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Background: Respiratory illness affects individuals across all age demographics on a global scale, often precipitated by viral infections. The symptomatic manifestations of these diseases bear clinical resemblance, complicating the accurate determination of their etiological origins. Furthermore, the diagnostic panels for respiratory pathogens used within local medical practices, may not encompass the full spectrum of viral agents responsible for such ailments. Consequently, a significant number of clinically important viral pathogens may remain undetected. Methods and findings: In the light of this, we conducted a metagenomic examination of 66 nasopharyngeal swab specimens, obtained from patients presenting with acute respiratory conditions yet tested negative by the standard diagnostic panels available locally. These specimens were obtained from the Public Health Laboratory, Maceio, State of Alagoas. Our findings indicate a predominant diagnostic escape of rhinoviruses and notably enterovirus D68. Moreover, our study identified a substantial quantity of sequence reads attributed to human respirovirus 3 (human parainfluenza 3) along with various herpresviruses including human herpesvirus-1, Epstein-Barr virus (Human herpesvirus-4), Human herpesviruses 6 and 7 and human parvovirus B19 (B19V). Notably, the metagenomic analysis uncovered a widespread presence of the emerging human vientovirus FB in most of sample pools, though its clinical importance remains to be elucidated. Conclusions: The obtained results in this study underscore the invaluable role of viral metagenomics in the identification of underrecognized viruses bearing clinical relevance. Furthermore, it offers insights into the dissemination of these pathogens within the studied area, thereby informing public health strategies aimed at enhancing diagnostic accuracy and improving patient care. Author summary: The emergence of SARS-CoV-2 has reshaped our understanding of respiratory viruses, highlighting the challenges in etiological diagnosis due to symptom similarities. Metagenomics, an innovative approach, has revolutionized respiratory infection diagnosis by unbiasedly sequencing all genetic material in a sample, enabling the identification of previously unknown or unsuspected viruses where traditional methods often fail. In a study conducted in Alagoas, a Northeast Brazilian state with low human development indexes, samples obtained from patients with flu-like symptoms negative for locally applied diagnostic kits revealed diagnostic escape of rhinoviruses and a notably prevalent enterovirus D68. Additionally, substantial reads attributed to human respirovirus 3 (parainfluenza virus 3) and various herpesviruses, including human herpesvirus-1, Epstein-Barr virus, human herpesviruses 6 and 7, and human parvovirus B19, were identified. These findings are pivotal for differentiating viruses not detected by routinely implemented diagnostic procedures. Metagenomics shows great promise in diagnosing and surveilling respiratory viruses, providing insights into their epidemiology, evolution, and public health impact. [ABSTRACT FROM AUTHOR]

The main goal of this study was to pinpoint functional candidate genes associated with multiple economically important traits in Nellore cattle. After quality control, 1830 genomic regions sourced from 52 scientific peer-reviewed publications were used in this study. From these, a total of 8569 positional candidate genes were annotated for reproduction, 11,195 for carcass, 5239 for growth, and 3483 for morphological traits, and used in an over-representation analysis. The significant genes (adjusted p-values < 0.05) identified in the over-representation analysis underwent prioritization analyses, and enrichment analysis of the prioritized over-represented candidate genes was performed. The prioritized candidate genes were GFRA4, RFWD3, SERTAD2, KIZ, REM2, and ANKRD34B for reproduction; RFWD3, TMEM120A, MIEF2, FOXRED2, DUSP29, CARHSP1, OBI1, JOSD1, NOP58, and LOXL1-AS1 for the carcass; ANKRD34B and JOSD1 for growth traits; and no genes were prioritized for morphological traits. The functional analysis pinpointed the following genes: KIZ (plays a crucial role in spindle organization, which is essential in forming a robust mitotic centrosome), DUSP29 (involved in muscle cell differentiation), and JOSD1 (involved in protein deubiquitination, thereby improving growth). The enrichment of the functional candidate genes identified in this study highlights that these genes play an important role in the expression of reproduction, carcass, and growth traits in Nellore cattle. [ABSTRACT FROM AUTHOR]

