Biomedical subjects

Tom Goldammer

Publications and source records attributed to Tom Goldammer.

13 recordsLinked to original sources

PubMed2007

Generation of an improved cytogenetic and comparative map of Bos taurus chromosome BTA27.

Comparative genome analysis in cattle, human, and mouse identified various evolutionary breakpoints between Bos taurus 27 chromosome (BTA27) and corresponding segments in the Homo sapiens 4 and 8 chromosomes (HSA4, HSA8) and the Mus musculus 8 chromosome (MMU8). The fragmentary cytogenetic location of breaks is based on nine known loci and Zoo-FISH data on BTA27. A comparative mapping approach combining in-silico mapping and physical mapping by fluorescence in-situ hybridization (FISH) revealed an improved cytogenetic map of BTA27 based on 25 new and nine existing assignments of loci. Furthermore, hybrid cell mapping techniques identified and anchored three additional gene loci on BTA27. The BTA27 map was compared with available mapping and annotated sequence data for the chromosome and a generated comparative map displays conserved syntenic chromosome blocks between cattle, human, and mouse. The new anchor loci identify and narrow down evolutionary breakpoints on a cytogenetic level and can help to support the cattle genome assembly and annotation process.

Animals↗

PubMed2006

A gene-based high-resolution comparative radiation hybrid map as a framework for genome sequence assembly of a bovine chromosome 6 region associated with QTL for growth, body composition, and milk performance traits.

BACKGROUND: A number of different quantitative trait loci (QTL) for various phenotypic traits, including milk production, functional, and conformation traits in dairy cattle as well as growth and body composition traits in meat cattle, have been mapped consistently in the middle region of bovine chromosome 6 (BTA6). Dense genetic and physical maps and, ultimately, a fully annotated genome sequence as well as their mutual connections are required to efficiently identify genes and gene variants responsible for genetic variation of phenotypic traits. A comprehensive high-resolution gene-rich map linking densely spaced bovine markers and genes to the annotated human genome sequence is required as a framework to facilitate this approach for the region on BTA6 carrying the QTL. RESULTS: Therefore, we constructed a high-resolution radiation hybrid (RH) map for the QTL containing chromosomal region of BTA6. This new RH map with a total of 234 loci including 115 genes and ESTs displays a substantial increase in loci density compared to existing physical BTA6 maps. Screening the available bovine genome sequence resources, a total of 73 loci could be assigned to sequence contigs, which were already identified as specific for BTA6. For 43 loci, corresponding sequence contigs, which were not yet placed on the bovine genome assembly, were identified. In addition, the improved potential of this high-resolution RH map for BTA6 with respect to comparative mapping was demonstrated. Mapping a large number of genes on BTA6 and cross-referencing them with map locations in corresponding syntenic multi-species chromosome segments (human, mouse, rat, dog, chicken) achieved a refined accurate alignment of conserved segments and evolutionary breakpoints across the species included. CONCLUSION: The gene-anchored high-resolution RH map (1 locus/300 kb) for the targeted region of BTA6 presented here will provide a valuable platform to guide high-quality assembling and annotation of the currently existing bovine genome sequence draft to establish the final architecture of BTA6. Hence, a sequence-based map will provide a key resource to facilitate prospective continued efforts for the selection and validation of relevant positional and functional candidates underlying QTL for milk production and growth-related traits mapped on BTA6 and on similar chromosomal regions from evolutionary closely related species like sheep and goat. Furthermore, the high-resolution sequence-referenced BTA6 map will enable precise identification of multi-species conserved chromosome segments and evolutionary breakpoints in mammalian phylogenetic studies.

Animals↗

PubMed2005

Bovine NALP5, NALP8, and NALP9 genes: assignment to a QTL region and the expression in adult tissues, oocytes, and preimplantation embryos.

