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Biomedical subjects

J E Collins

Publications and source records attributed to J E Collins.

At least 19 recordsLinked to original sources
PubMed2004

The DNA sequence and analysis of human chromosome 13.

Chromosome 13 is the largest acrocentric human chromosome. It carries genes involved in cancer including the breast cancer type 2 (BRCA2) and retinoblastoma (RB1) genes, is frequently rearranged in B-cell chronic lymphocytic leukaemia, and contains the DAOA locus associated with bipolar disorder and schizophrenia. We describe completion and analysis of 95.5 megabases (Mb) of sequence from chromosome 13, which contains 633 genes and 296 pseudogenes. We estimate that more than 95.4% of the protein-coding genes of this chromosome have been identified, on the basis of comparison with other vertebrate genome sequences. Additionally, 105 putative non-coding RNA genes were found. Chromosome 13 has one of the lowest gene densities (6.5 genes per Mb) among human chromosomes, and contains a central region of 38 Mb where the gene density drops to only 3.1 genes per Mb.

Chromosome Mapping↗
PubMed2004

Lack of association of the vitamin D receptor gene with Graves' disease in UK Caucasians.

OBJECTIVE: Vitamin D modulates the immune system by suppressing the proliferation of activated T cells, with its actions being directed through the vitamin D receptor (VDR). A number of single nucleotide polymorphisms (SNPs) have been identified in the VDR gene, of which several have been associated with autoimmune diseases, including type 1 diabetes and Graves' disease (GD) in Japanese females. The aim of this study was to test for association of polymorphisms of the VDR gene in the genetic susceptibility to GD in UK Caucasians. DESIGN: Target DNA for five previously published SNPs, four novel SNPs and one microsatellite marker was amplified by the polymerase chain reaction (PCR). Subsequent genotyping was performed using restriction fragment length polymorphism (RFLP) or microsatellite genotyping analysis, according to the type of VDR polymorphism. PATIENTS: We obtained DNA from a case-control dataset consisting of 768 patients with GD and 864 control subjects. All patients and control subjects were Caucasians born in the UK, and all gave informed, written consent. MEASUREMENTS: Frequencies of the alleles and genotypes of the ten VDR gene polymorphisms were compared between patients and control subjects using the chi2 test. Odds ratios were calculated using Woolf's method with Haldane's modification for small numbers and D prime (D') was calculated to assess the level of linkage disequilibrium (LD) between the ten polymorphisms. RESULTS: No differences in allele or genotype frequencies were observed between GD cases and control subjects for any of the nine SNPs studied. The S allele of the PolyA microsatellite marker was slightly more frequent in GD cases when compared with control subjects (chi2= 4.364, P = 0.04). Strongest LD between markers was observed towards the 3' end of the VDR gene but there was no evidence of association with disease. CONCLUSION: This is the largest and most comprehensive study of the VDR gene in GD to date and these data suggest that these polymorphisms of the VDR gene do not contribute to GD susceptibility in the UK.

Case-Control Studies↗
PubMed2004

Evidence for a Type 1 diabetes-specific mechanism for the insulin gene-associated IDDM2 locus rather than a general influence on autoimmunity.

AIMS: The Type 1 diabetes susceptibility locus, IDDM2, has been mapped to a variable number of tandem repeats (VNTR) region 5' upstream of the insulin (INS) and insulin-like growth factor (IGF2) genes on chromosome 11p15. The function of the VNTR is uncertain; however, it may influence the thymic expression of the insulin gene and affect the development of immune self-tolerance. The aim of this study was to investigate whether the INS VNTR region is a Type 1 diabetes-specific locus or acting as a general autoimmunity gene. METHODS: We genotyped the INS-IGF2 VNTR [using the surrogate INS-23 HphI single nucleotide polymorphism (SNP)] in 823 Graves' disease (GD)/multiple sclerosis (MS) families, 1433 GD/MS patients and 837 healthy control subjects. RESULTS: We found no evidence of excess transmission of the allele associated with Type 1 diabetes to individuals affected by GD or MS within the families. Analysis of the case-control dataset showed no genotypic or allelic difference between the two populations. CONCLUSIONS: These data suggest that the INS-IGF2 VNTR is acting as a Type 1 diabetes-specific susceptibility gene rather than as an influence on general autoimmunity.

