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PubMed2002

Analyses of genotypic diversity among North, South, and Central American isolates of sugarcane yellow leaf virus: evidence for Colombian origins and for intraspecific spatial phylogenetic variation.

We have analyzed the genotypic diversity of sugarcane yellow leaf virus (SCYLV) collected from North, South, and Central America by fingerprinting assays and selective cDNA cloning and sequencing. One group of isolates from Colombia, designated the C-population, has been identified as residing at the root node between a separable superpopulation structure of SCYLV and other members of the family Luteoviridae, indicating that the progenitor viruses of the North, South, and Central American isolates of the SCYLV superpopulation most likely arose from a C-population structure. From a model of intrafamilial evolution (F. Moonan et al., Virology 269:156-171, 2000), a prediction could be made that within the SCYLV species, the capacity of genomic sequence divergence would range from lowest in the capsid protein open reading frame 3 (ORF 3) to highest in a region spanning across the carboxy-terminal end of the RNA-dependent RNA polymerase ORF. We have demonstrated the validity and applicability of this intrafamilial model for the prediction of intraspecies SCYLV diversity. Analysis of spatial phylogenetic variation (SPV) within the SCYLV isolates could not be assessed by application of a "partial likelihoods assessed through optimization" (PLATO)-derived intraspecies model alone. However, application of a PLATO-derived intrafamilial model with the intraspecies-derived model allowed distinction of three forms of SPV. Two of the SPV forms identified correspond to the extremes in a continuum of sequence evolution displayed in a SCYLV superpopulation structure, and the third form was diagnostic of a C-population structure. The application of these types of models has value in terms of predicting the types of SCYLV intraspecies diversity that may exist worldwide, and in general, may be useful in application for more informed design of transgenes for use in the elicitation of homology-dependent virus resistance mechanisms in transgenic plants.

Central America↗

PubMed2005

[16S rDNA RFLP analysis of endophytic bacteria from Brassica napus].

Endophytic bacteria reside in plant hosts without causing disease symptom. In this study, 122 endophytic bacteria strains isolated from healthy oilseed rape plant were categorized preliminarily to 35 groups based on colony morphology; 16S rDNAs were amplified with universal primers of bacteria, all the strains could produce a single band about 1500bp, the PCR products were digested with restriction endoenzyme Hae III and Msp I respectively, different patterns were obtained for each enzyme, by combining all the restriction patterns for the two enzymes, the 122 strains could be grouped into 39 16S rDNA genotypes. The results indicated that endophytic bacteria from Brassica napus were genetically diversity. By comparing two methods, colony morphology only showed limited and preliminary information, and PCR-RFLP could be as a rapid and accurate tool for the diversity analysis of endophytic bacteria from Brassica napus.

Bacteria↗

PubMed2006

Development of microsatellite markers and analysis of intraspecific genetic variability in chickpea (Cicer arietinum L.).

Paucity of polymorphic molecular markers in chickpea (Cicer arietinum L.) has been a major limitation in the improvement of this important legume. Hence, in an attempt to develop sequence-tagged microsatellite sites (STMS) markers from chickpea, a microsatellite enriched library from the C. arietinum cv. Pusa362 nuclear genome was constructed for the identification of (CA/GT)n and (CT/GA)n microsatellite motifs. A total of 92 new microsatellites were identified, of which 74 functional STMS primer pairs were developed. These markers were validated using 9 chickpea and one C. reticulatum accession. Of the STMS markers developed, 25 polymorphic markers were used to analyze the intraspecific genetic diversity within 36 geographically diverse chickpea accessions. The 25 primer pairs amplified single loci producing a minimum of 2 and maximum of 11 alleles. A total of 159 alleles were detected with an average of 6.4 alleles per locus. The observed and expected heterozygosity values averaged 0.32 (0.08-0.91) and 0.74 (0.23-0.89) respectively. The UPGMA based dendrogram was able to distinguish all the accessions except two accessions from Afghanistan establishing that microsatellites could successfully detect intraspecific genetic diversity in chickpea. Further, cloning and sequencing of size variant alleles at two microsatellite loci revealed that the variable numbers of AG repeats in different alleles were the major source of polymorphism. Point mutations were found to occur both within and immediately upstream of the long tracts of perfect repeats, thereby bringing about a conversion of perfect motifs into imperfect or compound motifs. Such events possibly occurred in order to limit the expansion of microsatellites and also lead to the birth of new microsatellites. The microsatellite markers developed in this study will be useful for genetic diversity analysis, linkage map construction as well as for depicting intraspecific microsatellite evolution.

