Use of testicular tone and echogenicity in identifying boars with low sperm quality / Uso de tônus e ecogenicidade testiculares na identificação de reprodutores suínos com baixa qualidade espermática

This study aimed to evaluate the use of some testicular traits to identify boars with low sperm morphological quality. The consistency (scores from 1 to 5), tone with tonometry (mm), parenchyma echogenicity and heterogeneity with ultrasound (pixel) were assessed in 402 mature boars (18.5 months on average). Sperm abnormality thresholds (≤ 25% of total sperm abnormalities, ≤ 5% of heads, acrosome, neck or midpiece defects, ≤ 10% tail defects, and 15% cytoplasmic droplets) were used to classify boars as approved or disapproved. Three classes of testicular traits were formed (extremely low and high values, approximately 15% each, were kept in separated classes). When the traits were individually evaluated, fewer boars were approved if the echogenicity or heterogeneity were high, or if the tone was rigid. When evaluated in combination, the interaction between heterogeneity and tone, and between heterogeneity and echogenicity were significant. The high heterogeneity combined with soft tone or with hypo-echogenicity resulted in lower approval of boars. Tonometry and ultrasonography have a moderate potential to be included in breeding soundness examination of boars. When combined, they provide more reliable information about the impact of testicular parenchymal alterations on morphology of sperm cells.(AU)

O estudo objetivou avaliar o uso de características testiculares para identificar reprodutores com baixa qualidade de morfologia espermática. A consistência (escore de 1 a 5), o tônus por tonometria (mm), a ecogenicidade e a heterogeneidade do parênquima testicular por ultrassonografia (pixel) foram avaliados em 402 machos suínos maduros (18,5 meses, em média). Limiares máximos de anormalidades espermáticas (≤ 25% de defeitos totais, ≤ 5% de defeitos de cabeça, acrossoma, colo e peça intermediária, ≤ 10% de defeitos de cauda e 15% de gota citoplasmática) foram utilizados para classificar os machos como aprovados ou reprovados. Três classes de características testiculares foram formadas (valores extremamente baixos e altos, aproximadamente 15% em cada, foram mantidos em classes separadas). Quando as características testiculares foram avaliadas individualmente, menos machos foram aprovados se a ecogenicidade ou a heterogeneidade foram altas, ou se o tônus era rígido. Quando avaliadas em combinação, a interação entre heterogeneidade e tônus e a interação entre heterogeneidade e ecogenicidade foram significativas. A alta heterogeneidade combinada com testículos flácidos ou com testículos hipoecogênicos resultou em menor aprovação de cachaços. A tonometria e a ultrassonografia possuem potencial moderado para serem incluídas no exame andrológico de cachaços. Quando combinadas, as técnicas fornecem uma informação mais consistente do impacto das alterações do parênquima testicular na morfologia das células espermáticas.(AU)

Risk factors for gastrointestinal parasite infections of dogs living around protected areas of the Atlantic Forest: implications for human and wildlife health / Fatores de risco para infecções parasitárias gastrointestinais em cães do entorno de áreas protegidas da Mata Atlântica: implicações para a saúde humana e da vida selvagem

Abstract Despite the ubiquity of domestic dogs, their role as zoonotic reservoirs and the large number of studies concerning parasites in urban dogs, rural areas in Brazil, especially those at the wildlife-domestic animal-human interface, have received little attention from scientists and public health managers. This paper reports a cross-sectional epidemiological survey of gastrointestinal parasites of rural dogs living in farms around Atlantic Forest fragments. Through standard parasitological methods (flotation and sedimentation), 13 parasite taxa (11 helminths and two protozoans) were found in feces samples from dogs. The most prevalent were the nematode Ancylostoma (47%) followed by Toxocara (18%) and Trichuris (8%). Other less prevalent (<2%) parasites found were Capillaria, Ascaridia, Spirocerca, Taeniidae, Acantocephala, Ascaris, Dipylidium caninum, Toxascaris, and the protozoans Cystoisospora and Eimeria. Mixed infections were found in 36% of samples, mostly by Ancylostoma and Toxocara. Previous deworming had no association with infections, meaning that this preventive measure is being incorrectly performed by owners. Regarding risk factors, dogs younger than one year were more likely to be infected with Toxocara, and purebred dogs with Trichuris. The number of cats in the households was positively associated with Trichuris infection, while male dogs and low body scores were associated with mixed infections. The lack of associations with dog free-ranging behavior and access to forest or villages indicates that infections are mostly acquired around the households. The results highlight the risk of zoonotic and wildlife parasite infections from dogs and the need for monitoring and controlling parasites of domestic animals in human-wildlife interface areas.

