Home About us Contact
|
Home About us Contact | ||
|
|
||
Gene Models (gene + models)
Selected AbstractsA unified framework for transmission-disequilibrium test analysis of discrete and continuous traitsGENETIC EPIDEMIOLOGY, Issue 1 2002Ying Liu Abstract This paper presents a unified framework for transmission-disequilibrium tests for discrete and continuous traits. A conditional score test is derived that maximizes power to detect small effects for any exponential family distribution, which includes binary and normal distributions, and distributions that are skewed or have non-normal kurtosis. The specific distributional form need not be specified, and the method applies to sibships of arbitrary size. Formulas for the distribution of the test statistic are given for models including complex genetic effects (additive, dominant, and recessive gene action), covariates, multiple gene models including gene-gene interactions or heterogeneity, and gene-environment interactions. We develop refinements of our method for trait-based sampling designs and multiple siblings that can have dramatic effects on power. Genet. Epidemiol. 22:26,40, 2002. © 2002 Wiley-Liss, Inc. [source] Manual superscaffolding of honey bee (Apis mellifera) chromosomes 12,16: implications for the draft genome assembly version 4, gene annotation, and chromosome structureINSECT MOLECULAR BIOLOGY, Issue 4 2007Hugh M. Robertson Abstract The euchromatic arms of the five smallest telocentric chromosomes in the honey bee genome draft Assembly v4 were manually connected into superscaffolds. This effort reduced chromosomes 12,16 from 30, 21, 25, 42, and 21 mapped scaffolds to five, four, five, six, and five superscaffolds, respectively, and incorporated 178 unmapped contigs and scaffolds totalling 2.6 Mb, a 6.4% increase in length. The superscaffolds extend from the genetically mapped location of the centromere to their identified distal telomeres on the long arms. Only two major misassemblies of 146 kb and 65 kb sections were identified in this 23% of the mapped assembly. Nine duplicate gene models on chromosomes 15 and 16 were made redundant, while another 15 gene models were improved, most spectacularly the MAD (MAX dimerization protein) gene which extends across 11 scaffolds for at least 400 kb. [source] The WRKY Gene Family in Rice (Oryza sativa)JOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 6 2007Christian A. Ross Abstract WRKY genes encode transcription factors that are involved in the regulation of various biological processes. These zinc-finger proteins, especially those members mediating stress responses, are uniquely expanded in plants. To facilitate the study of the evolutionary history and functions of this supergene family, we performed an exhaustive search for WRKY genes using HMMER and a Hidden Markov Model that was specifically trained for rice. This work resulted in a comprehensive list of WRKY gene models in Oryza sativa L. ssp. indica and L. ssp. japonica. Mapping of these genes to individual chromosomes facilitated elimination of the redundant, leading to the identification of 98 WRKY genes in japonica and 102 in indica rice. These genes were further categorized according to the number and structure of their zinc-finger domains. Based on a phylogenetic tree of the conserved WRKY domains and the graphic display of WRKY loci on corresponding indica and japonica chromosomes, we identified possible WRKY gene duplications within, and losses between the two closely related rice subspecies. Also reviewed are the roles of WRKY genes in disease resistance and responses to salicylic acid and jasmonic acid, seed development and germination mediated by gibberellins, other developmental processes including senescence, and responses to abiotic stresses and abscisic acid in rice and other plants. The signaling pathways mediating WRKY gene expression are also discussed. [source] A gene repertoire for nitrogen transporters in Laccaria bicolorNEW PHYTOLOGIST, Issue 2 2008Eva Lucic Summary ,,Ectomycorrhizal interactions established between the root systems of terrestrial plants and hyphae from soil-borne fungi are the most ecologically widespread plant symbioses. The efficient uptake of a broad range of nitrogen (N) compounds by the fungal symbiont and their further transfer to the host plant is a major feature of this symbiosis. Nevertheless, we far from understand which N form is preferentially transferred and what are the key molecular determinants required for this transfer. ,,Exhaustive in silico analysis of N-compound transporter families were performed within the genome of the ectomycorrhizal model fungus Laccaria bicolor. A broad phylogenetic approach was undertaken for all families and gene regulation was investigated using whole-genome expression arrays. ,,A repertoire of proteins involved in the transport of N compounds in L. bicolor was established that revealed the presence of at least 128 gene models in the genome of L. bicolor. Phylogenetic comparisons with other basidiomycete genomes highlighted the remarkable expansion of some families. Whole-genome expression arrays indicate that 92% of these gene models showed detectable transcript levels. ,,This work represents a major advance in the establishment of a transportome blueprint at a symbiotic interface, which will guide future experiments. [source] Mass spectrometric genomic data mining: Novel insights into bioenergetic pathways in Chlamydomonas reinhardtiiPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 23 2006Jens Allmer Abstract A new high-throughput computational strategy was established that improves genomic data mining from MS experiments. The MS/MS data were analyzed by the SEQUEST search algorithm and a combination of de novo amino acid sequencing in conjunction with an error-tolerant database search tool, operating on a 256 processor computer cluster. The error-tolerant search tool, previously established as GenomicPeptideFinder (GPF), enables detection of intron-split and/or alternatively spliced peptides from MS/MS data when deduced from genomic DNA. Isolated thylakoid membranes from the eukaryotic green alga Chlamydomonas reinhardtii were separated by 1-D SDS gel electrophoresis, protein bands were excised from the gel, digested in-gel with trypsin and analyzed by coupling nano-flow LC with MS/MS. The concerted action of SEQUEST and GPF allowed identification of 2622 distinct peptides. In total 448 peptides were identified by GPF analysis alone, including 98 intron-split peptides, resulting in the identification of novel proteins, improved annotation of gene models, and evidence of alternative splicing. [source] Condition-dependent mutation rates and sexual selectionJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 4 2009S. COTTON Abstract ,Good genes' models of sexual selection show that females can gain indirect benefits for their offspring if male ornaments are condition-dependent signals of genetic quality. Recurrent deleterious mutation is viewed as a major contributor to variance in genetic quality, and previous theoretical treatments of ,good genes' processes have assumed that the influx of new mutations is constant. I propose that this assumption is too simplistic, and that mutation rates vary in ways that are important for sexual selection. Recent data have shown that individuals in poor condition can have higher mutation rates, and I argue that if both male sexual ornaments and mutation rates are condition-dependent, then females can use male ornamentation to evaluate their mate's mutation rate. As most mutations are deleterious, females benefit from choosing well-ornamented mates, as they are less likely to contribute germline-derived mutations to offspring. I discuss some of the evolutionary ramifications of condition-dependent mutation rates and sexual selection. [source] | ||||||||||