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PubMed2006

[Phylogenetic analysis of bacterial diversity in Pacific Arctic sediments].

Using PCR-DGGE (denaturing gradient gel electrophoresis) methods, bacterial phylogenetic diversity in three Pacific Arctic sediment samples were investigated, taken from different depths in the range of 47 m to 3850 m. DGGE profiles of different layers in the same sediment sample are not completely same. 16S rDNA sequences corresponding to 50 excised bands from three sediment samples were analyzed and fell into seven lineages of the domain Bacteria: alpha- beta-, gamma-, delta-, epsilon- Proteobacteria, the Cytophaga-Flavobacterium-Bacteroides (CFB) group and Actinobacteria. However, the composition of bacterial phylotypes in three sediments is different. Fourteen sequences obtained from sediment B78 collected from the Canadian Basin belong to beta-, gamma- Proteobacteria, Comamonadaceae and Acidobacteria. Bacterial phylotypes in submarine plateau sediment P24 are alpha-, gamma-, delta-Proteobacteria; While seventeen sequences from sediment S11 colleted from continental slop in the Chukchi Sea are grouped into alpha-, gamma-, delta-, epsilon-Proteobacteria, the Cytophaga-Flavobacterium-Bacteroides (CFB) group and Actinobacteria. It is suggested the different characteristics of three sediments may cause the difference in the composition of bacterial phylotypes. 16S rDNA sequences from members of gamma-Proteobacteria dominated three sediments samples. The majority of the sequences were most closely related to uncultured marine environmental sequences, especially marine sediment environmental sequences (88% - 100%).

Arctic Regions↗
PubMed2006

[Microsatellite analysis of genetic diversity of Aristichthys nobilis in China].

Seventeen microsatellite markers of Aristichthys nobilis previously discovered by our lab were selected to analyze the genetic diversity and characteristics of two populations of Aristichthys nobilis from Jiangxi and Sichuan provinces. The following parameters were calculated: heterozygosity, polymorphism information content (PIC), valid allele number, allele frequency, genetic distance, genetic similarity coefficient, Hardy-Weinberg balance deflection index and so on. Results show that there are 4 monomorphic and 13 polymorphic markers among the 17 selected microsatellite markers. The average of allele number in each microsatellite locus of the Jiangxi population and Sichuan populations is 3.325 and 3.882, respectively; the average valid allele number is 3.531 and 2.676, respectively; and the number of total alleles of these 17 microsatellite loci is 71. The PIC of polymorphic loci varies between 0.077-0.960, and the average PIC is 0.417. The average observed heterozygosity (Ho) of two populations is 0.385 and 0.360, respectively and the average expected heterzygosity (He) is 0.452 and 0.422, respectively. The genetic similarity coefficient of two populations of Aristichthys nobilis is 0.897 and the genetic distance of these populations is 0.109.

Alleles↗
PubMed2006

[Theoretical analysis of ecological diversity models and their application in Fukang of Xinjiang Uygur Autonomous Region].

Ecological diversity refers to a combination of the richness and evenness of an investigation object. Based on this, the widely used model, Shannon model, and a recently developed model, Scaling ecological diversity model, were theoretically analyzed in this paper. It was indicated that Shannon model had many limitations, e. g., it could be available only when the number of each type of investigation object was more than 100, did not include any information of scale, and could not express the richness of diversity. In other words, Shannon model could only express the evenness of diversity. A case-study in Fukang of Xinjiang Uygur Autonomous Region showed that the richness and Shannon evenness were always resolution-dependent, while the ecotope diversity calculated by Scaling ecological diversity model was resolution-independent when the spatial resolution ranged from 30 m x 30 m to 150 m x 150 m, and strictly increased when the spatial resolution ranged from 150 m x 150 m to 480 m x 480 m.

Biodiversity↗
PubMed1989

Analysis of junctional diversity in the preferential V delta 1-J delta 1 rearrangement of fresh T-acute lymphoblastic leukemia cells by in vitro gene amplification and direct sequencing.

To define the junctional diversity of T-cell antigen receptor delta gene rearrangements in fresh T-acute lymphoblastic cells and to correlate cell phenotype with the coding potential of rearrangements, we determined the junctional nucleotide sequences of 13 T-cell antigen receptor delta gene rearrangements involving the preferentially rearranged V (V delta 1) and J (J delta 1) segments using in vitro gene amplification and direct sequencing. We showed that, as in gamma delta+ cell lines, extensive junctional diversity exists in these clones and that this diversity is due both to random nucleotide deletions/additions and to the use of at least two D delta segments. We also showed that a high percentage of these rearrangements are potentially translatable (7:13) and that such functional rearrangements occur in both surface CD3+ and CD3- cells. Comparison of alpha beta versus gamma delta surface expression demonstrates that all CD3+ T acute lymphoblastic leukemias with a functional V delta 1-J delta 1 rearrangement express a surface gamma delta receptor and are recognized by the anti-delta monoclonal antibody delta TCS1, whereas a control CD3+ gamma delta+ leukemic case that had not undergone V delta 1 rearrangement was delta TCS1-. In addition, expression of this monoclonal antibody is not restricted by V gamma or C gamma usage or by the covalent or noncovalent link between gamma and delta chains.

