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At least 127 records · Page 7Linked to original sources
PubMed2003

Mitochondrial DNA analysis reveals diverse histories of tribal populations from India.

We analyzed 370 bp of the first hypervariable region of the mitochondrial DNA (mtDNA) control region in 752 individuals from 17 tribal and four nontribal groups from the Indian subcontinent, to address questions concerning the origins, genetic structure and relationships of these groups. Southern Indian tribes showed reduced diversity and large genetic distances, both among themselves and when compared with other groups, and no signal of prehistoric demographic expansions. These results probably reflect enhanced genetic drift because of small population sizes and/or bottlenecks in these groups. By contrast, northern groups exhibited more diversity and signals of prehistoric demographic expansions. Phylogenetic analyses revealed that southern and northern groups (except northeastern ones) have related mtDNA sequences albeit at different frequencies, further supporting the larger impact of drift on the genetic structure of southern groups. The Indian mtDNA gene pool appears to be more closely related to the east Eurasian gene pool (including central, east and southeast Asian populations) than the west Eurasian one (including European and Caucasian populations). Within India, northeastern tribes are quite distinct from other groups; they are more closely related to east Asians than to other Indians. This is consistent with linguistic evidence in that these populations speak Tibeto-Burman languages of east Asian origin. Otherwise, analyses of molecular variance suggested that caste and tribal groups are genetically similar with respect to mtDNA variation.

Cluster Analysis↗
PubMed1999

An analysis of diversity in the cognitive performance of elderly community dwellers: individual differences in change scores as a function of age.

This longitudinal study investigated whether age is associated with increases in interindividual variability across 4 ability domains using a sample of 426 elderly community dwellers followed over 3.5 years. Interindividual variability in change scores increased with age for memory, spatial functioning, and speed but not for crystallized intelligence for the full sample and in a subsample that excluded dementia or probable dementia cases. Hierarchical regression analyses indicated that being female, having weaker muscle strength, and having greater symptoms of illness and greater depression were associated with overall greater variability in cognitive scores. Having a higher level of education was associated with reduced variability. These findings are consistent with the view that there is a greater range of responses at older ages, that certain domains of intelligence are less susceptible to variation than others and that variables other than age affect cognitive performance in later life.

Activities of Daily Living↗
PubMed2003

Multivariate analysis of diversity of tef (Eragrostis tef (Zucc.) Trotter) germplasm from western and southern Ethiopia.

Sixty tef germplasm populations consisting of 3,000 panicle-derived lines from six western and southern regions of Ethiopia were evaluated for 17 pheno-morphic and agronomic traits on pellic Vertisols at Debre Zeit Agricultural Research Center during the 1999 main season. The objectives were to study the extent and pattern of variation of the germplasm with respect to regions and altitude zones, to classify the populations into relatively homogenous groups and to identify the major traits contributing to the overall diversity of the populations. At 75 % similarity level, the 60 populations aggregated into nine complexes of two to 10, with 12 populations remaining un-grouped. Five principal components (PC) extracted about 81 % of the gross variance among the populations. About 40 % of the variance accounted for by the first PC alone resulted largely from variations in diameters of the two basal culm internodes, grain yield and number of spikelets/panicle, shoot phytomass and grain yield/plant, and number of culm internodes. The entire regional as well as the clinal (altitude zone) variation was explained by five and two PCs, respectively. The discriminant analyses depicted about 77 % correct grouping of the 47 populations into nine clusters and about 62 % and 68 % correct origin-based classification of the germplasm in terms of altitude zones and regions, respectively. In general, the study demonstrated the existence of regional and clinal (altitude zone) variation patterns in the tef germplasm populations. The broad trait variation in the germplasm implies ample opportunities for genetic improvement of tef through selection and hybridization.

Agriculture↗
PubMed2005

Metagenomic analysis reveals diverse polyketide synthase gene clusters in microorganisms associated with the marine sponge Discodermia dissoluta.

