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Leukotriene D4 and E4 induce transmembrane signaling in human epithelial cells. Single cell analysis reveals diverse pathways at the G-protein level for the influx and the intracellular mobilization of Ca2+.

Leukotrienes are recognized as important mediators of the inflammatory process. Recently, increasing attention has been paid to the role of noninflammatory cells in the regulation of the inflammatory process. To further increase our knowledge of this matter we have, in the present study, investigated leukotriene-induced Ca2+ signaling, using a single cell technique in a human epithelial cell line, Intestine 407. It was evident that both LTD4 and LTE4, at physiological concentrations (10 nM), triggered rapid and pronounced cytosolic free Ca2+ transients, due to both influx across the plasma membrane and intracellular mobilization. Preincubation with pertussis toxin (1200 ng/ml) decreased the level of agonist-induced Ca2+ transients to an extent similar to that caused by depletion of extracellular Ca2+, suggesting that the toxin affected the influx but not the intracellular mobilization of Ca2+. Indeed, by using the Mn2+ quenching technique, it could be shown that pertussis toxin totally inhibited the influx of Ca2+. The fact that, even after pertussis toxin treatment, direct G-protein activation by AIF4- was still able to trigger a cytosolic free Ca2+ transient, indicates that, in these cells, G-proteins (GTP-binding proteins) that are insensitive to pertussis toxin are capable of mediating a Ca2+ signal. In order to test the idea that such G-proteins regulate mobilization of intracellular Ca2+ induced by LTD4 and LTE4, we electropermeabilized and preincubated the Intestine 407 cells with guanosine-5'-O-(2-thiodiphosphate) (GDP beta S), let them reseal, and, after loading with fura2, investigated the effects on agonist-stimulated Ca2+ signaling. Electropermeabiization and resealing alone did not significantly affect the Ca2+ responses triggered by LTD4 or LTE4. Addition of GDP beta S, in the presence of extracellular Ca2+, reduced the Ca2+ responses by approximately 60-70%. In Ca2(+)-depleted medium, GDP beta S also impaired the LTD4-induced response by 65%, however, it had no effect on the Ca2+ response induced by LTE4. In conclusion, LTD4 and LTE4 trigger cytosolic free Ca2+ signaling in a human epithelial cell line by causing both an influx of Ca2+ and mobilization of intracellular Ca2+. The Ca2(+)-signaling mechanism appears to consist of dual pathways, since the influx is regulated by a pertussis toxin-sensitive G-protein, but, the mobilization of Ca2+ is not. Furthermore, our data suggest that the LTD4-induced mobilization is regulated by a pertussis toxin-insensitive G-protein whereas the LTE4-induced mobilization is relatively insensitive to both pertussis toxin and GDP beta S.

Aluminum↗

Peripheral (somatic) expansion of the murine cytotoxic T lymphocyte repertoire. I. Analysis of diversity in recognition repertoire of alloreactive T cells derived from the thymus and spleen of adult or aged DBA/2J mice.

Cytotoxic T lymphocyte precursors (CTLp) in the spleen or thymus of individual adult (8 to 10 wk) or aged (greater than 20 mo) DBA/2J mice have been activated by irradiated H-2Kb antigens under limiting dilution conditions such that cytotoxic cells in responder wells result from stimulation of a single CTLp. After division into several equal samples and expansion in the presence of IL 2 and more irradiated H-2Kb stimulators, the contents of replicate individual wells were tested for their ability to lyse a panel of selected H-2Kb mutant targets. The heterogeneity within a given age group, and the similarity of CTLp repertoires between different age groups were then compared for splenic and thymic CTLp repertoires. Our data indicate a far greater mouse-to-mouse variation for the splenic CTLp repertoire of aged mice compared with young mice, despite the greater heterogeneity of the repertoire in the latter case. Less difference was seen for the thymic CTLp repertoire. When we studied the correlation between the repertoires present in the thymus and spleen within a given age group, it seemed that the most striking difference in aged mice was a loss of systematic expansion of the early appearing thymic CTLp repertoire. These findings are discussed in terms of a two-stage model of T cell differentiation.

