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PubMed1976

A mathematical approach to the analysis of diversity in antibody gene families.

In this article, we develop a mathematical approach for the analysis of diversity in antibody gene families. This approach is arrived at by examing two general questions about protein populations: (1) What is a relative measure of the diversity exhibited by one protein family when compared with a second? (2) What is the probability that two protein populations were derived from a single common population? These quantitative approaches permit a variety of precise evolutionary, genetic, and developmental questions to be asked of antibody gene families. Using this methodology, we demonstrate that the diversity in mouse K-immunoglobulin chains is considerably greater than in their human K counterparts. We also show that the variable (Vl) regions of light chains associated with IgG and IgA immunoglobulins in the mouse appear to have been derived from a common population of Vl genes. This approach also can be used to analyse sequence data from other informational multigene families.

Amino Acid Sequence↗
PubMed2003

Splice site prediction with quadratic discriminant analysis using diversity measure.

Based on the conservation of nucleotides at splicing sites and the features of base composition and base correlation around these sites we use the method of increment of diversity combined with quadratic discriminant analysis (IDQD) to study the dependence structure of splicing sites and predict the exons/introns and their boundaries for four model genomes: Caenorhabditis elegans, Arabidopsis thaliana, Drosophila melanogaster and human. The comparison of compositional features between two sequences and the comparison of base dependencies at adjacent or non-adjacent positions of two sequences can be integrated automatically in the increment of diversity (ID). Eight feature variables around a potential splice site are defined in terms of ID. They are integrated in a single formal framework given by IDQD. In our calculations 7 (8) base region around the donor (acceptor) sites have been considered in studying the conservation of nucleotides and sequences of 48 bp on either side of splice sites have been used in studying the compositional and base-correlating features. The windows are enlarged to 16 (donor), 29 (acceptor) and 80 bp (either side) to improve the prediction for human splice sites. The prediction capability of the present method is comparable with the leading splice site detector--GeneSplicer.

Algorithms↗
PubMed2004

Performance of the Celera Diagnostics ViroSeq HIV-1 Genotyping System for sequence-based analysis of diverse human immunodeficiency virus type 1 strains.

The Celera Diagnostics ViroSeq HIV-1 Genotyping System is a Food and Drug Administration-cleared, integrated system for sequence-based analysis of drug resistance mutations in subtype B human immunodeficiency virus type 1 (HIV-1) protease and reverse transcriptase (RT). We evaluated the performance of this system for the analysis of diverse HIV-1 strains. Plasma samples were obtained from 126 individuals from Uganda, Cameroon, South Africa, Argentina, Brazil, and Thailand with viral loads ranging from 2.92 to >6.0 log(10) copies/ml. HIV-1 genotyping was performed with the ViroSeq system. HIV-1 subtyping was performed by using phylogenetic methods. PCR products suitable for sequencing were obtained for 125 (99%) of the 126 samples. Genotypes including protease (amino acids 1 to 99) and RT (amino acids 1 to 321) were obtained for 124 (98%) of the samples. Full bidirectional sequence data were obtained for 95 of those samples. The sequences were categorized into the following subtypes: A1/A2 (16 samples), B (12 samples), C (13 samples), D (11 samples), CRF01_AE (9 samples), F/F2 (9 samples), G (7 samples), CRF02_AG (32 samples), H (1 sample), and intersubtype recombinant (14 samples). The performances of the individual sequencing primers were examined. Genotyping of duplicate samples in a second laboratory was successful for 124 of the 126 samples. The identity level for the sequence data from two laboratories ranged from 98 to 100% (median, 99.8%). The ViroSeq system performs well for the analysis of plasma samples with diverse non-B subtypes. The availability of this genotyping system should facilitate studies of HIV-1 drug resistance in non-subtype B strains of HIV-1.

Base Sequence↗
PubMed1992

Phylogeny of the genera Trichophyton using mitochondrial DNA analysis.

