Downregulation of growth plate genes involved with the onset of femoral head separation in young broilers

Femoral head separation (FHS) is characterized by the detachment of growth plate (GP) and articular cartilage, occurring in tibia and femur. However, the molecular mechanisms involved with this condition are not completely understood. Therefore, genes and biological processes (BP) involved with FHS were identified in 21-day-old broilers through RNA sequencing of the femoral GP. 13,487 genes were expressed in the chicken femoral head transcriptome of normal and FHS-affected broilers. From those, 34 were differentially expressed (DE; FDR ≤0.05) between groups, where all of them were downregulated in FHS-affected broilers. The main BP were enriched in receptor signaling pathways, ossification, bone mineralization and formation, skeletal morphogenesis, and vascularization. RNA-Seq datasets comparison of normal and FHS-affected broilers with 21, 35 and 42 days of age has shown three shared DE genes (FBN2, C1QTNF8, and XYLT1) in GP among ages. Twelve genes were exclusively DE at 21 days, where 10 have already been characterized (SHISA3, FNDC1, ANGPTL7, LEPR, ENSGALG00000049529, OXTR, ENSGALG00000045154, COL16A1, RASD2, BOC, GDF10, and THSD7B). Twelve SNPs were associated with FHS (p < 0.0001). Out of those, 5 were novel and 7 were existing variants located in 7 genes (RARS, TFPI2, TTI1, MAP4K3, LINK54, and AREL1). We have shown that genes related to chondrogenesis and bone differentiation were downregulated in the GP of FHS-affected young broilers. Therefore, these findings evince that candidate genes pointed out in our study are probably related to the onset of FHS in broilers.

Comparative study of different liquid diets for dairy calves and the impact on performance and the bacterial community during diarrhea

The liquid diet composition can affect dairy calves' performance and diarrhea incidence. The effect of three liquid diets on performance, incidence of diarrhea, and microbial community during diarrhea occurrence in dairy calves were evaluated. At birth, 35 dairy calves (20 male and 15 female) were randomly assigned to one of three treatments-refrigerated whole milk (WM), acidified whole milk (AWM), and milk replacer (MR). Intake, fecal score, and rectal temperature were evaluated daily, and performance and blood parameters were evaluated weekly during the preweaning period. Fecal samples from diarrheic calves were collected, and one initial and one final sample for each episode were selected. The bacterial community was assessed by sequencing the V3-V4 region of the 16S rRNA gene on the Illumina MiSeq platform and analyzed using the DADA2 pipeline. Calves fed WM had higher body weight at weaning, average daily gain, body measurements, and concentration of blood metabolites. The AWM-fed calves had a lower rectal temperature and fever days. Moreover, the MR-fed calves had lower beta-hydroxybutyrate concentration and a higher incidence of diarrhea. The fecal bacterial community of diarrheic calves showed dissimilarity among the AWM and the other treatments. At the compositional level, we observed a higher abundance of Fusobacterium and Ruminococcus genera (AWM), Prevotella (WM), and Lactobacillus (MR). In the AWM and MR diarrheic calves' feces, we also observed some beneficial bacterial genera. The performance and incidence of diarrhea of dairy calves were influenced by the liquid diet consumed and the bacterial composition of diarrhea.

Integrative Analysis Between Genome-Wide Association Study and Expression Quantitative Trait Loci Reveals Bovine Muscle Gene Expression Regulatory Polymorphisms Associated With Intramuscular Fat and Backfat Thickness

