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PubMed2003

Microsatellite analysis of genetic diversity and population genetic structure of a wild rice (Oryza rufipogon Griff.) in China.

Genetic diversity and population genetic structure of natural Oryza rufipogon populations in China were studied based on ten microsatellite loci. For a total of 237 individuals of 12 populations collected from four regions, a moderate to high level of genetic diversity was observed at population levels with the number of alleles per locus ( A) ranging from 2 to 18 (average 10.6), and polymorphic loci ( P) from 40.0% to 100% (average 83.3%). The observed heterozygosity ( H(O)) varied from 0.163 to 0.550 with the mean of 0.332, and the expected heterozygosity ( H(E)) from 0.164 to 0.648 with the mean of 0.413. The level of genetic diversity for Guangxi was the highest. These results are in good agreement with previous allozyme and RAPD studies. However, it was unexpected that high genetic differentiation among populations was found ( R(ST) = 0.5199, theta = 0.491), suggesting that about one-half of the genetic variation existed between the populations. Differentiation (pairwise theta) was positively correlated with geographical distance ( r = 0.464), as expected under the isolation by distance model. The habitat destruction and degradation throughout the geographic range of O. rufipogon may be the main factor attributed to high genetic differentiation among populations of O. rufipogon in China.

China↗
PubMed1999

Analysis of genetic diversity at the iron-containing superoxide dismutase locus in Plasmodium falciparum wild isolates.

In order to investigate the genetic diversity of iron-containing superoxide dismutase (FeSOD) from Plasmodium falciparum, a potential anti-malarial therapeutic target, we cloned and sequenced Plasmodium FeSOD from 26 blood samples from non-infected patients. Fifteen clones had the same nucleotide sequence as that of the FeSOD gene of the P. falciparum strain HB3 cultivated in vitro. The other 11 clones presented mutations responsible for punctual amino acid changes which did not modify key residues for the function or the structure of the enzyme. The high sequence conservation between FeSOD from the isolates confirms that this enzyme could represent a therapeutic target.

Amino Acid Sequence↗
PubMed1991

An analysis of the diverse factors concerned with the development of pressure sores in spinal cord injured patients.

Patients with spinal cord injuries (SCI) admitted to the Institut Guttmann, Barcelona, from the years 1985 to 1988 with pressure sores (PS) are reviewed. Demographic, pathological and psychological factors are analysed in an attempt to identify organic and/or behavioural patterns which might imply an added risk for the development of pressure sores in the spinal cord injured. About 30% of 884 SCI patients admitted during this period had one or more PS (mean 1.5), most of these were localised to the ischial, trochanteric and sacral regions, and about 70% were grade 3 or 4 (Enis and Sarmiento classification). The study supports the generally acknowledged view that a precarious state of health and certain psycho-social conditions are contributing factors to a higher risk in the development and severity of PS in SCI patients.

Adult↗
PubMed2004

Analysis of microbial diversity in oligotrophic microbial fuel cells using 16S rDNA sequences.

Molecular ecological techniques were applied to analyze the bacterial diversity of two oligotrophic microbial fuel cells (MFCs) enriched using river water or artificial wastewater (AWW) as fuel. Denaturing gradient gel electrophoresis (DGGE) of the PCR amplified 16S rDNA showed that different microbial communities were present in the two MFCs and these were different from the river sediment used to initiate the enrichment. Nearly complete 16S rDNA was amplified and sequenced. Over 80% of the clones were Proteobacteria. Betaproteobacteria were the dominant clones (46.2%) in MFCs fed with river water, and about 64.4% of the clones in MFCs fed with AWW were Alphaproteobacteria. Actinobacteria were found only in the MFC fed with AWW, and Deltaproteobacteria, Acidobacteria, Chloroflexi and Verrucomicrobia in the MFC fed with river water. Many clones were related to uncultured bacteria, some with homology less than 95%, indicating that many novel bacteria were enriched in the oligotrophic MFCs.

