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Understanding what people believe the causes of autism to be has implications for experiences of familial guilt and stigma. Using a qualitative approach, we investigated how Brazilian healthcare professionals, parents of young and adult autistic people and young and adult autistic people consider the origins of autism and the interaction between the biological and social environment concerning the challenges autistic people encounter. Eight health professionals who assist autistic people, five young autistic people, six family members of young autistic people, five autistic adults, and four parents of autistic adults participated in the research. After analysis, two major coding themes emerged from the interviews: (T1) Perceived origins of autism: genetic, environmental, or both, (T2) The impact of the structured family environment. Our respondents consider autism in Brazil strongly related to genetic origins and little to environmental and social origins. At the same time, the context of the structured social and family environment can influence challenges and opportunities for autistic people. [ABSTRACT FROM AUTHOR]

Colistin resistance is a global health concern, with antibiotics being the last treatment for Gram-negative bacteria infections. We aimed to identify colistin-resistant enterobacteria on environmental surfaces of a long-term care facility (LTCF) for the elderly in southern Brazil. Samples were collected and screened on MacConkey agar plus colistin, followed by API20E identification and PCR. Two isolates were founded and identified as Klebsiella pneumoniae and Providencia stuartii harboring mcr-1 gene with MICs > 128 µg mL−1 for colistin. This is the first isolation of microorganisms resistant to colistin in the environment of a LTCF for the elderly in south Brazil, urging monitoring programs to reduce environmental contamination by multiresistant microorganisms. [ABSTRACT FROM AUTHOR]

Wheat is a globally important crop, and its production is critically challenged by heat stress. To understand the heat tolerance mechanism at grain-filling stage in wheat, two genotypes, W156 (tolerant) and Brazil 32 (susceptible) were evaluated for their morphological responses and expressions of TaAP2/ERF super-family transcription factor genes under heat stress (at 37/27 °C) at 11 days and 13 days post-anthesis. The W156 showed significantly higher thousand kernel weight (TKW), chlorophyll fluorescence (Fv/Fm) and delayed senescence of flag leaf and exposed peduncle. Twenty-two differentially expressed genes (DEGs) were selected from in silico expression analysis of 630 TaAP2/ERF genes under abiotic stress and their RT-qPCR expression validation identified twenty major DEGs responsive to heat stress. Co-expression network analysis of these DEGs identified hub TF genes including TraesCS1A02G221900, TraesCS6D02G324200, TraesCS6B02G331000, TraesCS4D02G298600, TraesCS5B02G193200, and TraesCS1A02G058400. Gene Ontology analysis and Gene Set Enrichment Analysis further revealed that 16 (80%) out of the 20 DEGs were involved in the ethylene-activated signaling pathway. Those DEGs involved in ethylene signaling pathway were further validated in an additional pair of contrasting genotypes (Perenjori and Yitpi). Therefore, heat tolerance regulated by TaAP2/ERF genes at grain filling stage of wheat may be mainly through ethylene signaling pathway while maintaining seed development under heat stress. [ABSTRACT FROM AUTHOR]

Introduction: Lynch syndrome (LS) is an inherited cancer predisposition syndrome characterized by a high risk of colorectal and extracolonic tumors. Germline pathogenic variants (GPV) in the PMS2 gene are associated with <15% of all cases. The PMS2CL pseudogene presents high homology with PMS2, challenging molecular diagnosis by next-generation sequencing (NGS). Due to the high methodological complexity required to distinguish variants between PMS2 and PMS2CL, most laboratories do not clearly report the origin of this molecular finding. Objective: The aim of this study was to confirm the GPVs detected by NGS in regions of high homology segments of the PMS2 gene in a Brazilian sample. Methods: An orthogonal and gold standard long-range PCR (LR-PCR) methodology to separate variants detected in the PMS2 gene from those detected in the pseudogene. Results: A total of 74 samples with a PMS2 GPV detected by NGS in exons with high homology with PMS2CL pseudogene were evaluated. The most common was NM_000535.6:c.2182_2184delinsG, which was previously described as deleterious mutation in a study of African-American patients with LS and has been widely reported by laboratories as a pathogenic variant associated with the LS phenotype. Of all GPVs identified, only 6.8% were confirmed by LR-PCR. Conversely, more than 90% of GPV were not confirmed after LR-PCR, and the diagnosis of LS was ruled out by molecular mechanisms associated with PMS2. Conclusion: In conclusion, the use of LR-PCR was demonstrated to be a reliable approach for accurate molecular analysis of PMS2 variants in segments with high homology with PMS2CL. We highlight that our laboratory is a pioneer in routine diagnostic complementation of the PMS2 gene in Brazil, directly contributing to a more assertive molecular diagnosis and adequate genetic counseling for these patients and their families. [ABSTRACT FROM AUTHOR]

The drug-resistant temporal lobe epilepsy (TLE) has recently been associated with single nucleotide variants (SNVs) in microRNA(miR)-146a (MIR-146A) (rs2910164) and Sodium Voltage-Gated Channel Alpha Subunit 1 (SCN1A) (rs2298771 and rs3812718) genes. Moreover, no studies have shown an association between these SNVs and susceptibility to drug-resistant and drug-responsive TLE in Brazil. Thus, deoxyribonucleic acid (DNA) samples from 120 patients with TLE (55 drug-responsive and 65 drug-resistant) were evaluated by real-time polymerase chain reaction (RT-PCR). A total of 1171 healthy blood donor individuals from the Online Archive of Brazilian Mutations (ABraOM, from Portuguese Arquivo Brasileiro On-line de Mutações), a repository containing genomic variants of the Brazilian population, were added as a control population for the studied SNVs. MIR-146A and SCN1A relative expression was performed by quantitative RT-PCR (qRT-PCR). The statistical analysis protocol was performed using an alpha error of 0.05. TLE patient samples and ABraOM control samples were in Hardy–Weinberg equilibrium for all studied SNVs. For rs2910164, the frequencies of the homozygous genotype (CC) (15.00% vs. 9.65%) and C allele (37.80% vs. 29.97%) were superior in patients with TLE compared to controls with a higher risk for TLE disease [odds ratio (OR) = 1.89 (95% confidence interval (95%CI) = 1.06–3.37); OR = 1.38 (95%CI = 1.04–1.82), respectively]. Drug-responsive patients also presented higher frequencies of the CC genotype [21.81% vs. 9.65%; OR = 2.58 (95%CI = 1.25–5.30)] and C allele [39.09% vs. 29.97%; OR = 1.50 (95%CI = 1.01–2.22)] compared to controls. For rs2298771, the frequency of the heterozygous genotype (AG) (51.67% vs. 40.40%) was superior in patients with TLE compared to controls with a higher risk for TLE disease [OR = 2.42 (95%CI = 1.08–5.41)]. Drug-resistant patients presented a higher AG frequency [56.92% vs. 40.40%; OR = 3.36 (95%CI = 1.04–17.30)] compared to the control group. For rs3812718, the prevalence of genotypes and alleles were similar in both studied groups. The MIR-146A relative expression level was lower in drug-resistant compared to drug-responsive patients for GC (1.6 vs. 0.1, p-value = 0.049) and CC (1.8 vs. 0.6, p-value = 0.039). Also, the SCN1A relative expression levels in samples from TLE patients were significantly higher in AG [2.09 vs. 1.10, p-value = 0.038] and GG (3.19 vs. 1.10, p-value < 0.001) compared to the AA genotype. In conclusion, the rs2910164-CC and rs2298771-AG genotypes are exerting significant risk influence, respectively, on responsive disease and resistant disease, probably due to an upregulated nuclear factor kappa B (NF-kB) and SCN1A loss of function. [ABSTRACT FROM AUTHOR]

