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At least 451 records · Page 25Linked to original sources
PubMed2025

Extensive Analysis of Genetic Diversity in HLA-DMA, HLA-DMB, HLA-DOA and HLA-DOB: Characterisation of 236 Novel Alleles.

HLA-DMA, -DMB, -DOA and -DOB are non-classical HLA Class II genes that play a crucial role in the selection of highly stable HLA Class II/peptide complexes on antigen-presenting cells. Although the genes were initially thought to have a limited diversity with less than 13 alleles per gene documented in the IPD-IMGT/HLA Database in 2022, recent studies suggest a potential impact of certain alleles on the outcome of hematopoietic cell transplantation. To gain a deeper understanding of allelic diversity, we sequenced HLA-DMA, -DMB, -DOA and -DOB of 1880 potential stem cell donors from Germany, Poland, Great Britain and Chile, achieving full-gene resolution. Remarkably, we identified 3968 previously undescribed sequences, including 28 distinct novel proteins. The observed allele frequencies were consistent across all studied populations with one dominating protein for each gene: HLA-DMA*01:01 (> 77%), HLA-DMB*01:01 (> 63%), HLA-DOA*01:01 (> 97%) and HLA-DOB*01:01 (> 77%). Notably, a much higher diversity was observed in full-genomic resolution. Finally, we submitted 51 distinct novel sequences for HLA-DMA, 58 for HLA-DMB, 80 for HLA-DOA and 47 for HLA-DOB to the IPD-IMGT/HLA Database. This comprehensive reference database update will not only simplify future genotyping of HLA-DMA, -DMB, -DOA and -DOB but will hopefully also enhance our understanding of the complex process of peptide selection and loading to the HLA Class II proteins.

Humans↗
PubMed1990

Analysis of junctional diversity during B lymphocyte development.

Immunoglobulin rearrangement is central to generating antibody diversity because of heterogeneity generated during recombination by deletion or addition of nucleotides at coding joints by the recombinase machinery. Examination of these junctional modifications revealed that the addition of nongermline-encoded nucleotides was more prevalent in adult versus fetal B cells, thus partially limiting the fetal antibody repertoire. In contrast, deletion of nucleotides occurs equivalently in B cells at different stages of development and at different points in B cell ontogeny. Finally, the bias in murine immunoglobulins for one DH segment reading frame occurs at the DHJH intermediate.

Aging↗
PubMed2005

Diversity and functional analysis of bacterial communities associated with natural hydrocarbon seeps in acidic soils at Rainbow Springs, Yellowstone National Park.

In this paper we describe the bacterial communities associated with natural hydrocarbon seeps in nonthermal soils at Rainbow Springs, Yellowstone National Park. Soil chemical analysis revealed high sulfate concentrations and low pH values (pH 2.8 to 3.8), which are characteristic of acid-sulfate geothermal activity. The hydrocarbon composition of the seep soils consisted almost entirely of saturated, acyclic alkanes (e.g., n-alkanes with chain lengths of C15 to C30, as well as branched alkanes, predominately pristane and phytane). Bacterial populations present in the seep soils were phylogenetically characterized by 16S rRNA gene clone library analysis. The majority of the sequences recovered (>75%) were related to sequences of heterotrophic acidophilic bacteria, including Acidisphaera spp. and Acidiphilium spp. of the alpha-Proteobacteria. Clones related to the iron- and sulfur-oxidizing chemolithotroph Acidithiobacillus spp. were also recovered from one of the seep soils. Hydrocarbon-amended soil-sand mixtures were established to examine [14C]hexadecane mineralization and corresponding changes in the bacterial populations using denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments. Approximately 50% of the [14C]hexadecane added was recovered as 14CO2 during an 80-day incubation, and this was accompanied by detection of heterotrophic acidophile-related sequences as dominant DGGE bands. An alkane-degrading isolate was cultivated, whose 16S rRNA gene sequence was identical to the sequence of a dominant DGGE band in the soil-sand mixture, as well as the clone sequence recovered most frequently from the original soil. This and the presence of an alkB gene homolog in this isolate confirmed the alkane degradation capability of one population indigenous to acidic hydrocarbon seep soils.

Bacteria↗
PubMed1978

Analysis of antigenic diversity among human cytomegaloviruses by kinetic neutralization tests with high-titered rabbit antisera.

