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At least 829 records · Page 46Linked to original sources
PubMed2006

Lactobacillus siliginis sp. nov., isolated from wheat sourdough in South Korea.

The taxonomic position of two lactic-acid-producing bacterial strains, isolated from wheat sourdough in South Korea, was studied using a polyphasic approach. Phylogenetic analysis on the basis of 16S rRNA gene sequences and biochemical and physiological characteristics indicated these two strains to be members of the genus Lactobacillus. They had high 16S rRNA gene sequence similarity (98.5 %) with Lactobacillus rossiae DSM 15814(T) and very low (<94.0 %) similarity with any other recognized species of the genus Lactobacillus. These two strains (designated M1-212(T) and M2-236) were heterofermentative, facultatively anaerobic, Gram-positive, non-spore-forming, non-motile, short rod-shaped bacteria. The optimum growth temperature for these strains was 30 degrees C (no growth at 15 or 45 degrees C) and they were able to tolerate 5 % (w/v) NaCl. The G+C content of the genomic DNA of the two strains was 45.5 mol%, within the range of values reported for the genus Lactobacillus (32-53 mol%). The peptidoglycan was of the A3alpha (l-lys-d-glu-l-Ala) type. Physiological, biochemical and genotypic data, as well as results of DNA-DNA hybridization of the genomic DNA with one of the closest phylogenetic relatives, L. rossiae DSM 15814(T), indicated that the strains represent a novel species of the genus Lactobacillus, for which the name Lactobacillus siliginis sp. nov. is proposed. The type strain is M1-212(T) (=KCTC 3985(T)=NBRC 101315(T)).

Base Composition↗
PubMed2025

Post-traumatic stress disorder and REM-sleep behavior disorder: exploring genetic associations and causal links.

OBJECTIVE: To explore potential genetic and/or causal associations between Post-Traumatic Stress Disorder and neurodegeneration-related isolated/idiopathic rapid-eye-movement sleep behavior disorder. METHODS: We conducted polygenic risk score, genetic correlation, and Mendelian randomization analyses using the latest genome-wide association studies summary statistics and individual genotyping data. Next, a blinded observer examined dopamine transporter imaging binding status-a marker of neurodegeneration-in patients with isolated/idiopathic rapid-eye movement sleep behavior disorder, with (N = 6) and without Post-Traumatic Stress Disorder (N = 32). RESULTS: Polygenic risk scores for Post-Traumatic Stress Disorder were associated with isolated/idiopathic rapid-eye-movement sleep behavior disorder, with each standard deviation increase linked to 14.7% higher odds (odds ratio = 1.15, 95% confidence interval: 1.04 to 1.26, p = 0.005). However, genetic correlation was weak, and Mendelian randomization did not support a potential causal relationship. The proportion of individuals with abnormal dopamine transporter imaging binding status was significantly higher in the Post-Traumatic Stress Disorder group compared to those without the disorder (p=0.01, X2 = 6.62). INTERPRETATION: Polygenic risk scores analysis identified an association between Post-Traumatic Stress Disorder and neurodegeneration-related isolated/idiopathic rapid-eye-movement sleep behavior disorder, consistent with the result from the small exploratory substudy. The lack of strong genetic correlation or causation may reflect limited sample size. Further research with larger and more diverse cohorts is crucial to clarify the genetic, biological and physiological mechanisms underlying this association.

Journal Article↗
PubMed2005

Sequence features in regions of weak and strong linkage disequilibrium.