Diversity of mitochondrial DNA (mtDNA) was investigated in 92 Trichophyton rubrum strains, 2 T. mentagrophytes var. mentagrophytes, 2 T. m. var. interdigitale, 2 T. m. var. goetzii, 1 T. m. var. erinacei, 2 T. quinckeanum, 2 T. schoenleinii, 1 T. tonsurans, 2 T. verrucosum var. album, 2 T. v. var. discoides, 1 T. violaceum var. violaceum, 1 Arthroderma benhamiae, and 1 A. vanbreuseghemii using endonucleases, Hae III, Msp I, Hind III, Xba I, and Bgl II. Trichophyton species were divided into 7 groups, and a phylogenetic tree was produced based on sequence divergence within mtDNA. The following results were obtained: (1) T. rubrum was divided into 2 groups Type I and Type II, and was suggested to be a complex. (2) A. benhamiae was closely related to T. m. var. erinacei. (3) T. rubrum Type II, T. tonsurans, and A. vanbreuseghemii showed identical restriction profiles, and were suggested to be closely related to each other or identical. (4) T. quinckeanum and T. schoenlenii showed identical restriction profiles, which differed slightly from those of A. vanbreuseghemii. (5) mtDNA analysis was useful in identifying pleomorphic strains.

DNA, Fungal↗
PubMed1998

Comparative DNA analysis across diverse genomes.

We review concepts and methods for comparative analysis of complete genomes including assessments of genomic compositional contrasts based on dinucleotide and tetranucleotide relative abundance values, identifications of rare and frequent oligonucleotides, evaluations and interpretations of codon biases in several large prokaryotic genomes, and characterizations of compositional asymmetry between the two DNA strands in certain bacterial genomes. The discussion also covers means for identifying alien (e.g. laterally transferred) genes and detecting potential specialization islands in bacterial genomes.

Animals↗
PubMed2004

Quantitative analysis of diverse Lactobacillus species present in advanced dental caries.

Our previous analysis of 65 advanced dental caries lesions by traditional culture techniques indicated that lactobacilli were numerous in the advancing front of the progressive lesion. Production of organic acids by lactobacilli is considered to be important in causing decalcification of the dentinal matrix. The present study was undertaken to define more precisely the diversity of lactobacilli found in this environment and to quantify the major species and phylotypes relative to total load of lactobacilli by real-time PCR. Pooled DNA was amplified by PCR with Lactobacillus genus-specific primers for subsequent cloning, sequencing, and phylogenetic analysis. Based on 16S ribosomal DNA sequence comparisons, 18 different phylotypes of lactobacilli were detected, including strong representation of both novel and gastrointestinal phylotypes. Specific PCR primers were designed for nine prominent species, including Lactobacillus gasseri, L. ultunensis, L. salivarius, L. rhamnosus, L. casei, L. crispatus, L. delbrueckii, L. fermentum, and L. gallinarum. More than three different species were identified as being present in most of the dentine samples, confirming the widespread distribution and numerical importance of various Lactobacillus spp. in carious dentine. Quantification by real-time PCR revealed various proportions of the nine species colonizing carious dentine, with higher mean loads of L. gasseri and L. ultunensis than of the other prevalent species. The findings provide a basis for further characterization of the pathogenicity of Lactobacillus spp. in the context of extension of the carious lesion.

Colony Count, Microbial↗
PubMed2026

SimpleMicrobiome: An integrated web-based platform for streamlined microbiome data analysis and visualization.

Microbiome studies require multiple analytical steps after initial sequence processing. These steps commonly include data harmonization, preprocessing, taxonomic profiling, diversity analysis, differential abundance testing, predictive modeling, network inference, and preparation of publication-ready outputs. Although robust packages are available for many of these tasks, routine use often depends on command-line workflows, repeated data reformatting, and method-specific scripting. These requirements can limit accessibility for experimental researchers and complicate consistent analysis across interdisciplinary teams. We developed SimpleMicrobiome, a web-based R Shiny platform that integrates established microbiome analysis methods into a single interactive downstream workflow. The application accepts standard abundance, taxonomy, and metadata tables, supports interactive preprocessing and sample filtering, and provides modules for taxa profile visualization, alpha and beta diversity analysis, ANCOM-BC2 and MaAsLin2 differential abundance testing, Random Forest modeling with SHAP-based interpretation, microbial association network inference using SparCC and SPIEC-EASI through NetCoMi, correlation heatmaps, and dbRDA/CAP-style association biplots. The platform is implemented as a modular Shiny application so that preprocessing choices are propagated across downstream analyses, results can be exported as figures and tables, and the same application can be run through the public server, source-code installation, or a Docker image. SimpleMicrobiome consolidates major downstream microbiome analysis tasks in an accessible browser-based environment while retaining links to established analytical frameworks. The platform may reduce technical barriers for non-programming users, improve consistency across exploratory and reporting-oriented analyses, and support collaborative microbiome research. The public application is available at https://simplemicrobiome.mglab.org, the source code is available at https://github.com/yjcho2252/SimpleMicrobiome, and a Docker image for local deployment is available at https://hub.docker.com/r/mglab2252/simplemicrobiome.

differential abundance↗
PubMed1997

Mucosal inflammation in pediatric diversion colitis: a quantitative analysis.

