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At least 505 records · Page 28Linked to original sources
PubMed1999

Molecular variation in Leymus species and populations.

Icelandic populations of European lymegrass [Leymus arenarius (L.) Hochst.] were examined using amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP) of the major ribosomal genes (18S-5.8S-26S rDNA), in comparison with Alaskan populations of its closely related species L. mollis (Trin.) Pilger. The AFLP profiles emerged as two distinct entities, clearly separating the two species, and based on species-specific bands it was simple to distinguish these two morphologically similar species. The rDNA-RFLPs also differentiated the species. Within species, the Icelandic L. arenarius was more homogeneous than the Alaskan L. mollis, and its variation was dispersed over geographically different populations, suggesting a common gene pool. The variation among the Alaskan L. mollis was more extensive and its interrupted pattern may be the result of gene introgression at subspecies level. Within a 40-year-old population of L. mollis established in Iceland from Alaskan material, the molecular profiles separated old and new genotypes. Both AFLP and rDNA revealed the new genotypes to be extremely similar. This rapid change in allele frequency is thought to be the result of adaptation to a new environment.

Alaska↗
PubMed2001

There may never be a final cure for breast cancer.

This paper challenges the perception that the success of the human genome project has brought us to the threshold of a cure for many common cancers. Paradoxically, the message emerging from the genetics of breast cancer may be that the genetic damage associated with malignant transformation, and the mutations predisposing to the disease in our gene pool, may prove impossible to eliminate.

Breast Neoplasms↗
PubMed1988

Gc subtypes in Finns, Swedes and Swedish Lapps.

The group-specific component (Gc) subtypes were determined by isoelectric focusing and immunoblotting. The gene frequencies in the Swedish Lapps were Gc1F = 0.412, Gc1S = 0.367 and Gc2 = 0.221, which was significantly different from the frequencies found in Finns and in the populations of northern and central Sweden (p less than 0.001). The gene frequencies in the Swedish Lapps, although similar to those in Asiatic populations, are probably not reflecting an Asiatic influence, since the accumulated genetic information on the Swedish Lapps suggests that founder effect and genetic drift are to a large extent responsible for the peculiar gene pool of the original Lapp population.

Finland↗
PubMedDate not supplied

Improvement in the RFLP procedure for studying the diversity of nifH genes in communities of nitrogen fixers in soil.

Several specific primers for the nifH gene were tested with different pure telluric N2-fixing strains. A PolF/PolR primer set provided successful amplification of 19 representative N2-fixing strains. Three restriction enzymes, HaeIII, NdeII and MnlI, chosen for restriction fragment length polymorphism (RFLP) analyses, were the most discriminating for the study of nifH gene diversity as they resulted in differences between strains at the species level. Amplification by selected primers and RFLP were applied to assess the genetic diversity of the nifH gene pool in soil. Pair soils, one under cultivation, the second under permanent pasture, were found to harbor a contrasting diversity of nifH genes. Pure strain profiles could not be recognized in the nifH soil patterns. Using the simple procedure described, it was shown that the structure of nitrogen fixers in soil was influenced by soil functioning.

Bacteria↗
PubMed1999

The population genetic structure of a large temperate pollinator species, Bombus pascuorum (Scopoli) (Hymenoptera: Apidae)

The genetic population structure of the bumble bee Bombus pascuorum was studied using six microsatellite loci and a partial sequence of the mitochondrial gene cytochrome b. Eighteen populations from central and northern Europe were included in the analysis. Observed levels of genetic variability and heterozygosity were high. Estimates of population differentiation based on F- and phi-statistics revealed significant genetic differentiation among B. pascuorum populations and suggest that two partially isolated gene pools, separated by the Alps, do exist. The distribution of mtDNA haplo-types supports this view and presents direct evidence for gene flow across the Alps. Estimates of the number of migrants exchanged among populations north of the Alps suggest that historical events may have left a strong imprint on population structure.

Journal Article↗
PubMed2006

ADOA3R as a therapeutic target in experimental colitis: proof by validated high-density oligonucleotide microarray analysis.