Alleles↗

PubMed2003

How can we learn to live with pain? A Q-methodological analysis of the diverse understandings of acceptance of chronic pain.

An analysis is reported of the variety of understandings available in British culture to understand acceptance of chronic pain. Q-factor analysis is used within a critical framework as Q-methodology. Thirty participants completed the procedure. Eight factors or accounts of accepting chronic pain were derived. These are reported as taking control, living day to day, acknowledging limitations, empowerment, accepting loss of self, more to life than pain, don't fight battles that cannot be won, and spiritual strength. Common features of accepting chronic pain are (1) the acknowledgement that a cure for pain is unlikely, (2) a shift of focus away from pain to non-pain aspects of life, and (3) a resistance to any suggestion that pain is a sign of personal weakness. Where accounts of chronic pain differ is in the extent to which acceptance of pain means a change in core aspects of self. Implications of this study for the study of chronic pain are discussed. In particular, how identity is managed in the context of threatening chronic pain is suggested as a fruitful area of future investigation.

Adaptation, Psychological↗

PubMed2005

Microbial response to heavy metal-polluted soils: community analysis from phospholipid-linked fatty acids and ester-linked fatty acids extracts.

Heavy metal pollution of soil is of concern for human health and ecosystem function. The soil microbial community should be a sensitive indicator of metal contamination effects on bioavailability and biogeochemical processes. Simple methods are needed to determine the degree of in situ pollution and effectiveness of remediating metal-contaminated soils. Currently, phospholipid-linked fatty acids (PLFAs) are preferred for microbial profiling but this method is time consuming, whereas direct soil extraction and transesterification of total ester-linked fatty acids (ELFAs) is attractive because of its simplicity. The 1998 mining acid-metal spill of >4000 ha in the Guadiamar watershed (southwestern Spain) provided a unique opportunity to study these two microbial lipid profiling methods. Replicated treatments were set up as nonpolluted, heavy metal polluted and reclaimed, and polluted soils. Inferences from whole community-diversity analysis and correlations of individual fatty acids with metals suggested Cu, Cd, and Zn were the most important in affecting microbial community structure, along with pH. The microbial stress marker, monounsaturated fatty acids, was significantly lower for reclaimed and polluted soil over nonpolluted soils for both PLFA and ELFA extraction. Another stress marker, the monounsaturated to saturated fatty acids ratio, only showed this for the PLFA. The general fungal marker (18:2omega6c), the arbuscule mycorrhizae marker (16:1omega5c), and iso- and anteiso-branched PLFAs (gram positive bacteria) were suppressed with increasing pollution whereas 17:0cy (gram negative bacteria) increased with metal pollution. For both extraction methods, richness and diversity were greater in nonpolluted soils and lowest in polluted soils. The ELFA method was sensitive for reflecting metal pollution on microbial communities and could be suitable for routine use in ecological monitoring and risk assessment programs because of its simplicity and reproducibility.

Bacteria↗

PubMed2026

Brucellar spondylitis is associated with disturbance in gut microbiota and histamine metabolism associated inflammation.