We use genotype data generated by the International HapMap Project to dissect the relationship between sequence features and the degree of linkage disequilibrium in the genome. We show that variation in linkage disequilibrium is broadly similar across populations and examine sequence landscape in regions of strong and weak disequilibrium. Linkage disequilibrium is generally low within approximately 15 Mb of the telomeres of each chromosome and noticeably elevated in large, duplicated regions of the genome as well as within approximately 5 Mb of centromeres and other heterochromatic regions. At a broad scale (100-1000 kb resolution), our results show that regions of strong linkage disequilibrium are typically GC poor and have reduced polymorphism. In addition, these regions are enriched for LINE repeats, but have fewer SINE, DNA, and simple repeats than the rest of the genome. At a fine scale, we examine the sequence composition of "hotspots" for the rapid breakdown of linkage disequilibrium and show that they are enriched in SINEs, in simple repeats, and in sequences that are conserved between species. Regions of high and low linkage disequilibrium (the top and bottom quartiles of the genome) have a higher density of genes and coding bases than the rest of the genome. Closer examination of the data shows that whereas some types of genes (including genes involved in immune response and sensory perception) are typically located in regions of low linkage disequilibrium, other genes (including those involved in DNA and RNA metabolism, response to DNA damage, and the cell cycle) are preferentially located in regions of strong linkage disequilibrium. Our results provide a detailed analysis of the relationship between sequence features and linkage disequilibrium and suggest an evolutionary justification for the heterogeneity in linkage disequilibrium in the genome.

Base Composition↗
PubMed2006

Localization of a long-range cis-regulatory element of IL13 by allelic transcript ratio mapping.

It appears that, for many genes, the two alleles possessed by an individual may produce different amounts of transcript. When such allelic differences in transcription are observed for some individuals but not others, a plausible explanation is genetic variation in the cis-acting elements that regulate the gene in question. Here we describe a novel analytical approach that uses such observations, combined with genotyping data from the HapMap project, to define the genomic location of cis-acting regulatory elements. When applied to the human 5q31 chromosomal region, where complex regulatory mechanisms are known to exist, we demonstrate the sensitivity of this approach by locating a highly significant cis-regulatory element operating on IL13 at long range from a position 250 kb upstream from the gene (P = 2 x 10(-6)). As this method is unaffected by other sources of variation, such as environmental and trans-acting genetic factors, it provides a tractable approach for dissecting the complexities of genetic variation in gene regulation.

Alleles↗
PubMed2003

Genetic and geographic differentiation in the Rio Negro tuco-tuco (Ctenomys rionegrensis): inferring the roles of migration and drift from multiple genetic markers.

Among tuco-tucos, Ctenomys rionegrensis is especially amenable to the study of the forces driving population differentiation because of the restricted geographic range it occupies in Uruguay. Within this limited area, the Rio Negro tuco-tuco is limited to sandy soils. It nonetheless exhibits remarkable variation in pelage color, including melanic, agouti, and dark-backed individuals. Two hypotheses have been put forth to explain this pattern: (1) local differentiation and fixation of alternative pelage types by genetic drift under limited gene flow; or (2) fixation by natural selection that may take place even in the presence of gene flow. A previous allozyme study rejected the genetic drift hypothesis on the basis of high inferred levels of migration. New estimates of gene flow from microsatellites and mitochondrial cytochrome b sequences were obtained for C. rionegrensis populations to further test these hypotheses. Much lower levels of gene flow were estimated with these more sensitive markers. Microsatellite-based estimates of gene flow are close to zero and may come closest to estimating current levels of migration. A lack of equilibrium between migration and genetic drift is also strongly suggested by the absence of an isolation-by-distance pattern found in all three genetic datasets. The microsatellite genotype data show that the species is strongly structured geographically, with subpopulations constituting distinct genetic entities. If current levels of gene flow are very low, as indicated by the new data, the local fixation of alternative alleles, including those responsible for pelage color polymorphism, is possible by drift alone. A scenario is thus proposed in which the species expanded in the recent past from a more restricted geographic range and has subsequently differentiated in near isolation, with genetic drift possibly playing a primary role in overall genetic differentiation. The local fixation of pelage color types could also be due to drift, but selection on this trait cannot be ruled out without direct analysis.

Animals↗
PubMed2004

Genetic diversity and differentiation in Portuguese cattle breeds using microsatellites.