Background: Infectious illnesses are a serious health concern in Indonesia. Widespread use of self-medication by the community increases the risk of developing multi-drug resistant (MDR) bacteria. This study assessed the potential of sappan wood as an inhibitor of extended-spectrum beta-lactamase (ESBL) encoded by blaSHV, blaTEM and blaCTX-M genes. Method: In silico testing was conducted to develop an effective and economical starting strategy. Thereby, this study significantly advances the development of novel treatments to combat antibiotic resistance. Using clavulanic acid as the benchmark medicine, the potency of the beta-lactamase inhibitor brazilein was predicted. Using the Molegro Virtual Docker computer tool, docking was performed to estimate the chemical and physical properties of the compounds, as well as the biological activity of brazilein toward the required receptor. The receptors used were SHV-1 beta-lactamase, PDB code: 2H0T; TEM-1 beta-lactamase, PDB code: 4OQG and CTX-M-14 beta-lactamase, PDB code: 6VHS. Data analysis was performed by comparing the binding energies of the docking results between the ligands and the target receptor. The more stable the bond that formed between the ligand and the target receptor, the lower the bond energy. Results: The in silico test results on the blaSHV gene were as follows: binding energy of ligand MA4&lowbar;400[A] = -100.699, brazilein = -82.206, clavulanic acid = -79.3704; in the blaTEM gene: ligand bond energy 2UL&lowbar;301[B] = -107.681, brazilein = -82.0296, clavulanic acid = -103.3; in the blaCTX-M gene: X57&lowbar;301[A] ligand bond energy = -86.6197, and brazilein = -88.1586, clavulanic acid = -101.933. Conclusion: The findings of this study demonstrate the significant potential of brazilein sappan wood to block the beta-lactamase activity of blaCTX-M. [ABSTRACT FROM AUTHOR]

Pseudomonas aeruginosa is commonly associated with the ability to acquire antimicrobial resistance. The surveillance of resistance genes in various environmental matrices has gained prominence in recent years, being seen as a potential threat to public health. The objective of this study was to investigate genes encoding metallo-beta-lactamases (MBLs), which confer resistance to carbapenems, in wastewater. Fifteen isolates of P. aeruginosa were collected for five months from samples obtained from a municipal wastewater treatment plant in Rio Grande do Sul. These isolates were subjected to disk diffusion testing using 10 different antimicrobials. Phenotypic enzymatic tests for MBLs were conducted, and positive isolates underwent DNA extraction and gene detection using the polymerase chain reaction. The resistance rate to ceftazidime was 100%, cefepime 73.3%, piperacillin-tazobactam 66.67%, imipenem 53.30%, levofloxacin 46.67%, tobramycin 40%, and ciprofloxacin and amikacin 13.33%. Both meropenem and aztreonam resistances were rare accounting for 6.60% of the tested isolates. Among these isolates, 20% were classified as multidrug-resistant and were found to carry the blaNDM and blaSPM genes. The results suggest that evaluating resistance genes in bacteria from urban raw sewage can provide data that assist in surveillance, as this environment can stimulate increased bacterial resistance. [ABSTRACT FROM AUTHOR]

Background Brazil ranks second in the absolute number of transplants. However, the supply remains insufficient to meet the demands, resulting in a lengthy waitlist. This study aimed to analyze whether the frequency of human leukocyte antigen (HLA) and the value of calculated panel reactive antibody (cPRA) would influence the waiting time for kidney transplantation. Methods The HLA-A, single bondB, and -DRB1 frequencies and the cPRA value were analyzed in 11,186 kidney transplant candidates included in the waitlist from 2006 to 2016. Results The most frequent alleles were HLA-A*02, HLA-B*35, and HLA-DRB1*13. The overall mean length of stay on the list was 986 ± 1001 days. The mean waiting time for the three most frequent alleles of the HLA-A and single bondB loci showed no significant difference when compared with the least frequent alleles; however, for the HLA-DRB1 locus, the most frequent alleles showed a shorter waiting time. In the association between HLA and PRA, the average length of stay on the list increased according to the candidate's degree of sensitization, regardless of the analyzed HLA frequency. Conclusion The length of stay on the waitlist is influenced by the frequency of the HLA alleles of the DRB1 locus and the degree of sensitization. [ABSTRACT FROM AUTHOR]

Microcephaly presents heterogeneous genetic etiology linked to several neurodevelopmental disorders (NDD). Copy number variants (CNVs) are a causal mechanism of microcephaly whose investigation is a crucial step for unraveling its molecular basis. Our purpose was to investigate the burden of rare CNVs in microcephalic individuals and to review genes and CNV syndromes associated with microcephaly. We performed chromosomal microarray analysis (CMA) in 185 Brazilian patients with microcephaly and evaluated microcephalic patients carrying < 200 kb CNVs documented in the DECIPHER database. Additionally, we reviewed known genes and CNV syndromes causally linked to microcephaly through the PubMed, OMIM, DECIPHER, and ClinGen databases. Rare clinically relevant CNVs were detected in 39 out of the 185 Brazilian patients investigated by CMA (21%). In 31 among the 60 DECIPHER patients carrying < 200 kb CNVs, at least one known microcephaly gene was observed. Overall, four gene sets implicated in microcephaly were disclosed: known microcephaly genes; genes with supporting evidence of association with microcephaly; known macrocephaly genes; and novel candidates, including OTUD7A, BBC3, CNTN6, and NAA15. In the review, we compiled 957 known microcephaly genes and 58 genomic CNV loci, comprising 13 duplications and 50 deletions, which have already been associated with clinical findings including microcephaly. We reviewed genes and CNV syndromes previously associated with microcephaly, reinforced the high CMA diagnostic yield for this condition, pinpointed novel candidate loci linked to microcephaly deserving further evaluation, and provided a useful resource for future research on the field of neurodevelopment. [ABSTRACT FROM AUTHOR]

Fusarium wilt caused by Fusarium oxysporum f. sp. cubense (Foc) is one of the most destructive diseases in banana farming worldwide. Knowledge of the factors of genetic diversity and virulence of the pathogen contributes to the development of resistant cultivars and management strategies based on exclusion. In this study, phenotypic traits such as virulence and aggressiveness in a sample of 52 Foc isolates were analyzed and their relationship to the presence of putative effectors of gene SIX (Secreted in Xylem) pathogenicity homologs was verified. The similarity matrix revealed three isolates that were closest to the standard Foc race 1 strain. Isolates 229A and 218A were selected according to their aggressiveness profile in 'Grand Naine' and 'Prata-Anã', respectively, to replace the standard isolate of race 1 in the resistance screening process carried out by the breeding program. Two homologs of the SIX8 gene, SIX8a and SIX8b, are present in isolates of Foc from Brazil, and the SIX8b gene correlates with avirulence in the cultivar 'Grand Naine' (Cavendish). These results are important to support the banana genetic breeding program by identifying sources of resistance to Foc and contributing to the establishment of the function of SIX effector proteins. [ABSTRACT FROM AUTHOR]

For the purpose of understanding the molecular processes triggered during callus formation in macaw palm, the expression of seven genes potentially involved in this process, identified in previous studies and from the literature, was investigated by RT-qPCR. In addition, in situ hybridization of the SERK gene was performed. Leaf tissues from adult plants from two macaw palm accession were inoculated in a medium combined with Picloram at a concentration of 450 μM to induce callus. The expression analysis was performed from leaf samples from two accessions of different origins (Municipalities of Tiros, MG, and Buriti Vermelho, DF, Brazil), which are characterized as non-responsive (NR) and responsive (R), respectively. The material was collected before callus induction (0 DAI, initial day) and 120 days after callus induction (120 DAI). Genes related to development (SERK, OASA, EF1, ANN1) and stress (LEA, CAT2, and MDAR5) were evaluated. The results obtained showed that all the genes involved with the development had their expressions downregulated at 0 DAI when the accession R was compared with the accession NR. On the other hand, it was possible to observe that these genes were upregulated at 120 DAI. The LEA stress gene showed a tendency to increase expression in the NR accession, while the R accession showed decreased expression and the CAT2 and MDAR5 genes showed upregulation in both accessions. In situ hybridization showed SERK transcripts in the vascular bundles, indicating the expression of SERK in this region, in addition to its expression in calluses. The results obtained in this study support our hypothesis that the regulation of genes involved in the control of oxidative stress and development is crucial for the formation of calluses in macaw palm. [ABSTRACT FROM AUTHOR]