Understanding the architecture of gene expression is fundamental to unravel the molecular mechanisms regulating complex traits in bovine, such as intramuscular fat content (IMF) and backfat thickness (BFT). These traits are economically important for the beef industry since they affect carcass and meat quality. Our main goal was to identify gene expression regulatory polymorphisms within genomic regions (QTL) associated with IMF and BFT in Nellore cattle. For that, we used RNA-Seq data from 193 Nellore steers to perform SNP calling analysis. Then, we combined the RNA-Seq SNP and a high-density SNP panel to obtain a new dataset for further genome-wide association analysis (GWAS), totaling 534,928 SNPs. GWAS was performed using the Bayes B model. Twenty-one relevant QTL were associated with our target traits. The expression quantitative trait loci (eQTL) analysis was performed using Matrix eQTL with the complete SNP dataset and 12,991 genes, revealing a total of 71,033 cis and 36,497 trans-eQTL (FDR < 0.05). Intersecting with QTL for IMF, we found 231 eQTL regulating the expression levels of 117 genes. Within those eQTL, three predicted deleterious SNPs were identified. We also identified 109 eQTL associated with BFT and affecting the expression of 54 genes. This study revealed genomic regions and regulatory SNPs associated with fat deposition in Nellore cattle. We highlight the transcription factors FOXP4, FOXO3, ZSCAN2, and EBF4, involved in lipid metabolism-related pathways. These results helped us to improve our knowledge about the genetic architecture behind important traits in cattle.

Plant genetic diversity by DNA barcoding to investigate propolis origin

Identify the botanical origins of a certain type of propolis may be challenging and time demanding, since it involves bee's behavior observation, plant resins collection and chemical analysis. Thus, this study aimed to determine the plant genetic materials in propolis from southern Brazil using the DNA barcoding to investigate their botanical origins, as well as to compare it with the phytochemical composition determined by ultra-high-performance liquid chromatography coupled with high-resolution mass spectrometry (UHPLC-HRMS) and with the pollinic profile. As principal results, non-native Populus carolinensis Moench (Salicaceae) was almost the only DNA source in some propolis samples, which coincided with the presence of flavonoids typical from poplar exudates. Conversely, other propolis samples had DNA material coming mainly from native plant species, most of them characterized to the species level, although no specific chemical markers from those plants could be identified by UHPLC-HRMS. However, pollen from several plants identified by the DNA barcoding were extracted from some propolis samples. Despite the identification of typical diterpenes, DNA material from Araucaria angustifolia (Bertol.) Kuntze (Araucariaceae), which have been indicated as a major resin source for propolis from preservation areas in southern Brazil, was found in very small abundancies, likely because bees do not drag tissue material containing DNA when collecting resin from this native species. In conclusion, DNA barcoding analysis successfully provided information about the provenance of propolis, although, depending on the plant resin sources, this information is likely to come from pollen.

Simulation of group testing scenarios can boost COVID-19 screening power

The COVID-19 has severely affected economies and health systems around the world. Mass testing could work as a powerful alternative to restrain disease dissemination, but the shortage of reagents is a limiting factor. A solution to optimize test usage relies on ‘grouping’ or ‘pooling’ strategies, which combine a set of individuals in a single reaction. To compare different group testing configurations, we developed the poolingr package, which performs an innovative hybrid in silico/in vitro approach to search for optimal testing configurations. We used 6759 viral load values, observed in 2389 positive individuals, to simulate a wide range of scenarios. We found that larger groups (>100) framed into multi-stage setups (up to six stages) could largely boost the power to detect spreaders. Although the boost was dependent on the disease prevalence, our method could point to cheaper grouping schemes to better mitigate COVID-19 dissemination through identification and quarantine recommendation for positive individuals.

EEF1A1 transcription cofactor gene polymorphism is associated with muscle gene expression and residual feed intake in Nelore cattle

Cis-acting effects of noncoding variants on gene expression and regulatory molecules constitute a significant factor for phenotypic variation in complex traits. To provide new insights into the impacts of single-nucleotide polymorphisms (SNPs) on transcription factors (TFs) and transcription cofactors (TcoF) coding genes, we carried out a multi-omic analysis to identify cis-regulatory effects of SNPs on these genes' expression in muscle and describe their association with feed efficiency-related traits in Nelore cattle. As a result, we identified one SNP, the rs137256008C > T, predicted to impact the EEF1A1 gene expression (β = 3.02; P-value = 3.51E-03) and the residual feed intake trait (β = - 3.47; P-value = 0.02). This SNP was predicted to modify transcription factor sites and overlaps with several QTL for feed efficiency traits. In addition, co-expression network analyses showed that animals containing the T allele of the rs137256008 SNP may be triggering changes in the gene network. Therefore, our analyses reinforce and contribute to a better understanding of the biological mechanisms underlying gene expression control of feed efficiency traits in bovines. The cis-regulatory SNP can be used as biomarker for feed efficiency in Nelore cattle.