BACKGROUND: Diversion colitis commonly occurs in bypassed segments of colorectum, and has been described qualitatively in Hirschsprung's disease patients with colostomies. The objective of this study was to characterize quantitatively the changes in the inflammatory cell population in the mucosa of children with diversion colitis. METHODS: Paraffin blocks of well-oriented, full-thickness colorectal tissues were obtained from 15 children with diversion colitis (all with Hirschsprung's disease), four pediatric controls and four adult controls. Sections were immunostained for B and T lymphocytes, macrophages, IgG, IgM, and IgA. Measurements were made referent to a standard length of muscularis mucosae. Lymphoid follicles were counted and the areas occupied by B and T cells were determined by image analysis. Cells in the interfollicular lamina propria were counted separately, but IgA-containing plasma cells were too abundant to enumerate. RESULTS: Pediatric diversion colitis was characterized by enlarged and more numerous lymphoid follicles with approximately four times as many B lymphocytes and twice as many T lymphocytes in the follicular compartment of the mucosa when compared to pediatric controls. The interfollicular mucosa was thickened (499 +/- 27 versus 380 +/- 56 microns) and contained approximately six times as many B cells and eight times as many T cells as controls. Macrophages and plasma cells containing IgG and IgM were not significantly increased. CONCLUSIONS: These findings extend the qualitative observations of increased follicular and lamina propria lymphoid tissue in bypassed segments of colon, and are consistent with the hypothesis of persistent antigenic stimulation of the mucosa-associated lymphoid tissue.

Adult↗
PubMed2006

Dispersal and species diversity: a meta-analysis.

Species diversity in communities of interacting organisms is thought to be enhanced by dispersal, yet mechanisms predicting this have little to say about what effects differing rates of dispersal have on diversity and how dispersal affects diversity at larger spatial scales. I performed meta‐analyses on 23 studies comprising 50 experiments that manipulated species migration and measured community richness or diversity to test three hypotheses: that dispersal increases local diversity; that this effect depends on the rate of dispersal, specifically, that local diversity should be maximized at intermediate dispersal rates or else linearly related to dispersal rate; and that regional diversity may be either unaffected or negatively impacted by dispersal because dispersal tends to homogenize local communities. I found that immigration increased local diversity. Further, in animal studies, diversity appears maximized at intermediate dispersal rates but not with plant studies; however, more standardized studies are needed. Finally, results are ambiguous as to what happens at larger scales, with studies finding either declines or no change in regional diversity with dispersal. Taken together, these results reveal that dispersal has a complex, spatially contingent relationship with patterns of species diversity.

Animal Distribution↗
PubMed2003

Analysis of genetic diversity in red clover (Trifolium pratense L.) breeding populations as revealed by RAPD genetic markers.

Red clover is an important forage legume species for temperate regions and very little is known about the genetic organization of its breeding populations. We used random amplified polymorphic DNA (RAPD) genetic markers to address the genetic diversity and the distribution of variation in 20 breeding populations and cultivars from Chile, Argentina, Uruguay, and Switzerland. Genetic distances were calculated for all possible pairwise combinations. A high level of polymorphism was found and the proportion of polymorphic loci across populations was 74.2%. A population derived from a non-certified seedlot displayed a higher proportion of polymorphic loci than its respective certified seedlot. Gene diversity values and population genetics parameters suggest that the populations analyzed are diverse. An analysis of molecular variance (AMOVA) revealed that the largest proportion of variation (80.4%) resides at the within population level. RAPD markers are a useful tool for red clover breeding programs. A dendrogram based on genetic distances divided the breeding populations analyzed into three distinct groups. The amount and partition of diversity observed can be of value in identifying the populations that parents of synthetic cultivars are derived from and to exploit the variation available in the populations analyzed.

Analysis of Variance↗
PubMed2000

Transient T cell receptor beta-chain variable region-specific expansions of CD4+ and CD8+ T cells during the early phase of pediatric human immunodeficiency virus infection: characterization of expanded cell populations by T cell receptor phenotyping.

