Genetic relationships among mastitis and alternative somatic cell count traits in the first 3 lactations of Swedish Holsteins

The objectives of this study were to estimate heritabilities of, and genetic correlations among, clinical mastitis (CM), subclinical mastitis (SCM), and alternative somatic cell count (SCC) traits in the first 3 lactations of Swedish Holstein cows, and to estimate genetic correlations for the alternative traits across lactations. Data from cows having their first calving between 2002 and 2009 were used. The alternative SCC traits were based on information on CM and monthly test-day (TD) records of SCC traits of 178,613, 116,079, and 64,474 lactations in first, second, or third parity, respectively. Sires had an average of 230, 165, or 124 daughters in the data (parities 1, 2, or 3, respectively). Subclinical mastitis was defined as the number of periods with an SCC >150,000 cell/mL and without a treatment for CM. Average TD SCC between 5 and 150 d was used as a reference trait. The alternative SCC traits analyzed were 1) presence of at least 1 TD SCC between 41,000 and 80,000 cell/mL (TD41-80), 2) at least 1 TD SCC >500,000 cells/mL, 3) standard deviation of log SCC over the lactation, 4) number of infection peaks, and 5) average days diseased per peak. The same variables in different parities were treated as distinct traits. The statistical model considered the effects of herd-year, year, month, age at calving, animal, and residual. Heritability estimates were 0.07 to 0.08 for CM, 0.12 to 0.17 for SCM, and 0.14 for SCC150. For the alternative traits, heritability estimates were 0.12 to 0.17 for standard deviation of log SCC, TD SCC >500,000 cells/mL, and average days diseased per peak, and 0.06 to 0.10 for TD41-80 and number of infection peaks. Genetic correlations between CM with SCM were 0.62 to 0.74, and correlations for these traits with the alternative SCC traits were positive and very high (0.67 to 0.82 for CM, and 0.94 to 0.99 for SCM). Trait TD41-80 was the only alternative trait that showed negative, favorable, genetic correlations with CM (-0.22 to -0.50) and SCM (-0.48 to -0.85) because it is associated with healthy cows. Genetic correlations among the alternative traits in all 3 parities were high (0.93 to 0.99, 0.92 to 0.98, and 0.78 to 0.99, respectively). The only exception was TD41-80, which showed moderate to strong negative correlations with the rest of the traits. Genetic correlations of the same trait across parities were in general positive and very high (0.83 to 0.99). In conclusion, these alternative SCC traits could be used in practical breeding programs aiming to improve udder health in dairy cattle

Genetic variants of Anaplasma phagocytophilum from 14 equine granulocytic anaplasmosis cases

<p>Abstract</p> <p>Background</p> <p>Equine Granulocytic Anaplasmosis (EGA) is caused by <it>Anaplasma phagocytophilum</it>, a tick-transmitted, obligate intracellular bacterium. In Europe, it is transmitted by <it>Ixodes ricinus</it>. A large number of genetic variants of <it>A. phagocytophilum </it>circulate in nature and have been found in ticks and different animals. Attempts have been made to assign certain genetic variants to certain host species or pathologies, but have not been successful so far. The purpose of this study was to investigate the causing agent <it>A. phagocytophilum </it>of 14 cases of EGA in naturally infected horses with molecular methods on the basis of 4 partial genes (<it>16S rRNA</it>, <it>groEL</it>, <it>msp2</it>, and <it>msp4</it>).</p> <p>Results</p> <p>All DNA extracts of EDTA-blood samples of the horses gave bands of the correct nucleotide size in all four genotyping PCRs. Sequence analysis revealed 4 different variants in the partial <it>16S rRNA</it>, <it>groEL </it>gene and <it>msp2 </it>genes, and 3 in the <it>msp4 </it>gene. One <it>16S rRNA </it>gene variant involved in 11 of the 14 cases was identical to the "prototype" variant causing disease in humans in the amplified part [GenBank: <ext-link ext-link-id="U02521" ext-link-type="gen">U02521</ext-link>]. Phylogenetic analysis revealed as expected for the <it>groEL </it>gene that sequences from horses clustered separately from roe deer. Sequences of the partial <it>msp2 </it>gene from this study formed a separate cluster from ruminant variants in Europe and from all US variants.</p> <p>Conclusions</p> <p>The results show that more than one variant of <it>A. phagocytophilum </it>seems to be involved in EGA in Germany. The comparative genetic analysis of the variants involved points towards different natural cycles in the epidemiology of <it>A. phagocytophilum</it>, possibly involving different reservoir hosts or host adaptation, rather than a strict species separation.</p

