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PubMed1989

Intraspecific evolution of a gene family coding for urinary proteins.

The genome of the laboratory mouse contains about 35 major urinary protein (MUP) genes, many of which are clustered on chromosome 4. We have used distance and parsimony methods to estimate phylogenetic relationships between MUP genes from nucleotide sequence and restriction maps. By analyzing coding sequences we show that the genes fall into four main groups of related sequences (groups 1-4). Comparisons of restriction maps and the nucleotide sequences of hypervariable regions that lie 50 nucleotides 5' to the cap sites show that the group 1 genes and probably also the group 2 pseudogenes fall into subgroups. The most parsimonious trees are consistent with the evolution of the array of group 1 and 2 genes by mutation accompanied by a process tending toward homogenization such as unequal crossing-over or gene conversion. The phylogenetic grouping correlates with grouping according to aspects of function. The genomes of the inbred strains BALB/c and C57BL contain different MUP gene arrays that we take to be samples from the wild population of arrays.

Animals↗
PubMed1996

Allelic diversity at the primate Mhc-G locus: exon 3 bears stop codons in all Cercopithecinae sequences.

Twenty-seven major histocompatibility complex (Mhc)-G exon 2, exon 3, and exon 2 and 3 allelic sequences were obtained together with 12 different intron 2 sequences. Homo sapiens, Pan troglodytes, Pan paniscus, Gorilla gorilla, Pongo pygmaeus, Macaca fascicularis, Macaca mulatta, and Cercopithecus aethiops individuals were studied. Polymorphism does not follow the classical pattern of three hypervariable regions per domain and is found in all species studied; exon 3 (equivalent to the alpha 2 protein domain) shows stop codons in the Cercopithecinae group but not in the Pongidae and human groups. Dendrograms show that cotton top tamarin (Saguinus oedipus) Mhc-G sequences are closer to Homo sapiens and Pongidae than to Cercopithecinae, probably due to the stop codons existing at exon 3 of the latter. There is a clear trans-species evolution of allelism in Cercopithecinae and also in exon 2 of all the other apes studied, but a generation of allelism within each species may be present on exon 3 sequences. This discrepancy may be due to the preferential use of exon 2 over exon 3 at the mRNA splicing level within each species in order to obtain the appropriate functional G product. Mhc-G intron 2 shows conserved motifs in all species studied, particularly a 23 base pair deletion between positions 161 and 183 which is locus specific, and some of the invariant residues, important for peptide presentation, conserved in classical class I molecules from fish and reptiles to humans were not found in Mhc-G alleles; the intron 2 dendrogram also shows a particular pattern of allelism within each species. In summary, Mhc-G has substantial differences from other classical class I genes: polymorphism patterns, tissue distribution, gene structure, splicing variability, and probably an allelism variability within each species at exon 3. The G proteins may also be different. This indicates that the Mhc-G function may not be peptide presentation to the clonotypic T-cell receptor.

Alleles↗
PubMed1989

Two distinct subtypes of the HLA-DRw12 haplotypes in the Japanese population detected by nucleotide sequence analysis and oligonucleotide genotyping.

We determined the DNA sequence of the enzymatically amplified second exon of the DRB1 gene of the Drw12 haplotypes derived from three Japanese donors and found two distinct subtypes of the DRw12 haplotype. The two subtypes, designated DRw12a and DRw12b, had single-base substitutions that predicted one amino acid change at residue number 67. The sequence of the DRw12a and DRw12b subtypes differed from those of the other DR haplotypes, but in the first hypervariable region of the DRB1 gene the sequences were identical to those of the DRw8(Dw8.1) and DRw8(Dw8.3) haplotypes. The DRw12a and DRw12b subtypes were detected in a wide range of Japanese donors by genotyping with sequence-specific oligonucleotide probes synthesized according to the DNA sequences of the two subtypes. Results of this study demonstrated that the DRw12 haplotypes in the Japanese population are genetically diverse, as many other DR haplotypes are.

Asian People↗
PubMed2000

Sequence analysis of mitochondrial 16S ribosomal RNA gene fragment from seven mosquito species.