T cell receptor (TCR) repertoire perturbations are commonly detected in CD8+ T cells during adult primary human immunodeficiency virus (HIV) infection and have been associated with HIV-specific cytotoxic T cell responses. By use of flow cytometry, transient high-level TCR beta-chain variable region-specific expansions of CD4+ and CD8+ T cells were observed more frequently in HIV-infected children than in children exposed to HIV who remained uninfected. TCR beta-chain diversity analysis and diversity-specific polymerase chain reaction were used to study the clonality of expanded CD4+ and CD8+ subsets. In CD8+ T cells, structural features of the complement-determining regions 3 were altered during the course of the expansion, and persistent TCR clonotypes were observed, consistent with antigen-driven selection. In contrast, TCR beta-chain variable region-specific expansions without clonotypic overrepresentation or persistence were observed in CD4+ T cells, possibly related to HIV-specific helper T cell responses or to the progressive destruction of the CD4+ cell compartment.

CD4-Positive T-Lymphocytes↗
PubMed1980

Genetic structure of Pileolaria pseudomilitaris (Polychaeta: Spirorbidae).

The genetic structure of Pileolaria pseudomilitaris was studied by means of gene-diversity analysis of allozyme frequencies. At an esterase locus, most of the gene diversity was due to subdivision of the population into colonies and subpopulations separated by less than 100 meters. Gene frequencies at a phosphoglucose isomerase locus were similar over many kilometers, but differed between two habitat types. Differences between colonies are attributed to drift and founder effect; similarities over greater distances are attributed to similar selection pressures. A mathematical appendix details the method of gene diversity analysis for a multi-leveled, hierarchically subdivided population.

Animals↗
PubMed2004

Molecular diversity management strategies for building and enhancement of diverse and focused lead discovery compound screening collections.

This publication describes processes for the selection of chemical compounds for the building of a high-throughput screening (HTS) collection for drug discovery, using the currently implemented process in the Discovery Technologies Unit of the Novartis Institute for Biomedical Research, Basel Switzerland as reference. More generally, the currently existing compound acquisition models and practices are discussed. Our informatics, chemistry and biology-driven compound selection consists of two steps: 1) The individual compounds are filtered and grouped into three priority classes on the basis of their individual structural properties. Substructure filters are used to eliminate or penalize compounds based on unwanted structural properties. The similarity of the structures to reference ligands of the main proven druggable target families is computed, and drug-similar compounds are prioritized for the following diversity analysis. 2) The compounds are compared to the archive compounds and a diversity analysis is performed. This is done separately for the prioritized, regular and penalized compounds with increasingly stringent dissimilarity criterion. The process includes collecting vendor catalogues and monitoring the availability of samples together with the selection and purchase decision points. The development of a corporate vendor catalogue database is described. In addition to the selection methods on a per single molecule basis, selection criteria for scaffold and combinatorial chemistry projects in collaboration with compound vendors are discussed.

Computational Biology↗
PubMed1998

Analysis of genetic diversity in Chinese sweetpotato [Ipomoea batatas (L.) Lam.] germplasm using DNA amplification fingerprinting.

The genetic diversity and evolutionary relationships in a representative sample of Chinese sweetpotato collection were assessed using the DNA amplification fingerprinting approach. DNA fingerprint profiles were developed for all 42 accessions tested. There were 19-26 bands for each accession and an average of 20.7 such bands were polymorphic. Chinese sweetpotato germplasm tested exhibited a high degree of genetic diversity. Phenetic analysis revealed five major clusters with the following components: (1) landraces from Guangdong Province, (2) landraces from Fujian province, (3) Chinese cultivars, (4) those closely related to Japanese sweetpotato cultivars, and (5) those closely related to the US sweetpotato cv. Nancy Hall. The genetic association observed between accessions was largely consistent with the known pedigree records. The DNA amplification fingerprinting may provide reliable insights into the domestication history of the sweetpotato crop and may be useful in germplasm enhancement.

Base Sequence↗
PubMed2006

Analysis of diversity and activity of sulfate-reducing bacterial communities in sulfidogenic bioreactors using 16S rRNA and dsrB genes as molecular markers.