Sponge-associated bacteria are thought to produce many novel bioactive compounds, including polyketides. PCR amplification of ketosynthase domains of type I modular polyketide synthases (PKS) from the microbial community of the marine sponge Discodermia dissoluta revealed great diversity and a novel group of sponge-specific PKS ketosynthase domains. Metagenomic libraries totaling more than four gigabases of bacterial genomes associated with this sponge were screened for type I modular PKS gene clusters. More than 90% of the clones in total sponge DNA libraries represented bacterial DNA inserts, and 0.7% harbored PKS genes. The majority of the PKS hybridizing clones carried small PKS clusters of one to three modules, although some clones encoded large multimodular PKSs (more than five modules). The most abundant large modular PKS appeared to be encoded by a bacterial symbiont that made up < 1% of the sponge community. Sequencing of this PKS revealed 14 modules that, if expressed and active, is predicted to produce a multimethyl-branched fatty acid reminiscent of mycobacterial lipid components. Metagenomic libraries made from fractions enriched for unicellular or filamentous bacteria differed significantly, with the latter containing numerous nonribosomal peptide synthetase (NRPS) and mixed NRPS-PKS gene clusters. The filamentous bacterial community of D. dissoluta consists mainly of Entotheonella spp., an unculturable sponge-specific taxon previously implicated in the biosynthesis of bioactive peptides.

Animals↗
PubMed1995

Hepatocarcinogenesis in BXH recombinant inbred strains of mice: analysis of diverse phenotypic effects of the hepatocarcinogen sensitivity loci.

The hepatocarcinogen sensitivity (Hcs) loci were originally identified as determinants of the approximately 50-fold higher susceptibility of male C3H/HeJ (C3H) mice to perinatally induced hepatocarcinogenesis relative to male C57BL/6J (B6) mice. These two inbred strains also differ in other phenotypes related to hepatocarcinogenesis, including their incidences of spontaneous liver tumors and the properties of neoplastic hepatic lesions. To test the hypothesis that the Hcs loci also influence these phenotypes, we characterized male mice from B6, C3H, and nine BXH recombinant inbred (RI) strains for spontaneous liver tumor development, the frequency of activating mutations in tumors, and the presence of cytoplasmic inclusions in preneoplastic lesions. By comparing these results to the relative susceptibilities of the parental and RI strains to N,N-diethylnitrosamine (DEN)- and N-ethyl-N-nitrosourea- induced hepatocarcinogenesis in preweanling male mice, we concluded that the C3H alleles of the Hcs loci also positively influence the spontaneous development of liver tumors in male animals. While strain-dependent differences in the frequency of Ha-ras-1 activation in DEN-initiated liver tumors were observed, this phenotype was not correlated with susceptibility to liver tumor induction. The formation of eosinophilic intracytoplasmic inclusion bodies observed specifically in B6 liver tumors, which has been suggested to be associated with the resistance of this strain to hepatocarcinogenesis, also segregated independently of the Hcs loci.

Animals↗
PubMed2000

Analysis of diversity of nucleotide and amino acid distributions in the VD and DJ joining regions in Ig heavy chains.

Nucleotide fill-in between the germ line V, D and J genes in the H3 loop of immunoglobulins contributes to the diversity of the antibody repertoire. This fill-in process is mediated by terminal deoxynucleotidyl transferase (TdT), which has been widely believed to insert nucleotides in a random fashion. Using a database of 2443 immunoglobulin sequences, we identified the regions of nucleotide fill-in between the V-D and D-J gene regions. We translated the fill-in nucleotides and measured the diversity within the two regions both at the nucleotide and amino acid level. We found that the nucleotide and amino acid distributions that resulted from nucleotide fill-in were in fact not random. Examination of the synonymous substitution rates of nucleotides revealed evidence suggesting that TdT plays a less significant role in generating antibody diversity than previously thought. We observed preferences for polar residues, which are more likely to encourage interaction with ligand than non-polar residues and are often found in loop regions in general. We also observed a preference for the insertion of smaller residues versus larger residues of similar biochemical properties, aiding in loop flexibility. We interpret these findings to reflect the significant influence of biochemical (i.e. folding) constraints and/or binding affinity constraints (at the cellular/selectional level) on the sequence diversity in the H3 region. These constraints act as a filter on the randomness generated by nucleotide addition by TdT, as well as other diversity generating processes such as recombination of VDJ gene segments and somatic mutation. The results of this study suggest that the antibody repertoire might be reduced from what is traditionally believed.