Mosquitoes are vectors for the transmission of many human pathogens that include viruses, nematodes and protozoa. For the understanding of their vectorial capacity, identification of disease carrying and refractory strains is essential. Recently, molecular taxonomic techniques have been utilized for this purpose. Sequence analysis of the mitochondrial 16S rRNA gene has been used for molecular taxonomy in many insects. In this paper, we have analysed a 450 bp hypervariable region of the mitochondrial 16S rRNA gene in three major genera of mosquitoes, Aedes, Anopheles and Culex. The sequence was found to be unusually A+T rich and in substitutions the rate of transversions was higher than the transition rate. A phylogenetic tree was constructed with these sequences. An interesting feature of the sequences was a stretch of Ts that distinguished between Ae-des and Culex on the one hand, and Anopheles on the other. This is the first report of mitochondrial rRNA sequences from these medically important genera of mosquitoes.

Animals↗
PubMed1996

Modified antigen-binding of human antibodies with glycosylation variations of the light chains produced in sugar-limited human hybridoma cultures.

We have characterized the effects of serum and N-acetylglucosamine in a glucose-deprived condition on the glycosylation of antibody light chains, as well as the resulting biological properties of those antibodies. We have chosen for our investigation the human hybridoma lines producing monoclonal antibodies reactive to lung adenocarcinoma. Each antibody possess a N-glycosylated carbohydrate chain in the hypervariable region of the light chains. When the cell lines were grown in the absence of glucose, variant light chains with varying molecular masses were found to be secreted. Analysis of these light chains produced in a glucose-deprived condition revealed that the changed molecular-mass of the variant light chains is due to different glycosylation. Addition of N-acetylglucosamine or fetal calf serum to the glucose-free medium led to the creation of other light chains that exhibit increased antigen binding activity.

Acetylglucosamine↗
PubMed1997

Molecular mechanisms involved in the association of HLA-DR4 and rheumatoid arthritis.

Susceptibility to developing rheumatoid arthritis (RA) maps to a highly conserved amino acid motif located in the third hypervariable region of different HLA-DRB1 chains. This motif, namely QKRAA, QRRAA, or RRRAA, helps the development of RA by an unknown mechanism. The QKRAA motif predisposes to more severe disease than the QRRAA or RRRAA motifs. The QKRAA motif carries particular properties: it is a strong B- and T-cell epitope, it shapes the T cell repertoire, it is overrepresented in protein databases, and it is a binding motif for bacterial and human 70-kDa heat-shock proteins. In this article, we propose different models to explain how the QKRAA motif might contribute to RA.

Amino Acid Sequence↗
PubMed2000

Forensic identification of skeletal remains from members of Ernesto Che Guevara's guerrillas in Bolivia based on DNA typing.

We report the positive identification of several members of the guerrillas led by Ernesto "Che" Guevara on the 1960 s in Bolivia by means of DNA fingerprinting. Successful DNA typing of both short tandem repeat loci and the hypervariable region of the human mitochondrial DNA was achieved after extracting total DNA from bones obtained from two burial sites. Given the size of the Cuban database for the STR allele frequencies, a conservative approach was followed to estimate the statistical significance of the genetic evidence. The estimated probabilities of paternity for the two cases in which the paternity logic was applied were higher than 99%. One case was analyzed using mitochondrial DNA and could not be excluded from the identity proposed by the forensic anthropology team. A fourth case was identified by exclusion, on the basis of the positive identification of the other remains, the historical and other anthropological evidence.

Alleles↗
PubMed2002

Identification and classification of S haplotypes in Raphanus sativus by PCR-RFLP of the S locus glycoprotein (SLG) gene and the S locus receptor kinase (SRK) gene.