Pemphigus foliaceus (PF) is an autoimmune skin blistering disease characterized by antidesmoglein-1 IgG production, with an endemic form (EPF) in Brazil. Genetic and epigenetic factors have been associated with EPF, but its etiology is still not fully understood. To evaluate the genetic association of histone (de)acetylation-related genes with EPF susceptibility, we evaluated 785 polymorphisms from 144 genes, for 227 EPF patients and 194 controls. Carriers of HDAC4_rs4852054*A were more susceptible (OR = 1.79, p = 0.0038), whereas those with GSE1_rs13339618*A (OR = 0.57, p = 0.0011) and homozygotes for PHF21A_rs4756055*A (OR = 0.39, p = 0.0006) were less susceptible to EPF. These variants were not associated with sporadic PF (SPF) in German samples of 75 SPF patients and 150 controls, possibly reflecting differences in SPF and EPF pathophysiology. We further evaluated the expression of histone (de)acetylation-related genes in CD4+ T lymphocytes, using RNAseq. In these cells, we found a higher expression of KAT2B, PHF20, and ZEB2 and lower expression of KAT14 and JAD1 in patients with active EPF without treatment compared to controls from endemic regions. The encoded proteins cause epigenetic modifications related to immune cell differentiation and cell death, possibly affecting the immune response in patients with PF. [ABSTRACT FROM AUTHOR]

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During the last decade, porcine rotavirus H was detected in the USA, Asian regions, South Africa, Brazil, and a couple of European countries. In the presented study, the virus was identified in piglets on a farrow-to-finish farm in Russia during metagenomic surveillance. Currently, it is the first identification of this species in the country. As a diagnostic method, nanopore-based metagenomic sequencing was applied. The obtained nanopore reads allowed for the assembly of 10 genome segments out of 11. The phylogenetic analysis revealed the virus belonged to the porcine cluster and had GX-P3-I3-R3-C3-M8-A7-N1-T5-E3-H3 genome constellation. Moreover, three potential new genotype groups for VP3, NSP1, and NSP3 genes were determined. Additionally, a recombination between RVH and RVC in the NSP3 gene was detected. The study provides significant information about a novel RVH strain. [ABSTRACT FROM AUTHOR]

Introduction: Several polymorphisms altering the NAT2 activity have already been identified. The geographical distribution of NAT2 variants has been extensively studied and has been demonstrated to vary significantly among different ethnic population. Here, we describe the genetic variability of human N-acetyltransferase 2 (NAT2) gene and the predominant genotype-deduced acetylation profiles of Brazilians. Methods: A total of 964 individuals, from five geographical different regions, were genotyped for NAT2 by sequencing the entire coding exon. Results: Twenty-three previously described NAT2 single nucleotide polymorphisms (SNPs) were identified, including the seven most common ones globally (c.191G>A, c.282C>T, c.341T>C, c.481C>T, c.590G>A, c.803A>G and c.857G>A). The main allelic groups were NAT2*5 (36%) and NAT2*6 (18.2%), followed to the reference allele NAT2*4 (20.4%). Combined into genotypes, the most prevalent allelic groups were NAT2*5/*5 (14.6%), NAT2*5/*6 (11.9%) and NAT2*6/*6 (6.2%). The genotype deduced NAT2 slow acetylation phenotype was predominant but showed significant variability between geographical regions. The prevalence of slow acetylation phenotype was higher in the Northeast, North and Midwest (51.3%, 45.5% and 41.5%, respectively) of the country. In the Southeast, the intermediate acetylation phenotype was the most prevalent (40.3%) and, in the South, the prevalence of rapid acetylation phenotype was significantly higher (36.7%), when compared to other Brazilian states (p < 0.0001). Comparison of the predicted acetylation profile among regions showed homogeneity among the North and Northeast but was significantly different when compared to the Southeast (p = 0.0396). The Southern region was significantly different from all other regions (p < 0.0001). Discussion: This study contributes not only to current knowledge of the NAT2 population genetic diversity in different geographical regions of Brazil, but also to the reconstruction of a more accurate phenotypic picture of NAT2 acetylator profiles in those regions. [ABSTRACT FROM AUTHOR]

Indoor residual spray (IRS), mainly employing pyrethroid insecticides, is the most common intervention for preventing malaria transmission in many regions of Latin America; the use of long-lasting insecticidal nets (LLINs) has been more limited. Knockdown resistance (kdr) is a well-characterized target-site resistance mechanism associated with pyrethroid and DDT resistance. Most mutations detected in acetylcholinesterase-1 (Ace-1) and voltage-gated sodium channel (VGSC) genes are non-synonymous, resulting in a change in amino acid, leading to the non-binding of the insecticide. In the present study, we analyzed target-site resistance in Nyssorhynchus darlingi, the primary malaria vector in the Amazon, in multiple malaria endemic localities. We screened 988 wild-caught specimens of Ny. darlingi from three localities in Amazonian Peru and four in Amazonian Brazil. Collections were conducted between 2014 and 2021. The criteria were Amazonian localities with a recent history as malaria hotspots, primary transmission by Ny. darlingi, and the use of both IRS and LLINs as interventions. Fragments of Ace-1 (456 bp) and VGSC (228 bp) were amplified, sequenced, and aligned with Ny. darlingi sequences available in GenBank. We detected only synonymous mutations in the frequently reported Ace-1 codon 280 known to confer resistance to organophosphates and carbamates, but detected three non-synonymous mutations in other regions of the gene. Similarly, no mutations linked to insecticide resistance were detected in the frequently reported codon (995) at the S6 segment of domain II of VGSC. The lack of genotypic detection of insecticide resistance mutations by sequencing the Ace-1 and VGSC genes from multiple Ny. darlingi populations in Brazil and Peru could be associated with low-intensity resistance, or possibly the main resistance mechanism is metabolic. [ABSTRACT FROM AUTHOR]

Background: Androgenetic alopecia (AGA) and alopecia areata (AA) are the most common types of non-cicatricial alopecia. Both diseases have limited effective therapeutic options and affect patient quality of life. Pharmacogenetic tests can help predict the most appropriate treatment option by evaluating the single nucleotide polymorphisms (SNPs) corresponding to genes related to alopecia. The objective of the study was to evaluate and compare selected SNPs and genes in AA and AGA patients from Romania and Brazil. Materials and Methods: We performed a retrospective study regarding the associations between AA and AGA and 45 tag SNPs of 15 genes in 287 Romanian and 882 Brazilian patients. The DNA samples were collected from oral mucosa using a swab. The SNPs were determined by the qPCR technique. Each genetic test displays the subject's genotype of the selected gene and the prediction of a successful treatment (e.g., genotype AA of the GR-alpha gene is related to a predisposition to normal sensibility to topical glucocorticoid, and, therefore, glucocorticoids should be effective). Results: The GR-alpha, GPR44-2, SULT1A1, and CRABP2 genes were statistically significantly different in Brazil compared to Romania. The SULT1A1 activity that predicts the response to minoxidil treatment showed in our analysis that minoxidil is recommended in half of the cases of AGA and AA. Patients with AGA and a high expression of SRD5A1 or PTGFR-2 may benefit from Dutasteride or Latanoprost treatment, respectively. Most of the studied genes showed no differences between the two populations. Conclusions: The DNA analysis of the patients with alopecia may contribute to a successful treatment. [ABSTRACT FROM AUTHOR]

