Identification and in silico characterization of structural and functional impacts of genetic variants in milk protein genes in the Zebu breeds Guzerat and Gyr.

Whole genome sequencing of bovine breeds has allowed identification of genetic variants in milk protein genes. However, functional repercussion of such variants at a molecular level has seldom been investigated. Here, the results of a multistep Bioinformatic analysis for functional characterization of recently identified genetic variants in Brazilian Gyr and Guzerat breeds is described, including predicted effects on the following: (i) evolutionary conserved nucleotide positions/regions; (ii) protein function, stability, and interactions; (iii) splicing, branching, and miRNA binding sites; (iv) promoters and transcription factor binding sites; and (v) collocation with QTL. Seventy-one genetic variants were identified in the caseins (CSN1S1, CSN2, CSN1S2, and CSN3), LALBA, LGB, and LTF genes. Eleven potentially regulatory variants and two missense mutations were identified. LALBA Ile60Val was predicted to affect protein stability and flexibility, by reducing the number the disulfide bonds established. LTF Thr546Asn is predicted to generate steric clashes, which could mildly affect iron coordination. In addition, LALBA Ile60Val and LTF Thr546Asn affect exonic splicing enhancers and silencers. Consequently, both mutations have the potential of affecting immune response at individual level, not only in the mammary gland. Although laborious, this multistep procedure for classifying variants allowed the identification of potentially functional variants for milk protein genes.

Schistosoma mansoni: Off-target analyses using nonspecific double-stranded RNAs as control for RNAi experiments in schistosomula.

RNA interference is a well established and widely used reverse genetic tool available for gene functional studies in trematodes. This technique requires the use of nonrelevant double-stranded RNA as control. However, several authors have reported inconsistencies associated with RNAi. We used RNASeq to analyze genes affected by nonspecific dsRNA exposure. We found only few genes presenting altered expression in schistosomula exposed to GFP or mCherry nonspecific-dsRNAs, most of them encoding uncharacterized proteins. Correlation analysis revealed that there are more differences among biological replicates, than due to treatment with nonspecific controls. These observations are of key relevance to other RNAi gene function assessment in other organisms.

Expression of myogenes in longissimus dorsi muscle during prenatal development in commercial and local Piau pigs.

This study used qRT-PCR to examine variation in the expression of 13 myogenes during muscle development in four prenatal periods (21, 40, 70 and 90 days post-insemination) in commercial (the three-way Duroc, Landrace and Large-White cross) and local Piau pig breeds that differ in muscle mass. There was no variation in the expression of the CHD8, EID2B, HIF1AN, IKBKB, RSPO3, SOX7 and SUFU genes at the various prenatal ages or between breeds. The MAP2K1 and RBM24 genes showed similar expression between commercial and Piau pigs but greater expression (p < 0.05) in at least one prenatal period. Pair-wise comparisons of prenatal periods in each breed showed that only the CSRP3, LEF1, MRAS and MYOG genes had higher expression (p < 0.05) in at least one prenatal period in commercial and Piau pigs. Overall, these results identified the LEF1 gene as a primary candidate to account for differences in muscle mass between the pig breeds since activation of this gene may lead to greater myoblast fusion in the commercial breed compared to Piau pigs. Such fusion could explain the different muscularity between breeds in the postnatal periods.

Sequence and structural analysis of the 5' noncoding region of hepatitis C virus in patients with chronic infection.

Hepatitis C virus (HCV), exhibits considerable genetic diversity, but presents a relatively well conserved 5' noncoding region (5' NCR) among all genotypes. In this study, the structural features and translational efficiency of the HCV 5' NCR sequences were analyzed using the programs RNAfold, RNAshapes and RNApdist and with a bicistronic dual luciferase expression system, respectively. RNA structure prediction software indicated that base substitutions will alter potentially the 5' NCR structure. The heterogeneous sequence observed on 5' NCR led to important changes in their translation efficiency in different cell culture lines. Interactions of the viral RNA with cellular transacting factors may vary according to the cell type and viral genome polymorphisms that may result in the translational efficiency observed.

