Design and analysis of genetical genomics studies and their potential applications in livestock research

Quantitative Trait Loci (QTL) mapping has been widely used to identify genetic loci attributable to the variation observed in complex traits. In recent years, gene expression phenotypes have emerged as a new type of quantitative trait for which QTL can be mapped. Locating sequence variation that has an effect on gene expression (eQTL) is thought to be a promising way to elucidate the genetic architecture of quantitative traits. This thesis explores a number of methodological aspects of eQTL mapping (also known as “genetical genomics”) and considers some practical strategies for applying this approach to livestock populations. One of the exciting prospects of genetical genomics is that the combination of expression studies with fine mapping of functional trait loci can guide the reconstruction of gene networks. The thesis begins with an analysis in which correlations between gene expression and meat quality traits in pigs are investigated in relation to a pork meat quality QTL previously identified. The influence on power due to factors including sample size and records of matched subjects is discussed. An efficient experimental design for two-colour microarrays is then put forward, and it is shown to be an effective use of microarrays for mapping additive eQTL in outbred crosses under simulation. However, designs optimised for detecting both additive and dominance eQTL are found to be less effective. Data collected from livestock populations usually have a pedigreed structure. Many family-based association mapping methods are rather computationally intensive, hence are time-consuming when analysing very large numbers of traits. The application of a novel family-based association method is demonstrated; it is shown to be fast, accurate and flexible for genetical genomics. Furthermore, the results show that multiple testing correction alone is not sufficient to control type I errors in genetical genomics and that careful data filtering is essential. While it is important to limit false positives, it is desirable not to miss many true signals. A multi-trait analysis based on grouping of functionally related genes is devised to detect some of the signals overlooked by a univariate analysis. Using an inbred rat dataset, 13 loci are identified with significant linkage to gene sets of various functions defined by Gene Ontology. Applying this method to livestock species is possible, but the current level of annotations is a limiting factor. Finally, the thesis concludes with some current opinions on the development of genetical genomics and its impact on livestock genetics research

Neural processes of proactive and reactive controls modulated by motor-skill experiences

This study investigated the experience of open and closed motor skills on modulating proactive and reactive control processes in task switching. Fifty-four participants who were open-skilled

Rapid and robust association mapping of expression quantitative trait loci

We applied a simple and efficient two-step method to analyze a family-based association study of gene expression quantitative trait loci (eQTL) in a mixed model framework. This two-step method produces very similar results to the full mixed model method, with our method being significantly faster than the full model. Using the Genetic Analysis Workshop 15 (GAW15) Problem 1 data, we demonstrated the value of data filtering for reducing the number of tests and controlling the number of false positives. Specifically, we showed that removing non-expressed genes by filtering on expression variability effectively reduced the number of tests by nearly 50%. Furthermore, we demonstrated that filtering on genotype counts substantially reduced spurious detection. Finally, we restricted our analysis to the markers and transcripts that were closely located. We found five times more signals in close proximity (cis-) to transcripts than in our genome-wide analysis. Our results suggest that careful pre-filtering and partitioning of data are crucial for controlling false positives and allowing detection of genuine effects in genetic analysis of gene expression

Long-term evaluation of cantilevered versus fixed–fixed resin-bonded fixed partial dentures for missing maxillary incisors

