Fine-mapping of a QTL influencing pork tenderness on porcine chromosome 2

<p>Abstract</p> <p>Background</p> <p>In a previous study, a quantitative trait locus (QTL) exhibiting large effects on both Instron shear force and taste panel tenderness was detected within the Illinois Meat Quality Pedigree (IMQP). This QTL mapped to the q arm of porcine chromosome 2 (SSC2q). Comparative analysis of SSC2q indicates that it is orthologous to a segment of human chromosome 5 (HSA5) containing a strong positional candidate gene, calpastatin (<it>CAST</it>). <it>CAST </it>polymorphisms have recently been shown to be associated with meat quality characteristics; however, the possible involvement of other genes and/or molecular variation in this region cannot be excluded, thus requiring fine-mapping of the QTL.</p> <p>Results</p> <p>Recent advances in porcine genome resources, including high-resolution radiation hybrid and bacterial artificial chromosome (BAC) physical maps, were utilized for development of novel informative markers. Marker density in the ~30-Mb region surrounding the most likely QTL position was increased by addition of eighteen new microsatellite markers, including nine publicly-available and nine novel markers. Two newly-developed markers were derived from a porcine BAC clone containing the <it>CAST </it>gene. Refinement of the QTL position was achieved through linkage and haplotype analyses. Within-family linkage analyses revealed at least two families segregating for a highly-significant QTL in strong positional agreement with <it>CAST </it>markers. A combined analysis of these two families yielded QTL intervals of 36 cM and 7 cM for Instron shear force and taste panel tenderness, respectively, while haplotype analyses suggested further refinement to a 1.8 cM interval containing <it>CAST </it>markers. The presence of additional tenderness QTL on SSC2q was also suggested.</p> <p>Conclusion</p> <p>These results reinforce <it>CAST </it>as a strong positional candidate. Further analysis of <it>CAST </it>molecular variation within the IMQP F₁boars should enhance understanding of the molecular basis of pork tenderness, and thus allow for genetic improvement of pork products. Furthermore, additional resources have been generated for the targeted investigation of other putative QTL on SSC2q, which may lead to further advancements in pork quality.</p

Random Networks with Tunable Degree Distribution and Clustering

We present an algorithm for generating random networks with arbitrary degree distribution and Clustering (frequency of triadic closure). We use this algorithm to generate networks with exponential, power law, and poisson degree distributions with variable levels of clustering. Such networks may be used as models of social networks and as a testable null hypothesis about network structure. Finally, we explore the effects of clustering on the point of the phase transition where a giant component forms in a random network, and on the size of the giant component. Some analysis of these effects is presented.Comment: 9 pages, 13 figures corrected typos, added two references, reorganized reference

Psychological Safety and Norm Clarity in Software Engineering Teams

In the software engineering industry today, companies primarily conduct their work in teams. To increase organizational productivity, it is thus crucial to know the factors that affect team effectiveness. Two team-related concepts that have gained prominence lately are psychological safety and team norms. Still, few studies exist that explore these in a software engineering context. Therefore, with the aim of extending the knowledge of these concepts, we examined if psychological safety and team norm clarity associate positively with software developers' self-assessed team performance and job satisfaction, two important elements of effectiveness. We collected industry survey data from practitioners (N = 217) in 38 development teams working for five different organizations. The result of multiple linear regression analyses indicates that both psychological safety and team norm clarity predict team members' self-assessed performance and job satisfaction. The findings also suggest that clarity of norms is a stronger (30\% and 71\% stronger, respectively) predictor than psychological safety. This research highlights the need to examine, in more detail, the relationship between social norms and software development. The findings of this study could serve as an empirical baseline for such, future work.Comment: Submitted to CHASE'201

Some homogenization and corrector results for nonlinear monotone operators

This paper deals with the limit behaviour of the solutions of quasi-linear equations of the form \ \ds -\limfunc{div}\left(a\left(x, x/{\varepsilon _h},Du_h\right)\right)=f_h on $\Omega$ with Dirichlet boundary conditions. The sequence $(\varepsilon _h)$ tends to $0$ and the map $a(x,y,\xi )$ is periodic in $y$, monotone in $\xi$ and satisfies suitable continuity conditions. It is proved that $u_h\rightarrow u$ weakly in $H_0^{1,2}(\Omega )$, where $u$ is the solution of a homogenized problem \ -\limfunc{div}(b(x,Du))=f on $\Omega$. We also prove some corrector results, i.e. we find $(P_h)$ such that $Du_h-P_h(Du)\rightarrow 0$ in $L^2(\Omega ,R^n)$