The Divergent Pattern of SARS-CoV-2 Variant Predominance and Transmission Dynamics in the Brazilian Island of Ilhabela

Our effort in SARS-CoV-2 genomic surveillance in Brazil has detected the Alpha Variant of Concern with a predominance higher than 75% in the population of Ilhabela island (São Paulo State) at a time when the Gamma VOC was already predominating the mainland raised concerns for closer surveillance on this island. Therefore, we intensified the surveillance for 24 weeks by generating data from 34% of local positive cases. Our data show that the patterns of VOC predominance dynamics and infection rates were in general distinct from the mainland. We report here the first known case of Alpha predominance in a Brazilian population, a delay greater than 3 months for the Gamma to dominate the previous variants compared to the mainland, and a faster dispersion rate of Gamma and Delta VOCs compared to the mainland. Phylogenetic analysis revealed the SARS-CoV-2 transmission dynamics in Ilhabela were characterized by multiple independent introduction events of Gamma and Delta, with a few events of Alpha introduction, two of them followed by community transmission. This study evidenced the peculiar behavior of SARS-CoV-2 variants in an isolated population and brought to light the importance of specific programs for SARS-CoV-2 genomic surveillance in isolated populations.

SARS-CoV-2 epidemic in Brazil: how the displacement of variants has driven distinct epidemic waves

Brazil ranks as third in terms of total number of reported SARS-CoV-2 cases globally. The COVID-19 epidemic in Brazil was characterised by the co-circulation of multiple variants as a consequence of multiple independent introduction events occurring through time. Here, we describe the SARS-CoV-2 variants that are currently circulating and co-circulating in the country, with the aim to highlight which variants have driven the different epidemic waves. For this purpose, we retrieved metadata information of Coronavirus sequences collected in Brazil and available at the GISAID database. SARS-CoV-2 lineages have been identified along with eleven variants, labelled as VOCs (Alpha, Gamma, Beta, Delta and Omicron) VOIs (Lambda and Mu) VUMs (B.1.1.318) and FMVs (Zeta, Eta and B.1.1.519). Here we show that, in the Brazilian context, after 24 months of sustained transmission and evolution of SARS-CoV-2, local variants (among them the B.1.1.28 and B.1.1.33) were displaced by recently introduced VOCs firstly with the Gamma, followed by Delta and more recently Omicron. The rapid spread of some of those VOCs (such as Gamma and Omicron) was also mirror by a large increase in the number of cases and deaths in the country. This in turn reinforces that, due to the emergence of variants that appear to induce a substantial evasion against neutralizing antibody response, it is important to strengthen genomic effort within the country and how vaccination still remains a critical process to protect the vulnerable population, still at risk of infection and death.

Differential Gene Expression Associated with Soybean Oil Level in the Diet of Pigs

The aim of this study was to identify the differentially expressed genes (DEG) from the skeletal muscle and liver samples of animal models for metabolic diseases in humans. To perform the study, the fatty acid (FA) profile and RNA sequencing (RNA-Seq) data of 35 samples of liver tissue (SOY1.5, n = 17 and SOY3.0, n = 18) and 36 samples of skeletal muscle (SOY1.5, n = 18 and SOY3.0, n = 18) of Large White pigs were analyzed. The FA profile of the tissues was modified by the diet, mainly those related to monounsaturated (MUFA) and polyunsaturated (PUFA) FA. The skeletal muscle transcriptome analysis revealed 45 DEG (FDR 10%), and the functional enrichment analysis identified network maps related to inflammation, immune processes, and pathways associated with oxidative stress, type 2 diabetes, and metabolic dysfunction. For the liver tissue, the transcriptome profile analysis revealed 281 DEG, which participate in network maps related to neurodegenerative diseases. With this nutrigenomics study, we verified that different levels of soybean oil in the pig diet, an animal model for metabolic diseases in humans, affected the transcriptome profile of skeletal muscle and liver tissue. These findings may help to better understand the biological mechanisms that can be modulated by the diet.