Aging↗

Molecular genetic diversity in 5 populations of Madhya Pradesh, India.

This paper presents data on the distribution of 3 amplified fragment length polymorphisms (D1S80, APOB, and YNZ22) in 5 populations of Central India. Using the polymerase chain reaction technique, 3 caste (Brahmin, Khatri, and Dhimer) and 2 tribal (Gond and Baiga) populations were studied for the 3 loci. The allelic variations observed in the caste populations are compatible with those of many Caucasian populations, but the caste populations showed significant overall and interpopulation variability within the region. D1S80 allele *24 varied from 32% (Dhimers) to 42% (Brahmins). Allele *18 was not observed in Baiga tribal populations, but in caste populations it varied from 11% (Dhimers) to 24% (Brahmins). Both tribal populations showed higher frequencies of allele *31 (17%-18%). For APOB, caste populations again showed bimodal distribution of alleles *35 and *37, but in tribal populations higher allele numbers (*47, *49) were also frequent. For YNZ22, extensive variation was observed for all populations studied. Allele *4 was the most common in caste populations, while alleles *2, *7, and *10 were prominent in tribal populations. The level of gene differentiation is not very high for the 3 systems studied in the 5 populations. Overall, allele frequency distribution, heterozygosity, and genetic diversity analysis show that the genetic diversity observed is socially and geographically structured.

Alleles↗

[Quantitative evaluation of gene variation and interpopulation differentiation of parthenogenetic species of Darevskia lizards based on mini- and microsatellite DNA markers].

Methods of estimating within- and between-population gene diversity in parthenogenetic species using mini- and microsatellite DNA markers and modified Wright's FST statistic are presented with special reference to model populations of lizards of the genus Darevskia (D. dahli, D. armeniaca, D. unisexualis). We used DNA fingerprinting data for several populations of these species examined earlier. The effects of variation in M13, minisatellite, (GACA)n and (TCC)n microsatellite loci on the formation of within-population gene diversity in parthenogenetic species D. dahli and D. armeniaca were shown to be different. The equality of the realized gene diversity H and its maximum possible value Hmax in two populations of D. dahli (Hmax = 0.032, H = 0.031, P < < 0.0431; Hmax = 0.024, H = 0.027, P = 0.09) and D. armeniaca (Hmax = 0.05, H = 0.053, P = 0.03; Hmax = 0.054, H = 0.055, P = 0.02) suggests that variation in (GACA)n loci substantially contributes to the maintenance of within-population genetic diversity. Analysis of between-population genetic diversity using loci M13, (GACA)n, and (TCC)n showed differentiation of D. dahli populations from northeastern and northwestern Armenia (FST = 0.0272, P = 3 x 10(-13)) and genetic homogeneity of the Armenian and Introduced to the Ukraine populations of D. armeniaca characteristic of one clone (FST = 0, P = 1).

Animals↗

Analysis of methanogen diversity in a hypereutrophic lake using PCR-RFLP analysis of mcr sequences.

The incidence and diversity of methanogens in Priest Pot, a dynamic and active lake, were monitored by analysing mcrA gene sequences generated from total DNA samples obtained at different times of the year and amplified using the polymerase chain reaction. A number of mcrA clones were analysed by developing an RFLP-based protocol to generate a number of restriction patterns that were assigned to a number of classes. The RFLP patterns for each class were compared with published sequence information for mcrA from cultured methanogens as well as with those from other experimental studies. They could be used to assign tentative identification for some of the Priest Pot clones and also revealed the presence of a number of clones that could not be affiliated to any known methanogens. The limitations of using RFLP profiles of mcrA gene sequences for studying methanogen ecology are discussed.