Amino Acid Sequence↗
PubMed1977

Analysis of the diversity of murine antibodies to dextran B1355. II. Demonstration of multiple idiotypes with variable expression in several strains.

We have developed radioimmunoassays that detect idiotypic (variable region) differences among the alpha(1 leads to 3) dextran-binding meyloma proteins U102, J558, and M104 as well as an assay that detects variable region determinants common to all three proteins. Using these assays, we have examined 7S and 19S anti-alpha(1 leads to 3) dextran antibodies induced in five murine strains of the a1 IgCH linkage group and the recombinant strain BAB/14. All idiotypes were expressed in both 19S and 7S antibodies from all strains, but with considerable strain-specific variability in penetrance. In two strains, one additional type of antibody, which lacked all four idiotypic determinants, generally constituted the bulk of total anti-alpha(1 leads to 3) dextran antibodies.

Animals↗
PubMed1976

Analysis of the diversity of murine antibodies to dextran B1355. I. Generation of a larger, pauci-clonal response by a bacterial vaccine.

Mice immunized with a combination of dextran B1355 in adjuvant followed by three injections of 2 x 10(9) Escherichia coli B organisms produced an average of 14.5 mg/ml of anti-dextran antibodies. It was demonstrated that the stimulating effect of E. coli B was due to antigenic determinants cross-reactive with B1355 and not solely because of adjuvant properties of the organism. The anti-dextran antibodies were distributed among both 7S and 19S components. Isoelectric focusing of the 7S antibodies showed several spectrotypes of antibody, most of which were shared by the majority of the individual sera. The limited spectrotypic heterogeneity of the 7S antibodies was supported by idiotypic studies. Thus, a heterologous, anti-idiotypic serum, rabbit anti-M104, was prepared which distinguished between two closely related myeloma proteins, M104 and J558,with specificity for alpha-(1 leads to 3) dextran. This antiserum demonstrated that some, but not all, of the 7S and 19S anti-dextran antibodies possessed variable region determinants cross-reactive with M104.

Antibodies↗
PubMed1994

[Analysis of the diversity of tropomyosin isoforms].

Tropomyosins are a family of actin filament binding proteins. Like many structural proteins, tropomyosin isoform expression involves the use of multiple genes, but diversity is to a large extent generated by alternative processing of RNA. The tropomyosin family consists of 15 to 20 different protein isoforms which are coded by four genes. Each of these genes code for multiple proteins ranging from two up to as many as nine different isoforms. These genes have been named alpha CTM, alpha FTM, alpha STM and beta TM after to the striated muscle specific subunit of tropomyosin which they code. Their multiple coding potential is based upon the existence of multiple exons associated with initiation of transcription, multiple exons associated with polyadenylation signals and multiple mutually exclusive internal exons which are alternatively spliced. The regulation of this process of alternative splicing have been extensively studied both in the case of exons 2a/2b of the alpha FTM gene and in the case of exons 6a/6b of the beta TM gene. In both cases, one exon is specifically used in one type of muscle tissue, exon 2a is smooth muscle specific and exon 6b is skeletal muscle specific. In both cases, alternative splicing involves a combination of negative regulation, on exon 2b in smooth muscle and on exon 6b in non muscle tissues, and of competition in the alternative situation.

Animals↗
PubMed1998

Analysis of genetic diversity in the VP1 unique region gene of human parvovirus B19 using the mismatch detection method and direct nucleotide sequencing.

