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B Gene (b + gene)
Kinds of B Gene Terms modified by B Gene Selected AbstractsMechanism of Action of Low Recurrence of Gastritis Caused by Helicobacter pylori with the Type II Urease B GeneHELICOBACTER, Issue 2 2004Md. Badruzzaman ABSTRACT Background., Low recurrence of gastritis is seen in patients infected with Helicobacter pylori carrying the type II urease B gene, compared with H. pylori carrying types I and III. The underlying mechanism has been studied in terms of the urease activity and interleukin (IL)-8 production capacity of different strains of H. pylori. Materials and Methods., Forty-five patients infected with different strains of H. pylori (type I; 15, type II; 15 and type III; 15) were enrolled in the study. H. pylori was isolated from gastric mucosa and cultured in the presence of urea at pH 5.5 to evaluate urease activity. The capacity of different strains of H. pylori to induce IL-8 mRNA and IL-8 from a human gastric cancer cell line and human peripheral blood mononuclear cells was evaluated. Results., The urease activity of type II H. pylori[523 ± 228 µg of ammonia/dl/108 colony-forming units (CFU)/ml] was significantly lower than that of type I (1355 ± 1369 µg of ammonia/dl/108 CFU/ml) and type III (1442 ± 2229 µg of ammonia/dl/108 CFU/ml) (p < .05). Gastric cancer cells cocultured with type II H. pylori produced lower levels of IL-8 mRNA compared with type I and type III H. pylori. The levels of IL-8 were also significantly lower in cultures induced by type II H. pylori compared with those induced by type I and type III H. pylori. Peripheral blood mononuclear cells also produced lower levels of IL-8 when cocultured with type II compared with type I H. pylori. Conclusions., These results indicate that both the lower level of urease activity and the low IL-8-inducing capacity of type II H. pylori might underlie the lower recurrence rate of gastritis caused by type II H. pylori. [source] Characterization and expression analysis of the aspartic protease gene family of Cynara cardunculus L.FEBS JOURNAL, Issue 10 2007Catarina Pimentel Cardosin A and cardosin B are two aspartic proteases mainly found in the pistils of cardoon Cynara cardunculus L., whose flowers are traditionally used in several Mediterranean countries in the manufacture of ewe's cheese. We have been characterizing cardosins at the biochemical, structural and molecular levels. In this study, we show that the cardoon aspartic proteases are encoded by a multigene family. The genes for cardosin A and cardosin B, as well as those for two new cardoon aspartic proteases, designated cardosin C and cardosin D, were characterized, and their expression in C. cardunculus L. was analyzed by RT-PCR. Together with cardosins, a partial clone of the cyprosin B gene was isolated, revealing that cardosin and cyprosin genes coexist in the genome of the same plant. As a first approach to understanding what dictates the flower-specific pattern of cardosin genes, the respective gene 5, regulatory sequences were fused with the reporter ,-glucuronidase and introduced into Arabidopsis thaliana. A subsequent deletion analysis of the promoter region of the cardosin A gene allowed the identification of a region of approximately 500 bp essential for gene expression in transgenic flowers. Additionally, the relevance of the leader intron of the cardosin A and B genes for gene expression was evaluated. Our data showed that the leader intron is essential for cardosin B gene expression in A. thaliana. In silico analysis revealed the presence of potential regulatory motifs that lay within the aforementioned regions and therefore might be important in the regulation of cardosin expression. [source] The whorl-specific action of a petunia class B floral homeotic geneGENES TO CELLS, Issue 2 2000Suguru Tsuchimoto Background GREEN PETAL (GP) is thought to be a petunia class B floral homeotic gene, because the gp mutant flower displays a severe homeotic conversion of petals into sepals in the second whorl. However, since the third whorl stamens remain unaffected in the gp null mutant, gp is different from class B mutants in Arabidopsis and Antirrhinum, which also show a conversion