Search PubMed⌕ Search

Biomedical subjects

D C Ward

Publications and source records attributed to D C Ward.

At least 73 records · Page 4Linked to original sources
PubMed1995

Metaphase and interphase fluorescence in situ hybridization mapping of the rice genome with bacterial artificial chromosomes.

Fluorescence in situ hybridization (FISH) is a powerful tool for physical mapping in human and other mammalian species. However, application of the FISH technique has been limited in plant species, especially for mapping single- or low-copy DNA sequences, due to inconsistent signal production in plant chromosome preparations. Here we demonstrate that bacterial artificial chromosome (BAC) clones can be mapped readily on rice (Oryza sativa L.) chromosomes by FISH. Repetitive DNA sequences in BAC clones can be suppressed efficiently by using rice genomic DNA as a competitor in the hybridization mixture. BAC clones as small as 40 kb were successfully mapped. To demonstrate the application of the FISH technique in physical mapping of plant genomes, both anonymous BAC clones and clones closely linked to a rice bacterial blight-resistance locus, Xa21, were chosen for analysis. The physical location of Xa21 and the relationships among the linked clones were established, thus demonstrating the utility of FISH in plant genome analysis.

Animals↗
PubMed1995

Localization of the alpha 7 integrin gene (ITGA7) on human chromosome 12q13: clustering of integrin and Hox genes implies parallel evolution of these gene families.

Expression of the alpha 7 integrin gene (ITGA7) is developmentally regulated during the formation of skeletal muscle. Increased levels of expression and production of isoforms containing different cytoplasmic and extracellular domains accompany myogenesis. To determine whether a single or multiple alpha 7 genes underlie the structural diversity in this alpha chain that accompanies development, we have examined the rat and human genomes by Southern blotting and in situ hybridization. Our results demonstrate that there is only one alpha 7 gene in both the rat and the human genomes. In the human, ITGA7 is present on chromosome 12q13. Phylogenetic analysis of the integrin alpha chain sequences suggests that the early integrin genes evolved in two pathways to form the I-integrins and the non-I-integrins. The I-integrin alpha chains contain an additional sequence of approximately 180 amino acids and arose as a result of an early insertion into the non-I-gene. The I-chain subfamily further evolved by duplications within the same chromosome. The non-I-integrin alpha chain genes are localized in clusters on chromosomes 2, 12, and 17, and this closely coincides with the localization of the human homeobox gene clusters. Non-I-integrin alpha chain genes appear to have evolved in parallel and in proximity to the Hox clusters. Thus, the Hox genes that underlie the design of body structure and the Integrin genes that underlie informed cell-cell and cell-matrix interactions appear to have evolved in parallel and coordinate fashions.

Amino Acid Sequence↗
PubMed1995

Nuclear foci of mammalian Rad51 recombination protein in somatic cells after DNA damage and its localization in synaptonemal complexes.

Rad51 protein of Saccharomyces cerevisiae is a structural homolog of the Escherichia coli recombination enzyme RecA. In yeast, the Rad51 protein is required for mitotic and meiotic recombination and for repair of double-strand breaks in DNA. We have used antibodies raised against the homologous human protein, HsRad51, expressed in E. coli, to visualize the spatial distribution of the protein in mammalian somatic and meiotic cells. In cultured human cells, the HsRad51 protein is concentrated in multiple discrete foci in the nucleoplasm; it is largely absent from cytoplasm and nucleoli. After treatment of cells with methyl methanesulfonate, ultraviolet irradiation, or 137Cs irradiation, the percentage of cells with HsRad51 protein immunofluorescence increases; the same cells show unscheduled DNA synthesis. Induction of Rad51 foci is blocked by inhibitors of transcription. In mouse pachytene spermatocytes, the mouse homolog of Rad51 protein is highly enriched in synaptonemal complexes that are formed between the paired homologous chromosomes during meiotic prophase. We conclude that the mammalian proteins homologous to yeast Rad51 are involved in repair of DNA damage and recombinational repair during meiosis.

Animals↗
PubMed1995

Comparative genomic hybridization detects novel deletions and amplifications in head and neck squamous cell carcinomas.