A 3204-bp full-length cDNA of bovine NALP9 was cloned and its genomic organization was analyzed. The 2988-bp open reading frame covers 9 exons and encodes a deduced protein of 996 amino acids containing Pyrin, Nacht and leucine-rich repeat domains like the human NALP gene family members. Mapping with the WGRH5000 panel and fluorescence in situ hybridization assigned NALP9 in close vicinity to BM2078 (LOD score 25.71; distance 0.0 cR5000) on bovine chromosome 18, BTA18q25-q26, within a previously identified QTL region for reproductive traits flanked by the bovine marker BM2078 and TGLA227. BAC contig analysis revealed that NALP9, NALP8, and NALP5 map in this QTL region. Temporospatial expression of these members of the NALP gene family was monitored. Among the adult tissues examined, transcripts of NALP8 and NALP9 were detected exclusively in testis and ovary, whereas transcripts of the NALP5 gene are limited to the ovary. The transcripts of NALP9, NALP8, and NALP5 were detected in oocytes before and after in vitro maturation and with a gradual decline from 2-cell to 8-cell stage, suggesting no reactivation at the time of bovine maternal to embryonic transition. Assignment to a QTL region for reproductive traits and preferential expression of NALP9, NALP8, and NALP5 in oocyte, germinal lineage, and gonad cells may suggest their functional relevance to reproduction and possible contribution to phenotypic variation.

Age Factors↗

PubMed2005

Assignment of chromosome rearrangements between X chromosomes of human and cattle by laser microdissection and Zoo-FISH.

Cross-species fluorescence in-situ hybridization (Zoo-FISH) was performed on cattle metaphase spreads using Homo sapiens X chromosome (HSAX) painting probes specific for the p- and q-arms to identify the cytogenetic location of a chromosome breakpoint between HSAX and the Bos taurus X chromosome (BTAX). The existence of a breakpoint is strongly suggested by recent radiation hybrid and FISH mapping results. Hybridization probes were generated by microdissection of HSAX p- and q-arms using the contact-free technology of Laser Microdissection and Pressure Catapulting (LMPC), amplification of the isolated chromosome material by DOP-PCR, and labelling of the PCR products with digoxigenin in a secondary PCR. Independent Zoo-FISH of the two painting probes on bovine metaphase chromosomes (detected by antidigoxigenin-fluorescein) resulted in clear hybridization signals on BTAX. A breakpoint was identified between HSAXp and HSAXq on BTAX, and narrowed down between the G-bands BTAXq25 and BTAXq26. The assumed centromere transposition between HSAX and BTAX associated with the rearranged chromosome segments is supported by cytogenetic assignments of the genes BGN and G6PD to BTAX.

Animals↗

PubMed2005

The bovine PPARGC1A gene: molecular characterization and association of an SNP with variation of milk fat synthesis.

Several studies in a variety of breeds have reported at least two QTL for milk production traits, including milk fat synthesis on bovine chromosome 6 (BTA6), comprising a region that comparatively has been mapped to equivalent syntenic chromosome intervals in human, pig, and mouse harboring loci associated with type II diabetes and obesity-related traits. We identified the bovine peroxysome proliferator-activated receptor-gamma coactivator-1alpha gene (PPARGC1A) as a plausible positional and functional candidate gene for a previously described QTL for milk fat yield on BTA6 because of its chromosomal position and its key role in energy, fat, and glucose metabolism. To analyze the role of the bovine PPARGC1A gene in regulation of milk fat synthesis in dairy cattle, we determined its cDNA sequence, genomic organization, chromosomal localization, and expression pattern. The bovine PPARGC1A gene is organized in 13 exons comprising 6,261 bp and is expressed at different levels in a large number of tissues. Bovine PPARGC1A cDNA and protein sequences showed substantial similarity (92-95%) to its respective orthologs from human, rat, and mouse. Screening for polymorphisms in the coding sequence, exon/intron boundaries, 5'- and 3'-untranslated regions, and promoter region of the PPARGC1A gene in sires with a different genotype at the QTL for milk fat yield as well as in a multibreed panel revealed a total of 11 polymorphic loci. A significant association between an SNP in intron 9 of the PPARGC1A gene and milk fat yield was observed in a major dairy cattle population, indicating that the PPARGC1A gene could be involved in genetic variation underlying the QTL for milk fat synthesis on BTA6.

Amino Acid Sequence↗

PubMed2004

High-resolution comparative mapping between human chromosomes 4 and 8 and bovine chromosome 27 provides genes and segments serving as positional candidates for udder health in cattle.