of the third whorl stamens into the carpelloid tissue. BLIND (BL) is thought to be a petunia class A floral homeotic gene, because the bl mutant flower displays homeotic conversions of sepals into the stigmatoid tissue in the first whorl and of the corolla limb into antheroid structures in the second whorl. Results A double mutant line homozygous for both bl and gp mutations was constructed. The bl gp double mutant flower displays homeotic conversions of sepals into the stigmatoid tissue in the first whorl and of the corolla limb into antheroid structures with stigmatoid tips in the second whorl. In the third and fourth whorls of the mutant flower, organs remained unchanged. In the gp flower, a petunia B-type gene FBP1 is expressed strongly in the third whorl organs, but much more weakly in the second whorl organs. In the bl gp flower, FBP1 was found to be expressed strongly in the second whorl organs as well as in the third whorl organs. Conclusions Petunia has a class B gene other than GP that determines organ identities, both in the second and third whorls of the double mutant flower, and the action of the postulated class B gene (here called PhBX) is prevented by the BL gene in the second whorl of the gp flower. PhBX appears to be a gene that specifically interacts with the FBP1 gene, and is involved in the up-regulation of FBP1. [source] Development and Evaluation of a DNA Vaccine Based on Helicobacter pylori urease B: Failure to Prevent Experimental Infection in the Mouse ModelHELICOBACTER, Issue 6 2006Livania Zavala-Spinetti Abstract Background:, The development of a vaccine against Helicobacter pylori has become a priority to prevent major morbidity and mortality associated with this infection. Our goal was to prepare and evaluate a DNA vaccine based on the urease B gene (ureB). Methods:, The ureB gene of H. pylori was amplified and cloned into the eukaryotic expression vector pcDNA3.1/TOPO. Plasmid DNA was purified from transformed Escherichia coli cells and used to immunize mice by the intragastric, intramuscular, intrarectal (40 µg each) and intranasal (16 µg) route, three doses every 2 weeks, with CpG oligodeoxynucleotide (ODN) as adjuvant. Four weeks after the third dose, animals were orally challenged with Helicobacter felis and were sacrificed 6 weeks later. The stomach was stained to detect the presence of infection. Results:, Despite in vitro confirmation of successful cloning and functionality of the ureB gene with expression of a protein morphologically and antigenically identical to urease B, the DNA vaccine did not perform well in vivo. Immunization of mice produced a weak immune response. Overall, intrarectal and intranasal administration seemed more immunogenic than other routes. Protection against challenge was modest and nonsignificant, and slightly better on animals immunized by the intramuscular and intranasal route. Conclusion:, A DNA vaccine based on H. pylori urease B was poorly immunogenic and nonprotective at the conditions evaluated. Higher doses, better adjuvants or a prime-boost approach may circumvent these limitations. [source] Mechanism of Action of Low Recurrence of Gastritis Caused by Helicobacter pylori with the Type II Urease B GeneHELICOBACTER, Issue 2 2004Md. Badruzzaman ABSTRACT Background., Low recurrence of gastritis is seen in patients infected with Helicobacter pylori carrying the type II urease B gene, compared with H. pylori carrying types I and III. The underlying mechanism has been studied in terms of the urease activity and interleukin (IL)-8 production capacity of different strains of H. pylori. Materials and Methods., Forty-five patients infected with different strains of H. pylori (type I; 15, type II; 15 and type III; 15) were enrolled in the study. H. pylori was isolated from gastric mucosa and cultured in the presence of urea at pH 5.5 to evaluate urease activity. The capacity of different strains of H. pylori to induce IL-8 mRNA and IL-8 from a human gastric cancer cell line and human peripheral blood mononuclear cells was evaluated. Results., The urease activity of type II H. pylori[523 ± 228 µg of ammonia/dl/108 colony-forming units (CFU)/ml] was significantly lower than that of type I (1355 ± 1369 µg of