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At least 73 records · Page 4Linked to original sources
PubMed1999

Analysis of nifH gene pool complexity in soil and litter at a Douglas fir forest site in the Oregon cascade mountain range.

Nitrogen-fixing microbial populations in a Douglas fir forest on the western slope of the Oregon Cascade Mountain Range were analyzed. The complexity of the nifH gene pool (nifH is the marker gene which encodes nitrogenase reductase) was assessed by performing nested PCR with bulk DNA extracted from plant litter and soil. The restriction fragment length polymorphisms (RFLPs) of PCR products obtained from litter were reproducibly different than the RFLPs of PCR products obtained from the underlying soil. The characteristic differences were found during the entire sampling period between May and September. RFLP analyses of cloned nifH PCR products also revealed characteristic patterns for each sample type. Among 42 nifH clones obtained from a forest litter library nine different RFLP patterns were found, and among 64 nifH clones obtained from forest soil libraries 13 different patterns were found. Only two of the patterns were found in both the litter and the soil, indicating that there were major differences between the nitrogen-fixing microbial populations. A sequence analysis of clones representing the 20 distinct patterns revealed that 19 of the patterns had a proteobacterial origin. All of the nifH sequences obtained from the Douglas fir forest litter localized in a distinct phylogenetic cluster characterized by the nifH sequences of members of the genera Rhizobium, Sinorhizobium, and Azospirillum. The nifH sequences obtained from soil were found in two additional clusters, one characterized by sequences of members of the genera Bradyrhizobium, Azorhizobium, Herbaspirillum, and Thiobacillus and the other, represented by a single nifH clone, located between the gram-positive bacteria and the cyanobacteria. Our results revealed the distinctness of the nitrogen-fixing microbial populations in litter and soil in a Douglas fir forest; the differences may be related to special requirements for degradation and mineralization processes in the plant litter.

Bacteria↗
PubMed2001

[The Russian gene pool. Frequency of genetic markers].

Frequency distribution of several genetic markers was studied in ethnic Russians from the Moscow, Bryansk, Ryazan', Kostroma, Novgorod, Arkhangel'sk, and Sverdlovsk oblasts and Udmurtiya. Systems AB0, RH, HP, TF, GC, PI, C'3, ACP1, PGM1, ESD, GLO1, 6PGD, and AK were analyzed in most samples. New data on informative polymorphic genetic loci showed that the Russian gene pool mostly displays Caucasoid features. In addition, Y-chromosomal short tandem repeats (STRs) DYS19, DYS390, and YCAII were analyzed in the Russian samples. STRs of the chromosome are particularly valuable for elucidating ethnogenetic processes in Eastern Europe. Frequency distributions of the Y-chromosomal markers in Russians were intermediate between those of West European populations and eastern Finno-Ugric ethnoses of the Volga region. A marked longitudinal gradient was revealed for frequencies of several molecular markers.

DNA↗
PubMed1991

Autoantibodies and autoantigens: a conserved system that may shape a primary immunoglobulin gene pool.

Formation of certain autoantibodies is associated with a variety of autoimmune diseases, but the production of small amounts of autoantibodies also occurs in the normal immune system. Germline-encoded IgM antibodies that are autoreactive and bind to diverse antigen structures with low affinity are prominent in the primary antibody repertoire. Many IgG disease-related autoantibodies differ in structure and binding properties from these normally occurring IgM autoantibodies. The two sets may arise independently, but some properties, such as shared idiotypes, link some members of the two populations. Many autoantigen targets of both sets of autoantibodies are structurally conserved among species, as are certain features of the autoantibodies themselves. These elements, interacting before exposure of the system to foreign antigens, may constitute a conserved system that contributes to shaping and maintaining a primary immunoglobulin gene pool.

Autoantibodies↗
PubMed2005

Female gene pools of Berber and Arab neighboring communities in central Tunisia: microstructure of mtDNA variation in North Africa.

