eight weeks; wash gloves for 12 weeks; and single application of hot towel to the skin) and differences in outcome reporting. All three studies showed no clear difference in SCH at follow-up (ranging from 15 minutes after the intervention to 12 weeks from baseline), when compared with usual care. A clinical score of dryness was measured by three studies (including 245 participants); pooling was not appropriate. The treatment groups (different skin care regimens for eight weeks; a moisturising soap bar used for five days; and combinations of water soak, oil soak, and lotion for 12 days) may reduce dryness compared to standard care or no intervention (results measured at 5, 8, and 56 ± 4 days after treatment was initiated). However, the quality of evidence for this outcome is low. Outcomes of erythema and clinical score of itch were not assessed in any included studies. AUTHORS' CONCLUSIONS: Current evidence about the effects of hygiene and emollients in maintaining skin integrity in older people in residential and hospital settings is inadequate. We cannot draw conclusions regarding frequency of skin damage or side effects due to very low-quality evidence. Low-quality evidence suggests that in residential care settings for older people, certain types of hygiene and emollient interventions (two different standardised skin care regimens; moisturising soap bar; combinations of water soak, oil soak, and lotion) may be more effective in terms of clinical score of dryness when compared with no intervention or standard care. Studies were small and generally lacked methodological rigour, and information on effect sizes and precision was absent. More clinical trials are needed to guide practice; future studies should use a standard approach to measuring treatment effects and should include patient-reported outcomes, such as comfort and acceptability.

Genomic predictions combining SNP markers and copy number variations in Nellore cattle.

BACKGROUND: Due to the advancement in high throughput technology, single nucleotide polymorphism (SNP) is routinely being incorporated along with phenotypic information into genetic evaluation. However, this approach often cannot achieve high accuracy for some complex traits. It is possible that SNP markers are not sufficient to predict these traits due to the missing heritability caused by other genetic variations such as microsatellite and copy number variation (CNV), which have been shown to affect disease and complex traits in humans and other species. RESULTS: In this study, CNVs were included in a SNP based genomic selection framework. A Nellore cattle dataset consisting of 2230 animals genotyped on BovineHD SNP array was used, and 9 weight and carcass traits were analyzed. A total of six models were implemented and compared based on their prediction accuracy. For comparison, three models including only SNPs were implemented: 1) BayesA model, 2) Bayesian mixture model (BayesB), and 3) a GBLUP model without polygenic effects. The other three models incorporating both SNP and CNV included 4) a Bayesian model similar to BayesA (BayesA+CNV), 5) a Bayesian mixture model (BayesB+CNV), and 6) GBLUP with CNVs modeled as a covariable (GBLUP+CNV). Prediction accuracies were assessed based on Pearson's correlation between de-regressed EBVs (dEBVs) and direct genomic values (DGVs) in the validation dataset. For BayesA, BayesB and GBLUP, accuracy ranged from 0.12 to 0.62 across the nine traits. A minimal increase in prediction accuracy for some traits was noticed when including CNVs in the model (BayesA+CNV, BayesB+CNV, GBLUP+CNV). CONCLUSIONS: This study presents the first genomic prediction study integrating CNVs and SNPs in livestock. Combining CNV and SNP marker information proved to be beneficial for genomic prediction of some traits in Nellore cattle.

Misidentification of runs of homozygosity islands in cattle caused by interference with copy number variation or large intermarker distances.

BACKGROUND: Runs of homozygosity (ROH) islands are stretches of homozygous sequence in the genome of a large proportion of individuals in a population. Algorithms for the detection of ROH depend on the similarity of haplotypes. Coverage gaps and copy number variants (CNV) may result in incorrect identification of such similarity, leading to the detection of ROH islands where none exists. Misidentified hemizygous regions will also appear as homozygous based on sequence variation alone. Our aim was to identify ROH islands influenced by marker coverage gaps or CNV, using Illumina BovineHD BeadChip (777 K) single nucleotide polymorphism (SNP) data for Austrian Brown Swiss, Tyrol Grey and Pinzgauer cattle. METHODS: ROH were detected using clustering, and ROH islands were determined from population inbreeding levels for each marker. CNV were detected using a multivariate copy number analysis method and a hidden Markov model. SNP coverage gaps were defined as genomic regions with intermarker distances on average longer than 9.24 kb. ROH islands that overlapped CNV regions (CNVR) or SNP coverage gaps were considered as potential artefacts. Permutation tests were used to determine if overlaps between CNVR with copy losses and ROH islands were due to chance. Diversity of the haplotypes in the ROH islands was assessed by haplotype analyses. RESULTS: In Brown Swiss, Tyrol Grey and Pinzgauer, we identified 13, 22, and 24 ROH islands covering 26.6, 389.0 and 35.8 Mb, respectively, and we detected 30, 50 and 71 CNVR derived from CNV by using both algorithms, respectively. Overlaps between ROH islands, CNVR or coverage gaps occurred for 7, 14 and 16 ROH islands, respectively. About 37, 44 and 52% of the ROH islands coverage in Brown Swiss, Tyrol Grey and Pinzgauer, respectively, were affected by copy loss. Intersections between ROH islands and CNVR were small, but significantly larger compared to ROH islands at random locations across the genome, implying an association between ROH islands and CNVR. Haplotype diversity for reliable ROH islands was lower than for ROH islands that intersected with copy loss CNVR. CONCLUSIONS: Our findings show that a significant proportion of the ROH islands in the bovine genome are artefacts due to CNV or SNP coverage gaps.