ammonia/dl/108 CFU/ml) and type III (1442 ± 2229 µg of ammonia/dl/108 CFU/ml) (p < .05). Gastric cancer cells cocultured with type II H. pylori produced lower levels of IL-8 mRNA compared with type I and type III H. pylori. The levels of IL-8 were also significantly lower in cultures induced by type II H. pylori compared with those induced by type I and type III H. pylori. Peripheral blood mononuclear cells also produced lower levels of IL-8 when cocultured with type II compared with type I H. pylori. Conclusions., These results indicate that both the lower level of urease activity and the low IL-8-inducing capacity of type II H. pylori might underlie the lower recurrence rate of gastritis caused by type II H. pylori. [source] Six novel alleles identified in Italian hereditary fructose intolerance patients enlarge the mutation spectrum of the aldolase B gene,,HUMAN MUTATION, Issue 6 2004Gabriella Esposito Abstract Hereditary fructose intolerance (HFI) is a recessively inherited disorder of carbohydrate metabolism caused by impaired functioning of human liver aldolase (B isoform; ALDOB). To-date, 29 enzyme-impairing mutations have been identified in the aldolase B gene. Here we report six novel HFI single nucleotide changes identified by sequence analysis in the aldolase B gene. Three of these are missense mutations (g.6846T>C, g.10236G>T, g.10258T>C), one is a nonsense mutation (g.8187C>T) and two affect splicing sites (g.8180G>C and g.10196A>G). We have expressed in bacterial cells the recombinant proteins corresponding to the g.6846T>C (p.I74T), g.10236G>T (p.V222F), and g.10258T>C (p.L229P) natural mutants to study their effect on aldolase B function and structure. All the new variants were insoluble; molecular graphics data suggest this is due to impaired folding. © 2004 Wiley-Liss, Inc. [source] Validation of a real-time PCR for Haemophilus parasuisJOURNAL OF APPLIED MICROBIOLOGY, Issue 4 2010C. Turni Abstract Aims:, To validate a real-time PCR test for the diagnosis of Glässer's disease, a major pig disease caused by Haemophilus parasuis. Methods and Results:, The specificity of a real-time PCR amplifying the inf,B gene was validated with 68 H. parasuis isolates and 36 strains of closely related species. As well, 239 samples of DNA from tissues and fluids of 16 experimentally challenged animals were tested with the real-time PCR, and the results were compared with culture and a conventional PCR. The real-time PCR produced significantly more positive results than the conventional PCR (165 vs 86). Conclusions:, The sensitivity of the real-time PCR combined with high specificity makes it a very valuable tool for the diagnosis of Glässer's disease. Significance and Impact of Study:, This new method will improve the ability of laboratories to diagnose Glässer's disease, especially in laboratories where the culture method for H. parasuis is not optimal. [source] Modulation of expression of LDH isoenzymes in endothelial cells by laminin: Implications for angiogenesisJOURNAL OF CELLULAR BIOCHEMISTRY, Issue 6 2008V.B. Sameer Kumar Abstract Endothelial cell (EC) matrix interaction is critical in angiogenesis. Although matrix components can regulate the process of angiogenesis by acting as a reservoir of various cytokines, it is not clear if extracellular matrix (ECM) can modulate the production and activity of angiogenic cytokines. Investigations were therefore carried out to study the influence of the basement membrane (BM) protein, laminin (Ln) on the activity of vascular endothelial growth factor (VEGF), the major angiogenic cytokine, using isolated human umbilical vein ECs (HUVECs) in culture. Analysis of the biochemical markers of angiogenesis confirmed proangiogenic effect of Ln. The levels of VEGF protein and mRNA were not different in cells maintained on Ln, collagen I or polylysine substrata. Chorioallantoic membrane assay using VEGF isolated from cell extracts however revealed that Ln increased its angiogenic potency. Immunoblotting and HPLC analysis showed considerable reduction in poly adenosyl ribosylation of VEGF associated with a significant decrease in the levels of NAD+, in cells maintained on Ln substrata. Further, a shift in the isoenzymic pattern of LDH towards the B rich forms and an upregulation of LDH B gene were observed in cells maintained on Ln. Ln modulates expression of LDH gene through ,6,4 integrin mediated downstream signaling involving p38 mitogen activated protein kinases (MAPK) pathway. It thus appears that Ln can affect aerobic metabolism of ECs by modulating the expression of LDH isoenzymes resulting in a decrease in the level of NAD+ that can cause a reduction in the poly adenosyl ribosylation of VEGF altering its angiogenic potency. J. Cell. Biochem. 