North African populations are considered genetically closer to Eurasians than to sub-Saharans. However, they display a considerably high mtDNA heterogeneity among them, namely in the frequencies of the U6, East African, and sub-Saharan haplogroups. In this study, we describe and compare the female gene pools of two neighboring Tunisian populations, Kesra (Berber) and Zriba (non-Berber), which have contrasting historical backgrounds. Both populations presented lower diversity values than those observed for other North African populations, and they were the only populations not showing significant negative Fu's F(S) values. Kesra displayed a much higher proportion of typical sub-Saharan haplotypes (49%, including 4.2% of M1 haplogroup) than Zriba (8%). With respect to U6 sequences, frequencies were low (2% in Kesra and 8% in Zriba), and all belonged to the subhaplogroup U6a. An analysis of these data in the context of North Africa reveals that the emerging picture is complex, because Zriba would match the profile of a Berber Moroccan population, whereas Kesra, which shows twice the frequency of sub-Saharan lineages normally observed in northern coastal populations, would match a western Saharan population except for the low U6 frequency. The North African patchy mtDNA landscape has no parallel in other regions of the world and increasing the number of sampled populations has not been accompanied by any substantial increase in our understanding of its phylogeography. Available data up to now rely on sampling small, scattered populations, although they are carefully characterized in terms of their ethnic, linguistic, and historical backgrounds. It is therefore doubtful that this picture truly represents the complex historical demography of the region rather than being just the result of the type of samplings performed so far.

Arabs↗
PubMed1995

One of the two common mutations causing factor XI deficiency in Ashkenazi Jews (type II) is also prevalent in Iraqi Jews, who represent the ancient gene pool of Jews.

In recent years four mutations causing factor XI deficiency have been identified in Jews of Ashkenazi (European) origin. Two of them, type II (a nonsense mutation) and type III (a missense mutation), were found to prevail among 125 unrelated Ashkenazi Jews with severe factor XI deficiency. A finding of type II mutation in four unrelated Iraqi-Jewish families raised the possibility that this mutation is also common in Iraqi Jews, who represent the ancient gene pool of the Jews. A molecular-based analysis performed in 1,040 consecutively hospitalized patients disclosed the following results: Among 531 Ashkenazi-Jewish patients, the type II allele frequency was 0.0217 and among 509 Iraqi-Jewish patients, 0.0167 (P = .50). The type III allele frequency in the Ashkenazi-Jewish patients was 0.0254, whereas none of 502 Iraqi-Jewish patients examined had this mutation. These data suggest that the type II mutation was present in Jews already 2.5 millenia ago. The data also indicate that the estimated risk for severe factor XI deficiency in Ashkenazi Jews (due to either genotype) is 0.22% and in Iraqi Jews, 0.03%, and that the estimated risk of heterozygosity in Ashkenazi Jews is 9.0% and in Iraqi Jews, 3.3%. As patients with severe factor XI deficiency are prone to bleeding after injury and patients with partial deficiency may have similar bleeding complications when an additional hemostatic derangement is present, the observed high frequencies should be borne in mind when surgery is planned for individuals belonging to these populations.

Aged↗
PubMed2005

Population genetic analysis of cat populations from Mexico, Colombia, Bolivia, and the Dominican Republic: identification of different gene pools in Latin America.

In this paper we identify new genetic profiles of eight Latin American cat populations. In addition, we combine data from the present study and previously published data on 70 other American and European populations to discuss (1) the points of introduction of mutant alleles for cat coat phenotypes from Europe into Latin America, (2) the heterozygosity levels at these loci in the current Latin American cat populations, (3) the level of genetic heterogeneity among Latin American cat populations, and how this compares with levels found in North American and European cat populations, and (4) how many different cat gene pools are currently present in Latin America. We also include in our purview historical records of human migrations from Europe to and within the Americas. Our analyses clearly support the view that the current genetic profiles and structuring of cat populations in Latin America can be largely explained by the historical migration patterns of humans.