To get more information about the order of genes located in Bos taurus (BTA) chromosome 27 segments, supposed to harbor loci influencing clinical mastitis and somatic cell count, and to identify genes that serve as positional candidates for the mentioned traits, we constructed a high-resolution, comparative, and comprehensive gene map for BTA27. The map includes 57 loci in a 5000-rad cattle-hamster whole genome radiation hybrid panel supported by 50 syntenic assignments in a cattle-murine somatic hybrid cell panel. Thirty-eight new loci (36 genes, 2 microsatellites) together with repeated mappings of 5 genes and 7 microsatellites and integration of existing data from 7 microsatellites were used to generate a comprehensive RH5000 map. The RH map, constructed at lod score criterion 8 using the software RHMAP v.3.0, consisted of three linkage groups 23, 22, and 590 cR5000 in length. Gene assignments on BTA27 and the localization of 8 more genes on BTA8 and BTA14 previously predicted on BTA8/BTA27 and BTA14/BTA27 narrowed down significantly the chromosome break points between the three cattle chromosomes and segments on Homo sapiens chromosomes HSA4 and HSA8. Defined evolutionary break points increase the accuracy of comparative in silico mapping of further human genes in conserved chromosome segments of BTA27.

Animals↗

PubMed2004

Targeted generation of 16 sequence-tagged sites for bovine chromosome region 5q21-q25 by microdissection.

The cattle chromosome region BTA5q21-q25 is associated with immune defense and is linked with several economically important traits for growth, ovulation, twinning and milk yield. Chromosome microdissection of the region was performed to generate fragment-specific DNA libraries and to provide new bovine-specific DNA sequences as starting material for physical fine-mapping approaches or linkage studies. A first library screening resulted in the identification of 16 region-specific sequence-tagged sites (STS). Fifteen STS represent new unique cattle DNA sequences, of which one identifies a new microsatellite. Homology with the gene CDK2 was found for the remaining STS.

Animals↗

PubMed2004

A 1463 gene cattle-human comparative map with anchor points defined by human genome sequence coordinates.

A second-generation 5000 rad radiation hybrid (RH) map of the cattle genome was constructed primarily using cattle ESTs that were targeted to gaps in the existing cattle-human comparative map, as well as to sparsely populated map intervals. A total of 870 targeted markers were added, bringing the number of markers mapped on the RH(5000) panel to 1913. Of these, 1463 have significant BLASTN hits (E < e(-5)) against the human genome sequence. A cattle-human comparative map was created using human genome sequence coordinates of the paired orthologs. One-hundred and ninety-five conserved segments (defined by two or more genes) were identified between the cattle and human genomes, of which 31 are newly discovered and 34 were extended singletons on the first-generation map. The new map represents an improvement of 20% genome-wide comparative coverage compared with the first-generation map. Analysis of gene content within human genome regions where there are gaps in the comparative map revealed gaps with both significantly greater and significantly lower gene content. The new, more detailed cattle-human comparative map provides an improved resource for the analysis of mammalian chromosome evolution, the identification of candidate genes for economically important traits, and for proper alignment of sequence contigs on cattle chromosomes.

Animals↗

PubMed2003

The telomeric region of BTA18 containing a potential QTL region for health in cattle exhibits high similarity to the HSA19q region in humans.

We have applied a targeted physical mapping approach, based on the isolation of bovine region-specific large-insert clones using homologous human sequences and chromosome microdissection, to enhance the physical gene map of the telomeric region of BTA18 and to prove its evolutionary conservation. The latter is a prerequisite to exploit the dense human gene map for future positional cloning approaches. Partial sequencing and homology search were used to characterize 20 BACs targeted to the BTA18q2.4-q2.6 region. We used fluorescence in situ hybridization (FISH) to create physical maps of 11 BACs containing 15 gene loci; these BACs served as anchor loci. Using these approaches, 12 new gene loci (CKM, STK13, PSCD2, IRF3, VASP, ACTN4, ITPKC, CYP2B6, FOSB, DMPK, MIA, SIX5) were assigned on BTA18 in the bovine cytogenetic map. A resolved physical map of BTA18q2.4-q2.6 was developed, which encompasses 28 marker loci and a comparative cytogenetic map that contains 15 genes. The mapping results demonstrate the high evolutionary conservation between the telomeric region of BTA18q and HSA19q.

Animals↗

PubMed2003

Application of disease-associated differentially expressed genes--mining for functional candidate genes for mastitis resistance in cattle.