Actinobacteria↗
PubMed2004

Comparative analysis of genetic diversity and expression of amoA in wastewater treatment processes.

The genetic diversity and expression of amoA of autotrophic ammonia oxidizers in wastewater treatment processes were investigated by RT-PCR and denaturing gradient gel electrophoresis (DGGE) in order to identify active components of ammonia-oxidizer populations in a such processes. Ammonia oxidizers, evidenced by the presence of amoA mRNA, were regarded as metabolically active. The DGGE profiles derived from amoA mRNA and from its gene, which were amplified by RT-PCR or PCR using samples collected from a bench-scale reactor treating high concentration of inorganic ammonia, were similar. In contrast, RNA and DNA-derived DGGE profiles from three domestic wastewater treatment facilities were different from each other. These data indicate that the dominant ammonia oxidizers in the bench-scale reactor exhibited ammonia-oxidizing activity, whereas some ammonia oxidizers in the domestic wastewater treatment facilities apparently did not express high levels of amoA mRNA.

Ammonia↗
PubMed2005

Use of external ureteral catheters and internal double J stents in a modified ileal neobladder for continent diversion: a comparative analysis.

INTRODUCTION: Open-ended straight ureteral stents are typically used for the support of the ureteroileal anastomosis during the creation of an orthotopic 'S-pouch' ileal neobladder. The use of double J stents as an alternative in this setting is evaluated. MATERIALS AND METHODS: Medical charts from 43 patients undergoing radical cystectomy with formation of an ileal 'S-pouch' neobladder were retrospectively evaluated. In 30 patients (group A), a 6-Fr open-ended straight ureteral catheter was used to stent the ureteroileal anastomosis, while a double J stent was used for the same reason in 13 patients (group B). The ureteral catheter was removed 15 days after the procedure while the double J stent 3 weeks postoperatively. Hospital stay, early and late complications were evaluated for both groups during a mean follow-up period of 22.5 and 19.6 months respectively. RESULTS: Stricture of the ureteroileal anastomosis was observed in 2 (6.6%) and 1 (7.6%) patient of groups A and B respectively. All complications presented with similar rates, except for an increased but not statistically significant incidence of urethrovesical anastomotic leakage and early urinary tract infections in group B. Hospital stay was significantly (p<0.005) shorter for patients of group B (9.9 vs. 15.2 days). CONCLUSIONS: The use of double J stents to support the ureteroileal anastomosis can be used as an alternative to open-ended ureteral stents. With double J stents a shorter hospital stay was achieved with similar complication rates but a higher incidence of upper urinary tract infections.

Aged↗
PubMed2004

[Analysis of genetic diversity of preserved population of native chicken breeds by microsatellites and file foundation of markers].

The genetic diversity (allele frequency, mean heterozygosity, mean polymorphic information content(PIC), and Nei genetic distances) of preserved population of 11 native chicken breeds was analyzed by 20 microsatellite markers with high polymorphism. The clustering dendrogram was obtained eventually based on Nei genetic distances of 20 microsatellite. The results showed that 176 alleles were detected of 20 microsatellite loci in 11 native chicken breeds, the average number of alleles of each loci was 8.8 and the range of allele frequencies was 0.013-0.838, and 11 native chicken breeds shared 45 alleles. The average heterozygosity of 20 microsatellite loci was 0.6800-0.7432, the heterozygosity of Zang chicken was the highest (0.7432), and that of Langshang chicken was the lowest (0.6800). The range of PIC of 20 microsatellite loci were 0.6329-0.7023, which is higher than 0.5 and highly polymorphic. By the results of UPGMA tree, four groups were formed from 11 chicken breeds, the first group was Silky, Chahua, Xianju, Zang and Xiaoshan chicken; the second group was Luyuan and Langshan chicken; the third group was Gushi, Fatty and Dagu chicken; and the fourth group was Henan game chicken. The effect of preserved breeds and the differences among generations can be tested by the file foundation of molecular markers, which contained allele frequency, mean heterozygosity, and mean PIC of 20 microsatellite loci in different generation populations.