Background: The genotype-by-environment interaction (GxE) in beef cattle can be investigated using reaction norm models to assess environmental sensitivity and, combined with genome-wide association studies (GWAS), to map genomic regions related to animal adaptation. Including genetic markers from whole-genome sequencing in reaction norm (RN) models allows us to identify high-resolution candidate genes across environmental gradients through GWAS. Hence, we performed a GWAS via the RN approach using whole-genome sequencing data, focusing on mapping candidate genes associated with the expression of reproductive and growth traits in Nellore cattle. For this purpose, we used phenotypic data for age at first calving (AFC), scrotal circumference (SC), post-weaning weight gain (PWG), and yearling weight (YW). A total of 20,000 males and 7,159 females genotyped with 770k were imputed to the whole sequence (29 M). After quality control and linkage disequilibrium (LD) pruning, there remained ∼ 2.41 M SNPs for SC, PWG, and YW and ∼ 5.06 M SNPs for AFC. Results: Significant SNPs were identified on Bos taurus autosomes (BTA) 10, 11, 14, 18, 19, 20, 21, 24, 25 and 27 for AFC and on BTA 4, 5 and 8 for SC. For growth traits, significant SNP markers were identified on BTA 3, 5 and 20 for YW and PWG. A total of 56 positional candidate genes were identified for AFC, 9 for SC, 3 for PWG, and 24 for YW. The significant SNPs detected for the reaction norm coefficients in Nellore cattle were found to be associated with growth, adaptative, and reproductive traits. These candidate genes are involved in biological mechanisms related to lipid metabolism, immune response, mitogen-activated protein kinase (MAPK) signaling pathway, and energy and phosphate metabolism. Conclusions: GWAS results highlighted differences in the physiological processes linked to lipid metabolism, immune response, MAPK signaling pathway, and energy and phosphate metabolism, providing insights into how different environmental conditions interact with specific genes affecting animal adaptation, productivity, and reproductive performance. The shared genomic regions between the intercept and slope are directly implicated in the regulation of growth and reproductive traits in Nellore cattle raised under different environmental conditions. [ABSTRACT FROM AUTHOR]

Simple Summary: SCFAs are considered functional ingredients as they promote the growth and health of fish. This work aimed to assess the effect of short-chain fatty acids (SCFAs) on the immune status of the European sea bass gut through the ex vivo use of intestinal explants. The ex vivo technique significantly reduces the number of animals to be used, according to the guidelines of the 3Rs. The present results are important to understand how European sea bass respond to a bacterial infection after the administration of SCFAs and for the evaluation of functional ingredients used in aquaculture. This study aimed to evaluate the intestinal interactions between three short-chain fatty acids (SCFA), namely, acetate, propionate, and butyrate, and pathogenic bacteria (Vibrio anguillarum) in intestinal explants of European sea bass (Dicentrarchus labrax) juveniles. The anterior intestine of 12 fish with an average weight of 100 g (killed by excess anesthesia with 2-phenoxyethanol) were sampled and placed in 24-well plates. The experimental treatments consisted of a control medium and a control plus 1 mM or 10 mM of sodium acetate (SA), sodium butyrate (SB), and sodium propionate (SP). After 2 h of incubation, the explants were challenged with Vibrio anguillarum at 1 × 107 CFU/mL for 2 h. After the bacterial challenge, and regardless of the SCFA treatment, the oxidative stress-related genus catalase (cat) and superoxide dismutase (sod) were down-regulated and glutathione peroxidase (gpx) was up-regulated. Furthermore, the immune-related genes, i.e., the tumor necrosis factor (TNF-α), interleukin 8 (IL-8), transforming growth factor (TGF-β), and nuclear factor (NF-Kβ) were also up-regulated, and interleukin 10 (IL-10) was down-regulated. During the pre-challenge, sodium propionate and sodium butyrate seemed to bind the G-protein coupled receptor (grp40L), increasing its expression. During the challenge, citrate synthase (cs) was down-regulated, indicating that the SCFAs were used as an energy source to increase the immune and oxidative responses. Overall, our results suggest that sodium propionate and sodium butyrate may boost European sea bass immune response at the intestine level. [ABSTRACT FROM AUTHOR]