Adenosine A3 receptors (ADOA3Rs) are emerging as novel purinergic targets for treatment of inflammatory diseases. Our goal was to assess the protective effect of the ADOA3R agonist N(6)-(3-iodobenzyl)-adenosine-5-N-methyluronamide (IB-MECA) on gene dysregulation and injury in a rat chronic model of 2,4,6-trinitrobenzene sulfonic acid (TNBS)--induced colitis. It was necessary to develop and validate a microarray technique for testing the protective effects of purine-based drugs in experimental inflammatory bowel disease. High-density oligonucleotide microarray analysis of gene dysregulation was assessed in colons from normal, TNBS-treated (7 days), and oral IB-MECA-treated rats (1.5 mg/kg b.i.d.) using a rat RNU34 neural GeneChip of 724 genes and SYBR green polymerase chain reaction. Analysis included clinical evaluation, weight loss assessment, and electron paramagnetic resonance imaging/spin-trap monitoring of free radicals. Remarkable colitis-induced gene dysregulation occurs in the most exceptional cluster of 5.4% of the gene pool, revealing 2 modes of colitis-related dysregulation. Downregulation occurs in membrane transporter, mitogen-activated protein (MAP) kinase, and channel genes. Upregulation occurs in chemokine, cytokine/inflammatory, stress, growth factor, intracellular signaling, receptor, heat shock protein, retinoid metabolism, neural, remodeling, and redox-sensitive genes. Oral IB-MECA prevented dysregulation in 92% of these genes, histopathology, gut injury, and weight loss. IB-MECA or adenosine suppressed elevated free radicals in ex vivo inflamed gut. Oral IB-MECA blocked the colitis-induced upregulation ( 90% of genes tested (33 of 37 genes). We conclude that our validated high-density oligonucleotide microarray analysis is a powerful technique for molecular gene dysregulation studies to assess the beneficial effects of purine-based or other drugs in experimental colitis. ADOA3R is new potential therapeutic target for inflammatory bowel disease.

Adenosine↗
PubMed1990

Investigation of Lewis phenotypes in Polynesians: evidence of a weak secretor phenotype.

The salivary ABH and Lewis antigens of Polynesians were measured using a standardised red cell agglutination microplate assay and compared with the red cell defined Lewis phenotypes. Salivary ABH substances were detected in almost all saliva samples tested, with low levels (partial secretion) of ABH substances in the saliva from Le(a+b-) and Le(a+b+) individuals. Salivary Leb substance was detected in all Le(a-b+) and Le(a+b+) samples and in almost all Le(a+b-) samples. It is evident from the results obtained that Polynesian red cell phenotypes cannot be used to predict the presence or absence of salivary substances. If the presence of a coding secretor gene is presumed responsible for salivary ABH antigens and salivary Leb antigen expression, then the incidence of a coding secretor gene in Polynesians is 98%. These results indicate that the recessive non-secretor gene is absent or rare in a Polynesian derived gene pool. Two variants of secretor individuals are found among Polynesians, secretors with expression of normal amounts of the product of the secretor gene, similar to Caucasians, and partial secretors with weak expression of the secretor gene products.

ABO Blood-Group System↗
PubMed2004

Matrix gene of influenza a viruses isolated from wild aquatic birds: ecology and emergence of influenza a viruses.

Wild aquatic birds are the primary reservoir of influenza A viruses, but little is known about the viruses' gene pool in wild birds. Therefore, we investigated the ecology and emergence of influenza viruses by conducting phylogenetic analysis of 70 matrix (M) genes of influenza viruses isolated from shorebirds and gulls in the Delaware Bay region and from ducks in Alberta, Canada, during >18 years of surveillance. In our analysis, we included 61 published M genes of isolates from various hosts. We showed that M genes of Canadian duck viruses and those of shorebird and gull viruses in the Delaware Bay shared ancestors with the M genes of North American poultry viruses. We found that North American and Eurasian avian-like lineages are divided into sublineages, indicating that multiple branches of virus evolution may be maintained in wild aquatic birds. The presence of non-H13 gull viruses in the gull-like lineage and of H13 gull viruses in other avian lineages suggested that gulls' M genes do not preferentially associate with the H13 subtype or segregate into a distinct lineage. Some North American avian influenza viruses contained M genes closely related to those of Eurasian avian viruses. Therefore, there may be interregional mixing of the two clades. Reassortment of shorebird M and HA genes was evident, but there was no correlation among the HA or NA subtype, M gene sequence, and isolation time. Overall, these results support the hypothesis that influenza viruses in wild waterfowl contain distinguishable lineages of M genes.