Genotype data from 30 microsatellites were used to assess genetic diversity and relationships among 10 native Portuguese cattle breeds, American Charolais and the Brazilian Caracú. Hardy-Weinberg equilibrium was observed for all loci/population combinations except for five loci in Brava de Lide and one locus in Alentejana that exhibited heterozygote deficiency. Estimates of average observed and expected heterozygosities, total number of alleles (TNA) per breed and mean number of alleles (MNA) per locus/population were obtained. A total of 390 alleles were detected. TNA among Iberian cattle ranged from 170 to 237 and MNA ranged from 5.67 to 8.07. The highest observed heterozygosities were found in the Caracú, Maronesa, Garvonesa and Arouquesa and the lowest in Brava de Lide and Mirandesa. Estimation of population subdivision using Wright's FST index showed that the average proportion of genetic variation explained by breed differences was 9%. Neighbour-joining phylogenetic trees based on DA distances showed that the genetic relationships of present-day Portuguese native breeds are consistent with historical origins in the Brown Concave (Arouquesa, Mirandesa, Marinhoa) and Red Convex (Mertolenga, Alentejana, Garvonesa, Minhota) evolutionary groups. The Iberian Black Orthoide group, represented by Brava de Lide and Maronesa, and the Barrosã breed appeared to be more closely related to the Brown Concave group but may represent a separate lineage. The Caracú breed was not found to be closely associated with any of the native Portuguese breeds.

Analysis of Variance↗
PubMed2006

Globally dispersed Y chromosomal haplotypes in wild and domestic sheep.

To date, investigations of genetic diversity and the origins of domestication in sheep have utilised autosomal microsatellites and variation in the mitochondrial genome. We present the first analysis of both domestic and wild sheep using genetic markers residing on the ovine Y chromosome. Analysis of a single nucleotide polymorphism (oY1) in the SRY promoter region revealed that allele A-oY1 was present in all wild bighorn sheep (Ovis canadensis), two subspecies of thinhorn sheep (Ovis dalli), European Mouflon (Ovis musimon) and the Barbary (Ammontragis lervia). A-oY1 also had the highest frequency (71.4%) within 458 domestic sheep drawn from 65 breeds sampled from Africa, Asia, Australia, the Caribbean, Europe, the Middle East and Central Asia. Sequence analysis of a second locus, microsatellite SRYM18, revealed a compound repeat array displaying fixed differences, which identified bighorn and thinhorn sheep as distinct from the European Mouflon and domestic animals. Combined genotypic data identified 11 male-specific haplotypes that represented at least two separate lineages. Investigation of the geographical distribution of each haplotype revealed that one (H6) was both very common and widespread in the global sample of domestic breeds. The remaining haplotypes each displayed more restricted and informative distributions. For example, H5 was likely founded following the domestication of European breeds and was used to trace the recent transportation of animals to both the Caribbean and Australia. A high rate of Y chromosomal dispersal appears to have taken place during the development of domestic sheep as only 12.9% of the total observed variation was partitioned between major geographical regions.

Alleles↗
PubMed2004

Mild phenotype of familial cylindromatosis associated with an R758X nonsense mutation in the CYLD tumour suppressor gene.

Familial cylindromatosis is a rare dominantly inherited disease characterized by the development of multiple benign tumours of the skin appendages, including cylindromas, trichoepitheliomas and spiradenomas. The gene responsible was positionally cloned recently, and was designated CYLD. We describe a family with cylindromatosis, in which affected individuals have an inherited R758X nonsense mutation of CYLD. Affected members of this family manifest a relatively mild tumour phenotype; the largest tumour was only 30 mm in diameter. Thus far, there is no evident genotype-phenotype relationship in cylindromatosis, although the number of families reported with both phenotypic and genotypic data remains small.

Adult↗
PubMed1997

Isolation and characterization of coliforms from glacial ice and water in Canada's High Arctic.