Alleles↗
PubMed2004

Common allelic variants of exons 10, 12, and 33 of the thyroglobulin gene are not associated with autoimmune thyroid disease in the United Kingdom.

Thyroglobulin (Tg) is a major autoantigen for autoimmune thyroid disease (AITD). The Tg gene (Tg) has been mapped to chromosome 8q24, which has recently been linked in two independent studies to AITD. Association of specific alleles of microsatellite markers within Tg itself supports a role for Tg as a good candidate susceptibility locus for AITD. Resequencing of the Tg exons has led to the identification of a number of novel single nucleotide polymorphisms, four of which have been reported to be associated with AITD. Resequencing of Tg in Caucasian subjects in the United Kingdom (UK) has confirmed the presence of four single nucleotide polymorphisms in exons 10, 12, and 33. However, in the largest case-control association study to date with adequate power to detect the reported effect if present, we found no evidence for association of the Tg DNA variants with AITD in the UK. These data suggest that the recently identified single nucleotide polymorphisms do not have a causal role for AITD in the UK. At this stage, we cannot exclude the Tg region as harboring a susceptibility locus for AITD, and only large scale sequencing and fine mapping of the region, including neighboring genes, will allow us to identify any potential causal variants within this region.

Alleles↗
PubMed2003

The DNA sequence and analysis of human chromosome 6.

Chromosome 6 is a metacentric chromosome that constitutes about 6% of the human genome. The finished sequence comprises 166,880,988 base pairs, representing the largest chromosome sequenced so far. The entire sequence has been subjected to high-quality manual annotation, resulting in the evidence-supported identification of 1,557 genes and 633 pseudogenes. Here we report that at least 96% of the protein-coding genes have been identified, as assessed by multi-species comparative sequence analysis, and provide evidence for the presence of further, otherwise unsupported exons/genes. Among these are genes directly implicated in cancer, schizophrenia, autoimmunity and many other diseases. Chromosome 6 harbours the largest transfer RNA gene cluster in the genome; we show that this cluster co-localizes with a region of high transcriptional activity. Within the essential immune loci of the major histocompatibility complex, we find HLA-B to be the most polymorphic gene on chromosome 6 and in the human genome.

Animals↗
PubMed2003

Cadherins, catenins and APC in pleural malignant mesothelioma.

Malignant mesothelioma is an aggressive disease of the pleura, and less commonly the peritoneum, with a very poor prognosis. The present study has examined the expression of cell adhesion molecules including cadherins, catenins, and APC in order to determine whether abnormal expression of components of the Wnt signalling pathway contribute to the variable phenotype of malignant mesothelioma. Sixty-three malignant mesotheliomas and nine cases of reactive mesothelial hyperplasia were analysed by immunohistochemistry for E-cadherin, N-cadherin, alpha-catenin, beta-catenin, and the C- and N-terminals of APC. In addition, DNA was extracted from formalin-fixed, paraffin wax blocks, and a 226 bp fragment of exon 3 of the beta-catenin gene was amplified, sequenced, and screened for activating mutations in the glycogen synthase kinase 3beta (GSK-3beta) phosphorylation targets. E-cadherin expression was detected in 48% of the epithelioid mesotheliomas but was observed in only 7% of sarcomatoid mesotheliomas. N-cadherin, alpha-catenin, beta-catenin, and the C- and N-terminals of APC did not show differential expression between the mesothelioma phenotypes. Abnormal nuclear localization of beta-catenin was demonstrated in 19% of mesotheliomas. Mutations of beta-catenin phosphorylation sites were not detected in any of the 62 mesotheliomas examined. Positive staining for the N-terminal of APC was seen in all of the cases of reactive mesothelial hyperplasia, as well as in all the mesotheliomas. Staining for the C-terminal of APC was negative in 23% mesotheliomas, despite being present in all the cases of reactive hyperplasia. The present study provides the first evidence that beta-catenin accumulates in the nucleus in malignant mesotheliomas. In addition, APC expression was altered in some mesotheliomas, suggesting that a truncated APC gene product may contribute to abnormal Wnt signalling and dysregulation of cell proliferation in malignant mesothelioma.