GHap: an R package for genome-wide haplotyping.

UNLABELLED: The GHap R package was designed to call haplotypes from phased marker data. Given user-defined haplotype blocks (HapBlock), the package identifies the different haplotype alleles (HapAllele) present in the data and scores sample haplotype allele genotypes (HapGenotype) based on HapAllele dose (i.e. 0, 1 or 2 copies). The output is not only useful for analyses that can handle multi-allelic markers, but is also conveniently formatted for existing pipelines intended for bi-allelic markers. AVAILABILITY AND IMPLEMENTATION: https://cran.r-project.org/package=GHap CONTACT: ytutsunomiya@gmail.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Genome-Wide Association Study of Cell-Mediated Response in Dogs Naturally Infected by Leishmania infantum.

A genome-wide association study (GWAS) could unravel the complexity of the cell-mediated immunity (CMI) to canine leishmaniasis (CanL). Therefore, we scanned 110,165 single-nucleotide polymorphisms (SNPs), aiming to identify chromosomal regions associated with the leishmanin skin test (LST), lymphocyte proliferation assay (LPA), and cytokine responses to further understand the role played by CMI in the outcome of natural Leishmania infantum infection in 189 dogs. Based on LST and LPA, four CMI profiles were identified (LST-/LPA-, LST+/LPA-, LST-/LPA+, and LST+/LPA+), which were not associated with subclinically infected or diseased dogs. LST+/LPA+ dogs showed increased interferon gamma (IFN-γ) and tumor necrosis factor alpha (TNF-α) levels and mild parasitism in the lymph nodes, whereas LST-/LPA+ dogs, in spite of increased IFN-γ, also showed increased interleukin-10 (IL-10) and transforming growth factor ß (TGF-ß) levels and the highest parasite load in lymph nodes. Low T cell proliferation under low parasite load suggested that L. infantum was not able to induce effective CMI in the early stage of infection. Altogether, genetic markers explained 87%, 16%, 15%, 11%, 0%, and 0% of phenotypic variance in TNF-α, TGF-ß, LST, IL-10, IFN-γ, and LPA, respectively. GWAS showed that regions associated with TNF-α include the following genes: IL12RB1, JAK3, CCRL2, CCR2, CCR3, and CXCR6, involved in cytokine and chemokine signaling; regions associated with LST, including COMMD5 and SHARPIN, involved in regulation of NF-κB signaling; and regions associated with IL-10, including LTBP1 and RASGRP3, involved in T regulatory lymphocytes differentiation. These findings pinpoint chromosomic regions related to the cell-mediated response that potentially affect the clinical complexity and the parasite replication in canine L. infantum infection.

Revealing misassembled segments in the bovine reference genome by high resolution linkage disequilibrium scan.

BACKGROUND: Misassembly signatures, created by shuffling the order of sequences while assembling a genome, can be detected by the unexpected behavior of marker linkage disequilibrium (LD) decay. We developed a heuristic process to identify misassembly signatures, applied it to the bovine reference genome assembly (UMDv3.1) and presented the consequences of misassemblies in two case studies. RESULTS: We identified 2,906 single nucleotide polymorphism (SNP) markers presenting unexpected LD decay behavior in 626 putative misassembled contigs, which comprised less than 1 % of the whole genome. Although this represents a small fraction of the reference sequence, these poorly assembled segments can lead to severe implications to local genome context. For instance, we showed that one of the misassembled regions mapped to the POLL locus, which affected the annotation of positional candidate genes in a GWAS case study for polledness in Nellore (Bos indicus beef cattle). Additionally, we found that poorly performing markers in imputation mapped to putative misassembled regions, and that correction of marker positions based on LD was capable to recover imputation accuracy. CONCLUSIONS: This heuristic approach can be useful to cross validate reference assemblies and to filter out markers located at low confidence genomic regions before conducting downstream analyses.

Genome-wide CNV analysis reveals variants associated with growth traits in Bos indicus.

