Gene sequences and comparison of the fimbrial subunits representative of Bacteroides nodosus serotypes A to I: Class I and class II strains

We have determined the nucleotide sequences of the genes encoding the fimbrial subunits representative of the known Bacteroides nodosus serogroups. All of the genes are preceded by a highly conserved region which includes the likely promoter and transcriptional regulator sites as well as the ribosome-biding site, and are followed within a short but variable distance by a sequence with the characteristics of a transcription termination or attenuation signal. Based on sequence and organization, the subunits can be divided into two major classes called I (serogroups A, B, C, E, F, G, and I) and II (serogroups D and H). All contain the same seven-amino-acid positively charged leader sequence and conserved hydrophobic amino-terminal sequence typical of type 4 fibriae. Beyond this point the class II subunits are quite different from class I and share features more in common with those from other type 4 fimbriate bacteria, such as Moraxella bovis and Pseudomonas aeruginosa. The larger class I may be further subdivided into two subsets: (i) [A, E, F)(B, I)) and (ii) (C, G). These proteins exhibit three major clusters of variation, at either end of the presumptive disulphide loop which spans the central third of the protein, and near the carboxy-terimus, with dispersed changes in between. The length of the mature subunits varies from 152-156 amino acids, and the variation includes small insertions or deletions in the variable clusters between more conserved domains. The class II subunits are 149 amino acids in length and contain two pairs of cysteine residues: one is at the end of the amino-terminal conserved region, and the other is at the end of the protein. The major variation occurs in the central region of the molecule, and again small insertions or deletions are required to align adjacent conserved domains. There is also a striking absence of silent codon changes in the 5' coding region of all of these genes, indicating that these sequences have a secondary genetic function, probably in recombinational exchange

Molecular cytogenetics and gene mapping in sheep (Ovis aries, 2n = 54)

The development of a completely annotated sheep genome sequence is a key need for understanding the phylogenetic relationships and genetic diversity among the many different sheep breeds worldwide and for identifying genes controlling economically and physiologically important traits. The ovine genome sequence assembly will be crucial for developing optimized breeding programs based on highly productive, healthy sheep phenotypes that are adapted to modern breeding and production conditions. Scientists and breeders around the globe have been contributing to this goal by generating genomic and cDNA libraries, performing genome-wide and trait-associated analyses of polymorphism, expression analysis, genome sequencing, and by developing virtual and physical comparative maps. The International Sheep Genomics Consortium (ISGC), an informal network of sheep genomics researchers, is playing a major role in coordinating many of these activities. In addition to serving as an essential tool for monitoring chromosome abnormalities in specific sheep populations, ovine molecular cytogenetics provides physical anchors which link and order genome regions, such as sequence contigs, genes and polymorphic DNA markers to ovine chromosomes. Likewise, molecular cytogenetics can contribute to the process of defining evolutionary breakpoints between related species. The selective expansion of the sheep cytogenetic map, using loci to connect maps and identify chromosome bands, can substantially contribute to improving the quality of the annotated sheep genome sequence and will also accelerate its assembly. Furthermore, identifying major morphological chromosome anomalies and micro-rearrangements, such as gene duplications or deletions, that might occur between different sheep breeds and other Ovis species will also be important to understand the diversity of sheep chromosome structure and its implications for cross-breeding. To date, 566 loci have been assigned to specific chromosome regions in sheep and the new cytogenetic map is presented as part of this review. This review will also summarize the current cytogenomic status of the sheep genome, describe current activities in the sheep cytogenomics research sector, and will discuss the cytogenomics data in context with other major sheep genomics projects

Perfil fenotípico de linfócitos periféricos de bovinos de raças européias Phenotypic profile of peripheral blood lymphocytes from European bovines

<abstract language="eng">The phenotypic profile of bovine lymphocytes was evaluated in 18 bovines (Bos taurus) from three different breeds, being nine Holstein, six Hereford, and three Brown Swiss. All animals were free from ticks and hemoparasites, as determined after jugular vein blood sampling. The immunophenotypes of peripheral lymphocytes were evaluated by flow cytometry. Peripheral lymphocytes were exposed to bovine fluorescein-labeled monoclonal antibodies including anti-CD4, anti-CD8, and anti-purified bovine CD21 specificities. After lysing the erythrocytes with a commercial lysing solution (FACS TM ), the lymphocytes were washed, fixed, and evaluated by flow cytometry. Significant differences in the phenotypic profiles of peripheral lymphocytes among all breeds were found. Holstein animals showed a lower percentage of total T lymphocytes (CD4 and CD8) and higher percentage of B lymphocytes (CD21). In addition, the lymphocytes from Holstein animals showed a lower T/B ratio than the lymphocytes from Hereford animals. These results suggest the existence of different phenotypic profiles of peripheral lymphocytes from European breeds of cattle. Such differences may be related to the different pattern of immune response described for these breeds in the literature and may account to varying disease resistance among breeds