A common vaginal microbiota composition among breeds of Bos taurus indicus (Gyr and Nellore).

Describing the bovine vaginal microbiota is essential to better understand its physiology and its impact on health maintenance. Despite the economic importance of reproduction of these animals, bovine vaginal microbial community is still poorly described in comparison with rumen microbiome. Previous studies of our group described the vaginal microbiota of Nellore, an important Bos taurus indicus breed, using metagenomics. In order to better understand this microbiota, the present work aims to investigate another important breed, Gyr. Results have shown bacterial dominance over Archaea and Fungi was observed, with the most abundant bacterial phylum (Firmicutes) representing 40-50% of bacterial population, followed by Bacteroidetes, Proteobacteria, and Actinobacteria. The Fungi kingdom had the Mycosphaerella genus as its main representative, followed by Cladosporium. Archaea were observed at a very low abundance in all animals, with a high relative abundance of Methanobrevibacter genus. These results demonstrate a high microbial diversity on vaginal tract of Gyr, as demonstrated for Nellore and different from the previously described for other species. Our results indicate a great similarity between vaginal microbiota of Nellore and Gyr despite the differences in animal handling and genetic improvement. As observed for both breeds, individual variation is the largest source of microbial diversity between animals.

Pleiotropic alterations in gene expression in Latin American Fasciola hepatica isolates with different susceptibility to drugs.

BACKGROUND: Fasciola hepatica is the main agent of fasciolosis, a zoonotic disease affecting livestock worldwide, and an emerging food-borne disease in humans. Even when effective treatments are available, drugs are costly and can result in tolerance, liver damage and normally they do not prevent reinfection. Drug-resistant strains in livestock have been reported in various countries and, more worryingly, drug resistance in human cases has emerged in South America. The present study aims to characterize the transcriptome of two South American resistant isolates, the Cajamarca isolate from Peru, resistant to both triclabendazole and albendazole (TCBZR/ABZR) and the Rubino isolate from Uruguay, resistant to ABZ (TCBZS/ABZR), and compare them to a sensitive strain (Cenapa, Mexico, TCBZS/ABZS) to reveal putative molecular mechanisms leading to drug resistance. RESULTS: We observed a major reduction in transcription in the Cajamarca TCBZR/ABZR isolate in comparison to the other isolates. While most of the differentially expressed genes are still unannotated, several trends could be detected. Specific reduction in the expression levels of cytoskeleton proteins was consistent with a role of tubulins as putative targets of triclabendazole (TCBZ). A marked reduction of adenylate cyclase might be underlying pleiotropic effects on diverse metabolic pathways of the parasite. Upregulation of GST mu isoforms suggests this detoxifying mechanism as one of the strategies associated with resistance. CONCLUSIONS: Our results stress the value of transcriptomic approaches as a means of providing novel insights to advance the understanding of drug mode of action and drug resistance. The results provide evidence for pleiotropic variations in drug-resistant isolates consistent with early observations of TCBZ and ABZ effects and recent proteomic findings.

Differential impact of metacyclic and blood trypomastigotes on parasitological, serological and phenotypic features triggered during acute Trypanosoma cruzi infection in dogs.