Alleles↗
PubMed2001

To the research of the gene pool of the Gagauz population of Moldavia.

Population genetic data on Gagauzes from Moldavia are reported here for the first time. AB0 and Rhesus blood groups, serum protein group (HP, TF, GC) and the red cell enzyme polymorphism PGM1 were determined in 190 Gagauzes. In addition to this the ability to taste PTC was tested. The following allele frequencies were found: AB0*0 = 0.5241, AB0*A = 0.3279, AB0*B = 0.1480; RH*D = 0.6083, RH*d = 0.3917; HP*1 = 0.3544, HP*2 = 0.6456; TF*C1 = 0.7472, TF*C2 = 0.1770, TF*C3 = 0.0730, TF*B = 0.0028; GC*1F = 0.1025, GC*1S = 0.5932, GC*2 = 0.3043; PGM*1+ = 0.5932; PGM*1- = 0.1000, PGM*2+ = 0.2607, PGM*2- = 0.1107. The frequency of the PTC*T allele was found to be 0.5298. These frequencies and genetic distance analyses show that the gene pool of the Gagauzes is similar to that of neighbouring southeastern European populations.

ABO Blood-Group System↗
PubMed2006

Development of functional markers specific for seven Pm3 resistance alleles and their validation in the bread wheat gene pool.

In the ideal case, molecular markers used for marker-assisted selection are allele-specific even if the alleles differ only by a few nucleotide polymorphisms within the coding sequence of target genes. Such 'perfect' markers are completely correlated with the trait of interest. In hexaploid wheat (Triticum aestivum L.) the Pm3 locus encodes seven alleles (Pm3a-Pm3g) conferring resistance to different races of Blumeria graminis f.sp. tritici, the agent of powdery mildew, a major disease of bread wheat. All Pm3 alleles are known at the molecular level. Here, we generated specific markers for the Pm3 alleles based on nucleotide polymorphisms of coding and adjacent non-coding regions. The specificity of these markers was validated in a collection of 93 modern or historically important cultivars and breeding lines of wheat and spelt (Triticum spelta L.). These markers confirmed the presence of the predicted Pm3 alleles in 31 varieties and lines known to carry Pm3 resistance alleles. In a few varieties, Pm3 alleles different from alleles previously described based on pathogenicity tests or tightly linked markers were observed. In all these cases, the identity of the marker-detected Pm3 alleles was confirmed by DNA sequence analysis. Pm3 markers confirmed the absence of known Pm3 resistance alleles in 54 European wheat and spelt varieties in which Pm3 alleles had not been previously identified. These results indicate that the developed markers are highly diagnostic for specific Pm3 resistance alleles in a wide range of varieties and breeding lines, and will be useful (1) for identifying Pm3 alleles in the wheat gene pool, (2) for efficient marker-assisted selection of these genes, and (3) for combining multiple Pm3 alleles within a single cultivar through transgenic approaches.

Alleles↗
PubMed2000

MtDNA and Y chromosome polymorphisms in Hungary: inferences from the palaeolithic, neolithic and Uralic influences on the modern Hungarian gene pool.

Magyars imposed their language on Hungarians but seem not to have affected their genetic structure. To better investigate this point, we analysed some mtDNA and Y chromosome polymorphisms in a sample of the Hungarian Palóc who, for historical reasons, could have retained genetic traces of Magyars more than other groups. In addition, we examined a mixed sample from Budapest. About 100 individuals were tested for the markers defining all the European and Asian mtDNA haplogroups and about 50 individuals for some Y chromosome markers, namely the 12f2 and 49a,f/TaqI RFLPs, the YAP insertion, the microsatellites YCAIIa, YCAIIb, DYS19 and the Asian 50f2/C deletion. In the mtDNA analysis only two subjects belonged to the Asian B and M haplogroups. The Y chromosome analyses showed that the Palóc differed from the Budapest sample by the absence of YAP+ allele and by the DYS19 allele distribution; that the proto-European 49a,f Ht 15 and the neolithic 12f2-8Kb were rather uncommon in both groups; that there is a high prevalence of the 49a,f Ht 11 and the YCAII a5-b1; and that the Asian 50f2/C deletion is absent. These results suggest that the influence of Magyars on the Hungarian gene pool has been very low through both females and males and the Hungarian language could be an example of cultural dominance. Alternative explanations are discussed. An expansion centred on YAP-, 49a,f Ht 11 is revealed by the median network based on compound haplotypes. 49a,f Ht 11 could represent either a paleolithic marker of eastern Europe which underwent expansion after the last glacial period, or a marker of the more recent spread of the Yamnaia culture from southern Ukraine.