Avaliação clínica e hematológica em bezerros Nelore infectados experimentalmente com isolados de Babesia bigemina das regiões Sudeste, Nordeste e Norte do Brasil Clinical and hematological evaluation of Nelore calves experimentally infected with isolates of Babesia bigemina from the Southeastern, Northeastern and Northern regions of Brazil

O presente trabalho teve por objetivo estudar comparativamente as alterações clínicas e hematológicas desencadeadas por isolados de Babesia bigemina das regiões Sudeste, Nordeste e Norte do Brasil em bezerros Nelore infectados experimentalmente. Foram utilizados 18 bezerros com idade entre sete e nove meses, isentos de anticorpos contra Babesia sp. e criados livres de carrapatos. Três animais foram previamente inoculados com 2,0x10(9) eritrócitos parasitados (EP) para cada isolado. Os outros 15 bezerros foram subdivididos em três grupos de cinco animais, que foram subinoculados com 1,0x10(10) EP dos respectivos isolados. Foram avaliadas as alterações clínicas e hematológicas por meio da determinação da parasitemia, do hemograma, do fibrinogênio plasmático, da contagem de reticulócitos, da análise descritiva da medula óssea e da fragilidade osmótica eritrocitária, no decorrer de 30 dias, perfazendo um total de sete momentos de observação. O acompanhamento da resposta imunológica pelo teste de imunofluorescência indireta foi realizado diariamente até o 10&ordm; dia pós-inoculação (DPI) e posteriormente no 15&ordm;, 20&ordm;, 25&ordm; e 30&ordm; DPI. Clinicamente, observou-se uma manifestação muito branda da doença. Os achados laboratoriais revelaram baixos níveis de parasitemia; decréscimo nos valores do eritrograma; ausência de reticulócitos; diminuição inicial na contagem total dos leucócitos, neutrófilos e linfócitos com posterior elevação do número destas células; hipercelularidade da série eritrocítica e decréscimo da relação mielóide:eritróide mais acentuada entre o 8&ordm; e 12&ordm; DPI e um aumento da fragilidade osmótica eritrocitária nos grupos inoculados com os isolados sudeste e nordeste. Nenhum dos três isolados de B. bigemina desencadeou a forma clínica característica da enfermidade, apesar de induzirem uma resposta imune humoral.<br>A comparative study was made regarding the clinical and hematological alterations caused by isolates of Babesia bigemina from southeastern, northeastern and northern Brazil in experimentally infected Nelore calves. Eighteen calves between 7 and 9 months of age, without antibodies against Babesia sp and raised free from ticks, were used. Three animals were previously inoculated with 2.0x10(9) parasitic erythrocytes (PE) for each stabilate. The other 15 calves were subdivided into three groups, with five animals each, that were subinoculated with 1.0x10(10) PE of the respective isolates. The clinical and hematological alterations were evaluated by the determination of parasitaemia, haemogram, plasmatic fibrinogen, reticulocyte count, descriptive analysis of the bone marrow and erythrocytic osmotic fragility, for 30 days, totalizing seven moments of observation. The follow-up of the immunological response by the indirect fluorescent antibody test was carried out daily until the 10th day after inoculation (DAI) and after that, on the 15th, 20th, 25th and 30th DAI. A mild clinical manifestation of the disease was observed. The laboratory findings revealed low levels of parasitaemia; decrease of the erythrogram values; absence of reticulocytes, initial decrease in the total count of leukocytes, neutrophils and lymphocytes with a posterior elevation of the number of these cells; hypercellularity of the erythrocytic series and decrease of the myeloid: erythroid relation which was more accentuated between the 8th and 12th DAI, and an increase of the erythrocytic osmotic fragility in the groups inoculated with the Southeast and Northeast isolates. None of the three isolates of B. bigemina gave rise to the clinical characteristic form of the disease, although they induced an humoral immune response

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical science. © The Author(s) 2019. Published by Oxford University Press