BACKGROUND: The pathogenesis of brucellar spondylitis (BLS) has traditionally been considered to be primarily limited to local osteoarticular lesions. With the proposal of the "gut-spine axis" concept, the role of intestinal microecological dysbiosis in inflammatory spinal diseases has attracted in an increase of attention. The overactivated inflammatory cytokine network not only mediates bone destruction and intervertebral disc damage, but also forms a bidirectional interaction with gut microbiota dysbiosis through the "gut-spine axis," collectively driving disease progression. However, the inflammatory mechanism by which gut microbiota participates in the pathological process of BLS remains largely unclear. METHODS: This study recruited 20 BLS patients and 20 healthy donors. Multi-omics analysis including metagenomics, untargeted metabolomics, and targeted short-chain fatty acids (SCFAs) analysis, were used to compare the structural differences in gut microbiota between the two groups and screen for signature differential bacterial species. Plasma levels of histamine and histidine decarboxylase were measured by ELISA to clarify the role of differential histidine metabolic pathway in the disease. Additionally, plasma levels of lipopolysaccharide (LPS) and inflammatory cytokines (IL-1β, IL-6, IL-10, IL-17A, TNF-α) were detected by ELISA. The correlation between gut microbiota and inflammatory indicators was further analyzed. RESULTS: Compared to the healthy control group, the α-diversity of the gut microbiota in BLS patients was significantly reduced, with the microbial community structure exhibiting increased homogeneity. Beta diversity analysis revealed significant differences, suggesting that disease progression is associated with an overall imbalance in the gut microbiota and the deterioration of its specific structural composition. At the phylum level, the abundances of Actinomycetota, unclassified_d_Viruses, and Fusobacteriota were significantly increased in the gut microbiota of BLS patients compared to the control group, while the abundances of Bacillota and Pseudomonadota were significantly decreased. Further analysis revealed that, compared to the control group, the generic abundance of Enterococcus was significantly increased, while the proportions of Blautia, Faecalibacterium, Ruminococcus, Agathobacter, Roseburia, Clostridium, Eubacterium, Alistipes and Anaerobutyricum were significantly decreased. At the species level, the abundances of Enterococcus sp and Enterococcus-faecium were increased, whereas Blautia sp, Ruminococcus sp, Faecalibacterium sp, Faecalibacterium prausnitzii, Agathobacter rectalis, Eubacterium sp, Agathobacter sp, and Roseburia sp were decreased. Furthermore, untargeted metabolomics revealed that metabolites were enriched in the histidine metabolic pathway, and the levels of SCFAs including butyrate, isobutyrate, valerate, and 4-methylvalerate in the intestinal contents were reduced in BLS. Functional KEGG profiling revealed that key KOs involved in butyrate synthesis (e.g., K00074, K00172, K01640) and transport were globally downregulated in the patient group, whereas histidine decarboxylase KOs (K01693, K11755, K19787) that convert histidine to pro-inflammatory histamine were significantly enriched. The loss of butyrate-producing symbionts led to SCFAs deficiency and mucosal barrier disruption, creating ecological niches for facultatively anaerobic Enterococcus, which further exacerbated local inflammation via proteolytic fermentation and histamine production. Compared with the control group, BLS patients showed decreased plasma levels of IL-10, while levels of IL-1β, IL-6, IL-17A, and TNF-α were increased, and LPS levels were elevated. In addition, significantly elevated plasma pro-inflammatory LPS levels in patients with BLS suggest disruption of intestinal integrity and permeability. Correlation analysis indicated a close relationship between gut microbiota and inflammation. CONCLUSION: BLS is associated with gut microbiota dysbiosis and alterations in microbial metabolites, which may be linked to inflammatory responses and histamine metabolism. The differential microbial taxa identified in this study could be developed into a stool-based non-invasive diagnostic panel to facilitate early differentiation of BLS from other spinal disorders. Furthermore, restoring gut microbial balance through probiotic supplementation or dietary modulation may represent a promising adjunctive strategy to enhance the efficacy of standard antibiotic therapy and reduce disease recurrence.

Humans↗

PubMed2007

Development of microsatellite markers from tartary buckwheat.