Neutralizing antisera to human cytomegalovirus were produced in rabbits with alkaline-buffered extracts of infected cell cultures. The antibody activity was complement dependent and associated primarily with the 7S immunoglobulin fraction. Antisera with homologous K values greater than 10.00 were shown to be suitable for neutralization kinetic studies and were so used to examine the antigenic relatedness of strains AD169, Davis, Esp, C-87, Kerr, and Towne. Based upon the degree of relationship as determined by normalized K values, antisera to the Davis or AD169 strains discriminated three antigenic groups, and an antiserum to strain Esp discriminated two groups.

Animals↗
PubMed2001

Cloning of the Streptococcus mutans gene encoding glucan binding protein B and analysis of genetic diversity and protein production in clinical isolates.

Streptococcus mutans, the primary etiological agent of dental caries, produces several activities that promote its accumulation within the dental biofilm. These include glucosyltransferases, their glucan products, and proteins that bind glucan. At least three glucan binding proteins have been identified, and GbpB, the protein characterized in this study, appears to be novel. The gbpB gene was cloned and the predicted protein sequence contained several unusual features and shared extensive homology with a putative peptidoglycan hydrolase from group B streptococcus. Examination of gbpB genes from clinical isolates of S. mutans revealed that DNA polymorphisms, and hence amino acid changes, were limited to the central region of the gene, suggesting functional conservation within the amino and carboxy termini of the protein. The GbpB produced by clinical isolates and laboratory strains showed various distributions between cells and culture medium, and amounts of protein produced by individual strains correlated positively with their ability to grow as biofilms in an in vitro assay.

Amino Acid Sequence↗
PubMed2003

Analysis of genetic diversity of Streptococcus suis clinical isolates from pigs in Spain by pulsed-field gel electrophoresis.

Pulsed-field gel electrophoresis (PFGE) was used to investigate the diversity of Streptococcus suis isolates of various serotypes recovered from swine clinical samples in Spain. Capsular types 9 (64.9%) and 2 (14.8%) were the most frequently isolated serotypes followed by serotype 7 (5.9%) and serotype 8 (4.3%). The PFGE results of this study with 60 different pulsotypes indicate a great genetic diversity among the S. suis isolates, which is consistent with the broad distribution of S. suis in the swine population. Forty-five percent of the pulsotypes corresponded to single isolates, no pulsotype was common to all farms, and at least 3 different pulsotypes were isolated in 56% of herds in which more than 3 clinical isolates were analyzed. These results reveal a great diversity both between and within herds throughout the strains of S. suis studied, demonstrating that different strains of S. suis are associated with infection in pigs. Some pulsotypes were more frequently isolated and exhibited a wider distribution over herds than others, and were the unique or predominant strains in several herds, suggesting the existence of a prevalent or a few prevalent clones responsible for a large proportion of clinical cases. Overall, the great genetic heterogeneity of the clinical strains of S. suis, the isolation of different strains within the same herd, and the predominance of particular strains in some herds are evidence that infection by S. suis is a dynamic process and reinforce the idea that the epidemiology of S. suis infection is very complex.

Animals↗
PubMed1993

Genetic diversity and phylogeny analysis of Azolla based on DNA amplification by arbitrary primers.

The polymerase chain reaction was used to amplify random sequences of DNA from 25 accessions of Azolla to evaluate the usefulness of this technique for identification and phylogenetic analysis of this aquatic fern. Accessions were selected to represent all known species within the genus Azolla and to encompass the world-wide distribution of the fern. Primers of 10 nucleotides with 70% G + C content were used to generate randomly amplified polymorphic DNA from the symbiotic Azolla-Anabaena complex. Twenty-two primers were used and each primer gave 4-10 bands of different molecular weights for each accession. Bands were scored as present or absent for each accession and variation among accessions was quantified using Nei's genetic distances. A dendrogram summarizing phenetic relationships among the 25 accessions was generated using the unweighted pair-group method with arithmetic mean. Principal component analysis was also used to evaluate genetic similarities. Three distinct groups were identified: group 1 contains five species, group 2 contains the pinnata species, and group 3 contains the nilotica species. The analysis demonstrates that the major groups of Azolla species can be easily distinguished from one an other and, in addition, that closely related accessions within species can be identified. We further found that using 10 primers, a phylogeny that is essentially the same as that derived from 22 primers can be constructed. Our results suggest that total DNA extracted from the Azolla-Anabaena symbionts is useful for classification and phylogenetic studies of Azolla.