Adenomatous Polyposis Coli↗
PubMed2003

Association of a rare thyroglobulin gene microsatellite variant with autoimmune thyroid disease.

Genetic and environmental factors contribute to the development of Graves' disease and Hashimoto's thyroiditis. These diseases, although clinically distinct, share many immunological and histological features. Susceptibility genes for autoimmune thyroid disease (AITD) have been investigated, although only the human leukocyte antigen and cytotoxic T lymphocyte-associated antigen-4 gene regions have been consistently associated with disease. Recent data, however, have shown linkage and association of chromosome 8q24 (containing the thyroglobulin gene) to AITD. Therefore, we performed a case-control association study on patients with AITD and controls using previously associated markers (D8S284 and Tgms2). No differences in allele frequencies were observed between AITD cases and controls for D8S284. Compared with the three common alleles (frequencies >10%), the rare alleles of Tgms2 were increased (chi(2)= 10.6; P = 0.001) at Tgms2. This group included the 336-bp allele (increased in cases vs. controls: chi(2)= 24.97; P < 0.001), which has previously been reported to be associated with AITD. The rarity of this allele in the United Kingdom, however, precluded analysis in our family dataset. Although these findings may represent a random chance event, in view of previous reports of linkage and association of this gene region to AITD, this may be an example of a rare causal variant of a complex disease.

Adolescent↗
PubMed2001

Diagnostic investigation of chronic porcine reproductive and respiratory syndrome virus in a breeding herd of pigs.

Forty-five sows and 15 boars were selected at random from a breeding herd known to be chronically infected with porcine reproductive and respiratory syndrome virus (PRRSV) and lymphoid, immune-privileged, and non-lymphoid/non-immune-privileged tissues were tested for the presence of the virus by PCR, virus isolation, and immunohistochemistry. The virus was isolated from the lateral retropharyngeal lymph node of one sow; the isolate was nucleic acid sequenced and determined to be of field origin, and it was inoculated into two PRRSV-naive pregnant sows (A and B) at 95 days of gestation. They were necropsied 14 days later and samples of maternal and fetal tissue and blood samples were collected. Sow A had 10 fresh, six partially autolysed, and two mummified fetuses, and sow B had six fresh and viable fetuses. Viral nucleic acid was detected by PCR in tissue pools from each sow and also from pooled fetal tissues, and the virus was isolated from fetal pools from sow A.

Animals↗
PubMed2001

The physical maps for sequencing human chromosomes 1, 6, 9, 10, 13, 20 and X.

We constructed maps for eight chromosomes (1, 6, 9, 10, 13, 20, X and (previously) 22), representing one-third of the genome, by building landmark maps, isolating bacterial clones and assembling contigs. By this approach, we could establish the long-range organization of the maps early in the project, and all contig extension, gap closure and problem-solving was simplified by containment within local regions. The maps currently represent more than 94% of the euchromatic (gene-containing) regions of these chromosomes in 176 contigs, and contain 96% of the chromosome-specific markers in the human gene map. By measuring the remaining gaps, we can assess chromosome length and coverage in sequenced clones.

Chromosomes, Human, Pair 1↗
PubMed2001

Insertional events as well as translocations may arise during aberrant immunoglobulin switch recombination in a patient with multiple myeloma.

The majority of patients with multiple myeloma have translocations involving the immunoglobulin heavy chain switch regions on chromosome 14q32 and a promiscuous range of partner chromosomes. We describe a patient with an insertion of 132 bp of chromosome 22q12 sequence into the 5' region flanking S(mu) on chromosome 14q32. The 132 bp region from chromosome 22q12 contains the whole of exon 3 from a novel gene of unknown function in man. The significance of such insertional events remains unclear. The description of insertional events occurring as a result of abnormal switch recombination suggests that, in myeloma, dysregulation of oncogenes may occur by a mechanism other than chromosomal translocation.

Base Sequence↗
PubMed2001

CD8+ T cells in human uterine endometrial lymphoid aggregates: evidence for accumulation of cells by trafficking.