To assess the prevalent genetic types of human parvovirus B19 strains derived from various sources and their relation to particular clinical symptoms, the genetic diversity in the VP1 unique region, which is important for the neutralizing response to human parvovirus B19, was examined by the mismatch detection method using the Non-isotopic RNase Cleavage Assay (NIRCA) and direct nucleotide sequencing. Twenty three samples obtained between 1986 and 1997 were examined. Three electrophoresis patterns were observed with NIRCA. The nucleotide sequence showed that there were 14 nucleotide changes and 4 amino acid substitutions in comparison with Au strains employed as a standard strain. The nucleotide variability of all samples ranged from 0.3 to 2.7% and the amino acid variability ranged from 1.0 to 3.0%. They were classified into three types according to NIRCA. Types 1 and 3 had similar sequences, but the type 2 sequence was quite different. Although there were some nucleotide variations in the same NIRCA type, these were silent. However, there was no relationship between the clinical features and NIRCA types or between clinical features and the nucleotide sequence. All samples obtained before 1987 were NIRCA type 2. On the other hand, 19 of 20 samples obtained after 1989 were NIRCA type 1. The other sample obtained in 1992 was type 3. The results suggest that the B19 strain of type 2 disappeared by 1988 and changed to other B19 strains such as type 1 and type 3 after 1988, indicating a correlation between genome type and prevalence. NIRCA is a convenient method for screening mutations due to its simplicity and quickness.

Adolescent↗
PubMed2026

Genome-wide SNP-based genomic diversity and population structure analysis in alpaca populations from Europe and Peru.

This study aimed to analyze the genetic diversity and population structure of alpacas in Germany, Switzerland, and Austria (German-speaking regions, GSR) and to compare with that of the country of origin of the species (Peru). A total of 179 animals from GSR and 151 from Peru were genotyped with a species-specific 76k SNP array. The observed and expected heterozygosity was 0.305 and 0.311 for GSR and 0.310 and 0.312 for Peru. The mean FROH values were 0.029 for GSR and 0.023 for Peru. In general, results show that breeders in both analyzed regions efficiently maintain genetic diversity. Principal component analysis identified the GSR and Peru populations as separate from each other, but the relative proximity of both clusters indicates the shared genetic heritage. FST and XPEHH methods identified genomic regions under selection for traits such as coat color and adaptation. Genome-wide association studies comparing black and brown with white or gray alpacas identified associated genome regions containing the ASIP and KIT genes, respectively. The association of a recently identified keratin locus on chromosome 16 with differences in fleece type in alpacas was confirmed, while the putative causality of a TRPV3 variant was rejected.

Animals↗
PubMed1999

Methanotroph diversity in landfill soil: isolation of novel type I and type II methanotrophs whose presence was suggested by culture-independent 16S ribosomal DNA analysis.

The diversity of the methanotrophic community in mildly acidic landfill cover soil was assessed by three methods: two culture-independent molecular approaches and a traditional culture-based approach. For the first of the molecular studies, two primer pairs specific for the 16S rRNA gene of validly published type I (including the former type X) and type II methanotrophs were identified and tested. These primers were used to amplify directly extracted soil DNA, and the products were used to construct type I and type II clone libraries. The second molecular approach, based on denaturing gradient gel electrophoresis (DGGE), provided profiles of the methanotrophic community members as distinguished by sequence differences in variable region 3 of the 16S ribosomal DNA. For the culturing studies, an extinction-dilution technique was employed to isolate slow-growing but numerically dominant strains. The key variables of the series of enrichment conditions were initial pH (4. 8 versus 6.8), air/CH(4)/CO(2) headspace ratio (50:45:5 versus 90:9:1), and concentration of the medium (1x nitrate minimal salts [NMS] versus 0.2x NMS). Screening of the isolates showed that the nutrient-rich 1x NMS selected for type I methanotrophs, while the nutrient-poor 0.2x NMS tended to enrich for type II methanotrophs. Partial sequencing of the 16S rRNA gene from selected clones and isolates revealed some of the same novel sequence types. Phylogenetic analysis of the type I clone library suggested the presence of a new phylotype related to the Methylobacter-Methylomicrobium group, and this was confirmed by isolating two members of this cluster. The type II clone library also suggested the existence of a novel group of related species distinct from the validly published Methylosinus and Methylocystis genera, and two members of this cluster were also successfully cultured. Partial sequencing of the pmoA gene, which codes for the 27-kDa polypeptide of the particulate methane monooxygenase, reaffirmed the phylogenetic placement of the four isolates. Finally, not all of the bands separated by DGGE could be accounted for by the clones and isolates. This polyphasic assessment of community structure demonstrates that much diversity among the obligate methane oxidizers has yet to be formally described.

Base Sequence↗
PubMed2006

Analysis of retrotransposon structural diversity uncovers properties and propensities in angiosperm genome evolution.

