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We have recently reported a new pathogen discovery approach, ''computational subtraction''. With this approach, non-human transcripts are detected by sequencing cDNA libraries from infected tissue and eliminating those transcripts that match the human genome. We show now that this method is experimentally feasible. We generated a cDNA library from a tissue sample of post-transplant lymphoproliferative...
We applied an automatic and unsupervised system to a nearly complete database of mammalian odor receptor genes. The generated motifs and gene classification were subjected to extensive and systematic downstream analysis to obtain biological insights. Two major results from this analysis were: (1) a map of sequence motifs that may correlate with function and (2) the corresponding receptor classes in...
The canine species, including wolf and jackal, have four digits on the hind limb. It was thought that an extra first digit on the hind limb, named dewclaw, was a hereditary defect. For genetically related canine pedigrees with 73 members with dewclaws, we carried out a genome-wide scan for linkage with microsatellites. With an assumption of autosomal dominant mode of inheritance, significant linkages...
Medaka is one of the prominent model animals, which also include other fishes such as Fugu and zebrafish. Its genome is relatively compact but has not been well characterized. Here we have sequenced a 229-kb region of medaka, containing the Double anal fin (Da) locus, and compared its structure to those in Fugu, human, and mouse. This region, representing a gene-poor region, contains no major rearrangements...
In a previous study we demonstrated that repeated duplications of the tissue kallikrein gene (Klk1) had resulted in 24 paralogs in mouse. Here we demonstrate a different evolution of rat glandular kallikrein genes. Repeated duplications of an ~30-kb region, encompassing Klk1, Klk15, and Klk2-ps, resulted in 10 copies of each gene, but only the Klk1 paralogs are functional. The number of genes varies...
We report a comparative map of canine chromosome 1 (CFA1) incorporating single nucleotide polymorphisms (SNPs) and insertion/deletion (indel) polymorphisms, developed by using cross-species primers, radiation hybrid analysis, and pool-and-sequence identification of genetic variations. Fifty-five genes were chosen with relatively even spacing (approximately 3 Mb between the human homologues) and were...
HSP90 proteins are important molecular chaperones. Transcriptome and genome analyses revealed that the human HSP90 family includes 17 genes that fall into four classes. A standardized nomenclature for each of these genes is presented here. Classes HSP90AA, HSP90AB, HSP90B, and TRAP contain 7, 6, 3, and 1 genes, respectively. HSP90AA genes mapped onto chromosomes 1, 3, 4, and 11; HSP90AB genes mapped...
We have previously shown that GAA trinucleotide repeats have undergone significant expansion in the human genome. Here we present the analysis of the length distribution of all 10 nonredundant trinucleotide repeat motifs in 20 complete eukaryotic genomes (6 mammalian, 2 nonmammalian vertebrates, 4 arthropods, 4 fungi, and 1 each of nematode, amoebozoa, alveolate, and plant), which showed that the...
Blood genomic profiling has been applied to disorders of the blood and various organ systems including brain to elucidate disease mechanisms and identify surrogate disease markers. Since most studies have not examined specific cell types, we performed a preliminary genomic survey of major blood cell types from normal individuals using microarrays. CD4 + T cells, CD8 + T cells, CD19...
Transcriptional regulatory networks govern cell differentiation and the cellular response to external stimuli. However, mammalian model systems have not yet been accessible for network analysis. Here, we present a genome-wide network analysis of the transcriptional regulation underlying the mouse macrophage response to bacterial lipopolysaccharide (LPS). Key to uncovering the network structure is...
The mouse PancChip, a microarray developed for studying endocrine pancreatic development and diabetes, represents over 13,000 cDNAs. After computationally assigning the cDNAs on the array to known genes, manual curation of the remaining sequences identified 211 novel transcripts. In microarray experiments, we found that 196 of these transcripts were expressed in total pancreas and/or pancreatic islets...
Sarcomeric myosin heavy chains (MyHC) are the major contractile proteins of cardiac and skeletal muscles and belong to class II MyHC. In this study the sequences of nine sarcomeric MyHC isoforms were obtained by combining assembled contigs of the dog genome draft available in the NCBI database. With this information available the dog becomes the second species, after human, for which the sequences...
We identified a set of transcriptional elements that are conserved and overrepresented within the promoters of human, mouse, and rat GRIAs by comparing these promoters against a collection of 10,741 gene promoters. Cells regulate functional groups of genes by coordinating the transcriptional and/or posttranscriptional mRNA levels of interacting genes. As such, it is expected that functional groups...
Fascinating new data, revealed through gene sequencing, comparative genomics, and genetic engineering, precisely establish which genes are involved in mate choice and mating activity—behaviors that are surprisingly understudied from a genetic perspective. Discussed here are some of the recently identified visual and chemosensory genes that are involved in mate choice and mating behavior. These genes’...
Catfish is the major aquaculture species in the United States. To enhance its genome studies involving genetic linkage and comparative mapping, a bacterial artificial chromosome (BAC) contig-based physical map of the channel catfish (Ictalurus punctatus) genome was generated using four-color fluorescence-based fingerprints. Fingerprints of 34,580 BAC clones (5.6× genome coverage) were generated for...
Phytomonas spp. are members of the family Trypanosomatidae that parasitize plants and may cause lethal diseases in crops such as Coffee Phloem necrosis, Hartrot in coconut, and Marchitez sorpresiva in oil palm. In this study, the molecular karyotype of 6 isolates from latex plants has been entirely elucidated by pulsed-field gel electrophoresis and DNA hybridization. Twenty-one chromosomal linkage...
Giant axonopathy (gaxp), an autosomal recessive mouse mutation, exhibits ataxia of the hind legs with a slight side-to-side wobble while walking. Within the genomic region of the gaxp locus, a total of 94 transcripts were identified; the annotation of these genes using OMIM and PubMed yielded three potential candidate genes. By cDNA microarray analysis, 54 genes located on or near the gaxp locus were...
Repetitive elements (REs) constitute a substantial portion of the genomes of human and other species; however, the RE profiles (type, density, and arrangement) within the individual genomes have not been fully characterized. In this study, we developed an RE analysis tool, called REMiner, for a chromosome-wide investigation into the occurrence of individual REs and arrangement of clusters of REs,...
Codon bias is the phenomenon in which distinct synonymous codons are used with different frequencies. We define here the ''codonome value'' as the total number of codons present across all the expressed mRNAs in a given biological condition. We have developed the ''CODONOME'' software, which calculates the codon bias and, following integration with a gene expression profile, estimates the actual frequency...
The Japanese quail has several advantages as a laboratory animal for biological and biomedical investigations. In this study, the draft genome of the Japanese quail was sequenced and assembled using next-generation sequencing technology. To improve the quality of the assembly, the sequence reads from the Japanese quail were aligned against the reference genome of the chicken. The final draft assembly...
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