© 2016 Elsevier LtdObjectives To evaluate the long-term longevity and patient-reported outcomes of two-unit cantilevered (CL2) and three-unit fixed–fixed (FF3) resin-bonded fixed partial dentures (RBFPDs) for the replacement of a maxillary permanent incisor. Materials and methods Twenty-eight subjects were randomly assigned to receive either a CL2 or FF3 RBFPD placed by one operator. Prosthesis longevity was determined by clinical examination and history. Success was defined as absence of complications requiring intervention and survival as retention of the original prosthesis in mouth. Subjects’ satisfaction was assessed using visual analogue scale (VAS) and oral health-related quality of life (OHRQoL) using Oral Health Impact Profile (OHIP-49). Outcomes were analysed with t-test/Mann–Whitney U test, chi-square and log-rank test at significance level α = 0.05. Results Twenty-two subjects were reviewed. Thirteen of fifteen CL2 and ten of fourteen FF3 RBFPDs were examined (79.3 percent response rate) with a mean service life of 216.5 ± 20.8 months. All CL2 RBFPDs survived with no complications while only 10 percent of FF3 experienced no complications and only 50 percent of them survived (both P = 0.000). CL2 had a significantly better success and survival rate than FF3 (P = 0.000 and P = 0.009, respectively). There was no significant difference in subjects’ satisfaction and OHRQoL apart from CL2 group subjects had a higher satisfaction in cleaning of the prosthesis (84.1 ± 13.6) than FF3 group (72.6 ± 11.7) (P = 0.05). Conclusions Two-unit cantilevered RBFPDs were observed to have a significantly better success and survival than the FF3 design for the replacement of a maxillary incisor. Good patient-reported outcomes have been found for RBFPDs in single-tooth replacement in aesthetic zone.postprin

A combined strategy for quantitative trait loci detection by genome-wide association

We applied a range of genome-wide association (GWA) methods to map quantitative trait loci (QTL) in the simulated dataset provided by the 12th QTLMAS workshop in order to derive an effective strategy.A variance component linkage analysis revealed QTLs but with low resolution. Three single-marker based GWA methods were then applied: Transmission Disequilibrium Test and single marker regression, fitting an additive model or a genotype model, on phenotypes pre-corrected for pedigree and fixed effects. These methods detected QTL positions with high concordance to each other and with greater refinement of the linkage signals. Further multiple-marker and haplotype analyses confirmed the results with higher significance. Two-locus interaction analysis detected two epistatic pairs of markers that were not significant by marginal effects. Overall, using stringent Bonferroni thresholds we identified 9 additive QTL and 2 epistatic interactions, which together explained about 12.3% of the corrected phenotypic variance.The combination of methods that are robust against population stratification, like QTDT, with flexible linear models that take account of the family structure provided consistent results. Extensive simulations are still required to determine appropriate thresholds for more advanced model including epistasis

Restoring Ureagenesis in Hepatocytes by CRISPR/Cas9-mediated Genomic Addition to Arginase-deficient Induced Pluripotent Stem Cells.

Urea cycle disorders are incurable enzymopathies that affect nitrogen metabolism and typically lead to hyperammonemia. Arginase deficiency results from a mutation in Arg1, the enzyme regulating the final step of ureagenesis and typically results in developmental disabilities, seizures, spastic diplegia, and sometimes death. Current medical treatments for urea cycle disorders are only marginally effective, and for proximal disorders, liver transplantation is effective but limited by graft availability. Advances in human induced pluripotent stem cell research has allowed for the genetic modification of stem cells for potential cellular replacement therapies. In this study, we demonstrate a universally-applicable CRISPR/Cas9-based strategy utilizing exon 1 of the hypoxanthine-guanine phosphoribosyltransferase locus to genetically modify and restore arginase activity, and thus ureagenesis, in genetically distinct patient-specific human induced pluripotent stem cells and hepatocyte-like derivatives. Successful strategies restoring gene function in patient-specific human induced pluripotent stem cells may advance applications of genetically modified cell therapy to treat urea cycle and other inborn errors of metabolism

Satellite-derived Constraints on the Effect of Drought Stress on Biogenic Isoprene Emissions in the Southeast US