To gain a better understanding of genetic changes in squamous cell carcinomas of the head and neck we used comparative genomic hybridization for the analysis of 13 primary tumors. Copy number increases were most frequently observed on chromosomes 3q (10 cases) and 5p (8 cases) and less frequently on 1q (4 cases), 2 (1 case), 7 (2 cases), 8q (2 cases), 9 (1 case), 10p (2 cases), 13q (2 cases), 14q (1 case), 16 (1 case), 17 (2 cases), 20p (2 cases), 21q (1 case) and 22q (1 case). Copy number decreases occurred most frequently at 3p (5 cases), 5q (4 cases), 19p (6 cases), and 19q (5 cases). Copy number decreases also were observed on 1p (2 cases), 2q (2 cases), 4p (2 cases), 4q (2 cases), 7q (2 cases), 8p (1 case), 10q (1 case), 11p (2 cases), 11q (3 cases), 13q (3 cases), 14q (1 case), 16p (1 case), 17p (3 cases), 17q (1 case), 18q (1 case), and 22 (2 cases). Eight sites exhibiting significant sequence amplification were mapped to 3q26-->qter (3 cases), 11q13 (2 cases), 12p (2 cases), 2q33-36 (1 case), 7q21-22 (1 case), 7q33-->qter (1 case), 9p (1 case), and 13q32-->qter (1 case). Our data suggest that the regions 3q26-->qter and 5p may harbor oncogenes important for initiation or progression of squamous cell carcinomas of the head and neck. In addition, comparative genomic hybridization defines a subgroup of tumors with 11q13 involvement, the location of the PRAD1/(CCND1)/cyclin D1 gene.

Adult↗
PubMed1995

Higher order nuclear structure in mammalian sperm revealed by in situ hybridization and extended chromatin fibers.

The higher order organization of chromosomes in human and mouse sperm-cell nuclei has been visualized by fluorescence in situ hybridization. In mouse testicular sperm, centromeres form several linear higher order structures that are attached to a heterochromatic chromocenter at the center of the nucleus. Telomeres of the acrocentric mouse chromosomes are associated with either the heterochromatic center or the nuclear membrane. Whole chromosome domains are arranged parallel to the heterochromatic chromocenter and occasionally wrapped around it. We propose that constitutive heterochromatin serves as the nucleation point for a cell-type-specific organization of mouse sperm chromatin. In human mature sperm, individual chromosomes also appear as elongated territories. When human sperm nuclei are lysed with high salt and detergent, the normally condensed sperm chromatin unravels into linear arrays that exhibit a discrete nodular substructure (of < 300 nm diameter). These beads may represent a basic packaging unit of sperm chromatin. Larger superbead-like structures are also seen along the extended chromatin fibers and these could contain multiples of the basic packaging unit. These observations indicate that mammalian sperm nuclei have a highly defined nuclear architecture. The implications of an ordered organization of DNA in sperm are unknown, but it is possible that functional compartmentalization of the sperm-cell nucleus influences the initiation and regulation of paternal gene activity in the early embryo.

Animals↗
PubMed1995

Presence and abundance of CENP-B box sequences in great ape subsets of primate-specific alpha-satellite DNA.

CENP-B, a highly conserved centromere-associated protein, binds to alpha-satellite DNA, the centromeric satellite of primate chromosomes, at a 17-bp sequence, the CENP-B box. By fluorescence in situ hybridization (FISH) with an oligomer specific for the CENP-B box sequence, we have demonstrated the abundance of CENP-B boxes on all chromosomes (except the Y) of humans, chimpanzee, pygmy chimpanzee, gorilla, and orangutan. This sequence motif was not detected in the genomes of other primates, including gibbons, Old and New World monkeys, and prosimians. Our results indicate that the CENP-B box containing subtype of alpha-satellite DNA may have emerged recently in the evolution of the large-bodied hominoids, after divergence of the phylogenetic lines leading to gibbons and apes; the box is thus on the order of 15-25 million years of age. The rapid process of dispersal and fixation of the CENP-B box sequence throughout the human and great ape genomes is thought to be a consequence of concerted evolution of alpha-satellite subsets on both homologous and nonhomologous chromosomes.

Animals↗
PubMed1995

Isolation and chromosomal localization of a human ATP-regulated potassium channel.

KATP channels are K+ channels whose activity is inhibited by the presence of and enhanced by the absence of cytosolic ATP. This property allows KATP channels to sense cellular intermediary metabolism and directly couple this information to the modulation of membrane excitability. Indeed, recent studies from our laboratory and others have suggested that activation of KATP channels during anoxia is important in the response and adaptation of central neurons to hypoxia. In order to identify KATP channels from human brain, we performed a polymerase chain reaction (PCR) using human cerebral cortex mRNA and primers derived from the ROMK1 sequence, a cDNA clone encoding an ATP-regulated potassium channel, recently isolated from rat kidney. We thus identified a novel 308-bp PCR product, pKCNJ1, whose expression was found to be restricted to a 3.0-kb band in the kidney by probing a human multiple tissue northern blot, pKCNJ1 was then used to isolate genomic clones and, using fluorescence in situ hybridization (FISH) to human metaphase chromosomes, was mapped to chromosome 11q.

Adenosine Triphosphate↗
PubMed1995

Dynamic changes in Rad51 distribution on chromatin during meiosis in male and female vertebrates.