Killer cell immunoglobulin-like receptors (KIR) exhibit extensive diversity, giving rise to different KIR profiles in populations worldwide. This study aimed to investigate the distribution of KIR genes and HLA ligands in a population from Campinas, southeastern Brazil (n = 292), and to compare their results with other populations. A comprehensive analysis of population-specific genes, genotype, and haplotype frequencies of KIR may facilitate a better understanding of their evolution and role in immunity. The genotyping of 16 KIR genes and HLA class I alleles was performed by the reverse sequence-specific oligonucleotide methodology using the Luminex platform (One Lambda, Inc., Canoga Park, CA). The framework genes were present in all individuals, with the most common non-framework KIR genes detected being KIR2DP1(96.6%), KIR2DL1(95.5%), KIR3DL1(94.5%), KIR2DS4(93.8%) and KIR2DL3(87.3%). KIR2DS1, KIR2DS3, KIR2DS5, and KIR3DS1 presented frequencies below 40%. KIR2DL2, KIR2DL5, and KIR2DS2 showed intermediate frequencies (between53% and 58%). The activating gene KIR2DS5 was the least common in this population (30.8%). Forty-five KIR profiles were found with the commonest being the homozygous A haplotype (27.4%). The distribution of KIR genes in the Brazilian population is similar to Caucasian European and Euro-descendant populations. [ABSTRACT FROM AUTHOR]

The introduction of rotavirus A (RVA) vaccines has considerably reduced the RVA-associated mortality among children under 5 years of age worldwide. The ability of RVA to reassort gives rise to different combinations of surface proteins G (glycoprotein, VP7) and P (protease sensitive, VP4) RVA types infecting children. During the epidemiological surveillance of RVA in the Northwest Amazon region, an unusual rotavirus genotype G6P[8] was detected in feces of a 2-year-old child with acute gastroenteritis (AGE) that had been vaccinated with one dose of Rotarix® (RV1). The G6P[8] sample had a DS-1-like constellation with a Wa-like VP3 gene mono-reassortment similar to equine-like G3P[8] that has been frequently detected in Brazil previously. The results presented here reinforce the evolutionary dynamics of RVA and the importance of constant molecular surveillance. [ABSTRACT FROM AUTHOR]

Two new species, Newellia xakriaba sp. nov. and Centrotrombidium krenak sp. nov. (Trombidiformes: Parasitengona: Johnstonianidae) from Brazilian caves, are described based on vouchering material for which sequences from multiple genes are available. This article expands the geographical range of the genus NewelliaAndré, 1962 known previously only from Angola. [ABSTRACT FROM AUTHOR]

Genetic association studies in rheumatoid arthritis conducted in various populations have yielded heterogeneous results. The present systematic review was conducted to synthesize the results of the studies in order to establish the impact of polymorphisms in the ficolin-coding genes FCN1, FCN2, and FCN3 on the susceptibility to develop rheumatoid arthritis. A systematic literature review was performed using the following keywords "gene (FCN1/FCN2/FCN3)", "Polymorphism/Genetic Variant", and "rheumatoid arthritis" in different databases until January 2022. Authors assessed articles by title/abstract and then assessed by full text for data extraction. The risk of bias was assessed using the Newcastle-Ottawa scale. Data synthesis was performed qualitatively and quantitatively. A total of 1519 articles were eligible for inclusion in this review, 3 were identified as relevant for the quantitative synthesis with 670 patients and 1019 controls. For the FCN1 gene, an association was found in the dominant and recessive genetic models of the variants rs2989727 (genotype TT = OR: 0.577, 95% CI: 0.430-0.769) and rs1071583 (genotype GG = OR: 1.537, 95% CI: 1.153-2.049, p = 0.0032) with the development of rheumatoid arthritis as a protective or susceptibility factor. FCN2 and FCN3 genes did not show association with disease development. The FCN1 gene variants rs2989727 and rs1071583 are associated with the risk of developing rheumatoid arthritis in populations from Brazil and Belgium, but not in FCN2 and FCN3 gene variants. [ABSTRACT FROM AUTHOR]

Salmonella enterica subspecies enterica serovar Infantis (S. Infantis) is a non-typhoid, zoonotic and foodborne serovar with worldwide distribution, and often associated with increasing antimicrobial resistance. Efflux pumps are antimicrobial resistance mechanisms able to promote and increase resistance levels to multiple distinct drug classes. Heavy metal tolerance genes have been demonstrated to promote resistance against these compounds and act in the co-selection of antimicrobial resistant strains. Despite the relevance of S. Infantis in clinical and non-clinical fields, few studies worldwide have investigated the occurrence of such genes in strains from diverse sources. Therefore, the present study aimed at determining the prevalence of antimicrobial efflux pump and heavy metal tolerance genes and their genomic relatedness through core-genome multi-locus sequence typing (cgMLST) of 80 S. Infantis strains isolated from food, environmental, human and animal sources from 2013 to 2018 in Brazil. Twenty efflux pump encoding genes were detected, with 17 of these (acrA, acrB, baeR, crp, emrB, emrR, hns, kdpE, kpnF, marA, marR, mdtK, msbA, rsmA, sdiA, soxR and soxS) detected in all strains studied, golS in 98.75%, mdfA in 58.75% and tet(A) in 37.5%. Tolerance genes to arsenic (arsR) were detected in 100% of the strains, gold (golS and golT) in 98.75%, silver (silABCDEFPRS) in 36.25% and mercury (merR and merT) in 1.25%. cgMLST demonstrated a closer genetic relationship among strains harboring similar profiles of heavy metal and efflux pump encoding genes, despite their origin. In conclusion, the high prevalence of some efflux pump and heavy metal tolerance encoding genes alert us about the importance of strong surveillance measures to monitor resistance and the transmission of S. Infantis among diverse sources in Brazil. [ABSTRACT FROM AUTHOR]

RNA sequencing (RNA-Seq) and mass-spectrometry-based proteomics data are often integrated in proteogenomic studies to assist in the prediction of eukaryote genome features, such as genes, splicing, single-nucleotide (SNVs), and single-amino-acid variants (SAAVs). Most genomes of parasite nematodes are draft versions that lack transcript- and protein-level information and whose gene annotations rely only on computational predictions. Angiostrongylus costaricensis is a roundworm species that causes an intestinal inflammatory disease, known as abdominal angiostrongyliasis (AA). Currently, there is no drug available that acts directly on this parasite, mostly due to the sparse understanding of its molecular characteristics. The available genome of A. costaricensis, specific to the Costa Rica strain, is a draft version that is not supported by transcript- or protein-level evidence. This study used RNA-Seq and MS/MS data to perform an in-depth annotation of the A. costaricensis genome. Our prediction improved the reference annotation with (a) novel coding and non-coding genes; (b) pieces of evidence of alternative splicing generating new proteoforms; and (c) a list of SNVs between the Brazilian (Crissiumal) and the Costa Rica strain. To the best of our knowledge, this is the first time that a multi-omics approach has been used to improve the genome annotation of A. costaricensis. We hope this improved genome annotation can assist in the future development of drugs, kits, and vaccines to treat, diagnose, and prevent AA caused by either the Brazil strain (Crissiumal) or the Costa Rica strain. [ABSTRACT FROM AUTHOR]

Background: Psychosis rates are higher among some migrant groups. We hypothesized that psychosis in migrants is associated with cumulative social disadvantage during different phases of migration. Methods: We used data from the EUropean Network of National Schizophrenia Networks studying Gene-Environment Interactions (EU-GEI) case–control study. We defined a set of three indicators of social disadvantage for each phase: pre-migration, migration and post-migration. We examined whether social disadvantage in the pre- and post-migration phases, migration adversities, and mismatch between achievements and expectations differed between first-generation migrants with first-episode psychosis and healthy first-generation migrants, and tested whether this accounted for differences in odds of psychosis in multivariable logistic regression models. Results: In total, 249 cases and 219 controls were assessed. Pre-migration (OR 1.61, 95% CI 1.06–2.44, p = 0.027) and post-migration social disadvantages (OR 1.89, 95% CI 1.02–3.51, p = 0.044), along with expectations/achievements mismatch (OR 1.14, 95% CI 1.03–1.26, p = 0.014) were all significantly associated with psychosis. Migration adversities (OR 1.18, 95% CI 0.672–2.06, p = 0.568) were not significantly related to the outcome. Finally, we found a dose–response effect between the number of adversities across all phases and odds of psychosis (⩾6: OR 14.09, 95% CI 2.06–96.47, p = 0.007). Conclusions: The cumulative effect of social disadvantages before, during and after migration was associated with increased odds of psychosis in migrants, independently of ethnicity or length of stay in the country of arrival. Public health initiatives that address the social disadvantages that many migrants face during the whole migration process and post-migration psychological support may reduce the excess of psychosis in migrants. [ABSTRACT FROM AUTHOR]

