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R Deka

Publications and source records attributed to R Deka.

At least 55 records · Page 3Linked to original sources
PubMed1994

Conservation of human chromosome 13 polymorphic microsatellite (CA)n repeats in chimpanzees.

Tandemly repeated (dC-dA)n.(dG-dT)n sequences occur abundantly and are found in most eukaryotic genomes. To investigate the level of conservation of these repeat sequences in nonhuman primates, we have analyzed seven human chromosome 13 dinucleotide (CA)n repeat loci in chimpanzees by DNA amplification using primers designed for analysis of human loci. Comparable levels of polymorphism at these loci in the two species, revealed by the number of alleles, heterozygosity, and allele sizes, suggest that the (CA)n repeat arrays and their genomic locations are highly conserved. Even though the proportion of shared alleles between the two species varies enormously and the modal alleles are not the same, allelic lengths at each locus in the chimpanzees are detected within the bounds of the allele size range observed in humans. A similar observation has been noted in a limited number of gorillas and orangutans. Using a new measure of genetic distance that takes into account the size of alleles, we have compared the genetic distance between humans and chimpanzees. The genetic distance between these two species was found to be ninefold smaller than expected assuming there is no selection or mutational bias toward retention of (CA)n repeat arrays. These findings suggest a functional significance for these microsatellite loci.

Alleles↗
PubMed1994

Population genetic characteristics of the D1S80 locus in seven human populations.

We have analyzed the allele frequency distribution at the highly polymorphic variable number of tandem repeat (VNTR) locus D1S80 (pMCT118) in seven ethnic populations (namely, New Guinea Highlanders of Papua New Guinea, Dogrib Indians of Canada, Pehuenche Indians of Chile, American and Western Samoans, Kacharis of Northeast India, and German Caucasians) using the polymerase chain reaction (PCR) technique. In the pooled sample of 443 unrelated individuals 20 segregating alleles were detected. A trimodal pattern of allelic distribution is present in the majority of populations and is indicative of the evolutionary antiquity of the polymorphism at this locus. In spite of the observed high degree of polymorphism (expected heterozygosity 56%-86%), with a single exception--the marginally significant P value (0.04) of the exact test in American Samoans--the genotype distributions in all populations conform to their respective Hardy-Weinberg expectations. Summary statistics indicate that, in general, the allele frequency distribution at this locus may be approximated by the infinite allele model. The data also demonstrate that alleles that are shared by all populations have the highest average frequency within populations. Furthermore, the kinship bioassay analysis demonstrates that the extensive variation observed at the D1S80 locus is at the interindividual within population level, which dwarfs any interpopulation allele frequency variation, consistent with the population dynamics of hypervariable polymorphisms. These characteristics of the D1S80 locus make it a very useful marker for population genetic research, genetic linkage studies, forensic identification of individuals, and for determination of biological relatedness of individuals.

Alleles↗
PubMed1994

Cytogenetics and origins of pediatric germ cell tumors.

We present cytogenetic and DNA fingerprint analysis on 13 new cases of pediatric germ cell tumors; we analyze further four cases we have reported previously. The patients ranged in age from 23 weeks gestation to 16 years. The tumors were located in the ovary, sacrococcygeum, testis, mediastinum, and the craniofacial region, and represented benign, immature, and malignant cases. All of the new cases had a normal diploid karyotype. We have previously reported on multiple genetic mechanisms of origin for ovarian germ cell tumors, namely meiosis I nondisjunction, meiosis II nondisjunction, endoreduplication of a haploid ovum, mitotic division of premeiotic germ cell, and fusion of two ova. To determine the origin of extragonadal and testicular GCTs, Q-band centromeric heteromorphisms and DNA markers were analyzed in the host and the cognate tumor. Our data suggest that extragonadal and testicular GCTs do not arise by a meiosis I or II error, or by endoreduplication; rather, they arise mitotically from either a somatic or a germ cell.

Adolescent↗
PubMed1994

Preliminary localization of a gene for autosomal dominant hypoparathyroidism to chromosome 3q13.