Animals↗
PubMed1989

What is the potential of avirulent influenza viruses to complement a cleavable hemagglutinin and generate virulent strains?

A large pool of avirulent influenza viruses are maintained in the wild ducks and shorebirds of the world, but we know little about their potential to become virulent. It is well established that the hemagglutinin (HA) is pivitol in determining virulence and that a constellation of other genes is also necessary (R. Rott, M. Orlich, and C. Scholtissek, 1976, J. Virol. 19, 54-60). The question we are asking here is the ability of avirulent influenza viruses to provide the gene constellation that will complement the HA from a highly virulent virus and for the reassortant to be virulent. Reassortant influenza viruses were prepared between ultraviolet treated A/Chicken/Pennsylvania/1370/83 (H5N2) [Ck/Penn] and influenza viruses from natural reservoirs. These viruses included examples of the predominant subtypes in wild ducks, shorebirds, and domestic poultry. Attention was given to the influenza viruses from live poultry markets, for it is possible that these establishments may be important in mixing of influenza genes from different species and the possible transmission to domestic and mammalian species. The reassortants were genotyped by partial sequencing of each gene and were tested for virulence in chickens. Each of the reassortants contained the hemagglutinin and matrix (M) genes from Ck/Penn and a majority of genes from the viruses from natural reservoirs indicating a preferential association between the HA and M genes. The reassortants containing multiple genes from wild ducks and a cleavable HA were avirulent indicating that the gene pool in ducks may not have a high potential to provide genes that are potentially virulent. In contrast, a disproportionate number of viruses from shorebirds and all avirulent H5N2 influenza viruses from city markets provided a gene constellation that in association with cleavable H5 HA were highly virulent in chickens. An evolutionary tree based on oligonucleotide mapping established that the H5N2 influenza viruses from birds in city markets are closely related.

Animals↗
PubMed2003

Genetic structure of Mediterranean populations revealed by Y-chromosome haplotype analysis.

The allelic variability at six Y-chromosome-specific polymorphisms (YAP, DYS19, DYS389-I, DYS390, DYS391, and DYS392) was used to generate male-specific haplotypes in 333 males representing 12 population samples from the region around the Mediterranean sea. Extreme interindividual variation was observed, as more than 160 distinct Y-chromosome variants could be defined as six-locus haplotypes. Concomitant with this high variability, low levels of population genetic structure were observed. In particular, a "core" of populations directly facing the north and the east of the Mediterranean basin, from the Middle East to the Italian Peninsula, was found to be genetically undifferentiated. This observation, supported by a reanalysis of Y-specific binary polymorphisms in the same populations, suggests that at least part of the male-specific gene pools of these populations has either a very recent common origin (that could be related with the Neolithic demic diffusion hypothesis), and/or that gene flow has played a significant role in shaping the patterns of genetic variability in this region. In agreement with both hypotheses, we found that the spatial distribution of DYS392 alleles revealed a marked differentiation between the East and the West of the Mediterranean area. Through the analysis of microsatellite variation, the time to the most recent common ancestor (TMRCA) of the YAP(+) sublineage 4 has been estimated. The estimations, based on two different data sets, turn out to be quite recent (7,000-11,000 YBP), suggesting that this lineage may have been first introduced into Southern Europe through Neolithic migrations from the Middle East.

Chromosomes, Human, Y↗
PubMed1990

Inbred testing of tomato (Lycopersicon esculentum L.) F1 varieties by ultrathin-layer isoelectric focusing of seed protein.