Very effective genetic control of some root-knot nematode (RKN) species (Meloidogyne spp.) is obtained by the employment of the tomato (Solanum lycopersicum L.) dominant Mi-1.2 gene. However, the phenotypic expression conferred by the Mi-1.2 gene may be impaired by high soil temperatures (above 28 °C) and by previously reported virulent RKN species and/or populations. Here, a putative Mi-1.2 gene-virulent RKN population was found inducing severe gall symptoms in roots of the tomato rootstock 'Guardião' (a homozygous Mi-1.2 hybrid of S. lycopersicum × S. peruvianum) under protected crop conditions in Southern Brazil. Females were extracted from severely infected roots displaying large galls and used for biochemical characterization of α-esterase (EST) and confirmed by SCAR markers. Additional pathogenicity assays were carried out in order to confirm the virulence (= resistance-breaking) feature of this RKN population by employing other or the same Mi-1.2 gene-carrying rootstocks. This virulent RKN population was identified as M. javanica (EST J3 and J2). The pathogenicity tests confirmed that this M. javanica population can overcome the Mi-1.2 resistance gene, and it is able to induce severe root-gall symptoms and to reproduce in two dominant resistant rootstocks ('Muralha' and 'Guardião') under greenhouse conditions. In addition, an initial inoculum of 2000–7000 eggs was considered ideal for future studies with the virulent M. javanica population. It is the first report of a Mi-1.2 gene-virulent M. javanica population in Brazil, which may represent a potential threat to the tomato agribusiness sector. [ABSTRACT FROM AUTHOR]

Bacterial resistance is a public and one health problem. Free‐living birds can be reservoirs of multidrug‐resistant bacteria and resistance genes. This study aimed to characterize the antimicrobial resistance of Escherichia coli isolated from free‐living urban pigeons (Columba livia) in South Brazil. Ninety‐two animals were sampled, and one isolate was obtained from each one. The isolates were characterized, and the antimicrobial resistance profile and beta‐lactam and colistin resistance genes were investigated. The isolates were classified as phylogroups B1 (35%), B2 (33%), A (16%) and D (16%), and 14% of the strains had the eae virulence gene. All isolates were resistant to at least one antimicrobial, and 63% of them were multidrug‐resistant. Geographical location where the pigeons were captured and presence of the eae gene were associated with multidrug resistance. blaVIM and mcr‐1 genes were detected in one and two isolates, respectively. This is the first report of these genes in E. coli of pigeons. The blaVIM‐positive isolate was classified as Shiga toxin‐producing E. coli, and the isolates with mcr‐1 were classified as Enterohaemorrhagic E. coli and Enteropathogenic E. coli, which raise additional concerns related to public health since these are zoonotic pathotypes. The results reveal that pigeons carry multidrug‐resistant pathogenic E. coli, which may interest public health. Nonetheless, further studies on whether these animals are sources of contamination for humans must be performed to understand their role in spreading antimicrobial resistance. [ABSTRACT FROM AUTHOR]

The challenge in studying Neotropical tadpoles is identifying species using only their external morphology. However, the DNA barcode protocol is often implemented to help elucidate taxonomic issues. In fact, the identification of frogs through their unknown tadpoles has already been achieved accurately using this protocol. Despite the successful application of this tool, the efficiency of the 16S rRNA gene as a DNA barcode for Neotropical tadpoles has not been fully assessed. Herein we evaluate the efficacy of the 16S rRNA gene for identifying tadpoles from northeastern Brazil. Samples of 100 tadpole specimens from 12 locations were analyzed. The DNA sequences were individually submitted to a BLAST search and were then aligned with a matrix containing available sequences in the GenBank based on the anurans known to occur in the study area. The 16S rRNA fragment successfully identified the analyzed anuran species. Based on DNA barcoding, 8% of the tadpoles morphologically identified at the species level were incorrect. When an incongruence between morphological and molecular identifications was detected, the morphology of the target morphotype was reexamined, and previously neglected morphological characteristics were identified. DNA barcoding using the 16S rRNA gene facilitated the assessment of tadpole richness in northeastern Brazil. This DNA protocol can be used as a starting point for detecting high levels of genetic divergence, highlighting potential taxa that should be studied from phylogenetic and taxonomic perspectives. [ABSTRACT FROM AUTHOR]

ECO92, a United Nations Conference on Environment and Development, hosted by Brazil in 1992 was a catalyst for much activity on biodiversity in the State of São Paulo and eventually led to the establishment of BIOTA-FAPESP. BIOTA-FAPESP quickly evolved into a world-leading research program that has broadened to cover all aspects of biodiversity in the State from genes through species and to ecosystems and the interactions between them. Through the funding of multi-disciplinary projects, the development of collaborative links within the State, nationally and internationally, and the astute use of databases to link the program's project outputs it has set a platform for filling the biodiversity knowledge gaps. Having achieved much in the last two decades, it still has some way to go, but the stage is set. [ABSTRACT FROM AUTHOR]

Thielaviopsis and related taxa are responsible for losses in several agricultural crops. In carrot these pathogens can cause black rot, mainly after harvesting. Molecular studies using species‐specific DNA sequences are the principal tools for accurate identification of these pathogens. The objective of this work was to investigate which taxa are associated with black rot in carrot in Brazil using gene markers and Bayesian phylogenetic analysis. Eighteen isolates were obtained from carrots with symptoms of black rot. Through morphological characteristics all isolates were classified as Thielaviopsis‐like. Bayesian inference using only MCM7 sequences and a concatenated data set (LSU, MCM7 and 60S rRNA) allowed identification of all isolates as belonging to Berkeleyomyces basicola. All isolates induced black rot in carrot. Although our studies include a small number of isolates, the results indicate the likely predominance of B. basicola in causing black rot in carrot in Brazil, and that MCM7 sequences are enough to distinguish the Berkeleyomyces species by Bayesian inference. [ABSTRACT FROM AUTHOR]

This study aimed to perform a genome-wide association analysis (GWAS) using the Random Forest (RF) approach for scanning candidate genes for age at first calving (AFC) in Nellore cattle. Additionally, potential epistatic effects were investigated using linear mixed models with pairwise interactions between all markers with high importance scores within the tree ensemble non-linear structure. Data from Nellore cattle were used, including records of animals born between 1984 and 2015 and raised in commercial herds located in different regions of Brazil. The estimated breeding values (EBV) were computed and used as the response variable in the genomic analyses. After quality control, the remaining number of animals and SNPs considered were 3,174 and 360,130, respectively. Five independent RF analyses were carried out, considering different initialization seeds. The importance score of each SNP was averaged across the independent RF analyses to rank the markers according to their predictive relevance. A total of 117 SNPs associated with AFC were identified, which spanned 10 autosomes (2, 3, 5, 10, 11, 17, 18, 21, 24, and 25). In total, 23 non-overlapping genomic regions embedded 262 candidate genes for AFC. Enrichment analysis and previous evidence in the literature revealed that many candidate genes annotated close to the lead SNPs have key roles in fertility, including embryo pre-implantation and development, embryonic viability, male germinal cell maturation, and pheromone recognition. Furthermore, some genomic regions previously associated with fertility and growth traits in Nellore cattle were also detected in the present study, reinforcing the effectiveness of RF for pre-screening candidate regions associated with complex traits. Complementary analyses revealed that many SNPs top-ranked in the RF-based GWAS did not present a strong marginal linear effect but are potentially involved in epistatic hotspots between genomic regions in different autosomes, remarkably in the BTAs 3, 5, 11, and 21. The reported results are expected to enhance the understanding of genetic mechanisms involved in the biological regulation of AFC in this cattle breed. [ABSTRACT FROM AUTHOR]

