PEDE (Pig EST Data Explorer) has been expanded into Pig Expression Data Explorer, including 10 147 porcine full-length cDNA sequences

We formerly released the porcine expressed sequence tag (EST) database Pig EST Data Explorer (PEDE; ), which comprised 68 076 high-quality ESTs obtained by using full-length-enriched cDNA libraries derived from seven tissues. We have added eight tissues and cell types to the EST analysis and have integrated 94 555 additional high-quality ESTs into the database. We also fully sequenced the inserts of 10 147 of the cDNA clones that had undergone EST analysis; the sequences and annotation of the cDNA clones were stored in the database. Further, we constructed an interface that can be used to perform various searches in the database. The PEDE database is the primary resource of expressed pig genes that are supported by full-length cDNA sequences. This resource not only enables us to pick cDNA clones of interest for a particular analysis, but it also confirms and thus contributes to the sequencing integrity of the pig genome, which is now being compiled by an international consortium (). PEDE has therefore evolved into what we now call ‘Pig Expression Data Explorer’

Identification of a second gene associated with variation in vertebral number in domestic pigs

<p>Abstract</p> <p>Background</p> <p>The number of vertebrae in pigs varies and is associated with body size. Wild boars have 19 vertebrae, but European commercial breeds for pork production have 20 to 23 vertebrae. We previously identified two quantitative trait loci (QTLs) for number of vertebrae on <it>Sus scrofa </it>chromosomes (SSC) 1 and 7, and reported that an orphan nuclear receptor, <it>NR6A1</it>, was located at the QTL on SSC1. At the <it>NR6A1 </it>locus, wild boars and Asian local breed pigs had the wild-type allele and European commercial-breed pigs had an allele associated with increased numbers of vertebrae (number-increase allele).</p> <p>Results</p> <p>Here, we performed a map-based study to define the other QTL, on SSC7, for which we detected genetic diversity in European commercial breeds. Haplotype analysis with microsatellite markers revealed a 41-kb conserved region within all the number-increase alleles in the present study. We also developed single nucleotide polymorphisms (SNPs) in the 450-kb region around the QTL and used them for a linkage disequilibrium analysis and an association study in 199 independent animals. Three haplotype blocks were detected, and SNPs in the 41-kb region presented the highest associations with the number of vertebrae. This region encodes an uncharacterized hypothetical protein that is not a member of any other known gene family. Orthologs appear to exist not only in mammals but also birds and fish. This gene, which we have named <it>vertnin </it>(<it>VRTN</it>) is a candidate for the gene associated with variation in vertebral number. In pigs, the number-increase allele was expressed more abundantly than the wild-type allele in embryos. Among candidate polymorphisms, there is an insertion of a SINE element (PRE1) into the intron of the Q allele as well as the SNPs in the promoter region.</p> <p>Conclusions</p> <p>Genetic diversity of <it>VRTN </it>is the suspected cause of the heterogeneity of the number of vertebrae in commercial-breed pigs, so the polymorphism information should be directly useful for assessing the genetic ability of individual animals. The number-increase allele of swine <it>VRTN </it>was suggested to add an additional thoracic segment to the animal. Functional analysis of <it>VRTN </it>may provide novel findings in the areas of developmental biology.</p

Gravitational Quantum Foam and Supersymmetric Gauge Theories

We study K\"{a}hler gravity on local SU(N) geometry and describe precise correspondence with certain supersymmetric gauge theories and random plane partitions. The local geometry is discretized, via the geometric quantization, to a foam of an infinite number of gravitational quanta. We count these quanta in a relative manner by measuring a deviation of the local geometry from a singular Calabi-Yau threefold, that is a A_{N-1} singularity fibred over \mathbb{P}^1. With such a regularization prescription, the number of the gravitational quanta becomes finite and turns to be the perturbative prepotential for five-dimensional \mathcal{N}=1 supersymmetric SU(N) Yang-Mills. These quanta are labelled by lattice points in a certain convex polyhedron on \mathbb{R}^3. The polyhedron becomes obtainable from a plane partition which is the ground state of a statistical model of random plane partition that describes the exact partition function for the gauge theory. Each gravitational quantum of the local geometry is shown to consist of N unit cubes of plane partitions.Comment: 43 pages, 12 figures: V2 typos correcte

A Bayesian Method for Simultaneously Detecting Mendelian and Imprinted Quantitative Trait Loci in Experimental Crosses of Outbred Species

Genomic imprinting is interpreted as a phenomenon, in which some genes inherited from one parent are not completely expressed due to modification of the genome caused during gametogenesis. Subsequently, the expression level of an allele at the imprinted gene is changed dependent on the parental origin, which is referred to as the parent-of-origin effect. In livestock, some QTL for reproductive performance and meat productivity have been reported to be imprinted. So far, methods detecting imprinted QTL have been proposed on the basis of interval mapping, where only a single QTL was tested at a time. In this study, we developed a Bayesian method for simultaneously mapping multiple QTL, allowing the inference about expression modes of QTL in an outbred F2 family. The inference about whether a QTL is Mendelian or imprinted was made using Markov chain Monte Carlo estimation by comparing the goodness-of-fits between models, assuming the presence and the absence of parent-of-origin effect at a QTL. We showed by the analyses of simulated data sets that the Bayesian method can effectively detect both Mendelian QTL and imprinted QTL

Subordinate Fish Mediate Aggressiveness Using Recent Contest Information

Memorizing dominance relationships can help animals avoid unwinnable subsequent contests. However, when competitive ability changes over time—for example, as a function of condition—it may be adaptive to “forget” these dominance relationships and for subordinates to once again enter contests with previously dominant individuals. Here, we examined the behavior of pairs of male cichlid fish, Julidochromis transcriptus, in repeated contests separated by different time intervals. We found that the time taken to reach resolution of dominance relationships influenced subsequent aggressive behavior of the subordinate toward the dominant, with longer initial contests leading to higher subsequent aggression. Longer time intervals between contests also increased aggression from the subordinate toward the dominant. These results are consistent with increasing uncertainty due to ambiguous contest outcomes and increasing time intervals. Our results also show that a longer time was necessary to resolve contests between larger pairs, suggesting a self-assessment strategy, but not a mutual assessment strategy. Taken together, larger individuals appear to adaptively lose or ignore previously gathered social information because they have a higher fighting ability and better body condition. Therefore, we conclude that losing or ignoring unreliable information may be an adaptive strategy in the context of dominance relationships.publishe