Ellesmere Island is the northern most member of the Canadian Arctic Archipelago with over one-third of the land mass covered by ice. A joint services expedition to the island's Blue Mountains offered a unique opportunity for microbiological studies of resident bacteria in an environment uninhabited by man. Over 100 samples of water and ice were collected from stream, lake and glacier and the filtrate cultured under canvas. Bacterial growth was harvested onto swabs for transport back to the UK and 50 coliforms chosen at random for identification and antibiotic susceptibility testing. Most of the glacial strains were capsulated, pigmented and some over 2000 years old. Genera such as Serratia, Enterobacter, Klebsiella and Yersinia were found; speciation was inconclusive and some organisms remain unidentified. Ampicillin resistance was evident in 80% of water isolates as opposed to 30% of the glacial organisms, but the isolates were generally exquisitely susceptible to antibiotics. The facility for ampicillin resistance did not appear to be transferable. Plasmid DNA was found in 33% of the glacial organisms and over 50% of the water isolates. Similar profiles were identified within and apparently between species and required plasmid restriction analysis to help establish identity. Plasmid-free Serratia spp. were subjected to genomic fingerprinting. Indistinguishable patterns were found within sets of isolates both widely spaced by distance and collection date and it was postulated that coliforms able to survive an Arctic environment had spread extensively throughout the expedition area. In conclusion, this study contributes towards knowledge of naturally occurring antibiotic resistance, confirms the presence of plasmids and genotypic data provided evidence that potentially ancient organisms from glaciers can be cultured from water samples significantly distant.

Anti-Bacterial Agents↗
PubMed2004

How cryptic is the Scandinavian lynx?

A reanalysis of the existing genotypic data shows that they are compatible with the hypothesis that the present-day Scandinavian lynx represents a recent expansion from a single source. This contradicts earlier conclusions. The difference arises when it is assumed that the expansion and colonization have been stochastic processes and that the populations may not be at a drift-migration equilibrium.

Animal Migration↗
PubMed2005

Unbiased estimation of relative reproductive success of different groups: evaluation and correction of bias caused by parentage assignment errors.

Parentage assignment is widely applied to studies on mating systems, population dynamics and natural selection. However, little is known about the consequence of assignment errors, especially when some parents are not sampled. We investigated the effects of two types of error in parentage assignment, failing to assign a true parent (type A) and assigning an untrue parent (type B), on an estimate of the relative reproductive success (RRS) of two groups of parents. Employing a mathematical approach, we found that (i) when all parents are sampled, minimizing either type A or type B error insures the minimum bias on RRS, and (ii) when a large number of parents is not sampled, type B error substantially biases the estimated RRS towards one. Interestingly, however, (iii) when all parents were sampled and both error rates were moderately high, type A error biased the estimated RRS even more than type B error. We propose new methods to obtain an unbiased estimate of RRS and the number of offspring whose parents are not sampled (zW(z)), by correcting the error effects. Applying them to genotypic data from steelhead trout (Oncorhynchus mykiss), we illustrated how to estimate and control the assignment errors. In the data, we observed up to a 30% assignment error and a strong trade-off between the two types of error, depending on the stringency of the assignment decision criterion. We show that our methods can efficiently estimate an unbiased RRS and zW(z) regardless of assignment method, and how to maximize the statistical power to detect a difference in reproductive success between groups.

Animals↗
PubMed2006

Highly structured nucleotide variation within and among Arabidopsis lyrata populations at the FAH1 and DFR gene regions.

Nucleotide variation at the FAH1 and DFR gene regions was surveyed in four populations of Arabidopsis lyrata (two European A. l. petraea and two North American A. l. lyrata populations). In contrast to previous results, levels of variation were not consistently lower in A. l. lyrata than in A. l. petraea, and similar degrees of genetic differentiation were detected between and within subspecies. These observations and the significant genetic differentiation detected among populations suggest population substructure and no real subdivision between subspecies. For each gene studied, genotypic data were obtained, which allowed comparing nucleotide diversity within individuals (between sequences from the same individual) and within populations (between sequences from the same population). The generally lower level of variation within than among individuals detected in each population yielded a significant deviation from panmixia within populations. In three of the four populations studied, two highly divergent alleles were detected within populations at the highly variable DFR locus. This pattern and the significant excess of derived variants detected in most populations suggest that most variation segregating within populations results from rare migration events between relatively small and isolated populations exhibiting reduced panmixia.