A large family in which hypoparathyroidism was observed to segregate as an autosomal dominant trait in three generations was identified. Mutation in the PTH gene was excluded by linkage and single-stranded conformational analysis. The hypocalcemic phenotype in this family was mapped by linkage analysis using short, tandem-repeat polymorphisms to the region of chromosome 3q13. A maximum lod score of 2.71 at theta = 0.0 was observed with marker D3S1303. Positive lod scores were observed at theta = 0.0 with markers flanking D3S1303. Multipoint linkage analysis gave a lod score of 2.71 for the region flanking D3S1303. Simulation using the computer program SLINK showed that a lod score of 2.71 at theta = 0.0 was the maximum lod score possible given the pedigree structure. The simulation also showed that given the structure of the pedigree the probability of observing a lod score of 2.71 at theta = 0.0 by chance was 1 in 1000. The data presented above provide important preliminary evidence supporting linkage to chromosome 3q13. This region contains a Ca(2+)-sensing receptor gene that is proposed as a key signal transduction element for changes in extracellular Ca2+ concentrations in mechanisms of regulation of PTH secretion from parathyroid cells. The mutation in this family may activate the Ca(2+)-sensing receptor suppressing PTH secretion and lowering the "set point" for serum calcium levels.

Chromosome Mapping↗
PubMed1994

Genetic characterization of American and Western Samoans.

The Samoan islands were politically separated into American Samoa and Western Samoa in the early 1900s. Economic modernization is far more extensive in American Samoa. However, the Samoan archipelago has maintained a remarkable degree of sociocultural homogeneity, including intermarriage. The sociocultural exchanges presumably led to genetic homogeneity between the two Samoas. Detailed genetic comparisons and characterizations of Samoans are scanty, however. As part of a multidisciplinary study of modernization and cardiovascular risk factors in adults, we analyzed nine hypervariable nuclear DNA (HVR) and four serum protein polymorphisms in the two Samoan groups. The average heterozygosities at both DNA and serum protein loci are comparable in the two groups. As expected, the HVR loci reveal a high degree of variability (heterozygosity 30-87%) compared with the serum protein loci (heterozygosity 1-52%). A large proportion of alleles at the HVR loci, ranging from 50% to 100%, are shared between American and Western Samoa. With the exceptions of the D1S80 locus in American Samoa and the D13S118 locus in Western Samoa, the genotype distributions at all loci conform to their respective Hardy-Weinberg expectations. Sporadic occurrence of the F13B*2 allele at the F13B locus in Samoans indicates a low level of European admixture because this allele is unique to Europeans. The calculated zero values of kinship coefficients and standard genetic distances indicate minimal population differentiation between the two Samoan groups.

Alleles↗
PubMed1993

Characterization of the type I dehydroquinase from Salmonella typhi.

The type I dehydroquinase from the human pathogen Salmonella typhi was overexpressed in an Escherichia coli host and purified to homogeneity. The S. typhi enzyme was characterized in terms of its kinetic parameters, important active-site residues, thermal stability and c.d. and fluorescence properties. In all important respects, the enzyme from S. typhi behaves in a very similar fashion to the well-characterized enzyme from E. coli, including the remarkable conformational stabilization observed on reduction of the substrate/product mixture by NaBH4. This gives confidence that the information from X-ray studies on the S. typhi enzyme [Boys, Fawcett, Sawyer, Moore, Charles, Hawkins, Deka, Kleanthous and Coggins (1992) J. Mol. Biol. 227, 352-355] can be applied to other type I dehydroquinases. Studies of the quenching of fluorescence of the S. typhi enzyme by succinimide show that NaBH4 reduction of the substrate/product imine complex involves a dramatic decrease in the flexibility of the enzyme, with only very minor changes in the overall secondary and tertiary structure.

Circular Dichroism↗
PubMed1992

Crystallization of a type I 3-dehydroquinase from Salmonella typhi.