Base Sequence↗
PubMed1995

Analysis of genetic diversity in a sweetpotato (Ipomoea batatas) germplasm collection using DNA amplification fingerprinting.

A DNA amplification fingerprinting (DAF) approach was employed to develop individual-specific profiles and analyze genetic relationships among 73 plant introductions of sweetpotato (Ipomoea batatas (L.) Lam.) including unadapted lines from around the world and a few selected U.S.A. cultivars. Reliable and informative fingerprint profiles were obtained employing single octamer primers and Stoffel fragment Taq polymerase in the polymerase chain reaction, polyacrylamide-based vinyl polymer for electrophoresis, and silver staining to visualize the DNA. Using seven highly informative octamer primers, individual-specific DAF profiles were obtained for all accessions tested. The degree of polymorphism in the sweetpotato collection was very large, indicating a high level of genetic variability. Several accessions clustered together based on their geographic source. Most U.S.A. cultivars formed a separate cluster in the phenogram, while accessions from Papua New Guinea exhibited the highest genetic diversity. The wild species I. triloba and tetraploid I. batatas formed a group distinct from the cultivated sweetpotato. DAF appears to be useful in sweetpotato germplasm characterization and may be employed to identify duplicate accessions or for creation of core subsets. DAF data may also be useful for facilitating the selection of parents for a breeding program to ensure a broad genetic base.

Base Sequence↗
PubMed1999

Sentinel lymph node mapping for breast cancer: analysis in a diverse patient group.

PURPOSE: To evaluate sentinel lymph node mapping in patients with breast cancer. MATERIALS AND METHODS: Sixty-two patients with breast cancer scheduled to undergo axillary nodal dissection underwent scintigraphic localization of sentinel lymph nodes with filtered technetium 99m sulfur colloid. At surgery, isosulfan blue was injected. Sentinel nodes were identifiable by blue color and by radioactivity with hand-held gamma probe. Results were analyzed statistically. RESULTS: A sentinel lymph node was identified in 49 patients (79%). Lymph nodes were positive for metastatic disease in 26 patients (42%). The mapping success rate was 78% (n = 21) in the 27 patients with no prior surgery, 78% (n = 18) in the 23 patients with prior surgery, and 86% (n = 12) in the 14 patients with prior chemotherapy. Axillary nodes were positive in 11 (41%) of the 27 patients with no prior intervention, six (26%) of the 23 patients with prior surgery, and 10 (71%) of the 14 patients with prior chemotherapy. There were no false-negative findings in patients without prior intervention. Four patients with positive nodes had false-negative sentinel nodes. CONCLUSION: Sentinel lymph node mapping and biopsy without axillary dissection is appropriate in patients with breast cancer who have not undergone prior intervention. Further study is necessary to ascertain the accuracy of the procedure for patients who have undergone presurgical chemotherapy or previous excisional biopsy.

Adult↗
PubMed2024

Temporal analysis of genetic diversity and gene flow in the threatened catfish Pseudoplatystoma magdaleniatum from a dammed neotropical river.

The striped catfish Pseudoplatystoma magdaleniatum is a large-sized migratory species from the north Andes region, endemic to Magdalena basin and one of the major fishery resources. Despite the estimated reduction of over 80% of the fisheries production of this species throughout the basin in recent decades, its population in the lower Magdalena-Cauca basin showed healthy genetics after molecular analyses. However, the current conservation status of this species and several habitat disturbances demand the re-evaluation of its population genetics to infer evolutionary risks and assess potential changes. This work analyzed a total of 164 samples from the Cauca River collected downstream the Ituango Dam between 2019-2021 using species-specific microsatellite markers to compare the genetic diversity and structure in samples collected between 2010-2014 from the lower Magdalena-Cauca basin, previously analyzed. Our results showed a relatively stable panmictic population over time (4 to 10 years), with high genetic diversity and evidence of recent bottleneck. Promoting habitat connectivity to conserve gene flow, characterizing diversity and genetic structure over the entire basin, and integrating the results with future monitoring are important aspects for the management planning for P. magdaleniatum in the Magdalena-Cauca basin.

Animals↗
PubMed2005

An analysis of genetic diversity across the maize genome using microsatellites.