Land use and roles of soil bacterial community in the dissipation of atrazine

Atrazine (ATZ) is one of the most widely used herbicides in the world even though it is classified as a carcinogenic endocrine disruptor. This study focused on how land use (grazing versus cultivation in parallel soils, the latter under no-till with a seven-year history of ATZ application) and bacterial community diversity affected ATZ dissipation. Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, Acidobacteria, Verrucomicrobia, Planctomycetes, and Gemmatimonadetes were the dominant phyla in both soils. The mineralization of ATZ was much higher in soils under cultivation up to the onset of moderate diversity depletion (dilution =10^-3), corresponding to 44-52% of the amount applied (< 5% in the grazed soil). This was attributed to the higher diversity and complexity of the soils´ bacterial communities which consist of microbial groups that were more adapted as a result of previous exposure to ATZ. In these cases, ATZ dissipation was attributed mainly to mineralization (DT₅₀ = 4-11 d). However, formation of non-extractable ATZ residues was exceptionally important in the other cases (DT₅₀ = 17-44 d). The cultivated soils also presented a higher number of bacterial genera correlated with ATZ dissipation, in which Acidothermus, Aquicela, Arenimonas, Candidatus_Koribacter, Hirschia, MND1, Nitrospira, Occallatibacter, OM27_clade, and Ralstonia are suggested as potential ATZ-degraders. Finally, ATZ dissipation was mostly associated with an abundance of microbial functions related to energy supply and N-metabolism, suggesting co-metabolism is its first biodegradation step.

Effect of dietary soybean oil inclusion on liver-related transcription factors in a pig model for metabolic diseases

Dietary fatty acids (FA) are components of the lipids, which contribute to membrane structure, energy input, and biological functions related to cellular signaling and transcriptome regulation. However, the consumers still associate dietary FA with fat deposition and increased occurrence of metabolic diseases such as obesity and atherosclerosis. Previous studies already demonstrated that some fatty acids are linked with inflammatory response, preventing metabolic diseases. To better understand the role of dietary FA on metabolic diseases, for the first time, a study to identify key transcription factors (TF) involved in lipid metabolism and inflammatory response by transcriptome analysis from liver samples of animal models was performed. The key TF were identified by functional enrichment analysis from the list of differentially expressed genes identified in liver samples between 35 pigs fed with 1.5% or 3.0% soybean oil. The functional enrichment analysis detected TF linked to lipid homeostasis and inflammatory response, such as RXRA, EGFR, and SREBP2 precursor. These findings demonstrated that key TF related to lipid metabolism could be modulated by dietary inclusion of soybean oil. It could contribute to nutrigenomics research field that aims to elucidate dietary interventions in animal and human health, as well as to drive food technology and science.

DNA methylation may affect beef tenderness through signal transduction in Bos indicus

BACKGROUND

Beef tenderness is a complex trait of economic importance for the beef industry. Understanding the epigenetic mechanisms underlying this trait may help improve the accuracy of breeding programs. However, little is known about epigenetic effects on Bos taurus muscle and their implications in tenderness, and no studies have been conducted in Bos indicus.

RESULTS

Comparing methylation profile of Bos indicus skeletal muscle with contrasting beef tenderness at 14 days after slaughter, we identified differentially methylated cytosines and regions associated with this trait. Interestingly, muscle that became tender beef had higher levels of hypermethylation compared to the tough group. Enrichment analysis of predicted target genes suggested that differences in methylation between tender and tough beef may affect signal transduction pathways, among which G protein signaling was a key pathway. In addition, different methylation levels were found associated with expression levels of GNAS, PDE4B, EPCAM and EBF3 genes. The differentially methylated elements correlated with EBF3 and GNAS genes overlapped CpG islands and regulatory elements. GNAS, a complex imprinted gene, has a key role on G protein signaling pathways. Moreover, both G protein signaling pathway and the EBF3 gene regulate muscle homeostasis, relaxation, and muscle cell-specificity.

CONCLUSIONS

We present differentially methylated loci that may be of interest to decipher the epigenetic mechanisms affecting tenderness. Supported by the previous knowledge about regulatory elements and gene function, the methylation data suggests EBF3 and GNAS as potential candidate genes and G protein signaling as potential candidate pathway associated with beef tenderness via methylation.