Analyses of Birthdate and Growth in Beef Heifers Categorized by Puberty and Pregnancy Status

Heifer records were retrospectively evaluated to see if Julian birthdate, cycling status prior to breeding, and body weight collected from weaning through final pregnancy diagnosis differed when heifers were categorized by 5 different approaches: 1) pubertal status prior to estrous synchronization, 2) whether or not detected in estrus at AI, 3) heifers impregnated by AI vs all other heifers, 4) final pregnancy status, and 5) a 5-way classification accounting for AI and pregnancy status (AI pregnant, heifers subjected to AI that subsequently conceived to bull, heifers not AI that were impregnated by bull, heifers subjected to AI that were not pregnant, heifers not AI and not pregnant). Collectively, results support the concept that earlier birth in the calving season and greater preweaning growth are associated with desirable reproductive response in replacement beef heifers

Germ Cell Recovery, Cryopreservation and Transplantation in the California white sturgeon, Acipenser transmontanus

The white sturgeon (Acipenser transmontanus) is the largest freshwater fish in North America. Because of the unique life history characteristics of sturgeon, including longevity, late maturation and long spawning intervals, their aquaculture can be a significant investment of resources. As a result of habitat loss and overharvesting, natural populations of white sturgeon are threatened and there is a growing effort to improve conservation aquaculture programs. Germ cell transplantation is an innovative technology previously demonstrated in a variety of fish species to be able to produce a surrogate broodstock. The technique relies upon optimal donor germ cell recovery and transplantation into a recipient fish. In this study, we developed and optimized the harvest of donor cells for germline transplantation and evaluated methods for ovary cryopreservation for the first time in the white sturgeon. We found that harvesting gonads from juveniles between the ages of 1.5 and 2.5-years resulted in reliably high proportions of pre-meiotic cells regardless of sex, a critical feature for using white sturgeon for transplantation studies since the species shows no distinguishing external sex characteristics. From the viable cells, we identified germline cells using immunolabeling with the antibody DDX4, a marker specific to the germline. For in vivo tracking of donor cells during transplantations, gonadal cells were stained with a long half-life non-toxic cell membrane dye, PKH26, and microinjected into the peritoneal cavity of newly hatched white sturgeon larvae. Larvae were reared until 3 months post-transplantation to monitor for colonization and proliferation of PKH26-labeled cells within the recipient larval gonads. Furthermore, viable cell detection, assessment of germline-specificity, and transplantation was determined for cells recovered from cryopreserved ovarian tissue from sexually immature females. Transplantations using cells cryopreserved with media supplemented with dimethyl sulfoxide (DMSO) rather than ethylene glycol (EG) demonstrated the highest number of PKH26-labeled cells distributed along the gonadal ridges of the larval recipient. Determining optimal methods of tissue cryopreservation, and germ cell recovery and transplantation are foundational to the future development of germ cell transplantation as a strategy to improve the aquaculture and conservation of this species. Our study demonstrates that conservation actions, such as surrogate breeding, could be utilized by hatcheries to retain or improve natural gamete production without genetic modification, and provide an encouraging approach to the management of threatened sturgeon species

Ginzburg-Landau model with small pinning domains

We consider a Ginzburg-Landau type energy with a piecewise constant pinning term $a$ in the potential $(a^2 - |u|^2)^2$. The function $a$ is different from 1 only on finitely many disjoint domains, called the {\it pinning domains}. These pinning domains model small impurities in a homogeneous superconductor and shrink to single points in the limit $\v\to0$; here, \v is the inverse of the Ginzburg-Landau parameter. We study the energy minimization in a smooth simply connected domain $\Omega \subset \mathbb{C}$ with Dirichlet boundary condition $g$ on \d \O, with topological degree {\rm deg}_{\d \O} (g) = d >0. Our main result is that, for small \v, minimizers have $d$ distinct zeros (vortices) which are inside the pinning domains and they have a degree equal to 1. The question of finding the locations of the pinning domains with vortices is reduced to a discrete minimization problem for a finite-dimensional functional of renormalized energy. We also find the position of the vortices inside the pinning domains and show that, asymptotically, this position is determined by {\it local renormalized energy} which does not depend on the external boundary conditions.Comment: 39 page