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PubMed2002

Polymorphism patterns in two tightly linked developmental genes, Idgf1 and Idgf3, of Drosophila melanogaster.

A new developmental gene family, recently identified in D. melanogaster, has been called imaginal disc growth factors (IDGF) because the proteins promote growth of cell lineages derived from imaginal discs. These are the first genes reported that encode polypeptide factors with mitotic activity in invertebrates. Characteristics such as similar arrangement of introns and exons, small size, and different cytological localization make this family an excellent candidate for evolutionary studies. We focus on the loci Idgf1 and Idgf3, two genes that possess the most distinctive features. We examine the pattern of intra- and interspecific nucleotide variation in the sequences from 20 isogenic lines of D. melanogaster and sequences from D. simulans and D. yakuba. While MK, HKA, and Tajima's tests of neutrality fail to reject a neutral model of molecular evolution, Fu and Li's test with outgroup and McDonald's test suggest that balancing selection is modulating the evolution of the Idgf1 locus. The rate of recombination between the two loci is high enough to uncouple any linkage disequilibrium arising between Idgf1 and Idgf3, despite their close physical proximity.

Animals↗
PubMed2002

SNP genotyping using a simple and rapid single-tube modification of ARMS illustrated by analysis of 6 SNPs in a population of males with FRAXA repeat expansions.

Microsatellites have been used extensively in gene mapping, linkage and association studies but with the near completion of the human genome project (HGP) single nucleotide polymorphisms (SNP) have become the marker of choice. However, for association studies to be useful large numbers of SNPs must be analysed. To make these studies cost effective a simple and non-labour intensive method for SNP genotyping is essential. This work describes a single-tube modification of the amplification refractory mutation system (Biallelic-ARMS). Control amplimers flanking the SNP were amplified in a single-tube multiplex PCR with two SNP specific primers that prime in opposite directions. The SNP allele was identified on the basis of PCR product size after gel electrophoresis. Biallelic-ARMS was used to analyse six SNPs within 300 kb of the FRAXA repeat, two from the HGP SNP Database (ATL1 and FMRb) and four novel SNPs (WEX1, WEX10, WEX17 and WEX28). The study population consisted of 649 males with a range of FRAXA (10 to >200) repeat sizes. Each SNP correlated with distinct haplogroups, as identified by DXS548, FRAXAC1 and FRAXAC2 flanking microsatellite repeat patterns and confirmed the initial choice of haplogroups for FRAXA repeat stability defined by Enniset al.

Alleles↗
PubMed2005

Genealogical use of chloroplast DNA variation for intraspecific studies of Aegilops tauschii Coss.

Intraspecific patterns of chloroplast DNA variation was studied in Aegilops tauschii Coss., the D-genome progenitor of bread wheat. Nucleotide sequences of ten chloroplast microsatellite loci were analyzed for 63 accessions that cover the central part of the species distribution. As is often the case with nuclear microsatellites, those of chloroplasts of Ae. tauschii bear complex mutations. Several types of mutations other than change in the microsatellite repeat number were found, including base substitutions and length mutations in flanking regions. In total, eight mutations were present in the flanking regions of four loci. Most mutations in the flanking regions of microsatellite repeats are associated with biallelic polymorphisms. Phylogeographic analyses showed that such biallelic polymorphisms are useful to investigate intraspecific patterns of monophyletic lineage divergence. In contrast, most microsatellite repeat sites are multiallelic, variable within intraspecific lineages, and useful to compare degrees of genetic diversity between lineages. These findings show that the chloroplast genome harbors evolutionary variations informative for intraspecific studies of Ae. tauschii and can be analyzed by genealogical approaches.

Afghanistan↗
PubMedDate not supplied

A novel polymorphism of the porcine prolactin gene (PRL).