103: 1808,1825, 2008. © 2007 Wiley-Liss, Inc. [source] Construction and identification of a recombinant live attenuated Salmonella typhimurium vaccine strain carrying Helicobacter pylori heat shock protein subunit B geneJOURNAL OF DIGESTIVE DISEASES, Issue 4 2003Guo Qing LI OBJECTIVE: Because Helicobacter pylori is the principal cause of chronic active gastritis and peptic ulcer disease, the present study explored the possibility of constructing a recombinant live attenuated S. typhimurium vaccine strain carrying H. pylori heat shock protein subunit B (HspB) gene. METHODS: A 1640-bp HspB gene was cloned into a prokaryotic expression plasmid pTrc99A. After sequence analysis, the result was compared with the sequence of H. pylori -HspB gene and protein provided by the Genebank using BLAST analysis. The identified recombinant plasmid was then introduced into a live attenuated S. typhimurium strain SL3261. RESULTS: Using polymerase chain reaction (PCR) and restriction enzyme digestion, a recombinant prokaryotic expression plasmid pTrc99A-HspB harboring the HspB gene was constructed and successfully introduced into a live attenuated S. typhimurium strain SL3261. Most of the H. pylori -HspB in the recombinant plasmid pTrc99A-HspB was consistent with the H. pylori -HspB sequence provided by the Genebank. The exchange of A/T or C/G in the cloned sequence hardly changed the encoded amino acids; the homology for both the genes and proteins of H. pylori SS1 strain was 97%; the homology with other common H. pylori strains J99 and 26695 was 96% for both. CONCLUSION: A recombinant live attenuated S. typhimurium vaccine strain harboring H. pylori -HspB gene was successfully constructed and verified, which may help in the development of an oral vaccine against H. pylori infection. [source] Prenatal diagnosis of Larsen syndrome caused by a mutation in the filamin B genePRENATAL DIAGNOSIS, Issue 2 2009N. Winer No abstract is available for this article. [source] Identification of previously unrecognized predisposing factors for ankylosing spondylitis from analysis of HLA,B27 extended haplotypes in sardiniaARTHRITIS & RHEUMATISM, Issue 8 2007Isabella Cascino Objective To define the contribution of HLA genes other than HLA,B27 in conferring susceptibility to ankylosing spondylitis (AS), through analysis of HLA,B27 haplotypes in Sardinian subjects. Methods Ninety-eight patients with AS, 133 HLA,B27,positive controls (of whom 33 were positive for HLA,B*2709), and 190 randomly selected controls were genotyped for microsatellites and single-nucleotide polymorphisms (SNPs) spanning the HLA region. Results Haplotypes carrying either the B*2705 or the B*2709 allele were found to share a conserved region downstream of the HLA,B gene and a functional polymorphism in the HLA,E gene (R128G), while differing in all other markers. Notably, the presence of an A at SNP rs1264457, encoding for Arg-128, was significantly increased in the cohort of patients (P = 6 × 10,6, corrected P = 3 × 10,5) but not in B*2705- or B*2709-positive controls. Comparing the alleles co-occurring at each HLA marker, we identified a region differentiating patients with AS and B*2705-matched controls. In particular, there was a markedly increased prevalence of heterozygosity at rs1264457 among B27-positive controls (74%, versus 47% in patients and 54% in random controls), suggesting a protective role of G128 in AS. Moreover, other markers around the HLA,B gene were also differentially represented. Conclusion These results demonstrate a significant difference in the frequency of some HLA markers between AS patients and B*2705-positive controls, which could be attributed to the opposite chromosome. In particular, the differential