BACKGROUND: Apart from single nucleotide polymorphism (SNP), copy number variation (CNV) is another important type of genetic variation, which may affect growth traits and play key roles for the production of beef cattle. To date, no genome-wide association study (GWAS) for CNV and body traits in beef cattle has been reported, so the present study aimed to investigate this type of association in one of the most important cattle subspecies: Bos indicus (Nellore breed). RESULTS: We have used intensity data from over 700,000 SNP probes across the bovine genome to detect common CNVs in a sample of 2230 Nellore cattle, and performed GWAS between the detected CNVs and nine growth traits. After filtering for frequency and length, a total of 231 CNVs ranging from 894 bp to 4,855,088 bp were kept and tested as predictors for each growth trait using linear regression analysis with principal components correction. There were 49 significant associations identified among 17 CNVs and seven body traits after false discovery rate correction (P < 0.05). Among the 17 CNVs, three were significant or marginally significant for all the traits. We have compared the locations of associated CNVs with quantitative trait locus and the RefGene database, and found two sets of 9 CNVs overlapping with either known QTLs or genes, respectively. The gene overlapping with CNV100, KCNJ12, is a functional candidate for muscle development and plays critical roles in muscling traits. CONCLUSION: This study presents the first CNV-based GWAS of growth traits using high density SNP microarray data in cattle. We detected 17 CNVs significantly associated with seven growth traits and one of them (CNV100) may be involved in growth traits through KCNJ12.

Relationship between Arginase 1 and Arginase 2 levels and genetic polymorphisms with erectile dysfunction.

Arginase 1 and Arginase 2 are homologous enzymes that convert l-Arginine to Urea and l-ornithine and compete with nitric oxide synthases for l-Arginine. Increased Arginase 1 and 2 activity may reduce nitric oxide production by the endothelium in disease states, including erectile dysfunction (ED). Here we aimed at assessing whether Arginase 1 and 2 plasma levels, plasma arginase activity, or genetic factors are associated with ED risk and severity. Blood samples were collected from healthy controls (n = 106) and from patients with ED (n = 110) after completion of the IIEF questionnaire (international index of erectile function). Plasma Arginase 1 and 2 concentrations were assessed by ELISA, while plasma arginase activity was measured by spectrophotometry. Genotypes of ARG1 (rs2781659, rs2781667, rs2246012 and rs17599586) and ARG2 (rs3742879 and rs10483801) were determined by Taqman genotyping assays by real-time polymerase chain reaction. Increased Arginase 2 concentrations were found in clinical ED and are associated with increased risk for ED. ARG1 rs2781659 AA and rs2781667 TT genotypes are associated with lower IIEF scores (higher severity) only in clinical ED. Similarly, the ARG1 GTCC haplotype is associated with higher IIEF scores in clinical ED. This study shows that plasma Arginase 2 concentrations may serve as risk factor for ED. Besides, Arginase 1 genetic variations affect ED severity.

Low levels of taurine introgression in the current Brazilian Nelore and Gir indicine cattle populations.

BACKGROUND: Nelore and Gir are the two most important indicine cattle breeds for production of beef and milk in Brazil. Historical records state that these breeds were introduced in Brazil from the Indian subcontinent, crossed to local taurine cattle in order to quickly increase the population size, and then backcrossed to the original breeds to recover indicine adaptive and productive traits. Previous investigations based on sparse DNA markers detected taurine admixture in these breeds. High-density genome-wide analyses can provide high-resolution information on the genetic composition of current Nelore and Gir populations, estimate more precisely the levels and nature of taurine introgression, and shed light on their history and the strategies that were used to expand these breeds. RESULTS: We used the high-density Illumina BovineHD BeadChip with more than 777 K single nucleotide polymorphisms (SNPs) that were reduced to 697 115 after quality control filtering to investigate the structure of Nelore and Gir populations and seven other worldwide populations for comparison. Multidimensional scaling and model-based ancestry estimation clearly separated the indicine, European taurine and African taurine ancestries. The average level of taurine introgression in the autosomal genome of Nelore and Gir breeds was less than 1% but was 9% for the Brahman breed. Analyses based on the mitochondrial SNPs present in the Illumina BovineHD BeadChip did not clearly differentiate taurine and indicine haplotype groupings. CONCLUSIONS: The low level of taurine ancestry observed for both Nelore and Gir breeds confirms the historical records of crossbreeding and supports a strong directional selection against taurine haplotypes via backcrossing. Random sampling in production herds across the country and subsequent genotyping would be useful for a more complete view of the admixture levels in the commercial Nelore and Gir populations.

Indoor Tanning Practices of Colorado High School Students.