In this study the mRNA differential display method was applied to identify mastitis-associated expressed DNA sequences based on different expression patterns in mammary gland samples of non-infected and infected udder quarters of a cow. In total, 704 different cDNA bands were displayed in both udder samples. Five hundred-and-thirty two bands, (75.6%) were differentially displayed. Ninety prominent cDNA bands were isolated, re-amplified, cloned and sequenced resulting in 87 different sequences. Amongst the 19 expressed sequence tags showing a similarity with previously described genes, the majority of these sequences exhibited homology to protein kinase encoding genes (26.3%), to genes involved in the regulation of gene expression (26.3%), to growth and differentiation factor encoding genes (21.0%) and to immune response or inflammation marker encoding genes (21.0%). These sequences were shown to have mastitis-associated expression in the udder samples of animals with and without clinical mastitis by quantitative RT-PCR. They were mapped physically using a bovine-hamster somatic cell hybrid panel and a 5000 rad bovine whole genome radiation hybrid panel. According to their localization in QTL regions based on an established integrated marker/gene-map and their disease-associated expression, four genes (AHCY, PRKDC, HNRPU, OSTF1) were suggested as potentially involved in mastitis defense.

Animals↗

PubMed2002

A comparative radiation hybrid map of bovine chromosome 18 and homologous chromosomes in human and mice.

A comprehensive radiation hybrid (RH) map and a high resolution comparative map of Bos taurus (BTA) chromosome 18 were constructed, composed of 103 markers and 76 markers, respectively, by using a cattle-hamster somatic hybrid cell panel and a 5,000 rad whole-genome radiation hybrid (WGRH) panel. These maps include 65 new assignments (56 genes, 3 expressed-sequence tags, 6 microsatellites) and integrate 38 markers from the first generation WGRH(5,000) map of BTA18. Fifty-nine assignments of coding sequences were supported by somatic hybrid cell mapping to markers on BTA18. The total length of the comprehensive map was 1666 cR(5,000). Break-point positions within the chromosome were refined and a new telomeric RH linkage group was established. Conserved synteny between cattle, human, and mouse was found for 76 genes of BTA18 and human chromosomes (HSA) 16 and 19 and for 34 cattle genes and mouse chromosomes (MMU) 7 and 8. The new RH map is potentially useful for the identification of candidate genes for economically important traits, contributes to the expansion of the existing BTA18 gene map, and provides new information about the chromosome evolution in cattle, humans, and mice.

Animals↗

PubMed2002

Targeted construction of a high-resolution, integrated, comprehensive, and comparative map for a region specific to bovine chromosome 6 based on radiation hybrid mapping.

To resolve a candidate chromosome region on the middle part of bovine chromosome 6 (BTA6) containing several different quantitative trait locus (QTL) intervals, we constructed a high-resolution, integrated, comprehensive, and comparative map using a 12,000-rad, whole-genome, cattle-hamster radiation hybrid (RH) panel. The RH map includes a total of 71 loci either selected from bovine and comparative maps or targeted directly from a microdissection library specific for the BTA6 region. All loci typed were placed in one linkage group at a lod score threshold of 4.0. The length of the comprehensive RH map, which is the first high-resolution RH map in cattle, spans 2568.8 cR(12,000). The order of markers obtained principally agrees with the order on published bovine genetic maps. Our RH map integrates markers as well as genes and ESTs available from several physical and genetic maps of BTA6 and the orthologous ovine chromosome 6, human chromosome 4, and mouse chromosomes 5/3. Comparative analysis confirms and refines current knowledge about conservation and rearrangements in corresponding chromosomal regions on BTA6. We identified and localized two new breakpoints for intrachromosomal rearrangements between human chromosome 4 and BTA6. This RH map is a powerful tool in all aspects of genetic, physical, transcript, and comparative mapping. Due to its links to the gene-dense maps of human and mouse, it can serve as a prerequisite to identify possible candidate genes for quantitative trait loci localized in the targeted BTA6 region.

Animals↗

PubMed2002

Identification and chromosome assignment of 23 genes expressed in meat and dairy cattle.

Hepatic and intestinal expressed sequence tags (ESTs) of lactating German Holstein and Charolais cows were used to identify and map genes potentially involved in the regulation of metabolic processes in cattle. Seventeen ESTs were homologous to human gene sequences and six ESTs identified unknown coding sequences in human genomic DNA clones. A cattle-hamster somatic hybrid cell panel and cattle-hamster 5000 rad whole genome radiation hybrid (WGRH) panel were used to assign the ESTs in the bovine genome. Fifteen of the mapped genes and the six ESTs represent new assignments in the established cattle WGRH5000 map. Calculation of the radiation hybrid (RH) mapping data was performed with the software RHMAPPER. The new loci contribute to the completion of the bovine transcript maps and their comparative assignments increase our knowledge about genome evolution between cattle and human.

Animals↗