Bacteria↗

AFLP analysis of genetic diversity within and between Arabidopsis thaliana ecotypes.

The degree of genetic diversity within and between 21 Arabidopsis thaliana (L.) Heynh ecotypes was estimated by AFLP analysis. Within seven of the 21 ecotypes, a low but significant level of polymorphism was detected, and for five of these ecotypes two or three distinct subgroups could be distinguished. As these ecotypes represent natural populations, this intraecotypic diversity reflects natural genetic variation and diversification within the ecotypes. The source of this diversity remains unclear but is intriguing in view of the predominantly self-fertilizing nature of Arabidopsis. Interrelationships between the different ecotypes were estimated after AFLP fingerprinting using two enzyme combinations (EcoRI/MseI and SacI/MseI) and a number of selective primer pairs. SacI recognition sites are less evenly distributed in the genome than EcoRI sites, and occur more frequently in coding sequences. In most cases, AFLP data from only one enzyme combination are used for genetic diversity analysis. Our results show that the use of two enzyme combinations can result in significantly different classifications of the ecotypes both in cluster and ordination analysis. This difference most probably reflects differences in the genomic distribution of the AFLP fragments generated, depending on the enzymes and selective primers used. For closely related varieties, as in the case of Arabidopsis ecotypes, this can preclude reliable classification.

Arabidopsis↗

Hierarchical gene diversity and genetic structure of tribal populations of Andhra Pradesh, India.

Gene diversity and genetic structure of tribal populations of Andhra Pradesh, India, have been analyzed under a hierarchical model consisting of five regions of the state, tribes within the regions, and local subpopulations within the tribes. Average gene diversity has been estimated from gene frequency data for 15 polymorphic loci by using nested gene diversity analysis of GST. The intralocation coefficient of gene diversity was estimated at 96% of the total, whereas the intertribal, within--and between--regional gene diversities were found to be only 1.90, 0.95, and 1.43%, respectively. The estimate of gene diversity was higher for loci with higher degrees of polymorphism such as ABO, MN, ESD, and PTC and lower for loci with low-level polymorphism and extreme gene frequencies such as Hb, Tf, PHI, 6PGD, and Hp. The nature of selective preference or neutrality at the loci seems to be important in this respect. Tribes of the plains exhibit the least gene diversity, apparently because of higher gene flow among them. The contribution of loci with intermediate gene frequencies in intertribal and regional gene diversity was found to be higher than for loci with extreme allelic frequencies. These results suggest that the most significant component of variation is between individuals within locations and that variation between local subpopulations is negligible in the genetic structure of a population. Forces like selection, gene flow and drift also influence the diversity depending upon the nature of the locus.

Alleles↗

DISSIM: a program for the analysis of chemical diversity.

As interest in database searching and compound selection has grown, there has been a concomitant growth in interest in the quantification of chemical similarity. Described here is a computer program called DISSIM, which addresses the problem of selecting diverse subsets from larger collections of chemical compounds. It is a pragmatic solution combining a maximum dissimilarity search algorithm and a general multidimensional measure of chemical similarity based on the combination of different molecular descriptors. The problem of correlation between descriptors is addressed and appropriate schemes for weighting and normalisation are described. The specific application of these techniques to the comparative analysis of topological indices and their use in the area of chemical diversity analysis and compound selection are also described.

Algorithms↗

Natural fertility in northeastern Mexico: genetic structure by year of birth and birthplace.