Prolactin is a protein hormone playing a role in the maintenance of pregnancy in the pig by action on corpora lutea cells and possibly initiating production of progesterone. The prolactin gene is 10 kb in size and is composed of 5 exons and 4 introns. The present work is a report of the swine PRL gene--comparative DNA sequence analysis and the SNP revealed in the promoter region. Based on the bovine prolactin gene, three primer pairs were designed using the Primer3 on-line software. The overlapping fragments covered about 400 nucleotides of the promoter and 78 nucleotides of exon 1. The fragments were amplified; two of them were sequenced and deposited in the GenBank database (AY341908 and AY905690). All fragments were analyzed using multitemperature SSCP (MSSCP) technique. Only one fragment appeared to show a different MSSCP pattern. The samples of differing MSSCP conformers were sequenced and the C499T transition was identified in the 5'UTR region of the gene. The HphI restriction enzyme appeared to recognize the novel SNP. The alignment for homology analysis was performed with porcine, bovine (X01452) and human (NM_000948) DNA sequences available in GenBank database, using BLAST software. The comparative homology analysis results varied in dependence on the species and functional region of the gene.

5' Untranslated Regions↗
PubMed2005

Association analysis of common variants of STAT6, GATA3, and STAT4 to asthma and high serum IgE phenotypes.

BACKGROUND: Immune responses characterized by T H 2 type cells and IgE are important for the development of asthma and atopy. The transcription factors STAT6, GATA3, and STAT4 mediate the cytokine-induced development of naive CD4 + T cells into either T H 1 or T H 2 type. OBJECTIVE: We studied genetic variation of the STAT6, GATA3, and STAT4 genes and examined whether single nucleotide polymorphisms (SNPs) in these loci were associated with asthma or serum high IgE levels in the Finnish asthmatic families. METHODS: With denaturing high-performance liquid chromatography we screened all exons and exon-intron boundaries of the genes in 14 to 22 patients. All identified SNPs were genotyped in 120 nuclear families, and the haplotypes were analyzed by Haplotype Pattern Mining based statistical analysis. When potential association was observed, the analysis was replicated among 245 asthmatic patients and 405 population-based control subjects. RESULTS: A total of 23 SNPs were identified, of which 8 were not previously listed in the SNP database. Interestingly, a haplotype analysis of GATA3 showed 3 related haplotypes that associated with different asthma and atopy related phenotypes among both the family and case-control data sets. For STAT6 and STAT4, no significant association to asthma or serum total IgE levels was observed. CONCLUSIONS: We identified a panel of novel SNPs in genes coding for proteins important in the T H 1/T H 2 cell differentiation. SNPs of the GATA3 gene showed an initial association to asthma-related phenotypes. Elucidation of the importance of the identified panel of SNPs in other T H 1/T H 2 mediated diseases will be of great interest.

Adult↗
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↗
PubMed2002

Analysis of DNA methylation in Arabidopsis thaliana based on methylation-sensitive AFLP markers.

AFLP analysis using restriction enzyme isoschizomers that differ in their sensitivity to methylation of their recognition sites has been used to analyse the methylation state of anonymous CCGG sequences in Arabidopsis thaliana. The technique was modified to improve the quality of fingerprints and to visualise larger numbers of scorable fragments. Sequencing of amplified fragments indicated that detection was generally associated with non-methylation of the cytosine to which the isoschizomer is sensitive. Comparison of EcoRI/ HpaII and EcoRI/ MspI patterns in different ecotypes revealed that 35-43% of CCGG sites were differentially digested by the isoschizomers. Interestingly, the pattern of digestion among different plants belonging to the same ecotype is highly conserved, with the rate of intra-ecotype methylation-sensitive polymorphisms being less than 1%. However, pairwise comparisons of methylation patterns between samples belonging to different ecotypes revealed differences in up to 34% of the methylation-sensitive polymorphisms. The lack of correlation between inter-ecotype similarity matrices based on methylation-insensitive or methylation-sensitive polymorphisms suggests that whatever the mechanisms regulating methylation may be, they are not related to nucleotide sequence variation.

Arabidopsis↗
PubMed2006

Intron length and accelerated 3' gene evolution.