Alleles↗
PubMed2004

Global gene expression in human myocardium-oligonucleotide microarray analysis of regional diversity and transcriptional regulation in heart failure.

To obtain region- and disease-specific transcription profiles of human myocardial tissue, we explored mRNA expression from all four chambers of eight explanted failing [idiopathic dilated cardiomyopathy (DCM), n=5; ischemic cardiomyopathy (ICM), n=3], and five non-failing hearts using high-density oligonucleotide arrays (Affymetrix U95Av2). We performed pair-wise comparisons of gene expression in the categories (1) atria versus ventricles, (2) disease-regulated genes in atria and (3) disease-regulated genes in ventricles. In the 51 heart samples examined, 549 genes showed divergent distribution between atria and ventricles (272 genes with higher expression in atria, 277 genes with higher expression in ventricles). Two hundred and eighty-eight genes were differentially expressed in failing myocardium compared to non-failing hearts (19 genes regulated in atria and ventricles, 172 regulated in atria only, 97 genes regulated in ventricles only). For disease-regulated genes, down-regulation was 4.5-times more common than up-regulation. Functional classification according to Gene Ontology identified specific biological patterns for differentially expressed genes. Eleven genes were validated by RT-PCR showing a good correlation with the microarray data. Our goal was to determine a gene expression fingerprint of the heart, accounting for region- and disease-specific aspects. Recognizing common gene expression patterns in heart failure will significantly contribute to the understanding of heart failure and may eventually lead to the development of pathway-specific therapies.

Adult↗
PubMed2001

RAPD and ISSR fingerprints as useful genetic markers for analysis of genetic diversity, varietal identification, and phylogenetic relationships in peanut (Arachis hypogaea) cultivars and wild species.

Abstract: Twenty-one random and 29 SSR primers were used to assess genetic variation and interrelationships among subspecies and botanical varieties of cultivated peanut, Arachis hypogaea (2n = 4x = 40), and phylogenetic relationships among cultivated peanut and wild species of the genus Arachis. In contrast with the previous generalization that peanut accessions lack genetic variation, both random and SSR primers revealed 42.7 and 54.4% polymorphism, respectively, among 220 and 124 genetic loci amplified from 13 accessions. Moreover, the dendrograms based on RAPD, ISSR, and RAPD + ISSR data precisely organized the five botanical varieties of the two subspecies into five clusters. One SSR primer was identified that could distinguish all the accessions analysed within a variety. Although the polymorphic index content varied from 0.1 to 0.5 for both ISSR and RAPD markers, primer index values were substantially higher for RAPD primers (0.35-4.65) than for SSR primers (0.35-1.73). It was possible to identify accessions, particularly those of divergent origins, by RAPD and (or) ISSR fingerprints. Based on these results, marker-based genetic improvement in A. hypogaea appears possible. None of the 486 RAPD and 330 ISSR amplification products were found to be commonly shared among 13 species of section Arachis and one species each of sections Heteranthae, Rhizomatosae, and Procumbentes. Dendrograms constructed from RAPD, ISSR, and RAPD + ISSR data showed overall similar topologies. They could be resolved into four groups corresponding to the species grouped in four taxonomic sections. The present results strongly support the view that Arachis monticola (2n = 4x = 40) and A. hypogaea are very closely related, and indicate that A. villosa and A. ipaensis are the diploid wild progenitors of these tetraploid species.

Arachis↗
PubMed2002

Analysis of sequence diversity at the highly polymorphic Cpgp40/15 locus among Cryptosporidium isolates from human immunodeficiency virus-infected children in South Africa.