distribution of a functional polymorphism in the HLA,E gene suggests a possible role of natural killer function in AS pathogenesis. [source] ,B-crystallin: A novel p53-target gene required for p53-dependent apoptosisCANCER SCIENCE, Issue 12 2009Gou Watanabe The p53 protein is a transcription factor that trans -activates various genes in response to DNA-damaging stress. To search for new p53-target genes, we applied a cDNA microarray system using two independent p53-inducible cell lines, followed by in silico analysis to detect p53 response elements. Here, we report on crystallin alpha B gene (CRYAB), which encodes ,B-crystallin, and is one of the genes directly trans -activated by p53. We confirmed it is directly transcribed by p53 using promoter analysis, deletion reporter assay, ChIP assay and EMSA. ,B-crystallin is also upregulated in a p53-dependent manner and binds to the DNA-binding domain of p53. Overexpression of ,B-crystallin increased p53 protein and, in contrast, repression of ,B-crystallin decreased p53 protein. Interestingly, both overexpression and repression of ,B-crystallin reduced p53-dependent apoptosis. In conclusion, we identified that ,B-crystallin was a novel p53-target gene and required for p53-dependent apoptosis using two independent p53-inducible cell lines. This is the first report associating p53 directly with a heat shock protein through trans -activation and physical interaction. (Cancer Sci 2009; 100: 2368,2375) [source] Clonal dissemination of a toxin-A-negative/toxin-B-positive Clostridium difficile strain from patients with antibiotic-associated diarrhea in PolandCLINICAL MICROBIOLOGY AND INFECTION, Issue 8 2001H. Pituch Objective To determine the incidence of toxin-A-negative/toxin-B-positive Clostridium difficile strains and their genetic relatedness in the feces of patients suffering from antibiotic-associated diarrhea (AAD) in Polish hospitals. MethodsC. difficile strains were cultured from patients' stool samples. The present study characterises these strains with respect to their cytopathogenicity on McCoy cells and the absence of toxin A despite a functional toxin B as determined with commercial test kits (Culturette Brand Toxin CD-TCD toxin A test and C. difficile Tox A/B test). In addition, PCR using different primer pairs aiming at non-repeating or repeating regions of the toxin A and B genes were used to confirm the findings. All toxin A,B+ strains were genetically characterised by random amplification of polymorphic DNA (RAPD) analysis, PCR ribotyping and, in part, pulsed-field gel electrophoresis (PFGE) of DNA macrorestriction fragments. Results We here present the presence of 17 toxin A,B+ strains among 159 C. difficile strains (11%) isolated from fecal samples from 413 patients with antibiotic-associated diarrhea. All 17 strains possessed the toxin B gene, demonstrated a cytopathogenic effect on the McCoy cells, and were positive in the Tox A/B test. Molecular typing of these 17 C. difficile strains revealed that 7 of 17 (41%) toxin A,/B+C. difficile strains could not be discriminated. It appeared that these strains had a genotype that could not be distinguished from that of a Japanese control strain. Conclusion Our observations imply that a particular genotype of toxin A,B+C. difficile has spread extensively, not only in Poland but possibly even worldwide. [source] Characterization and expression analysis of the aspartic protease gene family of Cynara cardunculus L.FEBS JOURNAL, Issue 10 2007Catarina Pimentel Cardosin A and cardosin B are two aspartic proteases mainly found in the pistils of cardoon Cynara cardunculus L., whose flowers are traditionally used in several Mediterranean countries in the manufacture of ewe's cheese. We have been characterizing cardosins at the biochemical, structural and molecular levels. In this study, we show that the cardoon aspartic proteases are encoded by a multigene family. The genes for cardosin A and cardosin B, as well as those for two new cardoon aspartic proteases, designated cardosin C and cardosin D, were characterized, and their expression in C. cardunculus L. was analyzed by RT-PCR. Together with cardosins, a partial clone of the cyprosin B gene was isolated, revealing that cardosin