To test seed lots of tomato F1 hybrid varieties for the presence of undesirable inbred seeds by electrophoresis, a method has been developed on the basis of ultrathin-layer isoelectric focusing. The method is based on the genetic variation of the seed protein PRS-1 which could be visualized by isoelectric focusing of a 5 mM NaCl-soluble seed protein extract in a pH 6-9 gel followed by protein staining. Two genetic variants of the PRS-1 protein, PRS-1+ and PRS-1(1), were found among open-pollinated varieties, as well as among F1 hybrid varieties. The isoelectric points (pI) of the PRS-1 proteins are 7.1 and 6.1 for PRS-1+ and PRS-1(1), respectively. The PRS-1 protein is unique to seed tissue and is located primarily in the embryo. A genetic 1:2:1 segregation of the gene Prs-1 among several F2 populations shows monogenic inheritance. Analysis of commercial F1 hybrid varieties from several seed companies indicated that the Prs-1(1) allele, in contrast to the Prs-1+ allele, is primarily present in gene pools of "Money-maker type" tomatoes. The described method is generally applicable to all tomato F1 varieties that are heterozygous for the gene Prs-1. With the described method one person can routinely analyze more than 768 seeds per day.

Alleles↗
PubMed2006

Low level of genetic diversity in cultivated Pigeonpea compared to its wild relatives is revealed by diversity arrays technology.

Understanding the distribution of genetic diversity among individuals, populations and gene pools is crucial for the efficient management of germplasm collections and breeding programs. Diversity analysis is routinely carried out using sequencing of selected gene(s) or molecular marker technologies. Here we report on the development of Diversity Arrays Technology (DArT) for pigeonpea (Cajanus cajan) and its wild relatives. DArT tests thousands of genomic loci for polymorphism and provides the binary scores for hundreds of markers in a single hybridization-based assay. We tested eight complexity reduction methods using various combinations of restriction enzymes and selected PstI/HaeIII genomic representation with the largest frequency of polymorphic clones (19.8%) to produce genotyping arrays. The performance of the PstI/HaeIII array was evaluated by typing 96 accessions representing nearly 20 species of Cajanus. A total of nearly 700 markers were identified with the average call rate of 96.0% and the scoring reproducibility of 99.7%. DArT markers revealed genetic relationships among the accessions consistent with the available information and systematic classification. Most of the diversity was among the wild relatives of pigeonpea or between the wild species and the cultivated C. cajan. Only 64 markers were polymorphic among the cultivated accessions. Such narrow genetic base is likely to represent a serious impediment to breeding progress in pigeonpea. Our study shows that DArT can be effectively applied in molecular systematics and biodiversity studies.

Biodiversity↗
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

Approaches to prokaryotic biodiversity: a population genetics perspective.

The study of prokaryotic diversity has blossomed during the last 10-15 years as a result of the introduction of molecular identification, mostly based on direct 16S rRNA gene polymerase chain reaction (PCR) amplification and sequencing from natural samples. A large amount of information exists about the diversity of this specific gene. However, data from the field of bacterial population genetics and genomics make questionable the value of information regarding just one gene. Even if we accept 16S rRNA genes as useful for species identification, intraspecific variation in bacteria is so high that species catalogues are often of little value. The gene pools represented by an operational species are yet impossible to predict. On the other hand, adaptive features in prokaryotes are often coded in gene clusters (genomic islands) that can be cloned directly from the environment, sequenced and even expressed in a surrogate host. Thus, the study of the environmental genome or metagenome appears as an alternative that could eventually lead to a more realistic understanding of prokaryotic biodiversity, provide biotechnology with new tools and maybe even contribute to develop a model of prokaryotic evolution.

Biological Evolution↗
PubMed2000

Sequence diversity of Pseudomonas aeruginosa: impact on population structure and genome evolution.

Comparative sequencing of Pseudomonas aeruginosa genes oriC, citS, ampC, oprI, fliC, and pilA in 19 environmental and clinical isolates revealed the sequence diversity to be about 1 order of magnitude lower than in comparable housekeeping genes of Salmonella. In contrast to the low nucleotide substitution rate, the frequency of recombination among different P. aeruginosa genotypes was high, leading to the random association of alleles. The P. aeruginosa population consists of equivalent genotypes that form a net-like population structure. However, each genotype represents a cluster of closely related strains which retain their sequence signature in the conserved gene pool and carry a set of genotype-specific DNA blocks. The codon adaptation index, a quantitative measure of synonymous codon bias of genes, was found to be consistently high in the P. aeruginosa genome irrespective of the metabolic category and the abundance of the encoded gene product. Such uniformly high codon adaptation indices of 0.55 to 0.85 fit the ubiquitous lifestyle of P. aeruginosa.