Cryptosporidium sp. is a significant cause of diarrheal disease, particularly in human immunodeficiency virus (HIV)-infected patients in developing countries. We recently cloned and sequenced several alleles of the highly polymorphic single-copy Cryptosporidium parvum gene Cpgp40/15. This gene encodes a precursor protein that is proteolytically cleaved to yield mature cell surface glycoproteins gp40 and gp15, which are implicated in zoite attachment to and invasion of enterocytes. The most-striking feature of the Cpgp40/15 alleles and proteins is their unprecedented degree of sequence polymorphism, which is far greater than that observed for any other gene or protein studied in C. parvum to date. In this study we analyzed nucleic acid and amino acid sequence polymorphism at the Cpgp40/15 locus of 20 C. parvum isolates from HIV-infected South African children. Fifteen isolates exhibited one of four previously identified genotype I alleles at the Cpgp40/15 locus (Ia, Ib, Ic, and Id), while five displayed a novel set of polymorphisms that defined a new Cpgp40/15 genotype I allele, designated genotype Ie. Surprisingly, only 15 of these isolates exhibited concordant type I alleles at the thrombospondin-related adhesive protein of Cryptosporidium and Cryptosporidium oocyst wall protein loci, while five isolates (all of which displayed Cpgp40/15 genotype Ic alleles) displayed genotype II alleles at these loci. Furthermore, the last five isolates also manifested chimeric genotype Ic/Ib or Ic/II alleles at the Cpgp40/15 locus, raising the possibility of sexual recombination within and between prototypical parasite genotypes. Lastly, children infected with isolates having genotype Ic alleles were significantly older than those infected with isolates displaying other genotype I alleles.

AIDS-Related Opportunistic Infections↗
PubMed2003

Analysis of genomic diversity and evolution of the low-level antiseptic resistance gene smr in Staphylococcus aureus.

A multidrug efflux pump specified by the smr gene mediates low-level antiseptic resistance in staphylococci. We analyzed the genomic diversity of smr and its gene cassette, a structural unit containing smr and terminal direct repeats (DRs), in 22 clinical strains of Staphylococcus aureus isolated over 9 years in a Japanese hospital. Although open reading frames (ORFs) of all the smr genes examined were identical to those reported previously (e.g., qacD in pSK41), smr gene cassettes were classified into three groups (types 1, 2, and 3). The type 1 cassette had an identical genetic organization to that found in the plasmid pSK41, a putative prototype of the smr gene cassette, which contains DRs flanking smr. In the type 2 cassette, the rep gene and a putative replication nick site were found upstream of smr, between a SSOA (single-strand origin) sequence and DR1c, which are components of the type 1 cassette DR. In the type 3 cassette detected in a single strain, IS431 was located between the 3' end of smr and DR. It was suggested by genomic comparison that type 2 and type 3 cassettes might have been derived from the type 1 cassette via insertion of foreign DNA sequence, and that the type 2 cassette might be a precursor form of some previously reported smr cassettes, such as those in pSK108 and pNVH99. Although MICs of antiseptics and ethidium bromide were generally the same among strains having type 1, 2, or 3 smr gene cassette, the type 1 cassette was detected most frequently. Moreover, the copy number of the smr gene in the type 2 cassette was found to be much higher than that in the type 1 or type 3 cassette.

Anti-Bacterial Agents↗
PubMedDate not supplied

Wasatchian-Bridgerian (Eocene) paleoecology of the western interior of North America: changing paleoenvironments and taxonomic composition of omomyid (Tarsiiformes) primates.

