Assessment of autozygosity in Nellore cows (Bos indicus) through high-density SNP genotypes.

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Effectiveness of probiotic in preventing and treating antibiotic-associated diarrhoea and/or Clostridium difficile-associated diarrhoea in patients with spinal cord injury: a protocol of systematic review of randomised controlled trials

BACKGROUND: Probiotics may prevent antibiotic-associated and Clostridium difficile-associated diarrhoea (AAD/CDAD). Many spinal cord injury centre (SCIC) practitioners consider probiotics generically and may not realise that efficacy can be strain-, dose- and disease-specific. In order to confirm these effects and fully evaluate the extent of probiotic effectiveness in these patients, a systematic review and meta-analysis is indicated. METHODS: The following databases will be searched for relevant studies: Cochrane Library; Centre for Reviews and Dissemination (CRD) Database; CINAHL; PsycINFO; Embase; Medline; AMED; International Clinical Trials Registry Platform Search Portal and ISRCTN Registry and will hand search a list of conference proceedings. Any randomised controlled trials without restriction of publication status will be included with treatment of AAD/CDAD. Outcomes will include the effect of probiotic on the occurrence of AAD/CDAD and duration of diarrhoea, intensive care unit admission, hospital mortality and length of hospital stay. Two reviewers will independently screen the titles, abstracts or even full texts and extract data. Two other reviewers will assess study quality. Revman 5.1 software will be used to conduct meta-analysis and calculate the risk ratio for dichotomous data. Weighted mean difference or standard mean difference will be calculated for continuous data. The Cochrane Collaboration's tool will be used to assess the risk of bias. DISCUSSION: This systematic review protocol will provide information on probiotic therapy for AAD and CDAD in spinal cord injury (SCI) population. The results will be disseminated through peer-reviewed publication or conference presentation. SYSTEMATIC REVIEW REGISTRATION: PROSPERO CRD42015016976

A whole-genome assembly of the domestic cow, Bos taurus

Background: The genome of the domestic cow, Bos taurus, was sequenced using a mixture of hierarchical and whole-genome shotgun sequencing methods. Results: We have assembled the 35 million sequence reads and applied a variety of assembly improvement techniques, creating an assembly of 2.86 billion base pairs that has multiple improvements over previous assemblies: it is more complete, covering more of the genome; thousands of gaps have been closed; many erroneous inversions, deletions, and translocations have been corrected; and thousands of single-nucleotide errors have been corrected. Our evaluation using independent metrics demonstrates that the resulting assembly is substantially more accurate and complete than alternative versions. Conclusions: By using independent mapping data and conserved synteny between the cow and human genomes, we were able to construct an assembly with excellent large-scale contiguity in which a large majority (approximately 91%) of the genome has been placed onto the 30 B. taurus chromosomes. We constructed a new cow-human synteny map that expands upon previous maps. We also identified for the first time a portion of the B. taurus Y chromosome. © 2009 Zimin et al.; licensee BioMed Central Ltd

The Antioxidant Potential of the Mediterranean Diet in Patients at High Cardiovascular Risk: An In-Depth Review of the PREDIMED

Cardiovascular disease (CVD) is the leading global cause of death. Diet is known to be important in the prevention of CVD. The PREDIMED trial tested a relatively low-fat diet versus a high-fat Mediterranean diet (MedDiet) for the primary prevention of CVD. The resulting reduction of the CV composite outcome resulted in a paradigm shift in CV nutrition. Though many dietary factors likely contributed to this effect, this review focuses on the influence of the MedDiet on endogenous antioxidant systems and the effect of dietary polyphenols. Subgroup analysis of the PREDIMED trial revealed increased endogenous antioxidant and decreased pro-oxidant activity in the MedDiet groups. Moreover, higher polyphenol intake was associated with lower incidence of the primary outcome, overall mortality, blood pressure, inflammatory biomarkers, onset of new-onset type 2 diabetes mellitus (T2DM), and obesity. This suggests that polyphenols likely contributed to the lower incidence of the primary event in the MedDiet groups. In this article, we summarize the potential benefits of polyphenols found in the MedDiet, specifically the PREDIMED cohort. We also discuss the need for further research to confirm and expand the findings of the PREDIMED in a non-Mediterranean population and to determine the exact mechanisms of action of polyphenols