Genomic epidemiology reveals the impact of national and international restrictions measures on the SARS-CoV-2 epidemic in Brazil

Brazil has experienced some of the highest numbers of COVID-19 cases and deaths globally and from May 2021 made Latin America a pandemic epicenter. Although SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, important gaps remain in our understanding of virus transmission dynamics at the national scale. Here, we describe the genomic epidemiology of SARS-CoV-2 using near-full genomes sampled from 27 Brazilian states and a bordering country - Paraguay. We show that the early stage of the pandemic in Brazil was characterised by the co-circulation of multiple viral lineages, linked to multiple importations predominantly from Europe, and subsequently characterized by large local transmission clusters. As the epidemic progressed under an absence of effective restriction measures, there was a local emergence and onward international spread of Variants of Concern (VOC) and Variants Under Monitoring (VUM), including Gamma (P.1) and Zeta (P.2). In addition, we provide a preliminary genomic overview of the epidemic in Paraguay, showing evidence of importation from Brazil. These data reinforce the usefulness and need for the implementation of widespread genomic surveillance in South America as a toolkit for pandemic monitoring that provides a means to follow the real-time spread of emerging SARS-CoV-2 variants with possible implications for public health and immunization strategies.

Replacement of the Gamma by the Delta variant in Brazil: Impact of lineage displacement on the ongoing pandemic

The coronavirus disease 2019 (COVID-19) epidemic in Brazil was driven mainly by the spread of Gamma (P.1), a locally emerged variant of concern (VOC) that was first detected in early January 2021. This variant was estimated to be responsible for more than 96 per cent of cases reported between January and June 2021, being associated with increased transmissibility and disease severity, a reduction in neutralization antibodies and effectiveness of treatments or vaccines, and diagnostic detection failure. Here we show that, following several importations predominantly from the USA, the Delta variant rapidly replaced Gamma after July 2021. However, in contrast to what was seen in other countries, the rapid spread of Delta did not lead to a large increase in the number of cases and deaths reported in Brazil. We suggest that this was likely due to the relatively successful early vaccination campaign coupled with natural immunity acquired following prior infection with Gamma. Our data reinforce reports of the increased transmissibility of the Delta variant and, considering the increasing concern due to the recently identified Omicron variant, argues for the necessity to strengthen genomic monitoring on a national level to quickly detect the emergence and spread of other VOCs that might threaten global health.

Transcriptomic characterization of the molecular mechanisms induced by RGMa during skeletal muscle nuclei accretion and hypertrophy

Background

The repulsive guidance molecule a (RGMa) is a GPI-anchor axon guidance molecule first found to play important roles during neuronal development. RGMa expression patterns and signaling pathways via Neogenin and/or as BMP coreceptors indicated that this axon guidance molecule could also be working in other processes and diseases, including during myogenesis. Previous works from our research group have consistently shown that RGMa is expressed in skeletal muscle cells and that its overexpression induces both nuclei accretion and hypertrophy in muscle cell lineages. However, the cellular components and molecular mechanisms induced by RGMa during the differentiation of skeletal muscle cells are poorly understood. In this work, the global transcription expression profile of RGMa-treated C2C12 myoblasts during the differentiation stage, obtained by RNA-seq, were reported.

Results

RGMa treatment could modulate the expression pattern of 2,195 transcripts in C2C12 skeletal muscle, with 943 upregulated and 1,252 downregulated. Among them, RGMa interfered with the expression of several RNA types, including categories related to the regulation of RNA splicing and degradation. The data also suggested that nuclei accretion induced by RGMa could be due to their capacity to induce the expression of transcripts related to ‘adherens junsctions’ and ‘extracellular-cell adhesion’, while RGMa effects on muscle hypertrophy might be due to (i) the activation of the mTOR-Akt independent axis and (ii) the regulation of the expression of transcripts related to atrophy. Finally, RGMa induced the expression of transcripts that encode skeletal muscle structural proteins, especially from sarcolemma and also those associated with striated muscle cell differentiation.

Conclusions

These results provide comprehensive knowledge of skeletal muscle transcript changes and pathways in response to RGMa.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08396-w.