Many changes in mammalian faunas occurred across the early (Wasatchian) to middle (Bridgerian) Eocene boundary as documented in the fossil record from the Western Interior of North America. One of the more striking changes took place within the tarsiiform primate family Omomyidae. In the early Eocene, omomyids were dominated, both in abundance and diversity, by the subfamily Anaptomorphinae. In the middle Eocene, the subfamily Omomyinae dominated in abundance, while both subfamilies were nearly equally diverse. Examination of a series of paleoecological indicators including leaf-margin analysis, cenogram analysis, ecological diversity analysis of trophic structure, the distribution and development of ancient soil horizons (paleosols), and the distribution of lacustrine and fluvial facies in the Bighorn and southern Green River basins of Wyoming reveals factors that may have influenced the composition of omomyid primates. Subtle but important changes occurred in paleoclimates with mean annual temperatures reaching Cenozoic maximums at the end of the Wasatchian into the early Bridgerian. Both land mammal ages were typified by subtropical, closed forested conditions, but the Bridgerian was probably more humid and wetter than the Wasatchian. Paleohabitats most commonly sampled in the Wasatchian of the Bighorn Basin are proximal and distal floodplains, while those of the Bridgerian in the southern Green River Basin are lake margins and proximal floodplains. Changes in paleoclimate may have triggered a wave of omomyine immigration near the end of the Wasatchian with omomyines entering into habitats previously occupied by anaptomorphines. Lake margin and proximal floodplain habitats are those most commonly occupied by omomyines in the Bridgerian with anaptomorphines being more common in basin margin and distal floodplain areas not commonly sampled. Omomyine immigration and sampling of differing paleohabitats are two possible explanations for the changes documented in omomyid diversity and abundance.

Animals↗
PubMed1980

Experimental stress analysis of topographic diversity in early hominid gnathic morphology.

Reconstructing the biomechanics of early hominid mastication is a key element in most models of hominid differentiation. Traditionally, osteological features marking muscle attachment surfaces have served as a reference system from which the vector geometry of the masticatory force system and resultant force distributions could be predicted. To augment traditional morphological and computational approaches, we developed a simulation system capable of replicating human and non-human primate chewing motions. The forces of occlusion are recorded as photoelastic fringes in a urethane alveolar process. Simulation experiments evaluating the functional correlates of topographic diversity in zygomatic root position and mandibular ramus height in early hominids indicated that the mandibles and dentitions of robust australopithecines are well adapted to sustain high magnitude, low gradient load distributions.

Animals↗
PubMed1978

Analysis of the diversity of murine antibodies to dextran B1355. III. Idiotypic and spectrotypic correlations.

Examination of 19 S and 7 S anti-alpha(1 leads to 3) dextran (Dex) antibodies by serological assays and isoelectric focusing (IEF) has revealed substantial variation of idiotypic and spectrotypic expression between individuals of the same genotype. 7 S antibodies appeared to be more heterogeneous than 19 S by both methods. A strong, but complex, association was found between the IEF patterns of 19 S and 7 S anti-Dex antibodies and their expression of the idiotypic determinant(s) common to both the M104 and J558 dextran-binding myeloma proteins. However, no such relationship was found between the IEF pattern and the expression of idiotypic determinant(s) unique to the M104 myeloma protein. Rather, indistinguishable spectrotypes from different individuals have widely differing levels of expression of the determinant. In addition, this determinant(s) may be present on different spectrotypes of the same isotype. Both the M104 and J558-specific idiotypes were found on antibodies of the IgG3 subclass as well as in pools containing predominantly the IgG2a subclass. These data confirm and extend the picture of substantial structural variation among the antibodies comprising a response of restricted heterogeneity.

Animals↗
PubMed1994

Rapid DNA degradation in primary rat hepatocytes treated with diverse cytotoxic chemicals: analysis by pulsed field gel electrophoresis and implications for alkaline elution assays.