A genomic library enriched with (gT)(n) repeats from tartary buckwheat (Fagopyrum tataricum) was constructed using 5'-anchored PCR for the development of microsattellite markers. Sequencing analysis of 5 clones from the library showed that they all contained microsatellites (totally 10 loci), and each was unique. An additional locus-specific primer was designed according to flanking sequence. Two of the microsatellite loci of 10 tartary buckwheat varieties were amplified using an anchored primer and a locus-specific primer, which revealed a clear polymorphic pattern. The data confirmed that the degenerate primer was reliably anchoring at the 5'-end of the microsatellite, and the primers developed based on this technology could be used for diversity analysis of tartary buckwheat.

DNA Primers↗

PubMed2000

Comparative analysis of two different subunits of antigen B from Echinococcus granulosus: gene sequences, expression in Escherichia coli and serological evaluation.

Two different Echinococcus granulosus antigen B subunits (AgB8/1 and AgB8/2) were characterized and the structure of the genes encoding these two proteins were compared. DNA sequences were expressed in Escherichia coli and the antigens' diagnostic value was then assessed. The genomic sequence of AgB8/1 has a 92 bp intron in the position corresponding to amino acid 16; the AgB8/2 genomic sequence presents a 68 bp intron in the position corresponding to amino acid 20. Both introns are located between the putative N-terminal hydrophobic sequence and the secreted peptide. A comparison between the AgB8/1 and AgB8/2 nucleotide sequences showed a 53.5% identity among exons and a 50% identity between introns. According to the molecular diversity analysis, the elapsed time since both genes shared a common ancestor would be around 4.2x10(7) years. When the native AgB and the two recombinant antigens (rAgB8/1 and rAgB8/2) were tested in an anti-IgG ELISA, the sensitivity of the native antigen B was 77.41% and its specificity was 81.9%, while rAgB8/1 showed 54.84% of sensitivity and 80.17% of specificity and rAg138/2 had an 83.87% sensitivity and a 98.28% specificity. Statistical analysis confirms that rAgB8/2 has a better performance than rAgB8/1 and native AgB in ELISA.

Amino Acid Sequence↗

PubMed1999

Phage library-derived human anti-TETA and anti-DOTA ScFv for pretargeting RIT.

Pretargeting techniques have promise for radioimmunotherapy (RIT) in cancer because of the potential for markedly increasing the therapeutic ratio. Human antibody fragments can be retrieved from phage libraries and used to realize this potential. The library can be used to select the genetic material required to generate molecules with binding sites for both radiochelates and tumor antigens. In this study, human anti-chelate scFvs (single-chain fragments) for two metal chelates (Cu-TETA and Y-DOTA) were selected from a large, naive human scFv library. These anti-chelate scFvs were intended to serve as one arm of bispecific pretargeting molecules and to bind radiochelates given subsequently as Cu-67-TETA or Y-90-DOTA. Phage that displayed the anti-chelate scFv were selected by absorption to antibody (Lym-1) bound Cu-TETA or Y-DOTA. Enzyme-linked immunosorbent assays (ELISA) were performed to assess the intensity and specificity of phage binding to the specific chelate. Ninety-six clones demonstrating metal chelate binding seven times greater than to Lym-1 alone were chosen for diversity analysis. BstN I restriction digests were performed on DNA from these clones. Twenty-three and 43 different DNA fingerprint patterns were identified for anti-TETA and anti-DOTA clones, respectively. DNA sequencing of 39 anti-TETA clones for 23 different BstN I fingerprint patterns revealed 22 distinct sequences. Eleven of the anti-TETA clones were selected for further study. Five hundred to 1000 microg (100 to 320 microg per liter of culture) of purified scFv was produced from each of the 11 anti-TETA clones. Preliminary studies by BIAcore demonstrated evidence of 25- to 200-nM affinities. Comparable examination of the anti-DOTA clones is in progress. This study provides evidence that human scFv against unique synthetic targets can be readily selected from a large, naive human immunoglobulin phage library. Selections against metal chelated antibodies provided a wealth of scFvs with diverse binding affinities useful for engineering molecules for pretargeting RIT.

Antibodies, Monoclonal↗

PubMed1996

A computerized method for evaluating balance of occlusal load.