BACKGROUND: The aims of this population genetics study were 1) to ascertain whether 417 Mexican women with natural fertility (45 years of age, married, not using any family planning methods, residing in the state of Nuevo León) were genetically homogeneous, and 2) to compare the genetic structure of this selected population with the previously reported data of random populations of northeastern Mexico. METHODS: A sample of 417 women was interviewed and selected in seven medical units of the Mexican Social Security Institute. They were grouped by their year of birth (1896-1925 and 1926-1955) and birthplace [persons whose four grandparents were born in the northeastern states (NE) and outside the northeastern states (Not-NE) of Mexico]. Eight genetic marker systems were analyzed. RESULTS: Gene diversity analysis suggests that more than 99.1% of the total gene diversity can be attributed to variation between individuals within the population. Genetic admixture analysis suggests that this selected population, stratified by year of birth and birthplace, have received a predominantly Spanish contribution followed by a lesser Mexican Indian contribution. CONCLUSIONS: The genetic structure of this selected population was homogeneous and similar to the random populations of northeastern Mexico. This finding corroborates the utility of this selected population for genetic and epidemiological studies.

Alleles↗

Interaction of host gene-gut microbiota in male grading of Macrobrachium rosenbergii.

UNLABELLED: The giant freshwater prawn (GFP; Macrobrachium rosenbergii), a crustacean of high nutritional and economic value, is crucial for aquaculture. During the same growth cycle, male GFPs develop into three distinct forms: small males, orange claw males, and blue claw males. These morphotypes display varying social behaviors, which severely constrain their industrial development. To address this, this study collected male GFP samples at critical developmental time points (100, 110, and 120 days post-hatching) for phenotypic trait measurement and analysis to obtain external morphological data. Through gut microbiota diversity analysis, we identified key gut bacteria (Lactococcus garvieae and Lactobacillus taiwanensis) influencing male morphotype differentiation. Transcriptomic analysis revealed host Kyoto Encyclopedia of Gene and Genome pathways and key genes (Wnt-6, CTSB, CTSL, PPAE, and TP53) associated with morphotype differentiation. The interactions among phenotypic traits, gut microbiota, and key genes were systematically studied through association analysis. Weighted gene co-expression network analysis was employed to construct co-expression modules, from which critical gene modules influencing phenotypic variation were identified. Through association network analysis, we established an "Achromobacter-CD-TRINITY_DN93139_c0_g2 (calpain clp-1)" interaction model. Our findings provide novel insights into the genetic enhancement of GFPs and offer guidelines for future research regarding gut symbiotic bacteria and breeding initiatives. IMPORTANCE: Male Macrobrachium rosenbergii (giant freshwater prawn [GFP]) in the same growth cycle will develop into small males, orange claw males, and blue claw males. This individual heterogeneity in growth significantly impacts the benefits of aquaculture. However, the factors influencing the differentiation of male GFP morphotype remain unclear. This study analyzed the phenotypic data of various GFP levels, the structure of the intestinal microbiota, and the differential genes within the gonadal transcriptome at critical time points of male GFP-level type differentiation. The aim was to explore the potential role of intestinal microbiota and differential genes in this phenomenon. This study offers new insights into the research on the phenomenon of male GFP-level type differentiation.

Animals↗

[Genetic diversity of Beauveria bassiana (Bals.) Vuill. in forest ecosystem assessed by inter-simple sequence repeat (ISSR) markers].

In the present paper, the genetic diversity of 48 Beauveria bassiana strains from different altitudes and at different seasons in Dabie Mountains of western Anhui was estimated using inter-simple sequence repeat (ISSR) markers. Twelve among 33 ISSR primers were chosen for their reproducibility and high polymorphism. Seven (2 - 11) markers per primer were scored, and a total of 84 fragments were amplified, in which 73 (81%) were polymorphic. Genetic diversity analysis revealed a relatively high level of intraspecific genetic diversity of B. bassiana in Dabie Mountains of western Anhui: the percentage of polymorphic loci (PPL) was 81%, Nei's genetic diversity (He) was 0.3187 and Shannon's genetic diversity index (I) was 0.4782. The genetic differentiation, Gst was 0.1028, indicating that a low degree of genetic differentiation occurred in the B. Bassiana among populations.

Altitude↗

High level of male-biased Scandinavian admixture in Greenlandic Inuit shown by Y-chromosomal analysis.