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Context. The knowledge of the genetic variability of gestation length and its correlations with other traits is relevant for selection decisions in beef cattle. Aims. Genetic parameters and trends were estimated for gestation length (first (GL1), repeated measures range of 1--6 (GL)) and traits currently used as selection criteria (birth weight (BW), weight gain from birth to weaning (BWG), weight gain from weaning to yearling (WYG), scrotal circumference (SC), score of conformation (YC), score of precocity (YP), and score of muscling (YM)) in Brazilian Angus cattle. In addition, direct and correlated selection responses were predicted. Methods. A series of single- and two-trait Bayesian analyses were performed on beef cattle data from14 farms across different regions of Brazil, by using linear and threshold animal models. Key results. A moderate heritability was estimated for GL1 (0.356 ± 0.058); however, the estimate for GL was low (0.189 ± 0.028) as was that for repeatability (0.204 ± 0.027). Lower accuracies of breeding values were obtained for GL than for GL1, ranging from0.490 ± 0.161 to 0.687 ± 0.037. Direct heritability estimates for growth and body composition traits were low, except for SC and BWG (0.301 ± 0.060 and 0.241 ± 0.019 respectively). Genetic correlations of 0.558 ± 0.121 and 0.739 ± 0.131 were estimated between GL1 and BW, and between GL and BW respectively. The other traits studied were estimated to have weak or nearzero genetic correlations with gestation length traits. Positive and moderate genetic associations were estimated between BW and BWG, SC, and visual scores (ranging from 0.338 ± 0.095 to 0.458 ± 0.092), but a near-zero estimate was obtained with WYG (0.127 ± 0.150). Weight gains were more highly genetically correlated with visual scores than between themselves (BWG and WYG) and with SC. The SC was highly genetically correlated with visual scores (0.684 ± 0.054 to 0.714 ± 0.050). Genetic trends showed that all traits studied have been changing in a positive direction, being unfavourable for BW and GL. Higher genetic gains were expected from using direct selection than from using indirect selection for GL1. Conclusions. Rapid growth is genetically associated with superior conformation, precocity and musculature, as well as a large scrotal circumference in males. However, selection decisions that heavily focus on these traits are likely to lead to more calving difficulties in the longer term. Implications. Selection indices should incorporate traits that measure calving difficulty directly if relevant records are available. Currently, considering its practical implications in primiparous anoestrus, the first-gestation length could serve as a viable alternative for inclusion in selection indices. Due to the low repeatability of the gestation length, decisions to cull on the basis of only one or two records of GL are highly inaccurate. [ABSTRACT FROM AUTHOR]

Enhancing reproductive efficiency could lead to economic benefits for Nellore producers. However, several factors limit our understanding of the main genetic factors controlling reproduction traits in Nellore cattle, including genetic differences between populations and statistical limitations. A meta-analysis can assist in pinpointing the most likely functional candidate genes, quantitative trait loci, and biological processes simultaneously associated with several traits in a group. Hence, the goal of this study was to perform a meta-analysis of genomic regions previously associated with reproduction traits in Nellore cattle, to improve our comprehension of the main genetic mechanisms regulating these traits within the breed. This study incorporated a total of 549 genomic regions sourced from 21 scientific publications, published between 2014 to 2024. The reproduction traits included in this study are scrotal circumference at various ages (365, 450, and 550 d), early pregnancy (< 31 mo of age), early puberty (defined as pregnancy at 18 mo), age at first calving, antral follicle count, calving interval, calving ease, testicular hypoplasia, stayability, heifer rebreeding, gestation length, anti-mullerian hormone concentrations, preweaning calf mortality, and post-natal mortality. All genomic regions identified in the literature were up- dated to the ARS-UCD1.2 genome assembly, and the Gallo R package was used to identify positional candidate genes associated with each genomic region. A total of 8,441 positional candidate genes were annotated and used in an overrepresentation analysis performed inmeshr. The significant genes (adjusted P-values < 0.05) identified in the overrepresentation analysis underwent prioritization analyses using the GUILDify and Topp Gene software. Subsequently, enrichment analysis of the prioritized overrepresented candidate genes was performed using the Cluster Profiler R package. The 8,441 annotated genes generated 1,757 overrepresented genes, of which 17 candidate genes were prioritized (FDR P -value ≤ 10-3). The overrepresented candidate genes that were prioritized are: SERTAD2, RFWD3, C1QTNF9B, SLFN14, CATSPERE, GFRA4, ZNF408, NOP58, ADGRG3, KIZ, REM2, FSCN3, DCAF11, ACSM4, ANKRD34B, CMKLR2-AS, and TRV-AAC1-1. The functional enrichment analysis highlighted the following genes: FSCN3 (exhibits highly specific expression in testis), CATSPERE (has a vital role in cellular processes related to reproduction and is necessary for normal fertility), ANKRD34B (associated with cytoplasm found in oocytes or early embryos), and RFWD3 (regulates the transition be- tween phases of the mitotic cell cycle). All other prioritized genes also have roles in regulating metabolic pathways or biological processes related to reproduction, such as sperm capacitation, sperm motility, cilium or flagellum-dependent cell motility, mitotic cell cycle phase transition, and RNA endonuclease activity. The enrichment of the functional candidate genes identified highlights that these genes have an important role in the expression of reproduction traits in Nellore cattle. Candidate genes identified in this study can be used as target genes in gene expression studies, which are necessary to validate our findings. [ABSTRACT FROM AUTHOR]