Lymphoid aggregates (LA) develop during the proliferative phase of the menstrual cycle in the human uterine endometrium (EM). They contain mostly CD8+ T cells and B cells. As these LA are absent immediately following menses, they may arise by division of cells resident in the EM, or by division of a limited number of precursor cells that traffic into the EM during the early proliferative phase of the menstrual cycle. Alternatively, they may arise by the continuous trafficking of cells into the EM throughout the proliferative phase of the menstrual cycle. In this study we investigated the distribution and frequency of CD8+ T cells in the aggregates using expression of Vbeta2 or Vbeta8 as markers of clonality and Ki-67 as a marker of dividing cells. Confocal microscopic analysis of endometrial tissues showed the random distribution of CD8+ T cells within aggregates within the same sample and in aggregates from different samples. Furthermore, comparisons of the distribution of Vbeta2 and Vb8 with expected values predicted from Poisson distribution values were not significantly different, suggesting that CD8+ T cells do not arise by division from single precursors. A low level of T-cell division within LAs was confirmed by positive staining for Ki-67. Dividing T cells were randomly dispersed throughout the LA and the frequency of dividing cells did not vary greatly between aggregates within the same tissue. Nearest-neighbour analysis of dividing cells showed no statistically significant deviations from a random distribution. Taken together, these results suggest that LA develop during the menstrual cycle largely by the trafficking of cells to nucleation sites within the EM, rather than by division of a limited number of precursor cells.

Apoptosis↗
PubMed2001

Transmission of porcine reproductive and respiratory syndrome virus from persistently infected sows to contact controls.

The objective of this study was to determine if porcine reproductive and respiratory syndrome virus (PRRSV) could persist in non-pregnant sows and if persistently infected sows could transmit virus to naive contact controls. Twelve PRRSV-naive, non-pregnant sows (index sows) were infected with a field isolate of PRRSV and housed in individual isolation rooms for 42 to 56 days postinfection. Following this period, 1 naive contact sow was placed in each room divided by a gate allowing nose-to-nose contact with a single index sow. Index sows were not viremic at the time of contact sow entry. Virus nucleic acid was detected by polymerase chain reaction, and infectious virus was detected by virus isolation in sera from 3 of the 12 contact sows at 49, 56, and 86 days postinfection. All 3 infected contacts developed PRRSV antibodies. Virus nucleic acid was detected in tissues of all of the 12 index sows at 72 or 86 days postinfection. Nucleic acid sequencing indicated that representative samples from index and infected contacts were homologous (> 99%) to the PRRSV used to infect index sows at the onset of the study. This study demonstrates that PRRSV can persist in sows and that persistently infected sows can transmit virus to naive contact animals.

Animals↗
PubMed2000

Correlation between the presence of enzootic pneumonia lesions and detection of Mycoplasma hyopneumoniae in bronchial swabs by PCR.

In many diagnostic laboratories the diagnosis of mycoplasmal pneumonia in pigs is based on clinical signs and the presence of gross and histopathological lesions. The objective of this study was to evaluate the nested-PCR technique as an adjunct to the histopathological diagnosis of Mycoplasma hyopneumoniae infection. Respiratory disease of 184 swine cases submitted to the Minnesota Veterinary Diagnostic Laboratory between 1 January and 30 June 1998 were used. Bronchial swabs were collected and the nested-PCR performed. Lung samples were graded PCR positive or negative. Histopathological lesions were scored 0-4, depending on the mycoplasma-like characteristics of the lesions, with category 4 demonstrating strong evidence of mycoplasma infection.Nested-PCR correlated well with histopathological lesions characteristic of M. hyopneumoniae in categories 3 and 4 and approximately half of the histopathological categories 1 and 2 were nested-PCR positive. The results demonstrate that the nested-PCR is a valuable adjunct in the diagnosis of M. hyopneumoniae infection when non-diagnostic microscopic lesions of mycoplasmosis are found.

Animals↗
PubMed2000

Cloning and expression throughout mouse development of mfat1, a homologue of the Drosophila tumour suppressor gene fat.