Animals↗
PubMed2002

Phytosterols, phytostanols, and their conjugates in foods: structural diversity, quantitative analysis, and health-promoting uses.

Phytosterols (plant sterols) are triterpenes that are important structural components of plant membranes, and free phytosterols serve to stabilize phospholipid bilayers in plant cell membranes just as cholesterol does in animal cell membranes. Most phytosterols contain 28 or 29 carbons and one or two carbon-carbon double bonds, typically one in the sterol nucleus and sometimes a second in the alkyl side chain. Phytostanols are a fully-saturated subgroup of phytosterols (contain no double bonds). Phytostanols occur in trace levels in many plant species and they occur in high levels in tissues of only in a few cereal species. Phytosterols can be converted to phytostanols by chemical hydrogenation. More than 200 different types of phytosterols have been reported in plant species. In addition to the free form, phytosterols occur as four types of "conjugates," in which the 3beta-OH group is esterified to a fatty acid or a hydroxycinnamic acid, or glycosylated with a hexose (usually glucose) or a 6-fatty-acyl hexose. The most popular methods for phytosterol analysis involve hydrolysis of the esters (and sometimes the glycosides) and capillary GLC of the total phytosterols, either in the free form or as TMS or acetylated derivatives. Several alternative methods have been reported for analysis of free phytosterols and intact phytosteryl conjugates. Phytosterols and phytostanols have received much attention in the last five years because of their cholesterol-lowering properties. Early phytosterol-enriched products contained free phytosterols and relatively large dosages were required to significantly lower serum cholesterol. In the last several years two spreads, one containing phytostanyl fatty-acid esters and the other phytosteryl fatty-acid esters, have been commercialized and were shown to significantly lower serum cholesterol at dosages of 1-3 g per day. The popularity of these products has caused the medical and biochemical community to focus much attention on phytosterols and consequently research activity on phytosterols has increased dramatically.

Animals↗
PubMed2000

Analysis of diversity and genetic relationships between four Chinese indigenous pig breeds and one Australian commercial pig breed.

The genetic diversities and relationships of four Chinese indigenous pig breeds and one Australian commercial pig breed have been evaluated using 27 microsatellites recommended by the International Society of Animal Genetics (ISAG) and the Food and Agriculture Organization (FAO). The allele frequencies, effective numbers of alleles and the polymorphic information content have been calculated. Nei's standard genetic distances have been used to construct a UPGMA dendrogram, which has been evaluated by the Bootstrap test. The utility of microsatellites for evaluating genetic diversity of pigs is discussed.

Alleles↗
PubMed2003

Long-term temporal changes of genetic composition in brown trout (Salmo trutta L.) populations inhabiting an unstable environment.

The genetic structure of brown trout (Salmo trutta) populations inhabiting rivers on the island of Bornholm in the Baltic Sea was studied on a spatial and temporal scale. Low water levels in the rivers during the summer period are assumed to have a significant impact on the persistence of local populations, possibly resulting in a metapopulation structure. Extinctions may, however, also be buffered by a remnant strategy, whereby juveniles escape to river outlets during periods of drought. We compared polymorphism at seven microsatellite DNA loci in contemporary and past samples collected from 1944 to 1997. A principal component analysis, a hierarchical gene diversity analysis and assignment tests showed that the genetic composition of populations was not temporally stable, and that temporal genetic differentiation was much stronger than spatial differentiation. Genetic variability was high and stable over time. Effective population sizes (Ne) and migration rate (m) were estimated using a maximum-likelihood-based implementation of the temporal method. Ne estimates were low (ranging from 8.3 to 22.9) and estimates of m were high (between 0.23 and 0.99), in contrast to other Danish trout populations inhabiting larger and more environmentally stable rivers (Ne between 39.2 and 289.9 and m between 0.01 and 0.09). Thus, the observed spatio-temporal patterns of genetic differentiation can be explained by drift in small persisting populations, where levels of genetic variation are maintained by strong gene flow. However, observations of rivers devoid of trout suggested that population turnover also takes place. We suggest that Bornholm trout represent a metapopulation where the genetic structure primarily reflects strong drift and gene flow, combined with occasional extinction-recolonization events.