Resumo Apesar da ubiquidade dos cães domésticos, de seu papel como reservatório de doenças, e do grande número de estudos sobre parasitas de cães urbanos, as áreas rurais no Brasil, especialmente aquelas na interface entre animais silvestres - animais domésticos - humanos, tem recebido pouca atenção de cientistas e gestores de saúde pública. Este artigo relata um estudo epidemiológico seccional de parasitas gastrointestinais de cães rurais em propriedades no entorno de fragmentos de Mata Atlântica. Através de métodos parasitológicos como flutuação e sedimentação, 13 táxons de parasitas (11 helmintos e dois protozoários) foram encontrados em amostras de fezes dos cães. O mais prevalente foi o nematóide Ancylostoma (47%), seguido por Toxocara (18%) e Trichuris (8%). Outros parasitas menos prevalentes (<2%) encontrados foram Capillaria, Ascaridia, Spirocerca, Taeniidae, Acantocephala, Ascaris, Dipylidium caninum, Toxascaris, e os protozoários Cystoisospora and Eimeria. Infecções mistas foram detectadas em 36% das amostras, a maioria por Ancylostoma e Toxocara. Vermifugações prévias não foram associadas a infecções, indicando que esta medida preventiva está sendo realizada incorretamente pelos proprietários. Com relação aos fatores de risco, cães com menos de um ano tiveram maior probabilidade de infecção por Toxocara, e os cães de raça pura por Trichuris. O número de gatos na propriedade foi associado positivamente com a infecção por Trichuris, enquanto cães machos e baixos escores corporais foram associados a infecções mistas. A ausência de associações com comportamento de vida livre e acesso a florestas ou vilas pelos cães indica que as infecções estão sendo predominantemente adquiridas nas propriedades. Os resultados destacam o risco de infecções parasitárias zoonóticas e para animais silvestres a partir dos cães, e a necessidade de monitorar e controlar os parasitas de animais domésticos em áreas de interface entre humanos e a vida selvagem.

Risk factors for gastrointestinal parasite infections of dogs living around protected areas of the Atlantic Forest: implications for human and wildlife health.

Despite the ubiquity of domestic dogs, their role as zoonotic reservoirs and the large number of studies concerning parasites in urban dogs, rural areas in Brazil, especially those at the wildlife-domestic animal-human interface, have received little attention from scientists and public health managers. This paper reports a cross-sectional epidemiological survey of gastrointestinal parasites of rural dogs living in farms around Atlantic Forest fragments. Through standard parasitological methods (flotation and sedimentation), 13 parasite taxa (11 helminths and two protozoans) were found in feces samples from dogs. The most prevalent were the nematode Ancylostoma (47%) followed by Toxocara (18%) and Trichuris (8%). Other less prevalent (<2%) parasites found were Capillaria, Ascaridia, Spirocerca, Taeniidae, Acantocephala, Ascaris, Dipylidium caninum, Toxascaris, and the protozoans Cystoisospora and Eimeria. Mixed infections were found in 36% of samples, mostly by Ancylostoma and Toxocara. Previous deworming had no association with infections, meaning that this preventive measure is being incorrectly performed by owners. Regarding risk factors, dogs younger than one year were more likely to be infected with Toxocara, and purebred dogs with Trichuris. The number of cats in the households was positively associated with Trichuris infection, while male dogs and low body scores were associated with mixed infections. The lack of associations with dog free-ranging behavior and access to forest or villages indicates that infections are mostly acquired around the households. The results highlight the risk of zoonotic and wildlife parasite infections from dogs and the need for monitoring and controlling parasites of domestic animals in human-wildlife interface areas.

miRQuest: integration of tools on a Web server for microRNA research.

This report describes the miRQuest - a novel middleware available in a Web server that allows the end user to do the miRNA research in a user-friendly way. It is known that there are many prediction tools for microRNA (miRNA) identification that use different programming languages and methods to realize this task. It is difficult to understand each tool and apply it to diverse datasets and organisms available for miRNA analysis. miRQuest can easily be used by biologists and researchers with limited experience with bioinformatics. We built it using the middleware architecture on a Web platform for miRNA research that performs two main functions: i) integration of different miRNA prediction tools for miRNA identification in a user-friendly environment; and ii) comparison of these prediction tools. In both cases, the user provides sequences (in FASTA format) as an input set for the analysis and comparisons. All the tools were selected on the basis of a survey of the literature on the available tools for miRNA prediction. As results, three different cases of use of the tools are also described, where one is the miRNA identification analysis in 30 different species. Finally, miRQuest seems to be a novel and useful tool; and it is freely available for both benchmarking and miRNA identification at http://mirquest.integrativebioinformatics.me/.

Gastrointestinal parasites of maned wolf (Chrysocyon brachyurus, Illiger 1815) in a suburban area in southeastern Brazil.