Polymorphism of the S-locus glycoprotein (SLG) and S-locus receptor kinase (SRK) genes in Raphanus sativus was analyzed by PCR-RFLP using SLG- and SRK-specific primers. Twenty four inbred lines of R. sativus could be grouped into nine S haplotypes. DNA fragments of SLG alleles specifically amplified from five S haplotypes by PCR with Class-I SLG-specific primers showed different profiles upon polyacrylamide-gel electrophoresis after digestion with restriction endonucleases. The five R. sativus SLG alleles were determined for their nucleotide sequences of DNA fragments. Comparison of the amino-acid sequences with a reported Brassica SLG (S(6)) showed 77-84% homology. Deduced amino-acid sequences showed 12-conserved cystein residues and three hypervariable regions which are characteristic of Brassicsa SLG. A DNA fragment was also amplified by PCR from two of each S haplotype with Class-II SLG-specific primers, and showed polymorphism when cleaved with restriction endonucleases. The nucleotide sequences of amplified DNA fragments of the Class-II SLG revealed about 60% similarity with those of the Class-I SLG. It is concluded that there exist both Class I and Class II S alleles in R. sativus, as in Brassica campestris and Brassica oleracea. PCR using SRK-specific primers amplified a DNA fragment of about 1.0 kb from seven of each S haplotype out of 24 tested. These DNA fragments showed high polymorphism in polyacrylamide-gel electrophoresis after digestion with restriction endonucleases. Nucleotide sequences of the DNA fragments amplified from the seven S haplotypes showed that the fourth and the fifth exons of SRK are highly conserved, and that there is high variation in the fifth intron, the sixth intron and seventh exon of the SRK which may be responsible for the polymorphic band patterns in PCR-RFLP analysis. The PCR-RFLP method has proven useful for the identification of S alleles in inbred lines and for listing S haplotypes in R. sativus. Phylogenic analysis of the SLG and SRK sequences from Raphanus and Brassica revealed that the Raphanus SLGs and SRKs did not form an independent cluster, but were dispersed in the tree, clustering together with Brassica SLGs and SRKs. Furthermore, SLGs and SRKs from Raphanus were both grouped into Class-I or Class-II S haplotypes. Therefore, these results suggest that the diversification of the SLG and SRK alleles occurred prior to the differentiation of the two genera Brassica and Raphanus.

Journal Article↗
PubMed1998

A common mitochondrial DNA variant is associated with insulin resistance in adult life.

Mitochondrial DNA is maternally inherited. Mitochondrial DNA mutations could contribute to the excess of maternal over paternal inheritance of non-insulin-dependent diabetes mellitus (NIDDM). We therefore investigated the relationship between this variant, insulin resistance and other risk factors in a cohort which had been well characterised with respect to diabetes. Blood DNA was screened from 251 men born in Hertfordshire 1920-1930 in whom an earlier cohort study had shown that glucose tolerance was inversely related to birthweight. The 16189 variant (T--> C transition) in the first hypervariable region of mitochondrial DNA was detected using the polymerase chain reaction and restriction digestion. DNA analysis showed that 28 of the 251 men (11%) had the 16189 variant. The prevalence of the 16189 variant increased progressively with fasting insulin concentration (p < 0.01). The association was independent of age and body mass index and was present after exclusion of the patients with NIDDM or impaired glucose tolerance. We found that insulin resistance in adult life was associated with the 16189 variant. This study provides the first evidence that a frequent mitochondrial variant may contribute to the phenotype in patients with a common multifactorial disorder.

Adult↗
PubMed2000

The molecular evolutionary history of a winged bean alpha-chymotrypsin inhibitor and modeling of its mutations through structural analyses.

A serine protease inhibitor of the Kunitz-STI (soybean trypsin inhibitor) family, isolated from the legume seeds of winged bean, was found to inhibit chymotrypsin at a 1:2 stoichiometric ratio. When the structure was determined in our laboratory, it was found to form a characteristic beta-trefoil fold, which is also seen in other proteins from distant families and sources. The folding organization divides the protein into three approximately equal subdomains related by a pseudo-threefold axis of symmetry passing parallel to the barrel axis of the trefoil. Following the now established idea that the present-day genes originated from ancestral minigenes through evolution, the origin of the proteins having this beta-trefoil organization is scrutinized using its subdomain motif as the search probe. The results, based mainly on structural analyses, indicate the independent existence of such a motif, mimicking the unknown ancestral protein(s) that might have been distributed in nature, not only by gene duplication, but also by insertion and permutation in other folds. The understanding led to a hypothesis for the possible origin of the Kunitz-STI family. On the basis of this model of evolution, structurally hypervariable regions were located on the protein where mutations could be designed and a broad range of engineering of the protein's activity could be conceived.