Antibodies against human Rad51 protein were used to examine the distribution of Rad51 on meiotic chromatin in mouse spermatocytes and oocytes as well as chicken oocytes during sequential stages of meiosis. We observed the following dynamic changes in distribution of Rad51 during meiosis: (1) in early leptotene nuclei there are multiple, apparently randomly distributed, foci that by late leptonema become organized into tracks of foci. (2) These foci persist into zygonema, but most foci are now localized on Rad51-positive axes that correspond to lateral elements of the synaptonemal complex. As homologs synapse foci from homologous axes fuse. The distribution and involvement of Rad51 foci as contact points between homologs suggest that they may be components to early recombination nodules. (3) As pachynema progresses the number of foci drops dramatically; the temporal occurrence (mice) and physical and numerical distribution of foci on axes (chickens) suggest that they may be a component of late recombination nodules. (4) In early pachynema there are numerous Rad51 foci on the single axis of the X (mouse spermatocytes) or the Z (chicken oocytes) chromosomes that neither pair, nor recombine. (5) In late pachynema in mouse spermatocytes, but not oocytes, the Rad51 signal is preferentially enhanced at both ends of all the bivalents. As bivalents in spermatocytes, but not oocytes, begin to desynapse at diplonema they are often held together at these Rad51-positive termini. These observations parallel observations that recombination rates are exceptionally high near chromosome ends in male but not female eutherian mammals. (6) From diakinesis through metaphase I, Rad51 protein is detected as low-intensity fluorescent doublets that localize with CREST-specific antigens (kinetochores), suggesting that Rad51 participates, at least as a structural component of the materials involved, in sister kinetochore cohesiveness. Finally, the changes in Rad51 distribution during meiosis do not appear to be species specific, but intrinsic to the meiotic process.

Animals↗
PubMed1995

Toward a physical map of Aedes aegypti.

Labelled recombinant cosmids were used as in situ hybridization probes to Aedes aegypti metaphase chromosomes. The cosmid probes yielded paired signals, one on each arm of sister chromatids, and they were ordered along the three chromosomes. In total, thirty-seven different probes were mapped to the three chromosomes of Ae. aegypti (2n = 6): twenty-eight to chromosome 1, six to chromosome 2, and six to chromosome 3. These results represent an initial stage in the generation of a physical map of the Ae. aegypti genome.

Aedes↗
PubMed1995

Generation of monoclonal antibodies to Macaca mulatta (rhesus) IgA.

One IgG1 and five IgM murine monoclonal antibodies (mAb) specific for rhesus (Rh) IgA were generated. These mAbs bound to Rh IgA but not IgG or IgM when tested by enzyme-linked immunosorbent assay. Immunoblotting revealed that the mAbs reacted with the alpha heavy chain of Rh but not human IgA. The IgG1 anti-Rh IgA mAb detected IgA-producing cells in sections of monkey gut examined by immunofluorescent staining. These mAbs should be useful for characterizing IgA responses in the Rh monkey.

Animals↗
PubMed1995

Transcriptional activation by the parvoviral nonstructural protein NS-1 is mediated via a direct interaction with Sp1.

The nonstructural protein NS-1, encoded by the parvovirus minute virus of mice, is a potent regulator of viral gene expression. NS-1 does not bind DNA in a sequence-specific manner, and the mechanism by which it modulates viral promoter function is unclear. We have used Gal4-NS-1 fusion protein constructs to identify and characterize an activating domain encoded within the C-terminal 88 amino acids of NS-1 which competes effectively with the acidic activator domain of the herpes simplex virus VP16 protein. DNA affinity chromatography and immunoprecipitation experiments demonstrate that protein-protein interactions between the transcription factor Sp1 and NS-1 are required to bind NS-1 to promoter DNA in vitro. Cotransfection of Gal4-NS-1 and Sp1-VP16 acidic activator constructs into Drosophila melanogaster Schneider cells, which lack endogenous Sp1, stimulates transcription from a minimal promoter containing five Gal4 binding sites, while single-construct transfections do not. Cotransfection of Schneider cells with wild-type NS-1 and Sp1 constructs activates transcription from a simian virus 40 promoter 10- to 30-fold over that of either construct alone. Thus, Sp1-NS-1 interactions in vivo can stimulate transcription from a heterologous promoter containing Sp1 binding sites.

Animals↗
PubMed1995

Assignment of the human heart tetrodotoxin-resistant voltage-gated Na+ channel alpha-subunit gene (SCN5A) to band 3p21.

The chromosomal location of SCN5A, the gene encoding the principal voltage-gated Na+ channel expressed in human heart, has been determined by three independent methodologies: somatic cell hybrid mapping, chromosomal microdissection-polymerase chain reaction, and fluorescence in situ hybridization. The SCN5A gene was assigned to the short arm of chromosome 3 (band 3p21) by all three approaches. These data are further evidence that striated muscle Na+ channel genes are dispersed in the genome.