We examined 42 maned wolf scats in an unprotected and disturbed area of Cerrado in southeastern Brazil. We identified six helminth endoparasite taxa, being Phylum Acantocephala and Family Trichuridae the most prevalent. The high prevalence of the Family Ancylostomatidae indicates a possible transmission via domestic dogs, which are abundant in the study area. Nevertheless, our results indicate that the endoparasite species found are not different from those observed in protected or least disturbed areas, suggesting a high resilience of maned wolf and their parasites to human impacts, or a common scenario of disease transmission from domestic dogs to wild canid whether in protected or unprotected areas of southeastern Brazil.

CoffeebEST: an integrated resource for Coffea spp expressed sequence tags.

Coffee is one of the most important commodities in the world, and its production relies mainly on two species, Coffea arabica and Coffea canephora. Although there are diverse transcriptome datasets available for coffee trees, few research groups have exploited the potential knowledge contained in these data, especially with respect to fruit and seed development. Here, we present a comparative analysis of the transcriptomes of Coffea arabica and Coffea canephora with a focus on fruit development using publicly available expressed sequence tags (ESTs). Most of the fruit and seed EST data has been obtained from C. canephora. Therefore, we performed a fruit EST analysis of the 5 developmental stages of this species (18, 22, 30, 42, and 46 weeks after flowering) comprising 29,009 sequences. We compared C. canephora fruit ESTs to reference unigenes of C. canephora (7710 contigs and 8955 singletons) and C. arabica (15,656 contigs and 16,351 singletons). Additional analyses included functional annotation based on Gene Onthology, as well as an annotation using PlantCyc, a curated plant protein database. The Coffee Bean EST (CoffeebEST) is a public database available at http://bioinfo-02.cp.utfpr.edu.br/. This database represents an additional resource for the coffee scientific community, offering a user-friendly collection of information for non-specialists in coffee molecular biology to support experimental research on comparative and functional genomics.

Prediction of potential novel microRNAs in soybean when in symbiosis.

MicroRNAs (miRNAs) are small molecules, noncoding proteins that are involved in many biological processes, especially in plants; among these processes is nodulation in the legume. Biological nitrogen fixation is a key process, with critical importance to the soybean crop. This study aimed to identify the potential of novel miRNAs to act during the root nodulation process. We utilized a set of transcripts that were differentially expressed in soybean roots 10 days after inoculation with Bradyrhizobium japonicum, which were obtained in a previous study, and performed a set of computational analyses that led us to select new miRNAs potentially involved in nodulation. Among these analyses, the set of transcripts were submitted to an in silico annotation of noncoding RNAs, including a search of similarity against miRNA public databases, ab initio tools for miRNA identification, structural search against miRNA families, prediction of the secondary structure of miRNA precursors, and prediction of the sequences of mature miRNAs. Subsequently, we applied filter procedures based on miRNA selections described in the literature (e.g., free energy value). In the next step, a manual curation inspection of the annotation was performed and the top candidates were selected and used for prediction of potential target genes, which were later checked manually in the database of the soybean genome. This prediction led us to the identification of 9 potential new miRNAs; among these, 4 were conserved in other plants. Moreover, we predicted their target genes might play important roles in the regulation of nodulation.

High consumption of primates by pumas and ocelots in a remnant of the Brazilian Atlantic Forest.

We studied the diet of the ocelot and puma during the years 2007 and 2008 at the Feliciano Miguel Abdala Reserve, in Minas Gerais, south-eastern Brazil. We collected 49 faecal samples (scats) from cats, and identified the species of cat from 23 of them by the analysis of the microstructure patterns of hairs found in their faeces: 17 scats of the puma (Puma concolor) and six of the ocelot (Leopardus pardalis). In the puma scats, we identified three species of primates (Brachyteles hypoxanthus, Alouatta guariba and Sapajus nigritus), the remains of which were found in eight of 17 collected (47.1%), representing 26.7% of items consumed. For the ocelot, we detected capuchin monkey (S. nigritus) remains in three of the six scats (50%), accounting for 18.7% of items consumed by ocelot. We were unable to identify the cat species in the remaining 26 faecal samples, but we were able to analyse the food items present. Primates were found in five of these 26 faeces (19.2%) and represented 10.2% of the items found. Although the sample size is limited, our results indicate a relatively high consumption of primates by felines. We believe that this high predation may be the result of the high local density of primates as well as the greater exposure to the risks of predation in fragmented landscapes, which tends to increase the incidence of the primates using the ground.

Frequencia e causas de insucesso no tratamento das hernias inguinais. / Incidence and causes of failure in the treatment of inguinal hernias

Os autores assinalam a importancia do tratamento das hernias inguinais, ate agora exclusivamente cirurgico, entretanto acompanhado de recidivas que variam com a maior ou menor importancia com que se encare o problema. Sao analisados 312 casos operados, dos quais, compareceram a revisao pos-operatoria 73 pacientes. Destes, apresentaram recorrencia 11 pacientes. Sao analisadas as provaveis causas de recidiva, e sugeridas medidas para evita-las