In order to undertake a quantitative evaluation of balance occlusal load, the use of the Dental Prescale System was investigated. The method uses a test sheet that undergoes a colour-developing chemical reaction, for detecting contact area, and a computerized analysis system, for evaluating the balance of occlusal load. Twenty natural dentate subjects and 10 hemimaxillectomy patients participated in the study. Each subject bit a test sheet as hard as possible for 3 s. The balance of occlusal load was expressed as a percentage of the load on the side with the lesser occlusive load (%OLR). The %OLR ranged from 39.7% to 49.4% in the natural dentate subjects, and from 0% to 31.3% in the hemimaxillectomy patients at their resection site. The patients' low %OLRs were attributed to loss of sustaining structure and subjective occlusal adjustment by clinicians. Combining technical simplicity, relatively high reproducibility, and diverse analysis capability, this system is useful for quantitative evaluation of balance of occlusal load in clinical situations.

Adult↗

PubMed2006

RFLP and AFLP analysis of inter- and intraspecific variation of Brassica rapa and B. napus shows that B. rapa is an important genetic resource for B. napus improvement.

Fingerprinting of 29 accessions of oilseed rape, including seven accessions of Brassica napus, and 22 accessions of B. rapa (B. campestris) from Europe, North America, and China was analyzed using RFLP and AFLP markers. In total, 1,477 polymorphic RFLP bands and 183 polymorphic AFLP bands from 166 enzyme-probe combinations and two pairs of AFLP primers, respectively, were scored for the 29 accessions. On average, RFLP analysis showed that the Arabidopsis EST probe detected more polymorphic bands in Brassica than the random genomic probe performed. More polymorphic RFLP markers were detected with the digestion of EcoR I or BamH I than HindIII. According to the number of bands amplified from each accession, the copy numbers of each gene in the genomes of B. rapa and B. napus were estimated. The average copy numbers in B. rapa of China, B. rapa of Europe, and B. napus, were 3.2, 3.1, and 2.9, respectively. Genetic distance based on the AFLP data was well correlated with that based on the RFLP data (r = 0.72, P<0.001), but 0.39 smaller on average. Genetic diversity analysis showed that Chinese B. rapa was more polymorphic than Chinese B. napus and European materials. Some European B. napus accessions were clustered into European B. rapa, which were distinctly different from Chinese B. napus. The larger variations of Chinese accessions of B. rapa suggest that they are valuable in oilseed rape breeding. Novel strategies to use intersubgenomic heterosis between genome of B. rapa (A(r)A(r)) and genome of B. napus (A(n)A(n)C(n)C(n)) were elucidated.

Amplified Fragment Length Polymorphism Analysis↗

PubMed2005

[Molecular diversity and phylogenetic analysis of nitrogen-fixing (nifH) genes in alp prairie soil of Sanjiangyuan natural reserve].

Research on the diversity of microorganism community in natural environment has been concerned hot spot using the newly molecular biotechnology in the world now. This was the first description of the molecular diversity and phylogenetic analysis of nitrogen-fixing (nifH) genes in alp prairie soil of Sanjiangyuan natural reserve. DNA was directly extracted from the soil microorganism and amplified the nifH gene fragment using PCR by the primers of nifH-34F 5'-AAAGG(C/T)GG(A/T) ATCGG(C/T)AA(A/G) TCCACCAC-3' and nifH-491R 5'-TYGTT(G/C)GC(G/C)GC(A/G)TACAT(G/C)G CCATCAT-3'. For the gene fragment, diverse PCR products were characterized by cloning, restriction fragment length polymorphism (RFLP) analysis and sequencing. 143 clones and 35 different RFLP patterns were received in two samples by the restriction enzymes MspI and RsaI digested. ZD sample had 82 clones and 21 different RFLP patterns, and YS sample had 61 clones and 19 different RFLP patterns. There were shared 5 RFLP patterns in two samples. The analysis result found a significant dominant group of clones occurring in both samples which account for 29.3% and 32.8%, respectively, and several minor groups were also detected. 21 clones were sequenced, and their levels of nucleotide identity were from 71% to 98%. None of the sequenced nifH gene was completely identical to any deposited in the data banks, and therefore each of them belong to a noncharacterized bacterium. Finally, the phylogenetic tree was constructed by the Clustal W and Mega software. 21 sequences can be subdivided into 4 clusters in the phylogenetic tree, and most of them had the closely similar toalpha- , beta-, and gamma-Proteobacteria . The significant dominant group in YS sample and ZD sample had the closely related with Rhodobacter sphaeroides and Delftia tsuruhatensis, respectively. The YS-nifH-11 was the only sequence which had highly similar to Cyanobacteria .