Alu Elements↗
PubMed2006

Targeting polyketide synthase gene pool within actinomycetes: new degenerate primers.

Natural products provide a unique element of molecular diversity and biological functionality and they are still indispensable for drug discovery. The polyketides, comprising a large and structurally diverse family of bioactive natural products, have been isolated from a group of mycelia-forming Gram-positive microorganisms, the actinomycetes. Relatively high amino acid sequence identity of the actinomycetes type I polyketide synthases (PKSs) was used to design three degenerate primer pairs for homology-based PCR detection of novel PKS genes, with particular interest into PKSs involved in biosynthesis of immunosuppressive-like metabolites. The stepdown PCR method, described here, enables fast insight into the PKS arsenal within actinomycetes. Designed primers and stepdown PCR were applied for the analysis of two natural isolates, Streptomyces sp. strains NP13 and MS405. Sequence analysis of chosen clones revealed the presence of two distinctive sequences in strain Streptomyces sp. NP13, but only one of these showed homology to PKS-related sequences. On analysing PCR amplicons derived from Streptomyces sp. strain MS405, three different PKS-related sequences were identified demonstrating a potential of designed primers to target PKS gene pool within single organism.

Actinobacteria↗
PubMed1997

A global gene pool for high-level cephalosporin resistance in commensal Streptococcus species and Streptococcus pneumoniae.

Highly penicillin- and cephalosporin-resistant Streptococcus mitis and Streptococcus oralis were isolated in Spain, Hungary, and Berlin. With chromosomal DNA of these strains, resistant transformants of Streptococcus pneumoniae were obtained that expressed low-affinity variants of penicillin-binding proteins (PBPs) 2x, 1a, 2a, and 2b in different combinations, depending on the selective conditions. The transformants had cefotaxime MICs of up to 6 microg/mL, and those with a low-affinity PBP 2b were highly deficient in penicillin-induced lysis. Sequence analysis of the pbp2x genes confirmed the presence of a global gene pool of penicillin resistance determinants shared by commensal and pathogenic streptococci.

Amino Acid Sequence↗
PubMed1984

Accessory DNAs in the bacterial gene pool: playground for coevolution.

Chemostat studies of bacteria that harbour the prokaryotic transposable elements Tn5 and Tn10 and the temperate phages lambda, Mu, P1 and P2 have shown that these accessory DNA elements confer a selective advantage on their hosts. We propose that similar selective effects provided the initial impetus for the evolution of nascent accessory DNA elements in primitive bacterial populations. In subsequent evolution the elements acquired or perfected the 'selfish' characteristics of over-replication and horizontal transmission. Such selfish traits led to the dissemination of accessory DNAs among commensal strains, species and genera, genetically interconnecting them to create a 'commonwealth' of species that potentially share a common gene pool. The involvement of accessory DNAs in genetic exchange provides selection at the population level for refinement and diversification of the elements and for regulation of their replication, transposition and transfer among cells. The diversity of intracellular environments encountered by the elements imposes constraints on their evolution while at the same time altering the selection pressures operating on conventional chromosomal genes. This process of coevolution of accessory DNAs with the genomes of their diverse hosts has led to a unique population structure and mechanism of genetic exchange among bacteria, which constitutes the most effective adaptive strategy yet devised by selection.

Adaptation, Biological↗