A detailed follow-up investigation of the major parasitological, serological and phenotypic features in dogs experimentally infected with metacyclic (MT) and blood (BT) trypomastigotes of Trypanosoma cruzi strain Berenice-78, typifying vectorial and transfusional transmission of human Chagas disease, has been conducted. Although there were no changes with respect to the window of patent-parasitaemia, significant differences between MT- and BT-infected dogs in both the prepatent period (days 23 and 19, respectively) and the day of maximum parasitaemia (days 26 and 22, respectively) were recorded. A progressive enhancement in the level of T. cruzi-specific antibodies accompanied infection by both MT and BT forms, although higher IgG titres developed on days 14 and 21 following infection with MT forms. Higher Thy-1(+)/CD21(+) and lower CD4(+)/CD8(+) cell ratios, occasioned by increased levels of Thy-1(+) and CD8(+) T-cells and reduced frequencies of CD4(+) T-cells and CD21(+) B-lymphocytes, were observed in both MT- and BT-infected animals. The reduced frequency of CD14(+) leukocytes was revealed as the most relevant phenotypic feature intrinsic to T. cruzi infection independent of inoculum source. BT-specific phenotypic features included an early reduction in the percentage of circulating CD21(+) and CD14(+) leukocytes, together with a higher Thy-1(+)/CD21(+) cell ratio on day 42. On the other hand, higher levels of CD8(+) T-cells, together with a lower CD4(+)/CD8(+) cell ratio on day 28, were characteristic of MT infection. These findings emphasise the importance of inoculum source and suggest that vectorial or transfusional routes of T. cruzi infection may trigger distinct parasite-host interactions during acute Chagas disease.

Comparative sequence analysis reveals regulation of genes in developing schistosomula of Schistosoma mansoni exposed to host portal serum.

Once inside a vertebrate host after infection, individual schistosomula of the parasite Schistosoma mansoni find a new and complex environment, which requires quick adjustments for survival, such as those that allow it to avoid the innate immune response of the host. Thus, it is very important for the parasite to remain within the skin after entering the host for a period of about 3 days, at which time it can then reach the venous system, migrate to the lungs and, by the end of eighth day post-infection, it reach the portal venous system, while undergoing minimal changes in morphology. However, after just a few days in the portal blood system, the parasite experiences an extraordinary increase in biomass and significant morphological alterations. Therefore, determining the constituents of the portal venous system that may trigger these changes that causes the parasite to consolidate its development inside the vertebrate host, thus causing the disease schistosomiasis, is essential. The present work simulated the conditions found in the portal venous system of the vertebrate host by exposing schistosomula of S. mansoni to in vitro culture in the presence of portal serum of the hamster, Mesocricetus auratus. Two different incubation periods were evaluated, one of 3 hours and one of 12 hours. These time periods were used to mimic the early contact of the parasite with portal serum during the course of natural infection. As a control, parasites were incubated in presence of hamster peripheral serum, in order to compare gene expression signatures between the two conditions. The mRNA obtained from parasites cultured under both conditions were submitted to a whole transcriptome library preparation and sequenced with a next generation platform. On average, nearly 15 million reads were produced per sample and, for the purpose of gene expression quantification, only reads mapped to one location of the transcriptome were considered. After statistical analysis, we found 103 genes differentially expressed by schistosomula cultured for 3 hours and 12 hours in the presence of hamster portal serum. After the subtraction of a second list of genes, also differentially expressed between schistosomula cultured for 3 hours and 12 hours in presence of peripheral serum, a set of 58 genes was finally established. This pattern was further validated for a subset of 17 genes, by measuring gene expression through quantitative real time polymerase chain reaction (qPCR). Processes that were activated by the portal serum stimulus include response to stress, membrane transport, protein synthesis and folding/degradation, signaling, cytoskeleton arrangement, cell adhesion and nucleotide synthesis. Additionally, a smaller number of genes down-regulated under the same condition act on cholinergic signaling, inorganic cation and organic anion membrane transport, cell adhesion and cytoskeleton arrangement. Considering the role of these genes in triggering processes that allow the parasite to quickly adapt, escape the immune response of the host and start maturation into an adult worm after contact with the portal serum, this work may point to unexplored molecular targets for drug discovery and vaccine development against schistosomiasis.

Vaginal Microbiome Characterization of Nellore Cattle Using Metagenomic Analysis.