Genetic evolution depends in part upon a balance between negative selection and environmentally driven mutation. To explore whether this balance is affected by gene structure, we have used phylogenetic data mining to compare gene compositions across a range of species. Here we show that genomes of higher species exhibit a greater frequency of 5' CpG islands and of CpG-->TpG/CpA transitions. This latter mutational pattern exhibits a 5'-to-3' trend in higher species, consistent with a length-dependent effect on methylation-dependent CpG suppression. Associated strand asymmetry (TpG>CpA) declines with gene length, implying attenuation of transcription-coupled repair 3' to introns. A sharp 3' rise in coding region single-nucleotide polymorphism frequency further supports a mechanistic role for intron length in promoting genetic variation by reducing repair and/or weakening negative selection. Consistent with this, the Ka/Ks ratio of 3' exons exceeds that of centrally located exons in intron-containing, but not in intronless, genes (p<0.0003). We conclude that the efficiency of transcription-coupled repair decreases with gene length, suggesting in turn that 3' gene evolution is accelerated both by introns and by gene methylation.

3' Untranslated Regions↗
PubMed1991

Characterization of the molecular basis of the alpha 1-antitrypsin F allele.

alpha 1-Antitrypsin (alpha 1AT), the major serum inhibitor of neutrophil elastase, is a highly polymorphic serum protein associated with characteristic isoelectric-focusing (IEF) patterns for most variants. To characterize the molecular basis of the anodal F variant, the DNA sequence of the coding exons of an FZ individual was determined. The F allele differed from the normal M1(Val213) alpha 1AT allele by a single nucleotide transversion of cytosine to thymidine, which results in the amino acid substitution Arg223 CGT----Cys TGT. Inheritance of the F mutation was confirmed by family analysis using allele-specific amplification. In the context that the normal alpha 1AT molecule has only one cysteine residue, a mutation resulting in the addition of a second cysteine may influence the three-dimensional form of the protein and/or permit interaction with other plasma proteins with free-SH groups and may be responsible for the observation that the major F alpha 1AT bands often migrate as doublets in IEF gels.

Alleles↗
PubMed1997

Analysis of primate major histocompatibility complex (MHC)-DQA1 locus by PCR-single strand conformation polymorphism (SSCP).

Major histocompatibility complex (Mhc) gene products play an important role in the immune responses against pathogens and autoimmunity, disease resistance and transplantation. Non-human primates (NHPs) are increasingly being utilized as models to test the safety and efficacy of candidate vaccines. Mhc typing of NHPs is an important component of the vaccine trial studies and in the investigations of any associations between Mhc alleles and disease. Routine typing of primate Mhc alleles has been hampered by unavailability of well characterised immunological reagents. In this study, we have used PCR amplification and SSCP for screening polymorphisms in the primate DQA1 locus. Using this technique, 9 African primate species (36 individuals) were analyzed. Ten individuals showed three or four electrophoretic band patterns and the rest two-band patterns indicating this technique can be used to discriminate homozygous and heterozygous individuals prior to DNA sequencing. This method may also be used to screen primates for Mhc-DQA1 allelic polymorphism. However, practical application of this technique for routine typing of primate Mhc-DQA1 alleles depends on availability of adequate nucleotide sequence information.

Alleles↗
PubMed1995

A novel HLA-DR13 allele (DRB1*1314) identified by single-strand conformation polymorphism analysis and confirmed by direct sequencing.

A novel variant of the HLA-DR13 group is described. The new allele was found in a DR10, 13 heterozygous patient of Turkish origin, two HLA genotypically identical children of the patient typed as DR11,13, and one child typed as DR13,13. DR13 subtyping of the patient was initially performed by SSCP analysis of PCR-amplified DNA, using the 11th OHWS primers DRBAMP-3 and DRBAMP-B. Due to an unusual SSCP banding pattern, the PCR product was subjected to solid-phase sequencing. The sequence of the new allele, DRB1*1314, is different from that of DRB1*1307 by a single nucleotide substitution in codon 47, with T replacing consensus A. This results in a single amino acid change of tryptophan to phenylalanine in the first domain of the DR beta chain.

Anemia, Sickle Cell↗
PubMed2004

The influence of neighboring-nucleotide composition on single nucleotide polymorphisms (SNPs) in the mouse genome and its comparison with human SNPs.