Crystals have been grown of a type I 3-dehydroquinase from both Escherichia coli and Salmonella typhi. However, only those from S. typhi diffract to a resolution of 2.3 A on a conventional X-ray source and are suitable for structure determination. The space group has been determined as P2(1)2(1)2 with unit cell dimensions a = 48.01 A, b = 114.29 A, c = 42.87 A. There is one subunit in the asymmetric unit.

Bacterial Proteins↗
PubMed1992

A comparison of the enzymological and biophysical properties of two distinct classes of dehydroquinase enzymes.

This paper compares the biophysical and mechanistic properties of a typical type I dehydroquinase (DHQase), from the biosynthetic shikimate pathway of Escherichia coli, and a typical type II DHQase, from the quinate pathway of Aspergillus nidulans. C.d. shows that the two proteins have different secondary-structure compositions; the type I enzyme contains approx. 50% alpha-helix while the type II enzyme contains approx. 75% alpha-helix. The stability of the two types of DHQase was compared by denaturant-induced unfolding, as monitored by c.d., and by differential scanning calorimetry. The type II enzyme unfolds at concentrations of denaturant 4-fold greater than the type I and through a series of discrete transitions, while the type I enzyme unfolds in a single transition. These differences in conformational stability were also evident from the calorimetric experiments which show that type I DHQase unfolds as a single co-operative dimer at 57 degrees C whereas the type II enzyme unfolds above 82 degrees C and through a series of transitions suggesting higher orders of structure than that seen for the type I enzyme. Sedimentation and Mr analysis of both proteins by analytical ultracentrifugation is consistent with the unfolding data. The type I DHQase exists predominantly as a dimer with Mr = 46,000 +/- 2000 (a weighted average affected by the presence of monomer) and has a sedimentation coefficient s0(20,w) = 4.12 (+/- 0.08) S whereas the type II enzyme is a dodecamer, weight-average Mr = 190,000 +/- 10,000 and has a sedimentation coefficient, s0(20,w) = 9.96 (+/- 0.21) S. Although both enzymes have reactive histidine residues in the active site and can be inactivated by diethyl pyrocarbonate, the possibility that these structurally dissimilar enzymes catalyse the same dehydration reaction by the same catalytic mechanism is deemed unlikely by three criteria: (1) they have very different pH/log kcat. profiles and pH optima; (2) imine intermediates, which are known to play a central role in the mechanism of type I enzymes, could not be detected (by borohydride reduction) in the type II enzyme; (3) unlike Schiff's base-forming type I enzymes, there are no conserved lysine residues in type II amino acid sequences.

Bacterial Proteins↗
PubMed1992

Genetics and biology of human ovarian teratomas. III. Cytogenetics and origins of malignant ovarian germ cell tumors.

This report presents cytogenetic data on three cases of malignant ovarian germ cell tumors. All were diagnosed as malignant teratoma; case 1 with yolk sac elements; case 2 with elements of endodermal sinus tumor, embryonal carcinoma, and choriocarcinoma; and case 3 with yolk sac elements and embryonal carcinoma. Metaphase cells from each tumor, and normal tissue from the host, were karyotyped and scored for centromeric heteromorphisms in an attempt to determine the mechanism of origin. The karyotypes were 79,XXX,+1,+3,-6,+8,+12,+14,-15,+17, +20,+21,+22;49,XX,+8,+12,+22; and 48,XX,+3,+14, respectively. The analysis of centromeric heteromorphisms and DNA fingerprints of host and teratoma using the M13 probe revealed that one case originated from a germ cell before the first meiotic division. Normal host tissue was not available in case 2, but several centromeric markers were heterozygous in the tumor, indicating either meiosis I error or complete failure of germ cell meiosis. In the third case the centromeric heteromorphisms that were heterozygous in the host appeared to be homozygous for certain chromosomes and heterozygous for others in the tumor. These results suggest that germ cell teratomas could arise by the fusion of two ova.

Adolescent↗
PubMed1992

Comparison of five tandem repeat loci between humans and chimpanzees.