Animals↗
PubMed1995

Rabl orientation of CENP-B box sequences in Tupaia belangeri fibroblasts.

The chromosomes of the tree shrew Tupaia belangeri exhibit highly localized CENP-B box sequences in the centromeric regions of most chromosomes. Telomeric sequences are present at the ends of all chromosomes and, in addition, at specific interstitial chromosomal sites that likely represent remnants of ancestral telomeres. This suggests that Robertsonian and tandem chromosome fusion events have occurred in the karyotypic evolution of Tupaiidae. In Tupaia skin fibroblasts CENP-B boxes are almost always clustered together at one pole of the interphase nucleus, whereas the telomeric domains are relatively evenly distributed throughout the whole nuclear volume. The observed orientation of the centromeres is reminiscent of the Rabl polarization of chromosomes; this is the first mammalian cell substrate in which such an higher-order chromosomal organization has been observed. CENP-B box sequences are found in several other mammalian species. The implications for recent parallel evolution of CENP-B binding motifs and concerted evolution of these sequences are discussed.

Animals↗
PubMed1995

Localization of PURA, the gene encoding the sequence-specific single-stranded-DNA-binding protein Pur alpha, to chromosome band 5q31.

Pur alpha (PurA) is a sequence-specific single-stranded-DNA-binding protein implicated in control of both DNA replication and transcription. We have localized the Pur alpha gene (PURA) to human chromosome band 5q31 by fluorescence in situ hybridization with a 16-kb genomic probe together with hybridization of a cDNA probe to blots of DNA from human-hamster cell lines containing individual human chromosomes. Sequences with homology to the PURA locus are also present at 6q14. The 5q31 locus is frequently deleted in myelogenous leukemia and other cancers.

Animals↗
PubMed1995

Multicolor FISH with a telomere repeat and Sry sequences shows that Sxr (Sex reversal) in the mouse is a new type of chromosome rearrangement.

XYSxr (Sex reversal) mice carry a Y chromosome in which the chromatin (including Sry, the gene for testis determination) that normally resides on the short arm is duplicated and the second copy is relocated to the distal end of the long arm. Multicolor in situ hybridization to mitotic chromosomes of XYSxr males using probes for the telomere repeat sequence (TTAGGG)n and Sry shows that the rearranged chromatin is located distal to the telomeric signal. This suggests that the rearrangement arose from a recombination event involving the distal Y telomere sequences, i.e., within the telomere, a structure historically assumed to be incapable of participating in chromosome rearrangements.

Animals↗
PubMed1995

Congenital fibrosis of the extraocular muscles (autosomal dominant congenital external ophthalmoplegia): genetic homogeneity, linkage refinement, and physical mapping on chromosome 12.

Congenital fibrosis of the extraocular muscles (CFEOM) is an autosomal dominant syndrome of congenital external ophthalmoplegia and bilateral ptosis. We previously reported linkage of this disorder in two unrelated families to an 8-cM region near the centromere of human chromosome 12. We now present refinement of linkage in the original two families, linkage analysis of five additional families, and a physical map of the critical region for the CFEOM gene. In each of the seven families the disease gene is linked to the pericentromeric region of chromosome 12. D12S345, D12S59, D12S331, and D12S1048 do not recombine with the disease gene and have combined lod scores of 35.7, 35.6, 16.0, and 31.4, respectively. AFM136xf6 and AFMb320wd9 flank the CFEOM locus, defining a critical region of 3 cM spanning the centromere of chromosome 12. These data support the concept that this may be a genetically homogeneous disorder. We also describe the generation of a YAC contig encompassing the critical region of the CFEOM locus. This interval has been assigned cytogenetically to 12p11.2-q12 and spans the centromere of chromosome 12. These results provide the basis for further molecular analyses of the structure and organization of the CFEOM locus and will help in the identification of candidate genes.

Chromosome Mapping↗
PubMed1995

Network-based informatics support of research collaborations in the Human Genome Project and the Human Brain Project.

Sophisticated network-based informatics support will increasingly be required for collaborating biomedical laboratories located in different geographic locations, both to accommodate the massive amount of data being generated in certain fields, and to allow different types of data produced at different laboratories to be analyzed in an integrated fashion. The paper describes the experience of the Yale Center for Medical Informatics in providing informatics support for collaborative projects in gene mapping (as part of the national Human Genome Project) and neuroscience (as part of the national Human Brain Project). The paper describes the informatics needs of the two projects and the solutions being developed, describes certain lessons learned, and discusses certain broader issues that arise.

Brain Mapping↗