and cyprosin genes coexist in the genome of the same plant. As a first approach to understanding what dictates the flower-specific pattern of cardosin genes, the respective gene 5, regulatory sequences were fused with the reporter ,-glucuronidase and introduced into Arabidopsis thaliana. A subsequent deletion analysis of the promoter region of the cardosin A gene allowed the identification of a region of approximately 500 bp essential for gene expression in transgenic flowers. Additionally, the relevance of the leader intron of the cardosin A and B genes for gene expression was evaluated. Our data showed that the leader intron is essential for cardosin B gene expression in A. thaliana. In silico analysis revealed the presence of potential regulatory motifs that lay within the aforementioned regions and therefore might be important in the regulation of cardosin expression. [source] Recurrent familial hypobetalipoproteinemia,induced nonalcoholic fatty liver disease after living donor liver transplantationLIVER TRANSPLANTATION, Issue 7 2009Noboru Harada Familial hypobetalipoproteinemia (FHBL) is one of the causes of nonalcoholic steatohepatitis (NASH) and a codominant disorder. Patients heterozygous for FHBL may be asymptomatic, although they demonstrate low plasma levels of low-density lipoprotein (LDL) cholesterol and apolipoprotein B. Here we report a nonobese 54-year-old man with decompensated liver cirrhosis who underwent living donor liver transplantation with his son as the donor. Low albuminemia and refractory ascites persisted after transplantation. A biopsy specimen obtained 11 months after liver transplantation revealed severe steatosis and fibrosis, and recurrent NASH was diagnosed on the basis of pathological findings. Both the patient's and donor's laboratory tests demonstrated low LDL cholesterol and apolipoprotein levels. Because mutations in messenger RNAs of microsomal triglyceride transfer protein and apolipoprotein B genes were excluded neither in the recipient nor in the donor, both were clinically diagnosed as being heterozygous for FHBL. We successfully treated the recipient with heterozygous FHBL,induced recurrent NASH after liver transplantation using our diet and exercise programs. Liver Transpl 15:806,809, 2009. © 2009 AASLD. [source] Spatial pattern of MHC class II variation in the great snipe (Gallinago media)MOLECULAR ECOLOGY, Issue 7 2007ROBERT EKBLOM Abstract The genes of the major histocompatibility complex (MHC) code for proteins involved in antigen recognition and triggering of the adaptive immune response, and are therefore likely to be under selection from parasites. These selection regimes may vary in space and time. Here we report a strong geographical structure in MHC class II B genes of a migrating bird, the great snipe (Gallinago media). Genetic differentiation in the MHC between two ecologically distinct distributional regions (Scandinavian mountain populations vs. East European lowland populations) was still present after statistically controlling for the effect of selectively neutral variation (microsatellites) using partial Mantel tests. This suggests a role for selection in generating this spatial structure and that it represents local adaptation to different environments. Differentiation between populations within the two regions was negligible. Overall, we found a high number of MHC alleles (50, from 175 individuals). This, together with a tendency for a higher rate of nonsynonymous than synonymous substitutions in the peptide binding sites, and high Tajima's D in certain regions of the gene, suggests a history of balancing selection. MHC variation is often thought to be maintained by some form of balancing selection, but the nature of this selection remains unclear. Our results support the hypothesis that spatial variation in selection regimes contributes to the high polymorphism. [source] Isolation, sequence, and chromosomal localisation of the human I,BR gene (NFKBIL2)ANNALS OF HUMAN GENETICS, Issue 1 2000D. A. M. NORMAN The inhibitors of NF-,B (I,Bs) play an important role in the regulation of the NF-,B pathway. I,BR (for I,B -Related) is proposed to be a novel member of this family. We report the cloning and characterization