High-resolution haplotype block structure in the cattle genome

<p>Abstract</p> <p>Background</p> <p>The Bovine HapMap Consortium has generated assay panels to genotype ~30,000 single nucleotide polymorphisms (SNPs) from 501 animals sampled from 19 worldwide taurine and indicine breeds, plus two outgroup species (Anoa and Water Buffalo). Within the larger set of SNPs we targeted 101 high density regions spanning up to 7.6 Mb with an average density of approximately one SNP per 4 kb, and characterized the linkage disequilibrium (LD) and haplotype block structure within individual breeds and groups of breeds in relation to their geographic origin and use.</p> <p>Results</p> <p>From the 101 targeted high-density regions on bovine chromosomes 6, 14, and 25, between 57 and 95% of the SNPs were informative in the individual breeds. The regions of high LD extend up to ~100 kb and the size of haplotype blocks ranges between 30 bases and 75 kb (10.3 kb average). On the scale from 1–100 kb the extent of LD and haplotype block structure in cattle has high similarity to humans. The estimation of effective population sizes over the previous 10,000 generations conforms to two main events in cattle history: the initiation of cattle domestication (~12,000 years ago), and the intensification of population isolation and current population bottleneck that breeds have experienced worldwide within the last ~700 years. Haplotype block density correlation, block boundary discordances, and haplotype sharing analyses were consistent in revealing unexpected similarities between some beef and dairy breeds, making them non-differentiable. Clustering techniques permitted grouping of breeds into different clades given their similarities and dissimilarities in genetic structure.</p> <p>Conclusion</p> <p>This work presents the first high-resolution analysis of haplotype block structure in worldwide cattle samples. Several novel results were obtained. First, cattle and human share a high similarity in LD and haplotype block structure on the scale of 1–100 kb. Second, unexpected similarities in haplotype block structure between dairy and beef breeds make them non-differentiable. Finally, our findings suggest that ~30,000 uniformly distributed SNPs would be necessary to construct a complete genome LD map in <it>Bos taurus </it>breeds, and ~580,000 SNPs would be necessary to characterize the haplotype block structure across the complete cattle genome.</p

Lectin activity of the pneumococcal pilin proteins

Streptococcus pneumoniae is a leading cause of morbidity and mortality globally. The Pilus-1 proteins, RrgA, RrgB and RrgC of S. pneumoniae have been previously assessed for their role in infection, invasive disease and as possible vaccine candidates. In this study we have investigated the glycan binding repertoire of all three Pilus-1 proteins, identifying that the tip adhesin RrgA has the broadest glycan recognition of the three proteins, binding to maltose/cellobiose, α/β linked galactose and blood group A and H antigens. RrgB only bound mannose, while RrgC bound a subset of glycans also recognized by RrgA. Adherence of S. pneumoniae TIGR4 to epithelial cells was tested using four of the oligosaccharides identified through the glycan array analysis as competitive inhibitors. The blood group H trisaccharide provided the best blocking of S. pneumoniae TIGR4 adherence. Adherence is the first step in disease, and host glycoconjugates are a common target for many adhesins. This study has identified Pilus-1 proteins as new lectins involved in the targeting of host glycosylation by S. pneumoniae.Christopher J. Day, Adrienne W. Paton, Richard M. Harvey, Lauren E. Hartley-Tassell, Kate L. Seib, Joe Tiralongo, Nicolai Bovin, Silvana Savino, Vega Masignani, James C. Paton and Michael P. Jenning

Reliability of Bioelectrical Impedance Analysis for Estimating Whole‐Fish Energy Density and Percent Lipids

We evaluated bioelectrical impedance analysis (BIA) as a nonlethal means of predicting energy density and percent lipids for three fish species: Yellow perch Perca flavescens, walleye Sander vitreus, and lake whitefish Coregonus clupeaformis. Although models that combined BIA measures with fish wet mass provided strong predictions of total energy, total lipids, and total dry mass for whole fish, including BIA provided only slightly better predictions than using fish mass alone. Regression models that used BIA measures to directly predict the energy density or percent lipids of whole fish were generally better than those using body mass alone (based on Akaike’s information criterion). However, the goodness of fit of models that used BIA measures varied widely across species and at best explained only slightly more than one‐half the variation observed in fish energy density or percent lipids. Models that combined BIA measures with body mass for prediction had the strongest correlations between predicted and observed energy density or percent lipids for a validation group of fish, but there were significant biases in these predictions. For example, the models underestimated energy density and percent lipids for lipid‐rich fish and overestimated energy density and percent lipids for lipid‐poor fish. A comparison of observed versus predicted whole‐fish energy densities and percent lipids demonstrated that models that incorporated BIA measures had lower maximum percent error than models without BIA measures in them, although the errors for the BIA models were still generally high (energy density: 15‐18%; percent lipids: 82‐89%). Considerable work is still required before BIA can provide reliable predictions of whole‐fish energy density and percent lipids, including understanding how temperature, electrode placement, and the variation in lipid distribution within a fish affect BIA measures.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/141722/1/tafs1519.pd

Point of Care Nucleic Acid Testing for SARS-CoV-2 in Hospitalized Patients: A Clinical Validation Trial and Implementation Study

There is an urgent need for rapid SARS-CoV-2 testing in hospitals to limit nosocomial spread. We report an evaluation of point of care (POC) nucleic acid amplification testing (NAAT) in 149 participants with parallel combined nasal and throat swabbing for POC versus standard lab RT-PCR testing. Median time to result is 2.6 (IQR 2.3–4.8) versus 26.4 h (IQR 21.4–31.4, p < 0.001), with 32 (21.5%) positive and 117 (78.5%) negative. Cohen’s κ correlation between tests is 0.96 (95% CI 0.91–1.00). When comparing nearly 1,000 tests pre- and post-implementation, the median time to definitive bed placement from admission is 23.4 (8.6-41.9) versus 17.1 h (9.0–28.8), p = 0.02. Mean length of stay on COVID-19 “holding” wards is 58.5 versus 29.9 h (p < 0.001). POC testing increases isolation room availability, avoids bed closures, allows discharge to care homes, and expedites access to hospital procedures. POC testing could mitigate the impact of COVID-19 on hospital systems