We analyzed the neighboring-nucleotide composition of 433,192 biallelic substitutions, representing the largest public collection of SNPs across the mouse genome. Large neighboring-nucleotide biases relative to the genome- or chromosome-specific average were observed at the immediate adjacent sites and small biases extended farther from the substitution site. For all substitutions, the biases for A, C, G, and T were 0.21, 2.63, 0.71, and -3.55%, respectively, on the immediate adjacent 5' site and -3.67, 0.75, 2.69, and 0.23%, respectively, on the immediate adjacent 3' side. Further examination of the six categories of substitution revealed that the neighboring-nucleotide patterns for transitions were strongly influenced by the hypermutability of dinucleotide CpG and the neighboring effects on transversions were complex. Probability of a transversion increased with increasing A + T content of the two immediate adjacent sites, which was similarly observed in the human and Arabidopsis genomes. Overall, the bias patterns for the neighboring nucleotides in the mouse and human genomes were essentially the same; however, the extent of the biases was notably less in mice. Our results provide the first comprehensive view of the neighboring-nucleotide effects in the mouse genome and are important for understanding the mutational mechanisms and sequence evolution in the mammalian genomes.

Animals↗
PubMed2005

Detection of three single nucleotide polymorphisms in the gene encoding mannose-binding lectin in a single pyrosequencing reaction.

Mannose-binding lectin (MBL) is a key molecule of innate immunity. Binding of MBL to carbohydrates present on pathogens activates the lectin pathway of complement activation, resulting into opsonization and anti-microbial protection. Three frequently occurring single nucleotide polymorphisms (SNPs) are described in the coding region of the MBL2 gene that are associated with abnormal polymerization of the MBL molecule, decreased serum concentrations of high molecular weight MBL, and strongly impaired function. Clinical studies have shown that these MBL SNPs are associated with increased susceptibility to infections, especially in immune-compromised persons, as well as with accelerated progression of chronic diseases. The present study describes a novel method to detect the three major MBL SNPs by pyrosequencing. The close proximity of these SNPs allows their detection in one single pyrosequencing reaction, resulting in clearly distinguishable patterns for each allele combination described until now. This method can be used for the easy and reliable detection of MBL SNPs to identify the basis of functional MBL deficiency in clinical diagnostics and research.

Base Sequence↗
PubMed2001

Genetic variability of respiratory syncytial virus subgroup a strain in 15 successive epidemics in one city.

The genetic variability of 125 respiratory syncytial virus (RSV) subgroup A isolates over 15 successive epidemics from 1980 to 1995 in an urban population of Japan was determined. Allocation of isolates into lineages was archived by reverse transcriptase-polymerase chain reaction amplification of selected regions of the nucleoprotein (NP) and attachment (G) protein gene followed by restriction fragment length polymorphism (RFLP) analysis. Three and seven distinct restriction patterns of the NP and G gene were observed, respectively. When the NP and G gene RFLP analyses were combined, ten different genetic lineages were identified in the 125 isolates. The strains with the same genotype were isolated in each epidemic and the dominant lineages were replaced by others after every one to three consecutive epidemics. Nucleotide and amino acid sequencing of the variable region of G gene of these predominant isolates revealed differences of 5--28% between strains. There was, however, no apparent accumulation of diversity with age to indicate progressive changes. The dominant strains were often closely related to those isolated in other parts of the world at a similar time. These observations suggest that dominant RSV strains are replaced frequently by others that have been co-circulating or have recently entered the community from a worldwide reservoir. The change of dominant strains may be influenced by the buildup of immunological resistance in the community to successive epidemics of the same strain.

Amino Acid Sequence↗
PubMed1989

Hypervariable DNA fingerprinting in Escherichia coli: minisatellite probe from bacteriophage M13.

Extensive restriction-fragment-length polymorphism was revealed in Escherichia coli strains by using a region of the bacteriophage M13 genome as a DNA hybridization probe. This variation was observed across natural strains, in clinical samples, and to a lesser extent in laboratory strains. The sequence in M13 which revealed this fingerprint pattern was a region of the gene III coat protein, which contains two clusters of a 15-base-pair repeat. Oligonucleotides made to a consensus of these repeats also revealed the fingerprint profile. While this consensus sequence has significant homology to the lambda chi site sequence, an oligonucleotide made of the chi sequence did not reveal polymorphic fingerprint patterns in E. coli. The strain variation revealed by the M13 and M13-derived oligonucleotide probes will be useful for bacterial characterization and should find use in studies of bacterial evolution and population dynamics. The findings raise questions about what these repeated sequences are and why they are so variable.