We present the entire sequence of the mouse Fat orthologue (mFat1), a protein of 4,588 amino acids with 34 cadherin repeats, 27 potential N-glycosylation sites, five EGF repeats and a laminin A G-motif in its extracellular domain. A single transmembrane region is followed by a cytoplasmic domain containing putative catenin-binding sequences. mFat1 shows high homology to human FAT and lesser homology to Drosophila Fat. The sequence of this giant cadherin suggests that it is unlikely to have a homophilic adhesive function, but may mediate heterophilic adhesion or play a signalling role. Expression analysis shows that the mfat1 gene is expressed early in pre-implantation mouse development, at the compact eight cell stage. Whole-mount and section in situ analyses show that transcripts are widely expressed throughout post-implantation development, most notably in the limb buds, branchial arches, forming somites, and in particular in the proliferating ventricular zones in the brain, being down-regulated as cells cease dividing. RT-PCR detects widespread expression in the adult suggesting a role in proliferation and differentiation of many tissues and cell types.

Amino Acid Sequence↗
PubMed2000

Muscle force and range of motion as predictors of function in older adults.

BACKGROUND AND PURPOSE: Musculoskeletal impairments and functional limitations are linked to disability in older adults. The purposes of this study were to identify the extremity musculoskeletal impairments that best predict functional limitations in older adults and to assess the validity of measurements obtained for the Physical Performance Test (PPT) as a predictor of disability. SUBJECTS AND METHODS: Eighty-one older adults residing in independent and dependent care facilities were tested for extremity muscle force, range of motion, and function. Data were analyzed using multiple regression analysis to identify extremity impairments that predicted function scores and logistic regression analysis to determine whether PPT scores predicted subjects' living situation as dependent versus independent. RESULTS: Subject age, lower-extremity muscle force, and lower-extremity range of motion explained 77% of the variance in function as measured by the PPT. Results differed when analysis was done by subject living situation, with a higher percentage of the variance in function scores explained by musculoskeletal measures for the dependent living group as compared with the independent living group. CONCLUSION AND DISCUSSION: Extremity musculoskeletal impairments have a strong relationship to function, especially in older adults living in dependent care settings. The results of this study can be used to design interventions to address the musculoskeletal disorders most related to function in the older population.

Activities of Daily Living↗
PubMed1999

The DNA sequence of human chromosome 22.

Knowledge of the complete genomic DNA sequence of an organism allows a systematic approach to defining its genetic components. The genomic sequence provides access to the complete structures of all genes, including those without known function, their control elements, and, by inference, the proteins they encode, as well as all other biologically important sequences. Furthermore, the sequence is a rich and permanent source of information for the design of further biological studies of the organism and for the study of evolution through cross-species sequence comparison. The power of this approach has been amply demonstrated by the determination of the sequences of a number of microbial and model organisms. The next step is to obtain the complete sequence of the entire human genome. Here we report the sequence of the euchromatic part of human chromosome 22. The sequence obtained consists of 12 contiguous segments spanning 33.4 megabases, contains at least 545 genes and 134 pseudogenes, and provides the first view of the complex chromosomal landscapes that will be found in the rest of the genome.

Animals↗
PubMed1999

Porcine reproductive and respiratory syndrome virus infection in neonatal pigs characterised by marked neurovirulence.

Neonatal pigs from three herds of pigs were somnolent and inappetent and had microscopic lesions characterised by severe meningoencephalitis, necrotic interstitial pneumonia and gastric muscular inflammation. Porcine reproductive and respiratory syndrome virus (PRRSV) infection was diagnosed and confirmed by virus isolation, fluorescent antibody examination of frozen lung sections, serology, immunohistochemistry and in situ hybridisation. Each herd had a history of PRRSV infection and was using or had used a modified-live vaccine. The isolates from the affected pigs were genetically distinct from the modified-live vaccine strain of the virus when compared by restriction enzyme analysis and nucleotide sequencing of PRRSV open reading frames 5 and 6. The virus was identified in macrophages or microglia of brain lesions by immunohistochemical staining of brain sections with an anti-PRRSV monoclonal antibody and an anti-macrophage antibody. The replication of the virus in the brain was verified by in situ hybridisation. The meningoencephalitis induced by the virus in pigs from each of the herds was unusually severe and the brain lesions were atypical when compared with other descriptions of encephalitis induced by the virus, which should therefore be considered as a possible diagnosis for neonatal pigs with severe meningoencephalitis. In addition, field isolates of the virus which are capable of causing disease can emerge and coexist with modified-live vaccine virus in some pig herds.

Animals↗