While substantial progress has been made to improve our understanding of biogenic isoprene emissions under unstressed conditions, there remain large uncertainties in isoprene emissions under stressed conditions. Here we use the US Drought Monitor (USDM) as a weekly drought severity index and tropospheric columns of formaldehyde (HCHO), the key product of isoprene oxidation, retrieved from the Ozone Monitoring Instrument (OMI) to derive top-down constraints on the response of summertime isoprene emissions to drought stress in the Southeast U.S. (SE US), a region of high isoprene emissions and prone to drought. OMI HCHO column density is found to be 5.3 % (mild drought) &ndash; 19.8 % (severe drought) higher than that in no-drought conditions. A global chemical transport model, GEOS-Chem, with the MEGAN2.1 emission algorithm can simulate this direction of change, but the simulated increases at the corresponding drought levels are 1.4&ndash;2.0 times of OMI HCHO, suggesting the need for a drought-stress algorithm in the model. By minimizing the model-to-OMI differences in HCHO to temperature sensitivity under different drought levels, we derived a top-down drought stress factor (&gamma;d_OMI) in GEOS-Chem that parameterizes using water stress and temperature. The algorithm led to an 8.6 % (mild drought) &ndash; 20.7 % (severe drought) reduction in isoprene emissions in the SE US relative to the simulation without it. With &gamma;d_OMI the model predicts a non-uniform trend of increase in isoprene emissions with drought severity that is consistent with OMI HCHO and a single site&rsquo;s isoprene flux measurements. Compared with a previous drought stress algorithm derived from the latter, the satellite-based drought stress factor performs better in capturing the regional scale drought-isoprene responses as indicated by the close-to-zero mean bias between OMI and simulated HCHO columns under different drought conditions. The drought stress algorithm also reduces the model&rsquo;s high bias in organic aerosols (OA) simulations by 6.60 % (mild drought) to 11.71 % (severe drought) over the SE US compared to the no-stress simulation. The simulated ozone response to the drought stress factor displays a spatial disparity due to the isoprene suppressing effect on oxidants, with an &lt;1 ppb increase in O3 in high-isoprene regions and a 1&ndash;3 ppbv decrease in O3 in low-isoprene regions. This study demonstrates the unique value of exploiting long-term satellite observations to develop empirical stress algorithms on biogenic emissions where in situ flux measurements are limited.</p

Inconsistent Adoption of World Health Organization V (2010) Semen Analysis Reference Ranges in the United States Six Years After Publication

Objective To determine the percentage of laboratories in the United States that have adopted the World Health Organization 2010 (WHO 5) semen analysis (SA) reference values six years after their publication. Methods Laboratories were identified via three approaches: using the Clinical Laboratory Improvement Amendments (CLIA) website, the CDC's 2015 Assisted Reproductive Technology Fertility Clinical Success Rate Report, and automated web searches. Laboratories were contacted by phone or email to obtain de-identified SA reports and reference ranges. Results We contacted 617 laboratories in 46 states, of which 208 (26.7%) laboratories in 45 states were included in our analysis. 132 (63.5%) laboratories used WHO 5 criteria, 57 (27.4%) used WHO 4 criteria, and 19 (9.1%) used other criteria. WHO 5 criteria adoption rates varied by geographic region, ranging from 87.5% (35/40) in the Midwest to 50.0% (33/66) in the West. There was a greater adoption rate of WHO 5 reference values in academic affiliated (23/26, 88.5%) compared to non-academic affiliated laboratories (110/182, 60.4%) (P=0.028). Conclusion While the majority of laboratories have adopted WHO 5 criteria following its release six years ago, a large percentage (36.5%) use what is now considered outdated criteria. This variability could result in the characterization of a male's semen values as being “within reference range” at one center and “outside of reference range” at another. This inconsistency in classification may result in confusion for the both patient and physician and potentially shift the burden of infertility evaluation and treatment to the female partner

A pleurocidin analogue with greater conformational flexibility, enhanced antimicrobial potency and in vivo therapeutic efficacy.

Antimicrobial peptides (AMPs) are a potential alternative to classical antibiotics that are yet to achieve a therapeutic breakthrough for treatment of systemic infections. The antibacterial potency of pleurocidin, an AMP from Winter Flounder, is linked to its ability to cross bacterial plasma membranes and seek intracellular targets while also causing membrane damage. Here we describe modification strategies that generate pleurocidin analogues with substantially improved, broad spectrum, antibacterial properties, which are effective in murine models of bacterial lung infection. Increasing peptide-lipid intermolecular hydrogen bonding capabilities enhances conformational flexibility, associated with membrane translocation, but also membrane damage and potency, most notably against Gram-positive bacteria. This negates their ability to metabolically adapt to the AMP threat. An analogue comprising D-amino acids was well tolerated at an intravenous dose of 15 mg/kg and similarly effective as vancomycin in reducing EMRSA-15 lung CFU. This highlights the therapeutic potential of systemically delivered, bactericidal AMPs