Alcohol Oxidoreductases↗
PubMed2007

Linked vs unlinked markers: multilocus microsatellite haplotype-sharing as a tool to estimate gene flow and introgression.

We have explored the use of multilocus microsatellite haplotypes to study introgression from cultivated (Malus domestica) into wild apple (Malus sylvestris), and to study gene flow among remnant populations of M. sylvestris. A haplotype consisted of alleles at microsatellite loci along one chromosome. As destruction of haplotypes through recombination occurs much faster than loss of alleles due to genetic drift, the lifespan of a multilocus haplotype is much shorter than that of the underlying alleles. When different populations share the same haplotype, this may indicate recent gene flow between populations. Similarly, haplotypes shared between two species would be a strong signal for introgression. As the expected lifespan of a haplotype depends on the strength of the linkage, the length [in centiMorgans (cM)] of the haplotype shared contains information on the number of generations passed. This application of shared haplotypes is distinct from using haplotype-sharing to detect association between markers and a certain trait. We inferred haplotypes for four to eight microsatellite loci on Linkage Group 10 of apple from genotype data using the program phase, and then identified those haplotypes shared between populations and species. Compared with a Bayesian analysis of unlinked microsatellite loci using the program structure, haplotype-sharing detected a partially different set of putative hybrids. Cultivated haplotypes present in M. sylvestris were short (< 1.5 cM), indicating that introgression had taken place many generations ago, except for two Belgian plants that contained a haplotype of 47.1 cM, indicating recent introgression. In the estimation of gene flow, F(ST) based on unlinked loci indicated small (0.032-0.058) but statistically significant differentiation between some populations only. However, various M. sylvestris haplotypes were shared in nearly all pairwise comparisons of populations, and their length indicated recent gene flow. Hence, all Dutch populations should be considered as one conservation unit. The added value of using sharing of multilocus microsatellite haplotypes as a source of population genetic information is discussed.

Belgium↗
PubMed1998

HLA class II allele and haplotype frequencies in Ethiopian Amhara and Oromo populations.

HLA class II alleles were identified in 181 healthy unrelated Ethiopian children of both sexes and in 350 European controls from the South of France. The Ethiopian individuals belonged to the two major ethnic groups of the country: Oromo (N=83) and Amhara (N=98). In both panels, genetic polymorphism of HLA class II alleles was analysed for the first time by molecular typing of DRB1, DQA1 and DQB1 loci. Allelic and phenotypic frequencies were compared with those of European controls and other African populations. Construction of HLA class II three-locus haplotypes was also performed. The study revealed some differences between the two groups. Characteristic features of Central and North African populations appeared on the Ethiopian HLA genotypes. Surprisingly, DRB1*11 presented one of the lowest gene frequencies in both Ethiopian ethnic groups in contrast to Europeans and West Africans. Furthermore, this decrease was more marked than those observed using serological techniques in other geographically close East African countries. Oromo and Amhara only showed minor differences in spite of their different origins and histories. One significant difference consisted of a lower DRB1*01 gene frequency in Oromo as reported in most West African people. Some new or rare haplotypes were also observed in the Oromo group. Our results underline the distinctive features of the Ethiopian populations among the few HLA genotyping data available for East African groups and emphasise the major interest of such investigations in this region of Africa.

Alleles↗
PubMed2005

Contemporary gene flow and the spatio-temporal genetic structure of subdivided newt populations (Triturus cristatus, T. marmoratus).