How domestication bottlenecks and artificial selection shaped the amount and distribution of genetic variation in the genomes of modern crops is poorly understood. We analyzed diversity at 462 simple sequence repeats (SSRs) or microsatellites spread throughout the maize genome and compared the diversity observed at these SSRs in maize to that observed in its wild progenitor, teosinte. The results reveal a modest genome-wide deficit of diversity in maize relative to teosinte. The relative deficit of diversity is less for SSRs with dinucleotide repeat motifs than for SSRs with repeat motifs of more than two nucleotides, suggesting that the former with their higher mutation rate have partially recovered from the domestication bottleneck. We analyzed the relationship between SSR diversity and proximity to QTL for domestication traits and observed no relationship between these factors. However, we did observe a weak, although significant, spatial correlation for diversity statistics among SSRs within 2 cM of one another, suggesting that SSR diversity is weakly patterned across the genome. Twenty-four of 462 SSRs (5%) show some evidence of positive selection in maize under multiple tests. Overall, the pattern of genetic diversity at maize SSRs can be explained largely by a bottleneck effect with a smaller effect from selection.

DNA, Plant↗
PubMed2000

Analysis of the diversity of a sheep antibody repertoire as revealed from a bacteriophage display library.

We have applied bacteriophage display technology to construct and analyze the diversity of an IgG library of >1 x 108 clones from an adult sheep immunized against the hapten atrazine. We have identified eight new VH gene families (VH2-VH9) and five new Vkappa gene families (VkappaV-VkappaIX). The heavy and kappa light chain variable region gene loci were found to be far more diverse than previously thought.

Animals↗
PubMed1999

[RAPD analysis of genetic diversity and phylogenetic relationship of the Taihu pigs].

The genetic diversity and phylogenetic relationship of the Taihu pigs were studied using RAPD technique. A total of 57 individuals were used, and the phylogenetic tree was reconstructed using UPGMA method based on 198 RAPD markers which were amplified with 13 decamer primers. The results indicate as the following: (1) The similarity indexes within each strain and between the strains of the Taihu pigs are all high. The average genetic distance between the strains is 0.052. These results indicate that the Taihu pigs exhibit relatively low level of genetic variation and poor genetic diversity; (2) The Hongdenglong pig is also a strain of the Taihu pigs; (3) The Taihu pigs have close phylogenetic relationship with the Chinese wild boar occurred in the Taihu Lake area; (4) Two lineages diverged in the early stage during the course of the formation of the Taihu pigs. One of the lineage gave rise to the strains of Mizhu, Erhualian, Jiaxinhei and Hongdenglong, another lineage gave rise to the strains of Shawutou, Meishan, Fengjing and Hengjing. The strategy for genetic diversity conservation of the Taihu pigs was discussed.

Animals↗
PubMed2001

[Analysis of natural diversity of symbiotic relationships in the Paramecium bursaria--Holospora curviuscula system].

Bacteria of the genus Holospora belong to obligatory endonucleobionts of ciliates of the genus Paramecium. The bacteria show specificity towards the particular host species and the types of nuclei they infect: macro- or micronuclei. During a long-term screening of P. bursaria clones, belonging to three different syngens, Holospora inhibited cells of two syngens only. Using the number of host clones and symbiont isolates, it was shown that H. curviuscula was unable to pass successfully through the syngen barrier even under experimental infection. Considering the species level of specificity in Holospora associations of P. caudatum we suggest the existence of a greater evolutionary divergence in P. bursaria syngens than in syngens of P. caudatum. We have revealed that in incompatible combinations "host clone--symbionts isolate" the complicated bacterial life cycle may be blocked at definite stages depending on genetic features of both partners. Thus, the recognition of the full block spectrum could break the continuous infection process down to independently controlled steps. The block spectrum revealed in the system of P. bursaria--H. curviuscula demonstrates its significant similarity to block spectra of other systems within the Holospora--Paramecium complex. A block of transverse binding formation has been first revealed in Holospora dividing in the nucleus.

Animals↗
PubMed2002

[RAPD-PCR analysis of genetic diversity in the Manchurian pheasant].