Selecting sires with optimal genetic merit for mature weight (MWT) is crucial for profitability of beef producers, ensuring cost-effective production and increased economic returns per animal. The main objective of this study was to determine how different statistical approaches [e.g., including the fixed effects (FE) of age and body condition score (BCS) in the statistical model and/or pre-adjusting the weights for these effects] affect variance components estimation and genetic parameters for MWT, and their impact in the posterior selection decisions. The dataset provided by the American Angus Association (AAA) comprised 80,296 MWT records from 37,934 cows aged 2 to 15 yr. Contemporary groups (CG) were defined by con- catenating herd, year, and season of measurement. Model 1 analyzed unadjusted MWT with CG and BCS as categorical FE and age as a covariable (quadratic). Model 2 was model 1 without BCS, model 3 was model 1 without age, and model 4 considered CG as the only FE. In model 5, MWT was pre-adjusted for 6 yr of age and BCS of 6, and CG was the only FE included in the statistical model. Additive genetic and permanent environment (pe) random effects were included in all statistical models except model 5, which did not include pe (only one adjusted record per animal). Variance components were calculated using REML implemented in the BLUPf90+ family of programs. Sires with at least 10 offspring (n = 1,483) were ranked according to their breeding values (EBVs) predicted for MWT, and all and the top 10% sires were used to estimate the rank correlation across models. The heritability (± SE) estimated for MWT was 0.43 (± 0.011), 0.42 (± 0.011), 0.70 (± 0.008), 0.72 (± 0.082), and 0.37 (± 0.013) for models 1, 2, 3, 4, and 5, respectively. Repeatability values were 0.64, 0.67, 0.72, and 0.76 for models 1, 2, 3, and 4, respectively. The EBV ranks were highly correlated between models 1 and 2 (Top 10%: 0.96; All: 0.99), and models 3 and 4 (Top 10%: 0.99; All: 0.99). Inflated heritabilities in models 3 and 4 suggest that the effect of age is confounded with the additive genetic ef- fect, which will not translate to greater genetic progress. Therefore, disregarding age in the genetic evaluation of MWT is not recommended. Similarities between models 1 and 2 suggest that BCS has a relatively small impact on MWT, probably related to the relatively low genetic correlation between these traits. Models 1 and 5 cannot be directly compared, as they use slightly different response variables (body weight vs. pre-adjusted weight) and may lead to slightly different selection decisions (correlation between Top 10%: 0.85; All: 0.95). Further investigations in this field are warranted. [ABSTRACT FROM AUTHOR]

This study aimed to investigate functional variants in chromosome 14 (BTA14) and its impact in genomic selection for birth weight (BW), weaning weight (WW), and yearling weight (YW) in Nellore cattle. Genetic parameter estimation and the weighted single‐step genomic best linear unbiased prediction (WssGBLUP) analyses were performed. Direct additive heritability estimates were high for WW and YW, and moderate for BW. Trait‐associated variants distributed across multiple regions on BTA14 were observed in the weighted single‐step genome‐wide association studies (WssGWAS) results, implying a polygenic genetic architecture for weight in different ages. Several genes have been found in association with the weight traits, including the CUB And Sushi multiple domains 3 (CSMD3), thyroglobulin (TG), and diacylglycerol O‐acyltransferase 1 (DGAT1) genes. The variance explained per SNP was higher in six functional classes of gene regulatory regions (5UTR, CpG islands, downstream, upstream, long non‐coding RNA, and transcription factor binding sites (TFBS)), highlighting their importance for weight traits in Nellore cattle. A marginal increase in accuracy was observed when the selected functional variants (SV) information was considered in the WssGBLUP method, probably because of the small number of SV available on BTA14. The identified genes, pathways, and functions contribute to a better understanding of the genetic and physiological mechanisms regulating weight traits in the Nellore breed. [ABSTRACT FROM AUTHOR]