Biological Evolution↗
PubMed2005

Complex haplotypes, copy number polymorphisms and coding variation in two recently divergent mouse strains.

Inbred mouse strains provide the foundation for mouse genetics. By selecting for phenotypic features of interest, inbreeding drives genomic evolution and eliminates individual variation, while fixing certain sets of alleles that are responsible for the trait characteristics of the strain. Mouse strains 129Sv (129S5) and C57BL/6J, two of the most widely used inbred lines, diverged from common ancestors within the last century, yet very little is known about the genomic differences between them. By comparative genomic hybridization and sequence analysis of 129S5 short insert libraries, we identified substantial structural variation, a complex fine-scale haplotype pattern with a continuous distribution of diversity blocks, and extensive nucleotide variation, including nonsynonymous coding SNPs and stop codons. Collectively, these genomic changes denote the level and direction of allele fixation that has occurred during inbreeding and provide a basis for defining what makes these mouse strains unique.

Animals↗
PubMed2003

Y-chromosome lineages in Cabo Verde Islands witness the diverse geographic origin of its first male settlers.

The Y-chromosome haplogroup composition of the population of the Cabo Verde Archipelago was profiled by using 32 single-nucleotide polymorphism markers and compared with potential source populations from Iberia, west Africa, and the Middle East. According to the traditional view, the major proportion of the founding population of Cabo Verde was of west African ancestry with the addition of a minor fraction of male colonizers from Europe. Unexpectedly, more than half of the paternal lineages (53.5%) of Cabo Verdeans clustered in haplogroups I, J, K, and R1, which are characteristic of populations of Europe and the Middle East, while being absent in the probable west African source population of Guiné-Bissau. Moreover, a high frequency of J* lineages in Cabo Verdeans relates them more closely to populations of the Middle East and probably provides the first genetic evidence of the legacy of the Jews. In addition, the considerable proportion (20.5%) of E3b(xM81) lineages indicates a possible gene flow from the Middle East or northeast Africa, which, at least partly, could be ascribed to the Sephardic Jews. In contrast to the predominance of west African mitochondrial DNA haplotypes in their maternal gene pool, the major west African Y-chromosome lineage E3a was observed only at a frequency of 15.9%. Overall, these results indicate that gene flow from multiple sources and various sex-specific patterns have been important in the formation of the genomic diversity in the Cabo Verde islands.

Chromosomes, Human, Y↗
PubMed2002

Single-strand conformation polymorphism-based analysis of mitochondrial cytochrome c oxidase subunit 1 reveals significant substructuring in hookworm populations.

Sequence heterogeneity in a portion of the mitochondrial cytochrome c oxidase subunit 1 gene (pcox1) was measured for the hookworms, Ancylostoma caninum from Australia, A. duodenale from China, and Necator americanus from China and Togo using single-strand conformation polymorphism (SSCP) analysis combined with DNA sequencing. The pcox1 sequences were characterised for individual nematodes displaying genetic variation within each of the three species, and those were compared with pcox1 sequences of four other species of hookworm. While intraspecific variation in the pcox1 sequence ranged from 0.5 to 8.6% for A. caninum, 0.3 to 3.3% forA. duodenale, and 0.3 to 4.3% for N. americanus, interspecific differences varied from 4.8 to 12.9%. Sequence data also provided information on nucleotide compositions and substitution patterns. Genetically distinct groups were detected within A. caninum and A. duodenale, indicating significant population substructuring within these species. Also, N. americanus individuals from China all differed from those from Togo at four nucleotide positions, supporting a previous proposal (based on ribosomal DNA sequence data) that N. americanus may represent a species complex. The findings indicated the value of pcox1 sequence data and the mutation scanning approach for studying the genetic structures of hookworm populations, which should have important epidemiological relevance.

Ancylostomatoidea↗