Five tandem repeat loci were studied in humans and chimpanzees using VNTR probes derived from human DNA. Shared alleles were found at three loci and were often the modal allele in one species but never in both. There was no difference in the mean number of alleles per locus. However, these species exhibited substantially different levels of gene diversity, with chimpanzees monomorphic at two loci. Evidence of reduced variability in chimpanzees corroborates earlier comparisons using isozymes and plasma proteins. Molecular mechanisms, population dynamics, or both may be responsible for these differences. Equal numbers of alleles per locus may reflect high mutation rates. By one test, chimpanzees were out of equilibrium at one locus, which may reflect a typing error or population substructure. The long divergence time, and the high probability of backward mutations, precludes accurate estimation of genetic distance between these species.

Alleles↗
PubMed1992

Characteristics of polymorphism at a VNTR locus 3' to the apolipoprotein B gene in five human populations.

We have analyzed the allele frequency distribution at the hypervariable locus 3' to the apolipoprotein B gene (ApoB 3' VNTR) in five well-defined human populations (Kacharis of northeast India, New Guinea Highlanders of Papua New Guinea, Dogrib Indians of Canada, Pehuenche Indians of Chile, and a relatively homogeneous Caucasian population of northern German extraction) by using the PCR technique. A total of 12 segregating alleles were detected in the pooled sample of 319 individuals. A fairly consistent bimodal pattern of allele frequency distribution, apparent in most of these geographically and genetically diverse populations, suggests that the ApoB 3' VNTR polymorphism predates the geographic dispersal of ancestral human populations. In spite of the observed high degree of polymorphism at this locus (expected heterozygosity levels 55%-78%), the genotype distributions in all populations (irrespective of their tribal or cosmopolitan nature) conform to their respective Hardy-Weinberg predictions. Furthermore, analysis of the congruence between expected heterozygosity and the observed number of alleles reveals that, in general, the allele frequency distributions at this locus are in agreement with the predictions of the classical mutation-drift models. The data also show that alleles that are shared by all populations have the highest average frequency within populations. These findings demonstrate the potential utility of highly informative hypervariable loci such as the ApoB 3' VNTR locus in population genetic research, as well as in forensic medicine and determination of biological relatedness of individuals.

Alleles↗
PubMed1991

A population genetic study of six VNTR loci in three ethnically defined populations.

To investigate the population genetic characteristics of VNTR polymorphisms in human populations, we have studied the allele frequency distribution of six VNTR loci (D1S57, RB1, D1S77, D1S61, alpha-globin 5'HVR, D1S76) in three well-defined populations (Kachari of Northeast India; Dogrib Indian of Canada; and New Guinea Highlander of Papua New Guinea). Even though the number of alleles sampled is limited, 48 to 92 alleles per locus per population, significant variation is noticed in the number of alleles per locus for all the populations. Using alternate summary measures, we have observed that genotype distributions at the six VNTR loci apparently conform to their respective Hardy-Weinberg predictions. Multilocus genotype profiles of the individuals in each of the three populations suggest that the VNTR alleles are independently segregating with the exception of the two linked loci D1S76 and D1S77. Lack of fit of all VNTR loci to one particular model of mutational change, either the Infinite Allele Model or the Stepwise Mutation Model, suggests more than one mechanism for production of new VNTR alleles. This study also indicates that increased heterozygosity at VNTR loci in comparison to protein and blood group loci may lead to more accurate estimates of genetic distance.

Alleles↗
PubMed1990

The distribution of the Hb constant spring gene in Southeast Asian populations.

The distribution of the hemoglobin Constant Spring (Hb CS) gene in eight populations in Southeast Asia (including Assam) was determined using oligonucleotide hybridization. Hb CS was absent in two Assamese populations with a high prevalence of Hb E. The Hb CS gene frequency was 0.033 in northern Thailand and near 0.01 in central Thailand and Cambodia. High frequencies, between 0.05 and 0.06, were observed in northeastern Thailand. The present data and a similar study in Laotians suggest that the Lao-speaking populations of the Mekong River basin in northeastern Thailand and Laos have the highest frequencies of the Hb CS gene in Southeast Asia.