The use of genetic toxicology tests for hazard identification is complicated by the fact that some in vitro tests using cultured mammalian cells are subject to potential artifacts that can make it difficult to distinguish between direct, chemically-induced genotoxicity, and DNA damage that occurs secondary to chemically-induced cytotoxicity (e.g., mediated by endogenous nucleases). Recently, we demonstrated that cytotoxicity-induced DNA double strand breaks (dsb) can produce artifacts in the in vitro alkaline elution/rat hepatocyte assay [Elia et al., 1993]. To explore this further, we used pulsed field gel/DNA dsb assays to characterize the relationship between chemically-induced cytotoxicity and the degradation of genomic DNA to high molecular weight fragments. Two sets of compounds were tested: 17 cytotoxic agents judged to be neither genotoxic nor carcinogenic, and 10 known genotoxic carcinogens. We found a close correlation between chemically-induced cytotoxicity and the rapid degradation of DNA to high molecular weight, double-stranded fragments. In contrast, the classic genotoxic chemicals tested generally did not trigger DNA dsb fragmentation at doses that were genotoxic but not immediately cytotoxic. These data indicate that pulsed field gel/DNA dsb assays can be used with in vitro genetic toxicology assays to help distinguish between genotoxic and cytotoxic mechanisms of DNA damage.

Animals↗
PubMed1983

Analysis of antibody diversity: V-D-J mRNA nucleotide sequence of four anti-GAT monoclonal antibodies. A paucigene system using alternate D-J recombinations to generate functionally similar hypervariable regions.

The nucleotide sequence of four anti-(Glu60-Ala30-Tyr10)n (GAT) monoclonal gamma 1 heavy chain mRNAs was determined from codon 10 to 120. This sequence overlaps with the NH2-terminal amino acid sequence, allowing elucidation of the complete protein sequence encompassing regions VH, D and JH. These sequences, which are highly conserved, indicate that anti-GAT antibodies expressing the same public idiotypic specificities represent a paucigene system, which uses at least two D-J combinations leading to functionally similar hypervariable regions involved in the recognition of the dominant Glu-Tyr determinant. D regions are encoded by D genes which are closely related either to the D-SP2 or the D.FL16 germ line gene cores.

Amino Acid Sequence↗
PubMed2004

Proteome analysis of intraclonal diversity of two Pseudomonas aeruginosa TB clone isolates.

Two strains, Pseudomonas aeruginosa TB10839 and TB121838, which belong to the TB clonal lineage, have been isolated from sputa of cystic fibrosis patients. Despite the fact that the strains are closely related, their pathogenic potential differs dramatically: while strain TB10839 is capable of proliferating in polymorphonuclear granulocytes, strain TB121838 is not. Comparative two-dimensional polyacrylamide gel electrophoresis coupled to matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF)-mass spectrometry was employed to map the extracellular, intracellular, and surface sub-proteomes of TB10839 and TB121838 and to identify differentially expressed proteins. About 4% of all detected protein spots were differentially expressed between both strains including absent or present spots and spots with a more than 2-fold changed intensity. This percentage reflects a relatively high degree of intraclonal variability. Many of the protein spots in TB10839 that were missing or expressed at lower levels in TB121838 were identified as quorum-sensing regulated virulence factors. It might be speculated that the increased expression of these proteins contributes to pathogenic competence of TB10839.

Clone Cells↗
PubMed1993

Genetic analysis of the diversity in outer membrane protein P2 of non-encapsulated Haemophilus influenzae.

The molecular basis for the diversity of the major outer membrane protein (MOMP) P2 of non-encapsulated Haemophilus influenzae was analyzed by direct sequencing of fragments of the P2 genes, obtained by the polymerase chain reaction. Genetically divergent H. influenzae strains were isolated from patients with otitis media and from infected patients with chronic obstructive pulmonary disease (COPD). The nucleotide sequences of these P2 genes were determined and compared with P2 gene sequences of three non-encapsulated strains and with the P2 gene of encapsulated H. influenzae type b. Variation in the nucleotide sequence of the P2 genes of non-encapsulated H. influenzae was localized in eight distinct regions which were interchanged with relatively conserved regions. Regions 2, 4, 5 and 8 were found to be hypervariable, since they were characterized by multiple deletions or substitutions of nucleotides. According to the proposed structure of MOMP P2 the variable regions were localized in eight loop structures exposed at the outside of the outer membrane. Loops 2, 4, 5 and 8 were hypervariable in all isolates whereas loop 6 varied only in isolates from COPD patients with persistent infections.

Amino Acid Sequence↗