Animals↗
PubMedDate not supplied

Genetic variation at three VNTR loci in three tribal populations of Orissa, India.

BACKGROUND: The variable number of tandem repeats (VNTR) loci are robust, simple and rapid tools for genetic characterization of both individuals and populations. This paper presents data on the distribution of three VNTRs (APOB, YNZ22 and D1S80) in three tribal populations (Gadaba, Kuvi-Khond and Paroja) of the Koraput district of Orissa, India with a view to enlarge our understanding of molecular genetic diversity among these tribes and the usage of these VNTRs in anthropogenetic studies. SUBJECTS AND METHODS: Three tribal populations were genotyped for APOB, YNZ22 and D1S80 loci using the polymerase chain reaction (PCR) technique. Gadaba are an Austro-Asiatic tribe while Kuvi-Khond and Paroja are Dravidian tribes. All samples were collected, with consent, from unrelated individuals. RESULTS: The observed allelic variation in these tribes is comparable with many Indian populations, but they showed significant overall and inter-population variability within the region. Allele *24 was the most common allele at the D1S80 locus in all populations, with Gadabas having the highest frequency (50%) followed by Paroja (32%) and Kuvi-Khond (23%). Gadabas also showed a higher frequency of allele *19 (13%) and *31 (9%) compared to other Indian and European populations. In the Apo B system, allele *37 was the most common in all three populations, with Gadabas having the highest frequency (39%) followed by Paroja (24%) and Kuvi-Khond (21%). This allele is present in high frequencies in other Indian (except Gonds) and European populations. Alleles *33 (17%), *35 (20%) and *45 (12%) were also common in the Gadabas, but Kuvi-Khond showed higher frequencies of *31(10%), *35(13%) and the larger allele *49(16%). Paroja, on the other hand, had higher frequencies of *31 (14%), *33 (17%) and *45 (13%). Allele *49 was also present in Paroja (10%) but was absent in the Gadaba. For the YNZ22 system, allele *4 was the most common in Kuvi-Khond (25%) and Paroja (21.4%), and allele *2 was the predominant allele in the Gadaba (33%). However allele *4 still occurs at relatively high frequency in Gadaba (27%). Allele *2 also occurs at relatively high frequency in Kuvi-Khond (20%) and intermediate frequency in Paroja (11%). Average heterozygosity was relatively low for Gadaba (0.7597 +/- 0.0191) and high for Kuvi-Khond (0.8618 +/- 0.0149) and Paroja (0.8512 +/- 0.0190), perhaps a reflection of effective population size and limitations to mating. The level of gene differentiation is, however, low (3-4%) for the three systems studied in these tribal populations and in data compiled from previous studies from the region. CONCLUSIONS: The VNTRs are polymorphic in the tribal populations studied and there is extensive allelic variation. Gadabas are isolated but Kuvi-Khond and Paroja show clear affinities with the Gonds, a major tribal group of Central India. Overall, allele frequency distribution, heterozygosity and genetic diversity analysis show that genetic diversity observed is socially, linguistically and geographically structured in this region.

Alleles↗
PubMed2006

Do antiviral CD8+ T cells select hepatitis C virus escape mutants? Analysis in diverse epitopes targeted by human intrahepatic CD8+ T lymphocytes.