Amino Acid Sequence↗
PubMed2005

Extended HLA-DPB1 polymorphism: an RNA approach for HLA-DPB1 typing.

Most of the 119 human leukocyte antigen (HLA)-DPB1 alleles are defined by polymorphism in six hypervariable regions (HVRs) in exon 2 of the HLA-DPB1 gene. We investigated how DPB1 polymorphism is represented in the entire coding region. An RNA sequencing-based typing (SBT) approach was developed for the identification of HLA-DPB1 polymorphism from the 5' untranslated region (UTR) through the 3'-UTR. B-cell lymphoblastoid cell lines, encoding 16 different DPB1 alleles, were studied. Results show additional HLA-DPB1 polymorphism in exons 1, 3, 4 and 5 and the 5' and 3'-UTR. Four new HLA-DPB1 alleles were identified, DPB1*0502, DPB1*0602, DPB1*0802 and DPB1*0902, which have exon 2 sequences identical to other DPB1 alleles but differ in the extended region. The additional polymorphism represents two main polymorphic lineages in the DPB1 alleles. Among the HVRs in exon 2, only HVR F correlates with these two main lineages.

Alleles↗
PubMedDate not supplied

An extended HLA-DQ-DR haplotype rather than DRB1 alone contributes to RA predisposition.

In the present study, we tested our hypothesis on the role of a DQ-DR haplotype in rheumatoid arthritis (RA) predisposition. Using two groups of patients and controls, one from The Netherlands and one from Switzerland, we found that DQA1*0301-homozygous and DQA1*0301//DQA1*0101/04-heterozygous individuals are highly predisposed to RA in both populations, while DQA1*0101/04-homozygous are not. The DQA1*0301-DRB1*0403/06/07 and DQA1*0301-DRB1*0901 haplotypes are not associated with RA by themselves but strongly increase the risk of developing disease in DQA1*0301- and DQA1*0101/04-heterozygous. DRB1 alleles carrying the motif DERAA in their third hypervariable region, i.e., *0103, *0402, *1102, *1103, *1301, and *1302, provide a long-lasting protection against RA in DQA1*0101/04- but not in DQA1*0301-positive individuals. These data show that considering both DQ and DR gives a better distinction between patients and controls than the shared epitope hypothesis.

Arthritis, Rheumatoid↗
PubMed2001

Dog MHC alleles containing the human RA shared epitope confer susceptibility to canine rheumatoid arthritis.

To determine whether canine rheumatoid arthritis (CRA) is associated with dog MHC (DLA-DRB1) alleles which contain the QRRAA/RKRAA conserved third hypervariable region (3HVR) sequence, DNA samples were extracted from 61 dogs with clinically diagnosed small-joint polyarthritis and from 425 controls. Breed-matched controls were available for 41 cases. DLA-DRB1 genotypes were identified using molecular typing methods. Phenotype frequencies were compared between cases and controls and odds ratios with 95% confidence intervals calculated. Several DLA-DRB1 alleles were associated with increased risk for CRA: DLA-DRB1*002, DRB1*009, and DRB1*018. This was also observed for the presence of any shared epitope (SE)-bearing allele. The associations with DLA-DRB1*002 and the SE were maintained when only breed-matched cases and controls were compared. This study suggests that a conserved amino acid motif in the 3HVR present in some DRB1 alleles of both dogs and humans is associated with rheumatoid arthritis in both species.

Alleles↗
PubMed2003

Mitochondrial DNA heteroplasmy or artefacts--a matter of the amplification strategy?