Analysis of LTR retrotransposon structures in five diploid angiosperm genomes uncovered very different relative levels of different types of genomic diversity. All species exhibited recent LTR retrotransposon mobility and also high rates of DNA removal by unequal homologous recombination and illegitimate recombination. The larger plant genomes contained many LTR retrotransposon families with >10,000 copies per haploid genome, whereas the smaller genomes contained few or no LTR retrotransposon families with >1,000 copies, suggesting that this differential potential for retroelement amplification is a primary factor in angiosperm genome size variation. The average ratios of transition to transversion mutations (Ts/Tv) in diverging LTRs were >1.5 for each species studied, suggesting that these elements are mostly 5-methylated at cytosines in an epigenetically silenced state. However, the diploid wheat Triticum monococcum and barley have unusually low Ts/Tv values (respectively, 1.9 and 1.6) compared with maize (3.9), medicago (3.6), and lotus (2.5), suggesting that this silencing is less complete in the two Triticeae. Such characteristics as the ratios of point mutations to indels (insertions and deletions) and the relative efficiencies of DNA removal by unequal homologous recombination compared with illegitimate recombination were highly variable between species. These latter variations did not correlate with genome size or phylogenetic relatedness, indicating that they frequently change during the evolutionary descent of plant lineages. In sum, the results indicate that the different sizes, contents, and structures of angiosperm genomes are outcomes of the same suite of mechanistic processes, but acting with different relative efficiencies in different plant lineages.

Animals↗
PubMed2006

Multilocus microsatellite analysis reveals extensive genetic diversity in Neospora caninum.

Neospora caninum is a world-wide parasite that causes neuromuscular disorders in dogs and bovine abortion. Biological diversity among isolates has been proved in both in vivo and in vitro studies. In contrast, little is known about the genetic diversity of this parasite. Microsatellite sequence analysis constitutes a suitable tool that has been used for the genetic analysis of other apicomplexan parasites. In this report, we describe the identification and analysis of 13 microsatellite loci from N. caninum DNA sequences deposited in public databases, which were evaluated with the use of 9 isolates grown in vitro. One microsatellite was monomorphic, and the remaining 12 loci exhibited 3 to 9 separate alleles. Multilocus analysis showed that each of the 9 isolates investigated here displayed a unique profile and revealed no association between the genetic similarity and host or geographic origin. The multilocus analysis approach described here might nevertheless provide the powerful tool needed to study the genetic complexity of N. caninum and the molecular epidemiology of neosporosis.

Animals↗
PubMed2004

Approach to decreasing emergency department ambulance diversion hours.

Analysis between two local Emergency Departments (EDs) suggested an oscillatory phenomenon for ambulance diversion: When one hospital went on diversion it led to a disproportionate flow of ambulance traffic to a neighboring facility that subsequently was forced to go on divert. We hypothesized if one hospital could avoid diversion status, the need for diversion could be averted in the neighboring facility. ED A secured additional resources and made a commitment to no diversion for 1 week. No changes in operations occurred in hospital B. We found no differences in ambulance runs or ED census at either facility comparing the week before, during, and after the trial. There was a dramatic decline in diversion hours from 19.7 to 1.4 and 27.7 to 0 at hospitals A and B, respectively, during the trial period (p < 0.05) compared to the weeks before and after. We conclude that reciprocating effects can be decreased with one institution's commitment to avoid diversion, thus decreasing the need for diversion at a neighboring facility.

Ambulances↗
PubMed1991

[Leishmania tropica in Morocco. IV--Intrafocal enzyme diversity].

Ecoepidemiological analysis of a Moroccan focus of leishmaniasis caused by Leishmania tropica revealed considerable enzymatic diversity. Seven zymodemes belonging to the complex were identified in 149 strains isolated from humans, dogs, and the vector Phlebotomus sergenti. Three distinct subgroups were identifiable, two of which were in turn, composed of three "small variant" zymodemes. The diversity appears to be related to the age of the focus, which may have allowed colonization by zymodemes of different geographic origins. Diversification into "small variants" is apparently the result of recent mutation, possibly associated with genetic exchange.

Animals↗
PubMed1995

Babesia canis: evidence for genetic diversity among isolates revealed by restriction fragment length polymorphism analysis.

The genetic diversity of B. canis was investigated by restriction fragment length polymorphism analysis. For this purpose, we identified a Babesia canis specific DNA probe named pS8. This 1.2 kbp probe can detect as low as 20 pg of B. canis DNA. Results suggest that the pS8 probe is distributed in multiple copies throughout the genome though is probably not itself internally repetitious, i.e. not structured into blocks of tandem units. This probe reveals discrete hybridizing fragments in B. canis enzyme-digested genomic DNA. RFLP patterns obtained with the pS8 probe revealed a large genetic diversity between various isolates and led us to distinguish several clones derived from a single isolate. Results suggest that for a single isolate, the fingerprints obtained reflect those of a few quantitatively dominant clones. This technique can now be routinely applied and provides a convenient tool for the characterization and the identification of B. canis isolates, strains and clones.

Animals↗