Hepatitis C virus (HCV) is a variable RNA virus that can readily establish persistent infection. Cellular immune responses are important in the early control of the virus. Evidence from animal models suggests that mutation in epitopes recognized by CD8+ T lymphocytes may play an important role in the establishment of persistence but in human persistent infection, equivalent evidence is lacking. We investigated this by analysing a unique resource: viruses from a set of chronically HCV-infected individuals in whom the CD8+ T-cell responses in liver had previously been accurately mapped. Virus was sequenced in seven individuals at 10 epitopes restricted by 10 human leucocyte antigen (HLA) molecules. Two main patterns emerged: in the majority of epitopes sequenced, no variation was seen. In three epitopes, mutations were identified which were compatible with immune escape as assessed using phylogenetic and/or functional studies. These data suggest that - even where specific intrahepatic T cells are detectable - many epitopes do not undergo mutation in chronic human infection. On the contrary, virus may escape from intrahepatic CD8+ T-cell responses in a 'patchy' manner in certain specific epitopes. Furthermore, longitudinal studies to identify the differences between 'selecting' and 'nonselecting' intrahepatic CD8+ T-cell responses are needed in HCV infection.

CD8-Positive T-Lymphocytes↗
PubMed1998

Analysis of diversity of mutations in the mecI gene and mecA promoter/operator region of methicillin-resistant Staphylococcus aureus and Staphylococcus epidermidis.

Genomic diversity of mutation in the mecI gene or mecA promoter/operator region was analyzed for clinical isolates of methicillin-resistant Staphylococcus aureus (MRSA) and Staphylococcus epidermidis (MRSE). In most MRSA strains, a single base substitution was detected in either the mecI (three different positions) or the mecA promoter (two different positions), while a 28-base deletion in mecI was found in one strain. In contrast, no mutation was detected in these gene sequences of MRSE strains.

Bacterial Proteins↗
PubMed1996

Detection and analysis of diverse herpesviral species by consensus primer PCR.

A consensus primer PCR method which amplifies a region of herpesviral DNA-directed DNA polymerase (EC 2.7.7.7) and which uses degenerate primers in a nested format was developed. Primers were designed to target sequences coding for highly conserved amino acid motifs covering a region of approximately 800 bp. The assay was applied to 22 species of herpesviruses (8 human and 14 animal viruses), with PCR products obtained for 21 of 22 viruses. In the process, 14 previously unreported amino acid-coding sequences from herpesviral DNA polymerases were obtained, including regions of human herpesviruses 7 and 8. The 50 to 60 amino acid-coding sequences recovered in the present study were determined to be unique to each viral species studied, with very little sequence variation between strains of a single species when studied. Template dilution studies in the presence of human carrier DNA demonstrated that six human herpesviruses (herpesviruses 1, 2, 3, 4, 5, and 6B) could be detected at levels at or below 100 genome equivalents per 100 ng of carrier DNA. These data suggest that consensus primer PCR targeted to herpesviral DNA polymerase may prove to be useful in the detection and identification of known herpesviruses in clinical samples and the initial characterization of new herpesviral genomes.

Amino Acid Sequence↗
PubMed2004

Genetic analysis of diverse disease-causing pneumococci indicates high levels of diversity within serotypes and capsule switching.

We have used multilocus sequence typing (MLST) and serotyping to build a phylogenetic framework for pneumococcal disease isolates in Scotland that provides a snapshot of the relationships between capsular type and genotype. The results show that while the MLST type correlates with the serotype, isolates within a serotype can belong to a number of individual clonal complexes or sequence types (STs). We also show that isolates of the same ST can express different capsular polysaccharides, i.e., display capsular switching, and that this phenomenon is observed both for capsular types commonly isolated from patients with invasive disease and for serogroups less commonly isolated from patients with invasive disease but which may commonly be carried asymptomatically in the human nasopharynx.

Adolescent↗
PubMed2003

Exercise-induced improvement in endothelial dysfunction is not mediated by changes in CV risk factors: pooled analysis of diverse patient populations.