We compared two different PCR strategies for the amplification of mtDNA hypervariable region 1 (HV1) with regard to the detection and interpretation of point mutation heteroplasmy in human hair roots. We monitored the level of detected heteroplasmy using direct sequence analysis. PCR amplifications were performed in duplicate on each hair root, using 62 cycles of nested PCR versus 35 cycles of direct PCR. As a previous publication reported different sensitivities of heteroplasmy detection based on the number of PCR cycles used, we were interested in whether and how different PCR amplification strategies would impact sequence quality and the detection of point heteroplasmy. We identified 12 out of 93 hair roots as heteroplasmic (7 out of 31 persons) with direct PCR, whereas 2 of these heteroplasmic events could not be identified with the nested PCR approach. Generally, the quality of the sequence electropherograms in terms of background noise was significantly lower for the nested PCR amplification strategy, leading to ambiguous results in some of the nucleotide positions. Thus, the ability to clearly distinguish a genuine mixture of two nucleotides from background noise at a heteroplasmic position was substantially greater with direct PCR amplification, which generally resulted in higher quality sequence electopherograms.

Artifacts↗
PubMed2003

Genetic analysis of human remains found in two eighteenth century Yakut graves at At-Dabaan.

We extracted DNA from three skeletons belonging to the Yakut population, which were excavated from the At-Dabaan site (dating back 300 years) in the Sakha Republic (Russia). Ancient DNA was analyzed by autosomal STRs (short tandem repeats) and by the sequencing of the hypervariable region 1 (HV1) of the mitochondrial DNA (mtDNA) control region. The results showed that these three skeletons were not close relatives but probably linked to the same clan structure. Comparison of their haplotypes with the haplotypes of 8,774 Eurasian individuals suggested a relative specificity and continuity of part of the Yakut mitochondrial gene pool during the last 3 centuries.

Anthropology, Physical↗
PubMed2006

Forensic mass screening using mtDNA.

At the forensic autopsy of a sexual murder victim, some trace hairs, possibly belonging to the perpetrator, were saved. Initially, the analysis of a pubic hair shaft only revealed the presence of the mitochondrial (mt) DNA haplotype profile consisting of the (CA)(6) allele and the complete hypervariable region 1 (HV1) and 2 (HV2) sequence. Later, typing of some further telogene trace hairs, which had been stored for several years, yielded a nuclear short tandem repeat (STR) profile. We used both the mtDNA haplotype and the STR profile to start a DNA mass screening project involving 2,335 male citizens of the relevant communities. MtDNA screening was carried out by using the CA repeat amplification in combination with an SNP typing procedure based on the restriction site analysis of amplified d-loop sequences. The aim of our paper is to put mass screening with mtDNA up for discussion.

Alleles↗
PubMed1999

Influence of soil storage and exposure period on DNA recovery from teeth.

A study was performed to determine the influence of garden soil on the deoxyribonucleic acid (DNA) recovery from teeth depending on the duration of storage. In the first series 24 teeth supplied by dentists were exposed to garden soil storage for a maximum of 18 weeks. Selected samples were excavated for DNA extraction at time intervals of 6, 12 and 18 weeks. For the second series 20 teeth were stored for one year in garden soil. Following phenol/chloroform extraction with decalcification (first series) and without decalcification prior to extraction (second series) DNA was quantified, amplified using the polymerase chain reaction (PCR) for the tandem repeat loci D1S80, tyrosine hydroxylase, intron 1 (TH01) and Von Willebrand factor, intron A (VWA) (first series), human alpha fibrinogen (FGA) (second series) and sequenced in the hypervariable regions 1 and 2 (HV1, HV2) of the mitochondrial DNA (second series). The DNA concentration of the extracts after the first 6 weeks in soil was reduced by more than 90%. Amplification and direct sequencing of HV1 and HV2 of the mitochondrial genome was the most successful DNA technique.

Blood Stains↗
PubMed1999

Mitochondrial DNA in human hair shafts--existence of intra-individual differences?

The sequences of the hypervariable region 1 (HV1) of the mitochondrial DNA control region from multiple hair shafts from 10 unrelated individuals were compared to determine the frequency of differences in hairs from one individual. The extraction method described herein showed an average success rate of 67% for all 150 hair shafts tested in HV1. The mtDNA sequences from the hair shafts matched the sequences from the corresponding blood and saliva samples taken from the same donor and no evidence of heteroplasmy was found. The results emphasize the reliability of DNA extraction and mtDNA typing from human hair shafts for forensic purposes.

DNA, Mitochondrial↗