Bacteria↗

PubMed2026

Isolation of folate-producing probiotic candidates and their effects on homocysteine metabolism and gut microbiota composition.

BACKGROUND: Folate deficiency is a global nutritional problem associated with multiple adverse health outcomes, including impaired one-carbon metabolism and elevated homocysteine levels (hyperhomocysteinemia). Gut microbiota-mediated folate biosynthesis has emerged as a promising strategy for improving the host's folate status. This study aimed to isolate folate-producing probiotic strains, clarify their folate synthesis mechanisms, and evaluate their regulatory effects on folate metabolism and gut microbiota. METHODS: High-throughput cultivation and screening were performed to isolate folate-producing candidate probiotics. Whole-genome sequencing analysis, pathway reconstruction, and metabolite profiling in fermented milk were performed to explore folate biosynthesis pathways and microbial cross-feeding interactions. A folate-deficient mouse model was established to evaluate the effects of a candidate probiotic cocktail on serum folate, homocysteine (Hcy) levels, and gut microbiota composition using quantitative PCR (qPCR) and 16S rRNA gene sequencing. RESULTS: High-throughput screening identified 8 high-folate-producing candidate probiotic strains, including Lactiplantibacillus plantarum and Heyndrickxia coagulans, from over 1,000 isolates. Genomic analysis revealed that most commonly used probiotics lacked para-aminobenzoic acid (pABA) biosynthesis genes but retained downstream modules, suggesting a reliance on cross-feeding with pABA-producing gut commensals such as Bacteroides. Metabolite profiling of fermented milk demonstrated that selected strains significantly increased bioactive 5-methyltetrahydrofolate (5-MeTHF) and tetrahydrofolate levels. In vivo, only a high-dose candidate probiotic cocktail significantly elevated serum folate (p < 0.05) and reduced homocysteine levels (p < 0.05) in deficient mice. Fecal qPCR confirmed dose-dependent transient persistence of the administered bacterial species. Consistent with the qPCR data, 16S rRNA gene sequences demonstrated significant enrichment of these administered species observed in the high-dose group. Furthermore, beta-diversity analysis found that high-dose candidate probiotic supplementation promoted a shift in the gut microbiota composition toward a normal profile, partially mitigating the dysbiosis induced by the folate-deficient diet. This effect was accompanied by a significant enrichment of potential short-chain fatty acid producers (e.g., Lachnospiraceae and Oscillospiraceae) and the depletion of potential opportunistic pathogens. CONCLUSION: This study screened high-folate-producing candidate probiotic strains and demonstrated their ability to synthesize the active form of 5-MeTHF. Moreover, folate-producing candidate probiotic cocktail treatment significantly improved folate status and Hcy metabolism and modulated the gut microbiota by enriching potential beneficial bacterial taxa. These findings suggested that folate-producing probiotics may serve as a promising microbiota-based strategy to improve folate availability and homocysteine metabolism.

B vitamin↗

PubMed2026

Characterisation of the chloroplast genome of Macrotyloma species: comparative analysis and phylogenomic insights.