Gene flow and drift shape the distribution of neutral genetic diversity in metapopulations, but their local rates are difficult to quantify. To identify gene flow between demes as distinct from individual migration, we present a modified Bayesian method to genetically test for descendants between an immigrant and a resident in a nonmigratory life stage. Applied to a metapopulation of pond-breeding European newts (Triturus cristatus, T. marmoratus) in western France, the evidence for gene flow was usually asymmetric and, for demes of known census size (N), translated into maximally seven reproducing immigrants. Temporal sampling also enabled the joint estimation of the effective demic population size (Ne) and the immigration rate m (including nonreproductive individuals). Ne ranged between 4.1 and 19.3 individuals, Ne/N ranged between 0.05 and 0.65 and always decreased with N; m was estimated as 0.19-0.63, and was possibly biased upwards. We discuss how genotypic data can reveal fine-scale demographic processes with important microevolutionary implications.

Animals↗
PubMed2006

High-resolution characterization of linkage disequilibrium structure and selection of tagging single nucleotide polymorphisms: application to the cholesteryl ester transfer protein gene.

Full characterization of intragenic variation may improve candidate gene associations. This study selected tagging (t) single nucleotide polymorphisms (SNPs) to comprehensively represent genetic variability in the cholesteryl ester transfer protein (CETP) gene. Nineteen SNPs were identified in 50 unrelated individuals in the SNP discovery phase, and 13 intronic SNPs were added from the literature. These 32 SNPs were genotyped in 339 apparently healthy individuals and 190 coronary artery disease (CAD) patients. Using phased haplotypes, linkage disequilibrium (LD) structure was characterized and tSNPs selected using a principal component analysis (PCA) method. In healthy individuals, seven LD groups were identified that accounted for 93.4% of the observed genetic variation. These LD groups highlighted a complex LD structure for CETP, including both recombination and mutation, and eleven tSNPs were selected. Among CAD patients the results were essentially the same. Results from PCA using diploid genotype data were reasonably comparable. Finally, the selected tSNPs successfully represented the association evidence discovered for all of the other SNPs studied. This study provides an optimal set of tSNPs for association analyses of CETP. The observed complexity of LD structure highlights the importance of using methods, such as PCA, that allow for multiple dynamics in intragenic LD structure.

Aged↗
PubMed2006

Association study of G protein-coupled receptor kinase 4 gene variants with essential hypertension in northern Han Chinese.

To investigate the association between polymorphisms in the G protein-coupled receptor kinase 4 gene (GRK4) (R65L, A142V and A486V) and essential hypertension in northern Han Chinese, we conducted a case-control study consisting of 503 individuals with essential hypertension (HT) and 490 age-, gender-, and area-matched normotensive (NT) controls. The three GRK4 variants were genotyped by PCR-RFLP analysis. Both haplotype and single locus analysis were used to process the genotyping data. The A486 allele showed a significant association with HT (P < 0.001). A total of 6 haplotypes were observed in the entire population, with the haplotypes L-V-A and R-A-A being found to be significantly related to hypertension (P= 0.001).

Aged↗
PubMed2006

Septaplex PCR assay for rapid identification of Vibrio cholerae including detection of virulence and int SXT genes.

In this study, we describe a septaplex PCR assay for rapid identification of Vibrio cholerae including detection of the virulence and intsxt genes. Conditions were optimized to amplify fragments of ISRrRNA (encoding for 16S-23S rRNA gene, Intergenic spacer regions), O1rfb (O1 serogroup specific rfb), O139rfb (O139 serogroup specific rfb), ctxA (cholera toxin subunit A), tcpA (toxin coregulated pilus), and intsxt (sxt integron) simultaneously in a single PCR. The septaplex PCR was evaluated using 211 strains of V. cholerae and six water samples for in situ testing. PCR results were correlated with genotype data obtained by individual PCR and slot-blot assays. The one-step PCR described here can be used to identify V. cholerae accurately and rapidly. Also, the virulence and intsxt genes can be simultaneously detected, providing a useful method for monitoring pathogenic, intsxt-positive and nonpathogenic, intsxt-negative V. cholerae serogroups both in the environment and clinical settings.

Genes, Viral↗