Asia, Southeastern↗
PubMed1990

Genetics and biology of human ovarian teratomas. II. Molecular analysis of origin of nondisjunction and gene-centromere mapping of chromosome I markers.

Chromosomal heteromorphisms and DNA polymorphisms have been utilized to identify the mechanisms that lead to formation of human ovarian teratomas and to construct a gene-centromere map of chromosome 1 by using those teratomas that arise by meiotic nondisjunction. Of 61 genetically informative ovarian teratomas, 21.3% arose by nondisjunction at meiosis I, and 39.3% arose by meiosis II nondisjunction. Eight polymorphic marker loci on chromosome 1p and one marker on 1q were used to estimate a gene-centromere map. The results show clear linkage of the most proximal 1p marker (NRAS) and the most proximal 1q marker (D1S61) to the centromere at a distance of 14 cM and 20 cM, respectively. Estimated gene-centromere distances suggest that, while recombination occurs normally in ovarian teratomas arising by meiosis II errors, ovarian teratomas arising by meiosis I nondisjunction have altered patterns of recombination. Furthermore, the estimated map demonstrates clear evidence of chiasma interference. Our results suggest that ovarian teratomas can provide a rapid method for mapping genes relative to the centromere.

Adolescent↗
PubMed1989

Biology, cytogenetics, and sensitivity to immunological effector cells of new head and neck squamous cell carcinoma lines.

Twenty-one head and neck squamous cell carcinoma (HNSCC) cell lines were established from 89 fresh tumor specimens in order to study the biology of HNSCC lines, establish tumors in nude mice, and evaluate the sensitivity to immunological effector cells of these tumors in vitro and in vivo in nude mice. The lines were established from explants using differential trypsinization and culture for 2 to 20 mo. The explants were derived from 11 different sites. Three pairs of lines were derived from both the primary tumor and metastatic lymph nodes in the same patients. All cultures grew as either compact or diffuse adherent monolayers, and they had a median doubling time of 86 h (range, 33 to 531 h). DNA fingerprinting confirmed that the HNSCC lines were individual isolates. Thirteen of 14 lines tested induced tumors in athymic mice. The histology of each line growing in nude mice was similar to that of the original tumor tissue. Immunocytochemistry showed keratin production in all lines tested. Aneuploidy (36 to 87 chromosomes) was present in all 16 lines studied; the median chromosome number for lines derived from primary tumors was 70, whereas for lines originating from metastatic or recurrent tumors, it was 54. Karyotypic analysis showed deletion of the short arm of chromosome 3 (3p-) in 12 of 16 cell lines and trisomy 6 in 12 of 16 lines. In addition, translocations between chromosomes 9 and 11 or 9 and 12 were each present in five of 16 lines tested. The HNSCC lines were resistant to lysis by natural killer cells, but were efficiently lysed by lymphokine-activated killer cells in 4-h 51Cr release assays. These new lines have allowed us to establish a model of local adoptive immunotherapy of HNSCC in tumor-bearing nude mice, and they provide a resource for future studies of the biology of HNSCC.

Adult↗
PubMed1988

DNA haplotypes and frameworks associated with the beta-globin gene in the Kachari population of Assam (India).

DNA haplotypes and frameworks associated with the beta-globin gene were determined in a Tibeto-Burman group, the Kachari, from Upper Assam, India, using restriction analysis at eight restriction sites. Of the total of 59 subjects, 26 were homozygous for HBB*A and 33 homozygous for HBB*E. Complete haplotype determination in 33 subjects revealed a conspicuous difference in haplotype distribution between HBB*A- and HBB*E-bearing chromosomes. The Southeast Asian HBB*E-associated haplotype -+- +- (27-2 in the present terminology) predominated on HBB*E chromosomes. The previously established beta-globin-associated frameworks 1, 2 and 3 were evenly distributed among the HBB*A chromosomes, whereas all HBB*E chromosomes had framework 2. These findings favor a common origin of the HBB*E gene in Southeast Asia and Assam.

Adult↗