Here we describe the diversity and activity of sulfate-reducing bacteria (SRB) in sulfidogenic bioreactors by using the simultaneous analysis of PCR products obtained from DNA and RNA of the 16S rRNA and dissimilatory sulfite reductase (dsrAB) genes. We subsequently analyzed the amplified gene fragments by using denaturing gradient gel electrophoresis (DGGE). We observed fewer bands in the RNA-based DGGE profiles than in the DNA-based profiles, indicating marked differences in the populations present and in those that were metabolically active at the time of sampling. Comparative sequence analyses of the bands obtained from rRNA and dsrB DGGE profiles were congruent, revealing the same SRB populations. Bioreactors that received either ethanol or isopropanol as an energy source showed the presence of SRB affiliated with Desulfobulbus rhabdoformis and/or Desulfovibrio sulfodismutans, as well as SRB related to the acetate-oxidizing Desulfobacca acetoxidans. The reactor that received wastewater containing a diverse mixture of organic compounds showed the presence of nutritionally versatile SRB affiliated with Desulfosarcina variabilis and another acetate-oxidizing SRB, affiliated with Desulfoarculus baarsii. In addition to DGGE analysis, we performed whole-cell hybridization with fluorescently labeled oligonucleotide probes to estimate the relative abundances of the dominant sulfate-reducing bacterial populations. Desulfobacca acetoxidans-like populations were most dominant (50 to 60%) relative to the total SRB communities, followed by Desulfovibrio-like populations (30 to 40%), and Desulfobulbus-like populations (15 to 20%). This study is the first to identify metabolically active SRB in sulfidogenic bioreactors by using the functional gene dsrAB as a molecular marker. The same approach can also be used to infer the ecological role of coexisting SRB in other habitats.

Bacterial Typing Techniques↗
PubMed2000

The high performance liquid chromatography electrospray ionization mass spectrometry analysis of diverse basic pharmaceuticals on cyanopropyl and pentafluorophenylpropyl stationary phases.

Cyanopropyl (CN) and pentafluorophenylpropyl (PFPP) modified silica columns give good retention and good peak shape for the high performance liquid chromatography/electrospray ionization/mass spectrometry (HPLC/ESI/MS) analysis of several classes of basic drugs. These phases enhance the ESI-MS signal by providing good retention of basic drugs with a mobile phase containing 90% acetonitrile. With C18 columns, in order to achieve good retention of basic drugs, only a mobile phase containing less than 40% acetonitrile can be used. Higher concentrations of acetonitrile produce a larger MS signal in the ESI process; the MS signal was a factor of 9 and 12 times greater on the CN and PFPP phases when compared with the C18 phase for the analysis of codeine. The C18 phase required only 4.0-6.0% acetonitrile to obtain the same retention time for codeine. The CN and PFPP stationary phases can be used for the analysis of a range of basic drugs, including many compounds which are poorly retained on the popular C18 and C8 stationary phases. Applications of CN and PFPP columns in the HPLC/ESI/MS of basic drugs include the analysis of antimalarials, such as quinine, bronchodilators, such as salbutamol and tulobuterol, cardioactive drugs, such as procainamide and beta-blockers, tricyclic antidepressants (TCAs), such as protriptyline and trimipramine and alkaloids, such as morphine and codeine. The CN and PFPP phases are also useful for the analysis of bufuralol and its metabolite, hydroxy-bufuralol. All the above analyses were performed using the same mobile phase, 90% acetonitrile; thus the HPLC method development process was expedited. The CN and PFPP phases also gave reproducible retention times and peak shape after more than 8 h of analyses.

Chromatography, High Pressure Liquid↗
PubMed1998

Molecular analysis of diverse elements mediating VanA glycopeptide resistance in enterococci.

Differences were examined among 24 distinct elements mediating VanA-type glycopeptide resistance in enterococci isolated from hospital patients and non-human sources in the UK. The methods used included long-PCR restriction fragment length polymorphism (L-PCR RFLP) analysis and DNA hybridization. All elements had conserved vanRSHAX genes, but variation occurred upstream of vanR and downstream of vanX. Twenty-one VanA elements had significant alterations upstream of vanR in the transposition genes orf1 and orf2: either parts of these genes were absent or they were disrupted by IS1216V or IS3-like insertion sequences. Among VanA elements with alterations downstream of vanX, seven lacked vanY, one lacked both vanY and vanZ, and ten had copies of insertion sequence IS1216V between vanX and vanY. All VanA elements of group D (from geographically and temporally diverse enterococci) were characterized by the presence of an IS1216V/IS3-like/orf1 complex and a point mutation in vanX, both of which were absent from the other 23 groups of VanA elements. This finding is consistent with the dissemination of a stable resistance element. We conclude that L-PCR RFLP analysis, combined with DNA hybridization, merits further development for studying the evolution and epidemiology of VanA resistance elements in enterococci.

Animals↗