Understanding of microbial communities inhabiting cattle vaginal tract may lead to a better comprehension of bovine physiology and reproductive health being of great economic interest. Up to date, studies involving cattle microbiota are focused on the gastrointestinal tract, and little is known about the vaginal microbiota. This study aimed to investigate the vaginal microbiome in Nellore cattle, heifers and cows, pregnant and non-pregnant, using a culture independent approach. The main bacterial phyla found were Firmicutes (~40-50%), Bacteroidetes (~15-25%) and Proteobacteria (~5-25%), in addition to ~10-20% of non-classified bacteria. 45-55% of the samples were represented by only ten OTUs: Aeribacillus, Bacteroides, Clostridium, Ruminococcus, Rikenella, Alistipes, Bacillus, Eubacterium, Prevotella and non-classified bacteria. Interestingly, microbiota from all 20 animals could be grouped according to the respiratory metabolism of the main OTUs found, creating three groups of vaginal microbiota in cattle. Archaeal samples were dominated by the Methanobrevibacter genus (Euryarchaeota, ~55-70%). Ascomycota was the main fungal phylum (~80-95%) and Mycosphaerella the most abundant genus (~70-85%). Hormonal influence was not clear, but a tendency for the reduction of bacterial and increase of archaeal populations in pregnant animals was observed. Eukaryotes did not vary significantly between pregnant and non-pregnant animals, but tended to be more abundant on cows than on heifers. The present work describes a great microbial variability in the vaginal community among the evaluated animals and groups (heifers and cows, pregnant and non-pregnant), which is significantly different from the findings previously reported using culture dependent methods, pointing out the need for further studies on this issue. The microbiome found also indicates that the vaginal colonization appears to be influenced by the gastrointestinal community.

Complete genome sequence of Streptococcus agalactiae strain SA20-06, a fish pathogen associated to meningoencephalitis outbreaks.

Streptococcus agalactiae (Lancefield group B; GBS) is the causative agent of meningoencephalitis in fish, mastitis in cows, and neonatal sepsis in humans. Meningoencephalitis is a major health problem for tilapia farming and is responsible for high economic losses worldwide. Despite its importance, the genomic characteristics and the main molecular mechanisms involved in virulence of S. agalactiae isolated from fish are still poorly understood. Here, we present the genomic features of the 1,820,886 bp long complete genome sequence of S. agalactiae SA20-06 isolated from a meningoencephalitis outbreak in Nile tilapia (Oreochromis niloticus) from Brazil, and its annotation, consisting of 1,710 protein-coding genes (excluding pseudogenes), 7 rRNA operons, 79 tRNA genes and 62 pseudogenes.

Xerostomia, hyposalivation and sialadenitis in patients with chronic hepatitis C are not associated with the detection of HCV RNA in saliva or salivary glands.

OBJECTIVE: Salivary gland disorders in patients with chronic hepatitis C (CHC) have been considered oral extrahepatic manifestations, reinforcing the hepatitis C virus (HCV) as a sialotropic virus. Hence, the authors investigated the prevalence of HCV RNA in saliva and salivary glands and its possible association with xerostomia, hyposalivation and sialadenitis in patients with CHC. PATIENTS AND METHODS: In 65 patients with confirmed CHC, the HCV RNA was investigated by nested RT-PCR in saliva samples and minor salivary glands. Xerostomia, hyposalivation, clinical and histopathological evidence of sialadenitis were also evaluated. Univariate and multivariate analyses were employed to verify associations. RESULTS: HCV RNA was detected in the saliva of 26/65 (40.0%) patients and in 12/65 (18.5%) salivary glands. Xerostomia was reported by 23/65 (35.4%) patients, and hyposalivation was diagnosed in 13/65 (20.0%) patients. Sialadenitis was confirmed by histopathological features in 31/65 (47.7%) patients. Twelve (38.7%) of the 31 patients with sialadenitis presented HCV RNA in saliva and 2/31 (6.5%) in salivary glands. No associations were found between xerostomia, hyposalivation or sialadenitis and the detection of HCV RNA in saliva or in salivary glands. CONCLUSIONS: Although xerostomia, hyposalivation and sialadenitis are frequent findings in CHC patients, our study did not confirm the association between the detection of HCV RNA in saliva or salivary glands with these salivary gland disorders. However, an indirect role of HCV by immune-mediated virus mechanisms in the pathogenesis of salivary gland disorders in this group of patients cannot be ruled out.