SARS-COV-2 GENOMIC MONITORING IN THE STATE OF SÃO PAULO UNVEILS TWO EMERGING AY.43 SUBLINEAGES

Delta VOC is highly diverse with more than 120 sublineages already described as of November 30, 2021. In this study, through active monitoring of circulating severe acute respiratory syndrome coronavirus‐2 (SARS‐CoV‐2) variants in the state of São Paulo, southeast Brazil, we identified two emerging sublineages from the ancestral AY.43 strain which were classified as AY.43.1 and AY.43.2. These sublineages were defined by the following characteristic nonsynonymous mutations ORF1ab:A4133V and ORF3a:T14I for the AY.43.1 and ORF1ab:G1155C for the AY.43.2 and our analysis reveals that they might have a likely‐Brazilian origin. Much is still unknown regarding their dissemination in the state of São Paulo and Brazil as well as their potential impact on the ongoing vaccination process. However, the results obtained in this study reinforce the importance of genomic surveillance activity for timely identification of emerging SARS‐CoV‐2 variants which can impact the ongoing SARS‐CoV‐2 vaccination and public health policies.

GBS-MeDIP: A protocol for parallel identification of genetic and epigenetic variation in the same reduced fraction of genomes across individuals

The GBS-MeDIP protocol combines two previously described techniques, Genotype-by-Sequencing (GBS) and Methylated-DNA-Immunoprecipitation (MeDIP). Our method allows for parallel and cost-efficient interrogation of genetic and methylomic variants in the DNA of many reduced genomes, taking advantage of the barcoding of DNA samples performed in the GBS and the subsequent creation of DNA pools, then used as an input for the MeDIP. The GBS-MeDIP is particularly suitable to identify genetic and methylomic biomarkers when resources for whole genome interrogation are lacking.

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Our protocol combines two well-known techniques, GBS and MeDIP.

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The GBS-MeDIP allows for parallel interrogation of genetic/methylomic variants.

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Allows for cost-efficient analysis of reduced genomes from multiple individuals.

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Ideal for the identification of genetic and/or methylomic markers at reduced cost.

CNV detection and their association with growth, efficiency and carcass traits in Santa Inês sheep

Copy number variations (CNV) are an important source of genetic variation. CNV has been increasingly studied and frequently associated with diseases and productive traits in livestock animals. However, CNV-based genome-wide association studies (GWAS) in Santa Inês sheep, one of the principal sheep breeds in Brazil, have not yet been reported. Thus, the aim of this study was to investigate the association between CNV and growth, efficiency and carcass traits in sheep. The Illumina OvineSNP50 BeadChip array was used to detect CNV in 491 Santa Inês individuals. Then, CNV-based GWAS was performed with a linear mixed model approach considering a genomic relationship matrix, for ten traits: (1) growth: body weight at three (W3) and six (W6) months of age; (2) efficiency: residual feed intake (RFI) and feed efficiency (FE) and (3) carcass: external carcass length (ECL), leg length (LL), carcass yield (CY), commercial cuts weight (CCW), loin eye area (LEA) and subcutaneous fat thickness (SFT). We identified 1,167 autosomal CNV in 438 sheep, with 294 non-redundant CNV, ranging from 21.8 to 861.9 kb, merged into 216 distinct copy number variation regions (CNVRs). One significant CNV segment (p_FDR -value<0.05) in OAR3 was associated with CY, while another significant CNV in OAR6 was associated with RFI. Additionally, another 5 CNV segments were considered relevant for investigation in the future studies. The significant segments overlapped 4 QTLs and spanned 8 genes, including the SPAST, TGFA and ADGRL3 genes, involved in cell differentiation and energy metabolism. Therefore, the results of the present study increase knowledge about CNV in sheep, their possible impacts on productive traits, and provide information for future investigations, being especially useful for those interested in structural variations in the sheep genome.