We researched clinically relevant antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) in environmental samples from a recreation club in Brazil. A total of 172 amplicons (105 from soil and 67 from water) of 26 ARGs (20 among the soil and water samples; four only in soil samples; two only in water samples) were detected. Nine MGEs were detected, including plasmids and class 1 integron. The absolute abundance of the mcr-3 gene ranged from 1.12 × 102 to 1.81 × 103 copies/mL−1 in water samples. The rapid spread of mcr-like genes in several sources has generated a huge concern to public health. Accordingly, understanding of antimicrobial resistance, carry out surveillance studies may contribute to tackle antimicrobial resistance. As the environmental samples were collected from a popular recreation club in Brazil, this study points out to the risk and exposure to clinically relevant ARGs, especially to mcr-3 and mcr-7.1 genes. [ABSTRACT FROM AUTHOR]

In Brazil, 19 species of the genus Ornithodoros (Acari: Argasidae) have been reported. The medical and veterinary importance of Ornithodoros ticks has increased substantially in recent decades, with the discovery of various relapsing fever Borrelia infecting Ornithodoros ticks. Herein, argasid ticks were collected during 2019–2020 from caves, abandoned nests and homes in various regions of Ceará State, Brazilian semiarid—Caatinga biome. In total, 289 ticks were collected and identified into five species: Ornithodoros cavernicolous (176 specimens), Ornithodoros fonsecai (81), Ornithodoros mimon (12), Ornithodoros rietcorreai (4), and a fifth species provisionally retained as Ornithodoros sp. Ubajara. Tick identifications were corroborated by a phylogenetic analysis inferred using the 16S rRNA gene. To extend the molecular characterization, DNA samples were tested by an additional PCR assay targeting the nuclear Histone 3 (H3) gene. Because there were no H3 sequences of argasids in GenBank, we extended this PCR assay for additional Ornithodoros species, available in our laboratory. In total, 15 partial sequences of the H3 gene were generated for 10 Ornithodoros species, showing 0% intraspecific polymorphism, and 1.5–11.6% interspecific polymorphism. Phylogenetic analyses inferred segregated Ornithodoros sp. Ubajara as a potential novel species. Our results also highlight the potential of the H3 gene for deeper phylogenetic analyses of argasids. The present study provides new data for argasid ticks of the genus Ornithodoros in the Caatinga biome. Because some of these tick species are human-biting ticks, active surveillance for the incidence of human infection due to Ornithodoros-borne agents is imperative in the Caatinga biome. [ABSTRACT FROM AUTHOR]

Genetic variations in PCLO have been associated with different pathologies in global literature, but there are no data regarding this gene in Native American populations. The Amazonian Native American populations have lower genetic diversity and are more different from other continental groups. We investigated 18 genetic variants in the PCLO gene in Amazonian indigenous and compared our results with the ones found in global populations, which were publicly available in the 1000 Genomes Project, gnmAD and ABraOM databases. The results demonstrated that the variants of the PCLO, especially rs17156844, rs550369696, rs61741659 and rs2877, have a significantly higher frequency in Amerindian populations in comparison with other continental populations. These data outline the singular genetic profile of the Native American population from the Brazilian Amazon region. [ABSTRACT FROM AUTHOR]

Xeroderma pigmentosum (XP) is a rare genetic condition in which exposure to sunlight leads to a high tumor incidence due to defective DNA repair machinery. Herein, we investigated seven patients clinically diagnosed with XP living in a small city, Montanhas (Rio Grande do Norte), in the Northeast region of Brazil. We performed high-throughput sequencing and, surprisingly, identified two different mutated genes. Six patients carry a novel homozygote mutation in the POLH/XPV gene, c.672_673insT (p.Leu225Serfs*33), while one patient carries a homozygote mutation in the XPC gene, c.2251-1G>C. This latter mutation was previously described in Southeastern Africa (Comoro Island and Mozambique), Pakistan, and in a high incidence in Brazil. The XP-C patient had the first symptoms before the first year of life with aggressive ophthalmologic tumor progression and a melanoma onset at 7 years of age. The XP-V patients presented a milder phenotype with later onset of the disorder (mean age of 16 years old), and one of the six XP-V patients developed melanoma at 72 years. The photoprotection is minimal among them, mainly for the XP-V patients. The differences in the disease severity between XP-C (more aggressive) and XP-V (milder) patients are obvious and point to the major role of photoprotection in the XPs. We estimate that the incidence of XP patients at Montanhas can be higher, but with no diagnosis, due to poor health assistance. Patients still suffer from the stigmatization of the condition, impairing diagnosis, education for sun protection, and medical care. [ABSTRACT FROM AUTHOR]

Summary: The genus Manihot, with around 120 known species, is native to a wide range of habitats and regions in the tropical and subtropical Americas. Its high species richness and recent diversification only c. 6 million years ago have significantly complicated previous phylogenetic analyses. Several basic elements of Manihot evolutionary history therefore remain unresolved.Here, we conduct a comprehensive phylogenomic analysis of Manihot, focusing on exhaustive sampling of South American taxa.We find that two recently described species from northeast Brazil's Atlantic Forest were the earliest to diverge, strongly suggesting a South American common ancestor of Manihot. Ancestral state reconstruction indicates early Manihot diversification in dry forests, with numerous independent episodes of new habitat colonization, including into savannas and rainforests within South America. We identify the closest wild relatives to Manihot esculenta, including the crop cassava, and we quantify extensive wild introgression into the cassava gene pool from at least five wild species, including Manihot glaziovii, a species used widely in breeding programs. Finally, we show that this wild‐to‐crop introgression substantially shapes the mutation load in cassava.Our findings provide a detailed case study for neotropical evolutionary history in a diverse and widespread group, and a robust phylogenomic framework for future Manihot and cassava research. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Viticulture & Enology / Ciência e Técnica Vitivinícola is the property of EDP Sciences and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Urinary tract infections (UTI) are one of the most common diseases worldwide and Escherichia coli is the most common causative bacteria. Empirical treatment is challenging due to antimicrobial or multidrug-resistance. The aims of this study were to determine the uropathogens and their antimicrobial susceptibility profile, as well as to identify the phylogroups and virulence genes of E. coli strains, associated with community-acquired UTI in outpatients admitted at a Brazilian Hospital in southeast Brazil. In total, 47 bacterial strains were isolated from 47 patients, 44 women and 2 men (no gender record from one patient). The age of the patients whose urine culture were positive varied from 0 (less than one month) to 104 years. Most of the isolates were E. coli (41/47), followed by Klebsiella pneumoniae (2/47), Klebsiella variicola/Klebsiella aerogenes (1/47), Pseudomonas aeruginosa (1/47), Proteus mirabilis (1/47), and Citrobacter koseri (1/47). Most E. coli strains were classified as phylogroup B2 (15/41 = 36.59%) and B1 (12/41 = 29.27%) and the most common virulence genes among E. coli strains were fimH (31/41 = 75.61%), iutA (21/41 = 51.22%), and tratT (16/41 = 39.02%). Among the E. coli strains, 59% were multidrug-resistance and strains that were ampicillin, sulfamethoxazole/trimethoprim, or tetracycline-resistant exhibited more chance to be multidrug-resistance, with an odds ratio of 100.00 [95% confidence interval (CI) 9.44–1059.26], 22.50 (95% CI 3.95–128.30), and 12.83 (95% CI 2.68–61.45), respectively. Our results showed that E. coli was the main etiological agent identified and demonstrated high frequency of multidrug-resistance and virulence factors in bacterial strains isolated from UTIs. [ABSTRACT FROM AUTHOR]