A graph-search framework for associating gene identifiers with documents

BACKGROUND: One step in the model organism database curation process is to find, for each article, the identifier of every gene discussed in the article. We consider a relaxation of this problem suitable for semi-automated systems, in which each article is associated with a ranked list of possible gene identifiers, and experimentally compare methods for solving this geneId ranking problem. In addition to baseline approaches based on combining named entity recognition (NER) systems with a "soft dictionary" of gene synonyms, we evaluate a graph-based method which combines the outputs of multiple NER systems, as well as other sources of information, and a learning method for reranking the output of the graph-based method. RESULTS: We show that named entity recognition (NER) systems with similar F-measure performance can have significantly different performance when used with a soft dictionary for geneId-ranking. The graph-based approach can outperform any of its component NER systems, even without learning, and learning can further improve the performance of the graph-based ranking approach. CONCLUSION: The utility of a named entity recognition (NER) system for geneId-finding may not be accurately predicted by its entity-level F1 performance, the most common performance measure. GeneId-ranking systems are best implemented by combining several NER systems. With appropriate combination methods, usefully accurate geneId-ranking systems can be constructed based on easily-available resources, without resorting to problem-specific, engineered components

Sperm design and variation in the New World blackbirds (Icteridae)

Post-copulatory sexual selection (PCSS) is thought to be one of the evolutionary forces responsible for the rapid and divergent evolution of sperm design. However, whereas in some taxa particular sperm traits are positively associated with PCSS, in other taxa, these relationships are negative, and the causes of these different patterns across taxa are poorly understood. In a comparative study using New World blackbirds (Icteridae), we tested whether sperm design was influenced by the level of PCSS and found significant positive associations with the level of PCSS for all sperm components but head length. Additionally, whereas the absolute length of sperm components increased, their variation declined with the intensity of PCSS, indicating stabilizing selection around an optimal sperm design. Given the diversity of, and strong selection on, sperm design, it seems likely that sperm phenotype may influence sperm velocity within species. However, in contrast to other recent studies of passerine birds, but consistent with several other studies, we found no significant link between sperm design and velocity, using four different species that vary both in sperm design and PCSS. Potential reasons for this discrepancy between studies are discussed

Predicting the recipients of social work support and its impact on emotional and behavioural problems in early childhood

This paper examines the recipients of social work support in the Millennium Cohort Study. Using panel analysis and fixed effects models it investigates the factors that lead to the receipt of any type of social work support for individuals with young children, and the effects of this support on changes in the prevalence of emotional and behavioural problems in these children. We find that divorce or separation, and episodes of homelessness are two important factors that lead to the receipt of social work support. Mothers with male children are also more likely to receive social work support. However, we find no clear evidence that social work support has any effect on changes in children’s emotional and behavioural problems over time. The implications of these findings for social work research, and for practice and policy are discussed

The landscape of a Swedish boat-grave cemetery

This is the published PDF version of an article published in Landscapes© 2010. The definitive version is available at http://www.maneyonline.com/toc/lan/11/1The paper integrates topographical and experiential approaches to the mortuary landscape of a Viking period inhumation-grave excavated in 2005 within the cemetery at Skamby, Kuddy parish, Östergötland province, Sweden. We argue that the landscape context was integral to the performance of the funerary ceremonies and the subsequent monumental presence of the dead in the landscape. We offer a way to move beyond monocausal explanations for burial location based on single-scale analyses. Instead, we suggest that boat-inhumation at Skamby was a commemorative strategy that operated on multiple scales and drew its significance from multiple landscape attributes.British Academ

Fifteen new risk loci for coronary artery disease highlight arterial-wall-specific mechanisms

Coronary artery disease (CAD) is a leading cause of morbidity and mortality worldwide. Although 58 genomic regions have been associated with CAD thus far, most of the heritability is unexplained, indicating that additional susceptibility loci await identification. An efficient discovery strategy may be larger-scale evaluation of promising associations suggested by genome-wide association studies (GWAS). Hence, we genotyped 56,309 participants using a targeted gene array derived from earlier GWAS results and performed meta-analysis of results with 194,427 participants previously genotyped, totaling 88,192 CAD cases and 162,544 controls. We identified 25 new SNP-CAD associations (P &lt; 5 × 10(-8), in fixed-effects meta-analysis) from 15 genomic regions, including SNPs in or near genes involved in cellular adhesion, leukocyte migration and atherosclerosis (PECAM1, rs1867624), coagulation and inflammation (PROCR, rs867186 (p.Ser219Gly)) and vascular smooth muscle cell differentiation (LMOD1, rs2820315). Correlation of these regions with cell-type-specific gene expression and plasma protein levels sheds light on potential disease mechanisms