The genetic diversity of a local population of the Manchurian pheasant Phasianus colchicus pallasi was studied using RAPD-PCR. Based on the DNA patterns obtained in PCR with five arbitrary decanucleotide primers, we assessed genetic polymorphism of this population, estimated genetic distances between individuals, and constructed an NJ phylogenetic tree, and an UPGMA dendrogram of genetic similarity. The population was shown to exhibit high average genetic polymorphism (P = 79.4%) and genetic distances (D = 0.267). Possible reasons for the high genetic diversity of this local population are discussed.

Animals↗
PubMed2002

[Comparative analysis on species diversity of hillclosed afforested plant community in Beijing Jiulong Mountain].

The plant communities in Beijing Jiulong Mountain were surveyed with the Quadrate. The species diversity characteristics of the tree layer and the shrub layer and herb layer of these plant communities were measured by applying Shannon-Wiener diversity index(D), evenness index(J) and ecological dominance(C), and the comparison of the characteristics was conducted on shade slope and sun-faced slope. The results showed that these indices could effectively reveal the characteristics of species composition for plant communities in warm temperate zone. On shade slope or sun-faced slope, the D value of shrub layer in Jiulong shrub communities (SC) was higher than that of tree layer in arbor forest (AF), but lower than that of shrub layer in AF; the D value of herb layer in SC was lower than that of herb layer in AF; and the D value of herb layer was higher than that of shrub layer in AF, which was higher than that of tree layer in AF. C value presented quite the opposite with D value, and J presented the different feature in the comparison, respectively on shade slope and sun-faced slope. In addition, the succession series and the restoration measures on accelerating the progressive succession of the hillclosed afforested vegetation communities were tentatively discussed.

China↗
PubMed1992

Analysis of four diverse population groups indicates that a subset of cystic fibrosis mutations occur in common among Caucasians.

To determine the nature and frequency of non-delta F508 cystic fibrosis (CF) mutations among diverse populations, we have sequenced exons 9-12 and 19-23 of the CF transmembrane conductance regulator (CFTR) gene from 128 CF chromosomes (39 U.S. Caucasian, 27 African-American, 42 Northern Irish, and 20 Israeli chromosomes). These regions were chosen because they encode the two putative ATP-binding folds of CFTR, domains which appear to have functional significance. In addition, CFTR exons 1 and 2 were analyzed in the American patients. Mutations were found on 49 of the 128 CF chromosomes. Nineteen different mutations were observed; six were novel, while the remaining 13 had been reported previously by our group or by other investigators. Six of nine different mutations found in African-American patients were unique to that population. However, the vast majority of the mutations found in U.S. Caucasians (eight of nine), Northern Irish (four of five), and Israelis (three of three) also occurred in other Caucasian groups. The preponderance of previously reported mutations in these three groups suggested that a subset of the non-delta F508 mutations occur in common among Caucasians. A survey of mutation frequencies in other Caucasian groups confirmed this observation. Unfortunately, this subset accounts for less than half of non-delta F508 CF mutations in most groups. These data suggest that screening for delta F508 and this select group of mutations will efficiently and economically maximize the number of CF mutations identified in Caucasian groups. However, it will be difficult to detect more than 90% of mutant CFTR alleles except in ethnically and geographically discrete populations where CF is the result of founder effect.

Amino Acid Sequence↗
PubMed2005

[Comparative analysis of genetic diversity revealed by genomic-sSR, EST-SSR and pedigree in wheat (Triticum asetivum L.)].

Two SSR molecular markers, genomic-SSR and EST (expressed sequence tagged)-SSR, were used to measure the genetic diversity among 18 accessions of common wheat with known pedigrees, which were collected from winter wheat production region in Northern China. In addtion, the genetic diversity revealed by pedigree, EST-SSR and genomic-SSR was also compared. The results showed that the average number of alleles per genomic-SSR locus is 3.34, which is higher than that of EST-SSR (2.31), indicating that genomic-SSR is more polymorphic than EST-SSR. Genomic-SSR and EST-SSR were used to calculate the genetic distance (GD) in different materials. The mean GD value of EST-SSR for the 18 wheat genotypes is 0.3996,which is lower than that of genomic-SSR (0.5458). At the locus level, the mean GD calculated using pedigree information is higher (0. 9716) than that of genomic-SSR and EST-SSR markers (0.5458 and 0.3996). Therefore, although polymorphism of EST-SSR is low as compared to genomic SSR,it provides a more accurate evaluation of genetic relationship, especially when accessions are very closely related in pedigree. The strategy for improving the genetic diversity of wheat was also discussed.

Alleles↗