Macrotyloma is an underutilised legume genus within the tribe Phaseoleae (Fabaceae) that includes nutritionally and agronomically important crops such as horse gram (Macrotyloma uniflorum) and Kersting's groundnut (Macrotyloma geocarpum). Despite their importance, knowledge of the chloroplast (cp.) genome of this genus remains limited. In this study, we assembled and analysed the complete chloroplast genomes of three Macrotyloma species: M. uniflorum, M. geocarpum, and M. axillare. The chloroplast genomes were assembled into two isoforms that differ in the orientation of the small single-copy (SSC) region. Genome sizes ranged from 150,811 to 151,013 bp and exhibited the canonical quadripartite structure, comprising a pair of inverted repeats (IRa and IRb; 26,416-26,436 bp each), a large single-copy region (LSC; 80,229-80,446 bp), and a small single-copy region (SSC; 17,710-17,711 bp). Each genome encoded 110 unique genes, including 4 rRNA genes, 30 tRNA genes, and 76 protein-coding genes. All three species also possessed the ~ 50 kb inversion in the LSC region, a synapomorphy shared among a large clade within the Papilionoideae subfamily of Fabaceae. Although overall chloroplast genome structure and organisation were highly conserved among Macrotyloma species, gene-wise nucleotide diversity analysis identified seven relatively variable genes: rps18, rps15, ccsA, ndhA, ycf1, ycf4, and psaI. Phylogenomic analysis based on complete chloroplast genomes robustly resolved Macrotyloma as a monophyletic group within the Phaseolinae clade of the Papilionoideae subfamily. Within the genus, M. uniflorum and M. axillare formed a strongly supported sister pair, with M. geocarpum sister to this clade. Overall, this study provides valuable insights into chloroplast genome evolution in Macrotyloma and enhances understanding of its phylogenetic placement within Phaseoleae, offering genomic resources for future evolutionary, taxonomic, and conservation studies of this underutilised legume genus.

Genome, Chloroplast↗

PubMedDate not supplied

Ties in proximity and clustering compounds.

Hierarchical clustering algorithms such as Wards or complete-link are commonly used in compound selection and diversity analysis. Many such applications utilize binary representations of chemical structures, such as MACCS keys or Daylight fingerprints, and dissimilarity measures, such as the Euclidean or the Soergel measure. However, hierarchical clustering algorithms can generate ambiguous results owing to what is known in the cluster analysis literature as the ties in proximity problem, i.e., compounds or clusters of compounds that are equidistant from a compound or cluster in a given collection. Ambiguous ties can occur when clustering only a few hundred compounds, and the larger the number of compounds to be clustered, the greater the chance for significant ambiguity. Namely, as the number of "ties in proximity" increases relative to the total number of proximities, the possibility of ambiguity also increases. To ensure that there are no ambiguous ties, we show by a probabilistic argument that the number of compounds needs to be less than 2(n 1/4), where n is the total number of proximities, and the measure used to generate the proximities creates a uniform distribution without statistically preferred values. The common measures do not produce uniformly distributed proximities, but rather statistically preferred values that tend to increase the number of ties in proximity. Hence, the number of possible proximities and the distribution of statistically preferred values of a similarity measure, given a bit vector representation of a specific length, are directly related to the number of ties in proximities for a given data set. We explore the ties in proximity problem, using a number of chemical collections with varying degrees of diversity, given several common similarity measures and clustering algorithms. Our results are consistent with our probabilistic argument and show that this problem is significant for relatively small compound sets.

Journal Article↗

PubMed1984

[Dynamic urinary flow images in patients with ileal loop diversion assessed by I-123-hippuran scintigraphy. Detection of ileoureteral reflux].

To evaluate upper urinary tract and ileal loop functions, dynamic urinary flow studies using I-123 hippuran were performed in 52 kidneys of 27 patients with ileal loop urinary diversion. Analysis of regional renograms enabled easy assessment of the cortical, pelvic and loop functions. Normal pattern was found in 33 cortices (63.5%), 22 pelvis (45.8%) and 14 loops (51.9%). Most of the abnormal findings in the upper urinary tract were delayed excretion and/or retention of the pelvic and ureteral urines. Diagnosis of ileoureteral reflux under normal physiological circumstances was made to compare the pelvic and loop curves. Small peaks and/or irregular spike waves observed in the down slope of the pelvic curve concurrently with the increased activity of the loop curve indicate a production of the ileoureteral reflux associated with ileal movement. This reflux was noted in 22 of the 27 cases (81.5%). Bilateral reflux was evident in 3 cases, and unilateral reflux in 19 cases. Ileoureteral reflux was noticed in 14 of the 15 cases (90%) in which retrograde loopography was performed. Although bilateral reflux was found in 8 cases, the hippuran study revealed bilateral in only one case, unilateral in 5 and no reflux in 2. Thus, I-123 hippuran scintigraphy consisting of sequential renal images, loopograms and regional renograms enables the diagnosis of ileoureteral reflux and obstructive uropathies and is a useful tool to detect functional complications of the upper urinary tract in patients with ileal loop diversion.