Genetic effects of heat stress on milk fatty acids in a Brazilian Holstein cattle

The present study aimed to estimate covariance components of milk fatty acids (FA) and to compare the genomic estimated breeding values under general and heat-stress effects. Data consisted of 38,762 test-day records from 6,344 Holstein cows obtained from May 2012 through January 2018 on 4 dairy herds from Brazil. Single-trait repeatability test-day models with random regressions as a function of temperature-humidity index values were used for genetic analyses. The models included contemporary groups, parity order (1-6), and days in milk classes as fixed effects, and general and thermotolerance additive genetic and permanent environmental as random effects. Notably, differences in heritability estimates between environments (general and heat stress) increased (0.03 to 0.06) for unsaturated FA traits, such as unsaturated, monounsaturated, and polyunsaturated, at higher heat-stress levels. In contrast, heritability estimated between environments for saturated FA traits, including saturated FA, palmitic acid (C16:0), and stearic acid (C18:0) did not observe significant differences between environments. In addition, our study revealed negative genetic correlations between general and heat-stress additive genetic effects (antagonistic effect) for the saturated FA, C16:0, C18:0, and C18:1, which ranged from -0.007 to -0.32. Spearman's ranking correlation between genomic estimated breeding values ranged from -0.27 to 0.99. Results indicated a moderate to strong interaction of genotype by the environment for most FA traits comparing a heat-stress environment with thermoneutral conditions. Our findings point out novel opportunities to explore the use of FA milk profile and heat-stress models.

Genomic monitoring of the SARS-CoV-2 B1.1.7 (WHO VOC Alpha) in the Sao Paulo state, Brazil

The SARS-CoV-2 alpha VOC (also known as lineage B.1.1.7) initially described in the autumn, 2020 in UK, rapidly became the dominant lineage across much of Europe. Despite multiple studies reporting molecular evidence suggestive of its circulation in Brazil, much is still unknown about its genomic diversity in the state of São Paulo, the main Brazilian economic and transportation hub. To get more insight regarding its transmission dynamics into the State we performed phylogenetic analysis on all alpha VOC strains obtained between February and August 2021 from the Sao Paulo state Network for Pandemic Alert of Emerging SARS-CoV-2 variants. The performed phylogenetic analysis showed that most of the alpha VOC genomes were interspersed with viral strains sampled from different Brazilian states and other countries suggesting that multiple independent Alpha VOC introductions from Brazil and overseas have occurred in the São Paulo State over time. Nevertheless, large monophyletic clusters were also observed especially from the Central-West part of the São Paulo State (the city of Bauru) and the metropolitan region of the São Paulo city. Our results highlight the Alpha VOC molecular epidemiology in the São Paulo state and reinforce the need for continued genomic surveillance strategies for the real-time monitoring of potential emerging SARS-CoV-2 variants during the ever-growing vaccination process.

Liquid Biopsy as a Diagnostic and Prognostic Tool for Women and Female Dogs with Breast Cancer

INTRODUCTION

Breast cancer (BC) is the malignant neoplasm with the highest mortality rate in women and female dogs are good models to study BC.

OBJECTIVE

We investigated the efficacy of liquid biopsy to detect gene mutations in the diagnosis and follow-up of women and female dogs with BC.

MATERIALS AND METHODS

In this study, 57 and 37 BC samples were collected from women and female dogs, respectively. After core biopsy and plasma samples were collected, the DNA and ctDNA of the tumor fragments and plasma were processed for next generation sequencing (NGS) assay. After preprocessing of the data, they were submitted to the Genome Analysis ToolKit (GATK).

RESULTS

In women, 1788 variants were identified in tumor fragments and 221 variants in plasma; 66 variants were simultaneously detected in tumors and plasma. Conversely, in female dogs, 1430 variants were found in plasma and 695 variants in tumor fragments; 59 variants were simultaneously identified in tumors and plasma. The most frequently mutated genes in the tumor fragments of women were USH2A, ATM, and IGF2R; in female dogs, they were USH2A, BRCA2, and RRM2. Plasma of women showed the most frequent genetic variations in the MAP3K1, BRCA1, and GRB7 genes, whereas plasma from female dogs had variations in the NF1, ERBB2, and KRT17 genes. Mutations in the AKT1, PIK3CA, and BRIP genes were associated with tumor recurrence, with a highly pathogenic variant in PIK3CA being particularly prominent. We also detected a gain-of-function mutation in the GRB7, MAP3K1, and MLH1 genes.

CONCLUSION

Liquid biopsy is useful to identify specific genetic variations at the beginning of BC manifestation and may be accompanied over the entire follow-up period, thereby supporting the clinicians in refining interventions.