The Arapaima gigas is an endemic fish to the Amazon basin and with great potential for aquaculture, although its reproduction in captivity is limited by the absence of sexual dimorphism. The demand increase for pirarucu in the Northern region of Brazil, has led to new studies on the reproduction of the species. Thus, we aimed to investigate patterns of sex‐biased genes in brain and gonad tissues of A. gigas. A total of of 451,490,808 short sequencing reads were produced using the SOLiD v4 plus sequencing platform. An average of ~30% of sequencing reads were mapped to Asian arowana reference cDNAs, species that belong to the same group of bony‐tongue fishes. Gene expression analysis identified 305 sex‐biased genes for the brain, with 297 genes up‐regulated in females and only eight genes up‐regulated in males. The analysis of the gonads identified 120 sex‐biased genes, with 110 genes up‐regulated in females and only ten genes up‐regulated in males. Gene ontology analysis found more than 50 terms enriched for the sex‐biased genes in a wide range of pathways suggesting that multiple functions and processes differ between the sexes. Thus, the following areas of interest were approached: sex steroids/hormones, organism development process and macromolecule biosynthetic process, which exhibited sex‐biased gene expression; these areas are known to influence sexual development in other species. Lastly, the information obtained in this study concerning the sex‐biased genes in the A. gigas species is a contribution to further studies approaching the processes of gonadal development, and downstream molecular mechanisms in species. [ABSTRACT FROM AUTHOR]

The age at first calving has a great economic impact on the beef cattle system and calving at 24 months is an objective of selection for a more efficient herd. However, an age at first calving around 36 months has been observed for Nellore cattle in Brazil. Thus, a genome-wide association study (GWAS) was carried out with 8376 records of age at first calving and 3239 animals genotyped with the GGP-Indicus 35K, which has been developed specifically for Bos taurus indicus. The weighted single-step genomic best linear unbiased prediction method was used, with adjacent SNPs (single nucleotide polymorphisms) in genomic windows of 1.0 Mb. After quality control, 3239 (2161 males and 1078 females) animals genotyped for 30,519 SNPs were used in GWAS analysis. The average and standard deviation of age at first calving were 1041.7 and 140.6 days, respectively. The heritability estimate was 0.10 ± 0.02. The GWAS analysis found seven genomic regions in BTA1, 2, 5, 12, 18, 21, and 24, which explained a total of 11.24% of the additive genetic variance of age at first calving. In these regions were found 62 protein coding genes, and the genes HSD17B2 , SERPINA14 , SERPINA1 , SERPINA5 , STAT1 , NFATC1 , ATP9B , CTDP1 , THPO , ECE2 , PSMD2 , EIF4G1 , EIF2B2 , DVL3 , POLR2H , TMTC2, and GPC6 are possible candidates for age at first birth due their function. Moreover, two molecular functions ("serine-type endopeptidase inhibitor activity" and "negative regulation of endopeptidase activity") were significant, which depend on several serpin genes. The use of a SNP chip developed especially for Bos taurus indicus allowed to find genomic regions for age at first calving, which are close to QTLs previously reported for other reproduction-related traits. Future studies can reveal the causal variants and their effects on reproductive precocity of Nellore cows. • Heritability for age at first calving was estimated (0.10 ± 0.02). • Seven genome windows explained 11.24% of additive genetic variance of age at first calving. • Inside the genome windows, several candidate genes were found. • Five significant GO terms were found. [ABSTRACT FROM AUTHOR]

Copyright of Brazilian Journal of Biology is the property of Instituto Internacional de Ecologia and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Background Chagas disease is an infectious disease caused by the parasite Trypanosoma cruzi and is endemic from Latin American countries. The goal of our study was to identify novel genetic loci associated with chronic Chagas cardiomyopathy development in Chagas disease patients from different Latin American populations. Methods We performed a cross-sectional, nested case-control study including 3 sample collections from Colombia, Argentina, and Bolivia. Samples were genotyped to conduct a genome-wide association study (GWAS). These results were meta-analyzed with summary statistic data from Brazil, gathering a total of 3413 Chagas disease patients. To identify the functional impact of the associated variant and its proxies, we performed an in silico analysis of this region. Results The meta-analysis revealed a novel genome-wide statistically significant association with chronic Chagas cardiomyopathy development in rs2458298 (OR = 0.90, 95%CI = 0.87–0.94, P-value  = 3.27 × 10-08), nearby the SAC3D1 gene. In addition, further in silico analyses displayed functional relationships between the associated variant and the SNX15 , BAFT2, and FERMT3 genes, related to cardiovascular traits. Conclusions Our findings support the role of the host genetic factors in the susceptibility to the development of the chronic cardiac form of this neglected disease. [ABSTRACT FROM AUTHOR]

Background: We took advantage of the 2015-2016 Brazilian arbovirus outbreak (Zika [ZIKV]/dengue/chikungunya viruses) associated with neurological complications to type HLA-DRB1/DQA1/DQB1 variants in patients exhibiting neurological complications and in bone marrow donors from the same endemic geographical region.Methods: DRB1/DQA1/DQB1 loci were typed using sequence-specific oligonucleotides. In silico studies were performed using X-ray resolved dimer constructions.Results: The DQA1*01, DQA1*05, DQB1*02, or DQB1*06 genotypes/haplotypes and DQA1/DQB1 haplotypes that encode the putative DQA1/DQB1 dimers were overrepresented in the whole group of patients and in patients exhibiting peripheral neurological spectrum disorders (PSD) or encephalitis spectrum disorders (ESD). The DRB1*04, DRB1*13, and DQA1*03 allele groups protected against arbovirus neurological manifestation, being underrepresented in whole group of patients and ESD and PSD groups. Genetic and in silico studies revealed that DQA1/DQB1 dimers (1) were primarily associated with susceptibility to arbovirus infections; (2) can bind to a broad range of ZIKV peptides (235 of 1878 peptides, primarily prM and NS2A); and (3) exhibited hydrophilic and highly positively charged grooves when compared to the DRA1/DRB1 cleft. The protective dimer (DRA1/DRB1*04) bound a limited number of ZIKV peptides (40 of 1878 peptides, primarily prM).Conclusion: Protective haplotypes may recognize arbovirus peptides more specifically than susceptible haplotypes. [ABSTRACT FROM AUTHOR]

Copyright of Brazilian Journal of Biology is the property of Instituto Internacional de Ecologia and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Purpose: Genetic polymorphisms have been associated with variation in the metabolism of tacrolimus (TAC) in kidney transplant patients. This study is aimed at assessing the impact of allelic variants of CYP3A5 and PPARA genes on the pharmacokinetics (PK) of TAC in Brazilian kidney transplant recipients in the first-year post-transplant. Methods: A total of 127 patients were included for genetic evaluation. Genomic DNA was isolated from peripheral blood and real-time PCR was used to analyze the main polymorphisms described for the genes CYP3A5 (rs776746; C > G) and PPARA (rs4823613; A > G and rs4253728; G > A). Results: CYP3A5 expressors showed a lower Co/dose ratio than non-expressors, with the median values of this parameter <1.01 ng/mL/mg in the first group at all evaluated times. Additionally, PPARA variant homozygotes had a lower Co/D ratio than wild allele carriers in the 12-month post-transplant period, with a median value of 0.65 ng/mL/mg. In the CYP3A5 expressers, the presence of the variant homozygous genotype PPARA was associated with a lower value of Co/D compared with the other genotypic groups at month 12. Conclusion: In the population under study, polymorphisms on CYP3A5 and PPARA were identified as determining and independent factors associated with the reduction of Co/D of TAC. Thus, the genotyping of these genetic variants may be a useful tool for the individualized prescription of TAC in kidney transplant patients. [ABSTRACT FROM AUTHOR]