Biological Evolution↗
PubMed1981

HLA types in American black juvenile diabetics strong associations with Dw3 and Dw4.

The distributions of HLA-A, -B, -C and -D antigens in 38 black American insulin-dependent juvenile diabetics were studied. Antigens A1, A2, B8 and Cw3 were slightly increased, but the corrected probability values were not statistically significant. As determined by mixed lymphocyte culture, the frequency of Dw3 was 89% in the juvenile diabetics and that of Dw4 was 42% in comparison with 14 and 8%, respectively, in the controls. The relative risks for juvenile diabetes were 52 for Dw3 (p = 10(-8) and 9 for Dw4 (p = 10(-6). Dw2 was significantly decreased in the diabetics (p equals 0.008). All of these deviations in A, B, C and D locus specificities have been previously reported by others in white juvenile diabetics. Because there are white genes in the American black gene pool and juvenile diabetes is rare in blacks in western Africa, many cases of juvenile diabetes in American blacks could be the result of genes ultimately derived from the white genes. This hypothesis is supported by the similar HLA associations in juvenile diabetes in the black and white ethnic groups.

Black People↗
PubMed1989

Genetical variation and polyphyletic origin in Japanese Mus musculus.

Previous reports of mitochondrial DNA variation in Japanese mice have revealed the occurrence of two components, a M. m. musculus mtDNA type in central Japan and a M. m. castaneus one at both northern and southern ends. In the present study, we explore the genetic composition of nuclear genes from Japanese wild mice. Protein electrophoresis at 16 polymorphic loci was used to characterise mice from 20 localities and to compare them with samples from the surrounding countries. The results revealed a predominant M. m. musculus nuclear gene component on the main Japanese Islands. A M. m. castaneus contribution was detectable in south Kyushu, but, interestingly, not evident in Northern Honshu were the castaneus mtDNA predominates. On the other hand, the mouse populations from Ogasawara (Chichi Islands) showed a threefold origin with a strong M. m. domesticus component, probably resulting from a very recent admixture. This clearcut example of reticulate evolution, which does not give rise to an homogeneous gene distribution, is however very different from the situation observed in the European hybrid zone. This raises questions concerning the mechanisms that either impede or favour gene admixture when differentiated gene pools are brought together.

Alleles↗
PubMed2005

Identification of core and variable components of the Salmonella enterica subspecies I genome by microarray.

We have performed microarray hybridization studies on 40 clinical isolates from 12 common serovars within Salmonella enterica subspecies I to identify the conserved chromosomal gene pool. We were able to separate the core invariant portion of the genome by a novel mathematical approach using a decision tree based on genes ranked by increasing variance. All genes within the core component were confirmed using available sequence and microarray information for S. enterica subspecies I strains. The majority of genes within the core component had conserved homologues in Escherichia coli K-12 strain MG1655. However, many genes present in the conserved set which were absent or highly divergent in K-12 had close homologues in pathogenic bacteria such as Shigella flexneri and Pseudomonas aeruginosa. Genes within previously established virulence determinants such as SPI1 to SPI5 were conserved. In addition several genes within SPI6, all of SPI9, and three fimbrial operons (fim, bcf, and stb) were conserved within all S. enterica strains included in this study. Although many phage and insertion sequence elements were missing from the core component, approximately half the pseudogenes present in S. enterica serovar Typhi were conserved. Furthermore, approximately half the genes conserved in the core set encoded hypothetical proteins. Separation of the core and variant gene sets within S.enterica subspecies I has offered fundamental biological insight into the genetic basis of phenotypic similarity and diversity across S. enterica subspecies I and shown how the core genome of these pathogens differs from the closely related E. coli K-12 laboratory strain.

Conserved Sequence↗