We have pooled data from a series of our exercise training studies undertaken in groups with a broad range of vascular (dys) function to the examine the hypothesis that exercise-induced improvements in the conduit and/or resistance vessel function are related to improvements in risk factors for cardiovascular (CV) disease. Endothelium-dependent and -independent conduit vessel function were assessed by using wall tracking of high-resolution ultrasound images of the brachial artery response to flow-mediated dilation (FMD) and glyceryl trinitrate. Resistance vessel function was assessed using intrabrachial administration of acetylcholine (ACh), sodium nitroprusside, and NG-monomethyl-l-arginine. Randomized cross-over studies of 8-wk exercise training were undertaken in untreated hypercholesterolemic (n = 11), treated hypercholesterolemic (n = 11), coronary artery disease (n = 10), chronic heart failure (n = 12), Type 2 diabetic (n = 15), and healthy control subjects (n = 16). Exercise training did not significantly alter plasma lipids, blood pressure, blood glucose, waist-to-hip ratio, or body mass index values, despite significant improvement in both FMD and ACh responses. There were no correlations between changes in any risk factor variables and indexes of either resistance or conduit vessel function. We conclude that, in these subjects with antecedent vascular dysfunction, the beneficial effects of relatively short-term exercise training on vascular function are not solely mediated by the effects of exercise on CV risk factors.

Acetylcholine↗
PubMed2026

[Mechanism of Tianshu Capsules in treating migraine rats based on gut microbiota].

This study aims to investigate the therapeutic effect of Tianshu Capsules(TS) on migraine rat model and explore its potential mechanism of action from the perspectives of the structure of the gut microbiota and functional pathway regulation. A migraine rat model was established via subcutaneous injection of nitroglycerin. The Sprague-Dawley rats were randomly divided into a control group, a model group, a low-dose TS group, a medium-dose TS group, a high-dose TS group, and an ibuprofen group. The efficacy of TS in improving migraine was evaluated by general condition observation and measurement of the craniofacial pain threshold. The expression of the gene c-fos in the trigeminal ganglion was determined by quantitative real-time polymerase chain reaction(PCR). The contents of endothelin-1(ET-1), calcitonin gene-related peptide(CGRP), and 5-hydroxytryptamine(5-HT) in serum were measured by enzyme-linked immunosorbent assay(ELISA). Fecal samples were subjected to metagenomic sequencing for systematic analysis of gut microbial diversity, taxonomic composition difference, and functional pathway changes of Kyoto Encyclopedia of Genes and Genomes(KEGG), and their correlations with behavioral and biochemical indices were further evaluated. The results show that TS significantly improves the increased body temperature and decreased craniofacial pain threshold in migraine rats. It also markedly suppresses the elevated expression levels of the gene c-fos in the trigeminal ganglion and reduces the levels of ET-1, CGRP, and 5-HT in serum. Metagenomic beta diversity analysis and differential taxonomic abundance analysis reveal that the migraine model induces significant gut microbiota dysbiosis, characterized by enrichment of harmful genera, including Streptococcus and Enterococcus, as well as a decline in the abundance of beneficial bacteria such as Allobaculum, Eubacterium, and Muribaculum. Functional pathway analysis results of KEGG further reveal that the relative abundances of pathways associated with biosynthesis of phenylalanine, tyrosine, and tryptophan, bacterial secretion system, citrate cycle, and biosynthesis of secondary metabolites are significantly decreased in the model group. TS intervention increased the abundance of the genus, such as Parabacteroides, Eubacterium, Allobaculum, and Muribaculum, while decreasing levels of microbiota, including Staphylococcus. TS also significantly upregulated pathways associated with barrier function(tight junction), amino acid biosynthesis pathways, and biosynthesis pathways of neurotransmitter precursors such as cysteine and methionine metabolism. In addition, it downregulated inflammatory pathways(Toll and IMD signaling) and pathways related to Staphylococcus aureus infection, thereby restoring the structure and function of the microbiota to a state close to those of the normal group. Spearman correlation analysis reveals that partial gut microbiota are significantly associated with migraine-related behavioral and biochemical indices(c-fos, ET-1, CGRP, and 5-HT). In conclusion, TS can regulate the disrupted gut microbiota structure and microbial functions related to neurotransmitter metabolism, intestinal barrier function, and inflammatory regulation in migraine model rats, which may be one of the potential key ways through which TS exert its anti-migraine effect.

Animals↗