We have used binary markers and microsatellites on the Y chromosome to analyse diversity in a sample of Greenlandic Inuit males. This sample contains Y chromosomes typical of those found in European populations. Because the Y chromosome has a unique and robust phylogeny of a time depth that precedes the split between European and Native American populations, it is possible to assign chromosomes in an admixed population to either continental source. On this basis, 58+/-6% of these Y chromosomes have been assigned to a European origin. The high proportion of European Y chromosomes contrasts with a complete absence of European mitochondrial DNA and indicates strongly male-biased European admixture into Inuit. Comparison of the European component of Inuit Y chromosomes with European population data suggests that they have their origins in Scandinavia. There are two potential source populations: Norse settlers from Iceland, who may have been assimilated 500 years ago, and the Danish-Norwegian colonists of the eighteenth century. Insufficient differentiation between modern Icelandic and Danish Y chromosomes means that a choice between these cannot be made on the basis of diversity analysis. However, the extreme sex bias in the admixture makes the later event more likely as the source.

Asian People↗

Interethnic genetic differentiation: HLA class I antigens in the population of Mongolia.

A total of 1668 individuals representing 10 major Mongolian ethnic groups were serologically typed for HLA-A, -B, and -C antigens. Antigens A2, A24, B61, B51, B58, Cw3, Cw7, and Cw6 were the most frequent specificities in Mongolians and no case of B42 was noted in all ethnic groups. The cluster analysis of Principal Components I and II shows that Mongolian speaking groups form one cluster vs Turkic-speaking Kazakhs. The analysis reveals a low, but significant differentiation of Mongolian ethnic groups as measured by F(ST) = 0.0100 (P < 0.001). Gene diversity analysis shows that the genetic diversity of the Mongolian population can be attributed largely to its ethnic component, which makes up 64% of total genetic variation. The low degree of interpopulation variation and high level of intrapopulation diversity can be explained by the nomadic way of life of this indigenous population. Three-locus haplotypes A24-B61-Cw3, A33-B58-Cw3 are the most common haplotypic associations in Mongolians. The presence of antigens characteristic of Mongoloid, Caucasoid, and Negroid populations in Mongolians suggests a unique genetic background of this indigenous population. The three-locus haplotype distribution among Mongolians relative to other world populations supports the migration of ancient people from Central Asia to the New World, Korean Peninsula, and Southeast Asia. Am. J. Hum. Biol. 11:603-618, 1999. Copyright 1999 Wiley-Liss, Inc.

Journal Article↗

Genetic structure of the populations migrating from San Luis Potosi and Zacatecas to Nuevo León in Mexico.

The Mexicans residing in the Monterrey metropolitan area in Nuevo León, Mexico, were grouped by generation and birthplace [Monterrey Metropolitan Area (MMA), San Luis Potosi (SLP), and Zacatecas (ZAC)] of the four grandparents to determine the extent of genetic variation within this population and the genetic differences, if any, between the natives living in the MMA and the immigrant populations from SLP and ZAC. Nine genetic marker systems were analyzed. The genetic distance analysis indicates that SLP and ZAC are similar to the MMA, irrespective of birthplace and generation. Gene diversity analysis (GST) suggests that more than 96% of the total gene diversity (HT) can be attributed to individual variation within the population. The genetic admixture analysis suggests that the Mexicans of the MMA, SLP, and ZAC, stratified by birthplace and generation, have received a predominantly Spanish contribution (78.5%), followed by a Mexican Indian contribution (21.5%). Similarly, admixture analysis, conducted on the population of Nuevo León and stratified by generation, indicates a substantial contribution from the MMA (64.6%), followed by ZAC (22.1%) and SLP (13.3%). Finally, we demonstrate that there is no nonrandom association of alleles among the genetic marker systems (i.e., no evidence of gametic disequilibrium) despite the Mestizo origin of this population.

Alleles↗