of the region of the human gene encoding the previously reported mRNA. This region contains 13 exons, spread over 6550 bp of genomic sequence. The coding sequence is only weakly similar to other I,Bs and the exons display a more complicated structure than has been found in other members of the I,B gene family. Moreover, the positions of intron-exon junctions are different from those found in other I,B genes, even within the otherwise conserved ankyrin-like repeat region, suggesting that the I,BR gene is not a member of this extended gene family. We report a revised mRNA and protein sequence for I,BR, which predicts that the protein is larger than originally described. We also report the chromosomal localisation of the human I,BR gene (approved gene symbol NFKBIL2) to 8q24.3 using PCR-based somatic cell hybrid panel analysis and fluorescence in situ hybridization (FISH) mapping. [source] Crystallization and preliminary crystallographic studies of human RIG-I in complex with double-stranded RNAACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 6 2009Hyunjin Moon Retinoic acid inducible gene-I (RIG-I) is an essential component of the innate immune system that is responsible for the detection and elimination of invading viruses. RIG-I recognizes viral RNAs inside the cell and then initiates downstream signalling to activate the IRF-3 and NF-,B genes, which results in the production of type I interferons. RIG-I is composed of an N-terminal CARD domain for signalling and C-terminal helicase and repressor domains for RNA recognition. A RIG-I,RNA binding assay was performed to investigate the in vitro RIG-I,RNA binding properties. Selenomethionine-incorporated RIG-I was expressed using Escherichia coli and purified for crystallization. X-ray data were collected from RIG-I,dsRNA complex crystals to 2.8,Å resolution using synchrotron radiation. [source] Clonal dissemination of a toxin-A-negative/toxin-B-positive Clostridium difficile strain from patients with antibiotic-associated diarrhea in PolandCLINICAL MICROBIOLOGY AND INFECTION, Issue 8 2001H. Pituch Objective To determine the incidence of toxin-A-negative/toxin-B-positive Clostridium difficile strains and their genetic relatedness in the feces of patients suffering from antibiotic-associated diarrhea (AAD) in Polish hospitals. MethodsC. difficile strains were cultured from patients' stool samples. The present study characterises these strains with respect to their cytopathogenicity on McCoy cells and the absence of toxin A despite a functional toxin B as determined with commercial test kits (Culturette Brand Toxin CD-TCD toxin A test and C. difficile Tox A/B test). In addition, PCR using different primer pairs aiming at non-repeating or repeating regions of the toxin A and B genes were used to confirm the findings. All toxin A,B+ strains were genetically characterised by random amplification of polymorphic DNA (RAPD) analysis, PCR ribotyping and, in part, pulsed-field gel electrophoresis (PFGE) of DNA macrorestriction fragments. Results We here present the presence of 17 toxin A,B+ strains among 159 C. difficile strains (11%) isolated from fecal samples from 413 patients with antibiotic-associated diarrhea. All 17 strains possessed the toxin B gene, demonstrated a cytopathogenic effect on the McCoy cells, and were positive in the Tox A/B test. Molecular typing of these 17 C. difficile strains revealed that 7 of 17 (41%) toxin A,/B+C. difficile strains could not be discriminated. It appeared that these strains had a genotype that could not be distinguished from that of a Japanese control strain. Conclusion Our observations imply that a particular genotype of toxin A,B+C. difficile has spread extensively, not only in Poland but possibly even worldwide. [source] Phylogenetic Reanalysis of the Saudi Gazelle and Its Implications for ConservationCONSERVATION BIOLOGY, Issue 4 2001Robert L. Hammond The Saudi gazelle ( Gazella saudiya) was endemic to the Arabian peninsula but is now considered extinct in the wild and is potentially a candidate for captive breeding and reintroduction. Using 375 base pairs of mitochondrial DNA (mtDNA) cytochrome b gene derived from museum samples collected from the wild prior to the presumed