Adult↗

PubMed2000

Mitochondrial DNA variation in two South Siberian Aboriginal populations: implications for the genetic history of North Asia.

The mtDNAs of 76 individuals representing the aboriginal populations of South Siberia, the Tuvinians and Buryats, were subjected to restriction fragment length polymorphism (RFLP) analysis and control region hypervariable segment I (HVS-I) sequencing, and the resulting data were combined with those available for other Siberian and East Asian populations and subjected to statistical and phylogenetic analysis. This analysis showed that the majority of the Tuvinian and Buryat mtDNAs (94.4% and 92.5%, respectively) belong to haplogroups A, B, C, D, E, F, and M*, which are characteristic of Mongoloid populations. Furthermore, the Tuvinians and Buryats harbor four Asian- and Native American-specific haplogroups (A-D) with frequencies (72.2% and 55%, respectively) exceeding those reported previously for Mongolians, Chinese, and Tibetans. They represent, therefore, the populations that are most closely related to New World indigenous groups. Despite their geographical proximity, the Tuvinians and Buryats shared no HVS-I sequences in common, although individually they shared such sequences with a variety of other Siberian and East Asian populations. In addition, phylogenetic and principal component analyses data of mtDNA sequences show that the Tuvinians clustered more closely with Turkic-speaking Yakuts, whereas the Mongolic-speaking Buryats clustered closer to Korean populations. Furthermore, HVS-I sequences, comprising one-fourth of the Buryat lineages and characterized by the only C-to-T transition at nucleotide position 16223, were identified as different RFLP haplotypes (B, C, D, E, M*, and H). This finding appears to indicate the putative ancestral state of the 16223T HVS-I sequences to Mongoloid macrohaplogroup M, at least. Finally, the results of nucleotide diversity analysis in East Asian and Siberian populations suggest that Central and East Asia were the source areas from which the genetically heterogeneous Tuvinians and Buryats first emerged.

American Indian or Alaska Native↗

PubMedDate not supplied

Assessment of T-cell receptor beta-chain diversity by heteroduplex analysis.

The aim of this work was to search for a simple and alternative approach to the currently used methodologies for the analysis of T-cell receptor repertoire diversity. To this end we studied whether the heteroduplex analysis could be adapted to study the clonality of the T-cell receptor beta chain (TCRBV). We therefore analyzed, by sequencing, the molecular characteristics of the V-D-J junctions of numerous TCRBV chains from a variety of patients and from normal individuals, and compared the results with those obtained with the heteroduplex analysis. The latter procedure involves the amplification of the target TCRBV chains and the denaturation and renaturation of the amplified product to permit the random association of the distinct DNA strands encoding the different junctional regions. Whereas amplified material from polyclonal lymphoid cells migrates on a polyacrylamide gel as a "smear" of bands composed of different-sized polyclonal PCR fragments, the mismatched chains derived from oligoclonal populations migrate as discrete "heteroduplexes" and can be separated from the matched "homoduplex" obtained from homogeneous clonal cells. Our results provide evidence demonstrating that heteroduplex analysis can successfully be applied to the analysis of T-cell clonality in a variety of samples and can be complementary or substitute for the standard approach of TCR cloning and multiple sequencing of junctional regions. Thus, the procedure should facilitate the implementation of the analysis of TCR in diagnostic routine and should find applications in numerous physiologic and pathologic conditions.

Amino Acid Sequence↗