Variações nas regiões 5’ não traduzida e na proteína não estrutural NS5A do vírus da Hepatite C em pacientes infectados com o genótipo 1

Embora exibindo considerável variabilidade genética, a região 5' não codificante (5'RNC) do genoma viral é relativamente bem conservada entre todos os genótipos Existem evidências da presença nestes domínios de um sítio de entrada interno do ribossomo (IRES) que permite a tradução cap-independente do RNA viral. A variabilidade na região da proteína não estrutural NS5A, designada “Região Determinante da Suscetibilidade ao interferon” (ISDR), foi associada à resistência ou sensibilidade a terapia com interferon-α. A partir das seqüências obtidas, foram realizadas predições da estrutura secundária da 5' RNC pelos programas RNAfold, RNApdist e RNAshapes. Também foram realizados experimentos de transfecção in vivo a fim de testar a funcionalidade da 5' RNC. A correlação entre variações nas regiões 5' NRC e NS5A e resposta terapêutica, entre os grupos não respondedores e respondedores (NR e R) foram realizadas através de parâmetros de genética molecular. A Energia Livre Mínima (ELM) calculada através do RNAfold sofreu maior influência da posição do que com o número de substituições. Os resultados do RNAshapes mostraram diferenças na probabilidade de predição das shapes, reforçando a idéia de que as substituições alteram a estrutura secundária. Os resultados do RNApdist também mostraram que algumas substituições tem um impacto sobre a predição da estrutura secundária. A heterogeneidade da seqüência da 5' RNC conduziu importantes alterações na eficiência de tradução, implicando que as interações entre o RNA e fatores de tradução podem variar de acordo com o tipo de células. As regiões 5' RNC e NS5A apresentaram baixa variabilidade genética. Apenas a 5' RNC apresentou desvio da neutralidade e significativa variabilidade molecular nos dois grupos estudados (NR e R). A análise filogenética mostrou nenhuma correlação entre variações na seqüência e a. resposta terapêutica

Variações nas regiões 5’ não traduzida e na proteína não estrutural NS5A do vírus da Hepatite C em pacientes infectados com o genótipo 1 / Variations in the 5 'untranslated and non-structural protein NS5A of hepatitis C virus in patients infected with genotype 1

Embora exibindo considerável variabilidade genética, a região 5' não codificante (5'RNC) do genoma viral é relativamente bem conservada entre todos os genótipos Existem evidências da presença nestes domínios de um sítio de entrada interno do ribossomo (IRES) que permite a tradução cap-independente do RNA viral. A variabilidade na região da proteína não estrutural NS5A, designada “Região Determinante da Suscetibilidade ao interferon” (ISDR), foi associada à resistência ou sensibilidade a terapia com interferon-α. A partir das seqüências obtidas, foram realizadas predições da estrutura secundária da 5' RNC pelos programas RNAfold, RNApdist e RNAshapes. Também foram realizados experimentos de transfecção in vivo a fim de testar a funcionalidade da 5' RNC. A correlação entre variações nas regiões 5' NRC e NS5A e resposta terapêutica, entre os grupos não respondedores e respondedores (NR e R) foram realizadas através de parâmetros de genética molecular. A Energia Livre Mínima (ELM) calculada através do RNAfold sofreu maior influência da posição do que com o número de substituições. Os resultados do RNAshapes mostraram diferenças na probabilidade de predição das shapes, reforçando a idéia de que as substituições alteram a estrutura secundária. Os resultados do RNApdist também mostraram que algumas substituições tem um impacto sobre a predição da estrutura secundária. A heterogeneidade da seqüência da 5' RNC conduziu importantes alterações na eficiência de tradução, implicando que as interações entre o RNA e fatores de tradução podem variar de acordo com o tipo de células. As regiões 5' RNC e NS5A apresentaram baixa variabilidade genética. Apenas a 5' RNC apresentou desvio da neutralidade e significativa variabilidade molecular nos dois grupos estudados (NR e R). A análise filogenética mostrou nenhuma correlação entre variações na seqüência e a. resposta terapêutica