SAP30 Gene Is a Probable Regulator of Muscle Hypertrophy in Chickens

Animals with muscle hypertrophy phenotype are targeted by the broiler industry to increase the meat production and the quality of the final product. Studies characterizing the molecular machinery involved with these processes, such as quantitative trait loci studies, have been carried out identifying several candidate genes related to this trait; however, validation studies of these candidate genes in cell culture is scarce. The aim of this study was to evaluate SAP30 as a candidate gene for muscle development and to validate its function in cell culture in vitro. The SAP30 gene was downregulated in C2C12 muscle cell culture using siRNA technology to evaluate its impact on morphometric traits and gene expression by RNA-seq analysis. Modulation of SAP30 expression increased C2C12 myotube area, indicating a role in muscle hypertrophy. RNA-seq analysis identified several upregulated genes annotated in muscle development in treated cells (SAP30-knockdown), corroborating the role of SAP30 gene in muscle development regulation. Here, we provide experimental evidence of the involvement of SAP30 gene as a regulator of muscle cell hypertrophy.

Does algae β-glucan affect the fecal bacteriome in dairy calves?

β-glucans has been reported to be associated with many health-promoting and improvements in animal performance, however, information about their effects on the bacterial community remains unknown. This study aimed to investigate how the addition of β-glucans can affect the fecal bacterial community with possible consequences on animal growth and health. For this, newborn Holstein calves (n = 14) were individually housed in tropical shelters and blocked according to sex, date, and weight at birth and randomly assigned to one of the following treatments: (1) Control: milk replacer (14% solids, 24% CP, 18.5% fat); (2) β-glucans: milk replacer supplemented with β-glucans (2 g/d). All calves were bucket fed 6 L/d of milk replacer and received water and starter concentrate ad libitum starting on d 2. To evaluate the bacteriome, fecal samples were collected at weeks 1, 2, 4, and 8. The bacterial community was assessed through sequencing of the V3-V4 region of the 16S rRNA gene on the Illumina MiSeq platform and analyzed using the DADA2 pipeline. No differences for Shannon and Chao1 indexes were observed for treatments, but both indexes increased with age (P < 0.001). There were dissimilarities in the structure of the bacterial community during the pre-weaning period (P = 0.01). In a deeper taxonomic level, Collinsella (Actinobacteriota), Prevotella (Bacteroidota), and Lactobacillus (Firmicutes) were the most abundant genera (9.84, 9.54, and 8.82% of the sequences, respectively). β-glucans promoted a higher abundance of Alloprevotella and Holdemanella, which may indicate a beneficial effect of supplementation on dairy calves. The bacterial community was highly correlated with the fecal score at weeks 1 and 2 and with starter concentrate intake at week 8. In conclusion, algae β-glucan supplementation could be beneficial to fecal bacteriome and consequently to the health and performance of dairy calves.

Genome assembly and annotation of the tambaqui (Colossoma macropomum): an emblematic fish of the Amazon River Basin

Colossoma macropomum, known as "tambaqui", is the largest Characiformes fish in the Amazon River Basin and a leading species in Brazilian aquaculture and fisheries. Good quality meat and excellent adaptability to culture systems are some of its remarkable farming features. To support studies into the genetics and genomics of the tambaqui, we have produced the first high-quality genome for the species. We combined Illumina and PacBio sequencing technologies to generate a reference genome, assembled with 39× coverage of long reads and polished to a consensus quality value (QV) of 36 with 130× coverage of short reads. The genome was assembled into 1269 scaffolds (a total of 1,221,847,006 bases), with a scaffold N50 size of 40 Mb, where 93% of all assembled bases were placed in the largest 54 scaffolds corresponding to the diploid karyotype of the tambaqui. Furthermore, the NCBI Annotation Pipeline annotated genes, pseudogenes, and non-coding transcripts using the RefSeq database as evidence, guaranteeing a high-quality annotation. A Genome Data Viewer for the tambaqui was produced, which will benefit groups interested in exploring the unique genomic features of the species. The availability of a highly accurate genome assembly for tambaqui provides the foundation for the discovery of novel ecological and evolutionary insights, and is a helpful resource for aquaculture.