Background Our goal was to identify genetic risk factors for cutaneous leishmaniasis (CL) caused by Leishmania braziliensis. Methods Genotyping 2066 CL cases and 2046 controls using Illumina HumanCoreExomeBeadChips provided data for 4 498 586 imputed single-nucleotide variants (SNVs). A genome-wide association study (GWAS) using linear mixed models took account of genetic diversity/ethnicity/admixture. Post-GWAS positional, expression quantitative trait locus (eQTL) and chromatin interaction mapping was performed in Functional Mapping and Annotation (FUMA). Transcriptional data were compared between lesions and normal skin, and cytokines measured using flow cytometry and Bioplex assay. Results Positional mapping identified 32 genomic loci associated with CL, none achieving genome-wide significance (P < 5 × 10−8). Lead SNVs at 23 loci occurred at protein coding or noncoding RNA genes, 15 with eQTLs for functionally relevant cells/tissues and/or showing differential expression in lesions. Of these, the 6 most plausible genetic risk loci were SERPINB10 (P imputed_1000G = 2.67 × 10−6), CRLF3 (P imputed_1000G = 5.12 × 10−6), STX7 (P imputed_1000G = 6.06 × 10−6), KRT80 (P imputed_1000G = 6.58 × 10−6), LAMP3 (P imputed_1000G = 6.54 × 10−6), and IFNG-AS1 (P imputed_1000G = 1.32 × 10−5). LAMP3 (P adjusted = 9.25 × 10−12; +6-fold), STX7 (P adjusted = 7.62 × 10−3; +1.3-fold), and CRLF3 (P adjusted = 9.19 × 10−9; +1.97-fold) were expressed more highly in CL biopsies compared to normal skin; KRT80 (P adjusted = 3.07 × 10−8; −3-fold) was lower. Multiple cis-eQTLs across SERPINB10 mapped to chromatin interaction regions of transcriptional/enhancer activity in neutrophils, monocytes, B cells, and hematopoietic stem cells. Those at IFNG-AS1 mapped to transcriptional/enhancer regions in T, natural killer, and B cells. The percentage of peripheral blood CD3+ T cells making antigen-specific interferon-γ differed significantly by IFNG-AS1 genotype. Conclusions This first GWAS for CL identified multiple genetic risk loci including a novel lead to understanding CL pathogenesis through regulation of interferon-γ by IFNG antisense RNA 1. [ABSTRACT FROM AUTHOR]

Emergence of colistin-resistant bacteria harboring mobile colistin resistance genes (mcr genes) pose a threat for food-producing animals and humans. In this article, we aim to highlight the emergence of Escherichia fergusonii as an important new reservoir to mcr-1-harboring plasmid in poultry production. Three strains closely related were isolated from cloacal swabs. Their genome contains four plasmids, including a 182,869 bp IncHI2 plasmid harboring the colistin resistance gene mcr-1. These results will contribute to our understanding of plasmid-mediated mcr-1 gene presence and transmission in E. fergusonii. [ABSTRACT FROM AUTHOR]

A deficiência de alfa-1 antitripsina (DAAT) é um distúrbio genético raro causado por uma mutação no gene SERPINA1, que codifica o inibidor de protease alfa-1 antitripsina (AAT). A DAAT predispõe os indivíduos a DPOC e doença hepática. O diagnóstico precoce é essencial para a implementação de medidas preventivas e para limitar a carga da doença. Embora diretrizes nacionais e internacionais para o diagnóstico e manejo da DAAT estejam disponíveis há 20 anos, mais de 85% dos casos não são diagnosticados e, portanto, não são tratados. No Brasil, os motivos para o subdiagnóstico da DAAT incluem o desconhecimento dos médicos sobre a condição, a diversidade racial da população, o fato de os níveis séricos de AAT serem avaliados em um número limitado de indivíduos e a falta de ferramentas diagnósticas convenientes. O diagnóstico da DAAT baseia-se em resultados de exames laboratoriais. A abordagem diagnóstica padrão envolve a avaliação dos níveis séricos de AAT, seguida de fenotipagem, genotipagem, sequenciamento gênico ou suas combinações para detecção da mutação específica. Nos últimos 10 anos, novas técnicas foram desenvolvidas, oferecendo uma alternativa rápida, minimamente invasiva e confiável aos métodos tradicionais de teste. Um desses testes disponíveis no Brasil é o teste de genotipagem A1AT, que analisa simultaneamente as 14 mutações mais prevalentes da DAAT usando DNA extraído de swab bucal ou de sangue em papelfiltro. Esses avanços podem contribuir para a superação do problema do subdiagnóstico no Brasil e em outros países, bem como podem aumentar a taxa de detecção da DAAT e, portanto, mitigar os malefícios do diagnóstico tardio. [ABSTRACT FROM AUTHOR]

Background: Next generation sequencing (NGS) has been a handy tool in clinical practice, mainly due to its efficiency and cost-effectiveness. It has been widely used in genetic diagnosis of several inherited diseases, and, in clinical oncology, it may enhance the discovery of new susceptibility genes and enable individualized care of cancer patients. In this context, we explored a pan-cancer panel in the investigation of germline variants in Brazilian patients presenting clinical criteria for hereditary cancer syndromes or familial history.Methods: Seventy-one individuals diagnosed or with familial history of hereditary cancer syndromes were submitted to custom pan-cancer panel including 16 high and moderate penetrance genes previously associated with hereditary cancer syndromes (APC, BRCA1, BRCA2, CDH1, CDKN2A, CHEK2, MSH2, MSH6, MUTYH, PTEN, RB1, RET, TP53, VHL, XPA and XPC). All pathogenic variants were validated by Sanger sequencing.Results: We identified a total of eight pathogenic variants among 12 of 71 individuals (16.9%). Among the mutation-positive subjects, 50% were diagnosed with breast cancer and had mutations in BRCA1, CDH1 and MUTYH. Notably, 33.3% were individuals diagnosed with polyposis or who had family cases and harbored pathogenic mutations in APC and MUTYH. The remaining individuals (16.7%) were gastric cancer patients with pathogenic variants in CDH1 and MSH2. Overall, 54 (76.05%) individuals presented at least one variant uncertain significance (VUS), totalizing 81 VUS. Of these, seven were predicted to have disease-causing potential.Conclusion: Overall, analysis of all these genes in NGS-panel allowed the identification not only of pathogenic variants related to hereditary cancer syndromes but also of some VUS that need further clinical and molecular investigations. The results obtained in this study had a significant impact on patients and their relatives since it allowed genetic counselling and personalized management decisions. [ABSTRACT FROM AUTHOR]

This study used whole-genome sequencing to analyze the first case of NDM-1-producing Acinetobacter baumannii belonging to the novel sequence type 1465/CC216 recovered in Brazil. The study identified an unusual plasmid carrying blaNDM-1 gene, in which some genes of the Tn125 transposon were lost. Besides, on the chromosome, the strain reported here presented blaOXA-106 gene, a variant of blaOXA-51 gene, and blaADC-25 with ISAba1 upstream. The isolation of new STs of A. baumannii carrying blaNDM-1 genes elicits our concerns about the possible spread of these genes among clinically relevant bacteria. [ABSTRACT FROM AUTHOR]

Gymnodinium gracile, described from the coasts of Denmark in 1881, is one of the first described unarmored dinoflagellates. Individuals that morphologically fit with the original description were isolated from the English Channel (North‐East Atlantic). The SSU rRNA gene sequences were identical to the sequences identified as Balechina pachydermata and Gymnodinium amphora from the Mediterranean Sea and Brazil. We propose the transfer of Gymnodinium gracile into the genus Balechina as B. gracilis comb. nov. These sequences constitute an independent lineage, clustering with numerous environmental sequences from polar to tropical waters. The widespread distribution, the high plasticity in size, shape and coloration and the difficulties in discerning the fine longitudinal striae have contributed to the description of numerous synonyms: Amphidinium vasculum, Balechina pachydermata (=Gymnodinium pachydermatum), Gymnodinium achromaticum, G. abbreviatum, G. amphora, G. dogielii, G. lohmannii (=G. roseum sensu Lohmann 1908), G. situla, and Gyrodinium cuneatum (=G. gracile sensu Pouchet 1885). [ABSTRACT FROM AUTHOR]