For the first time, the 2013 Colorado Youth Risk Behavior Survey assessed indoor tanning practices of Colorado high school students. The survey revealed that girls are more likely to use indoor tanning devices than boys and that the majority of students who tan do so once or twice annually. Health care professionals and policymakers should focus on these groups in efforts to curtail indoor tanning and the associated risk of skin cancer in youth.

Genome-wide association analysis of feed intake and residual feed intake in Nellore cattle.

BACKGROUND: Feed intake plays an important economic role in beef cattle, and is related with feed efficiency, weight gain and carcass traits. However, the phenotypes collected for dry matter intake and feed efficiency are scarce when compared with other measures such as weight gain and carcass traits. The use of genomic information can improve the power of inference of studies on these measures, identifying genomic regions that affect these phenotypes. This work performed the genome-wide association study (GWAS) for dry matter intake (DMI) and residual feed intake (RFI) of 720 Nellore cattle (Bos taurus indicus). RESULTS: In general, no genomic region extremely associated with both phenotypic traits was observed, as expected for the variables that have their regulation controlled by many genes. Three SNPs surpassed the threshold for the Bonferroni multiple test for DMI and two SNPs for RFI. These markers are located on chromosomes 4, 8, 14 and 21 in regions near genes regulating appetite and ion transport and close to important QTL as previously reported to RFI and DMI, thus corroborating the literature that points these two processes as important in the physiological regulation of intake and feed efficiency. CONCLUSIONS: This study showed the first GWAS of DMI to identify genomic regions associated with feed intake and efficiency in Nellore cattle. Some genes and QTLs previously described for DMI and RFI, in other subspecies (Bos taurus taurus), that influences these phenotypes are confirmed in this study.

Accuracy of genotype imputation in Nelore cattle.

BACKGROUND: Genotype imputation from low-density (LD) to high-density single nucleotide polymorphism (SNP) chips is an important step before applying genomic selection, since denser chips tend to provide more reliable genomic predictions. Imputation methods rely partially on linkage disequilibrium between markers to infer unobserved genotypes. Bos indicus cattle (e.g. Nelore breed) are characterized, in general, by lower levels of linkage disequilibrium between genetic markers at short distances, compared to taurine breeds. Thus, it is important to evaluate the accuracy of imputation to better define which imputation method and chip are most appropriate for genomic applications in indicine breeds. METHODS: Accuracy of genotype imputation in Nelore cattle was evaluated using different LD chips, imputation software and sets of animals. Twelve commercial and customized LD chips with densities ranging from 7 K to 75 K were tested. Customized LD chips were virtually designed taking into account minor allele frequency, linkage disequilibrium and distance between markers. Software programs FImpute and BEAGLE were applied to impute genotypes. From 995 bulls and 1247 cows that were genotyped with the Illumina® BovineHD chip (HD), 793 sires composed the reference set, and the remaining 202 younger sires and all the cows composed two separate validation sets for which genotypes were masked except for the SNPs of the LD chip that were to be tested. RESULTS: Imputation accuracy increased with the SNP density of the LD chip. However, the gain in accuracy with LD chips with more than 15 K SNPs was relatively small because accuracy was already high at this density. Commercial and customized LD chips with equivalent densities presented similar results. FImpute outperformed BEAGLE for all LD chips and validation sets. Regardless of the imputation software used, accuracy tended to increase as the relatedness between imputed and reference animals increased, especially for the 7 K chip. CONCLUSIONS: If the Illumina® BovineHD is considered as the target chip for genomic applications in the Nelore breed, cost-effectiveness can be improved by genotyping part of the animals with a chip containing around 15 K useful SNPs and imputing their high-density missing genotypes with FImpute.

Assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle.

BACKGROUND: Signatures of selection are regions in the genome that have been preferentially increased in frequency and fixed in a population because of their functional importance in specific processes. These regions can be detected because of their lower genetic variability and specific regional linkage disequilibrium (LD) patterns. METHODS: By comparing the differences in regional LD variation between dairy and beef cattle types, and between indicine and taurine subspecies, we aim at finding signatures of selection for production and adaptation in cattle breeds. The VarLD method was applied to compare the LD variation in the autosomal genome between breeds, including Angus and Brown Swiss, representing taurine breeds, and Nelore and Gir, representing indicine breeds. Genomic regions containing the top 0.01 and 0.1 percentile of signals were characterized using the UMD3.1 Bos taurus genome assembly to identify genes in those regions and compared with previously reported selection signatures and regions with copy number variation. RESULTS: For all comparisons, the top 0.01 and 0.1 percentile included 26 and 165 signals and 17 and 125 genes, respectively, including TECRL, BT.23182 or FPPS, CAST, MYOM1, UVRAG and DNAJA1. CONCLUSIONS: The VarLD method is a powerful tool to identify differences in linkage disequilibrium between cattle populations and putative signatures of selection with potential adaptive and productive importance.