extinction of this species, we show that G. saudiya is the sister taxon of the African dorcas gazelle ( G. dorcas). Reciprocal monophyly of G. saudiya mtDNA haplotypes with G. dorcas, coupled with morphological distinctiveness, suggests that it is an evolutionarily significant unit. These data indicate that captive populations identified previously as potential sources of G. saudiya for captive breeding appear incorrectly designated and are irrelevant to the conservation of G. saudiya. The polymerase chain reaction,restriction fragment length polymorphism ( PCR-RFLP) analysis of several private collections of living gazelles in Saudi Arabia provides no evidence for the survival of G. saudiya. We recommend that field surveys be undertaken to establish whether G. saudiya is indeed extinct in the wild and that other private collections within the Arabian peninsula be screened genetically. We urge caution when captive animals of unknown provenance are used to investigate the phylogenetics of cryptic species groups. Resumen: La identificación de poblaciones taxonómicamente apropiadas de especies en peligro para programas de reproducción en cautiverio y de reintroducción es fundamental para su éxito. La Gacela Saudi (Gazella saudiya) fue endémica a la península de Arabia pero ahora está considerada como extinta en su medio y es un candidato potencial para reproducción en cautiverio y reintroducción. Utilizando 375 pares de bases de ADN mitocondrial (ADNmt) del gene citocromo b derivados de muestras de museos colectadas en el medio silvestre antes de la extinción de la especie, mostramos que G. saudiya es el taxón hermano de la gacela dorcas africana (G. dorcas). La monofilia recíproca de haplotipos de ADNmt de G. saudiya con G. dorcas, aunado a diferencias morfológicas, sugiere que es una unidad evolutiva significativa. Estos datos indican que las poblaciones cautivas identificadas previamente como fuente potencial de G. saudiya para reproducción en cautiverio están incorrectamente identificadas y son irrelevantes para la conservación de G. saudiya. El análisis PCR-RFLP de varias colecciones privadas de gacelas vivas en Arabia Saudita no proporcionan evidencia para la supervivencia de G. saudiya. Recomendamos que se realicen muestreos en el campo para establecer si en efecto G. saudiya está extinta en su hábitat y que se examinen genéticamente las otras colecciones privadas en la península Arábiga. Recomendamos precaución cuando animales cautivos de origen desconocido son utilizados para investigar la filogenia de grupos de especies crípticas. [source] Subpopulations of Cryptocephalus beetles (Coleoptera: Chrysomelidae): geographically close but genetically farDIVERSITY AND DISTRIBUTIONS, Issue 1 2003R. W. Piper Abstract. The leaf beetles Cryptocephalus coryli, C. decemmaculatus and C. nitidulus are of conservation concern and are included on the UK Biodiversity Action Plan. The distinctiveness of the disjunct remaining populations of these beetles was compared to that of more continuously distributed Cryptocephalus species. This was carried out with a view to defining evolutionary significant units (ESUs) in the rare species. A portion of the cytochrome b gene, an intergenic spacer and partial tRNA was analysed from 93 specimens of Cryptocephalus beetle (Coleoptera: Chrysomelidae). Considerable sequence divergence was apparent in all the species, even at an intersite scale when the distances between sampled localities were very small (< 1 km). Intrapopulation, intersite and interpopulation divergence observed in the rare species was reflected in the species that have a more continuous distribution, implying that dispersal ability in these species is poor and gene flow can be impeded by relatively trivial barriers to dispersal. The evidence suggests that the disjunct populations of the rare Cryptocephalus species can, tentatively, be considered as ESUs. This has important implications for management strategies and reintroductions. [source] MOLECULAR EVIDENCE FOR THE ORIGIN OF WORKERLESS SOCIAL PARASITES IN THE ANT GENUS POGONOMYRMEXEVOLUTION, Issue 10 2002Joel D. Parker Abstract., Speciation of two social parasites from their respective hosts is tested using a molecular phylogeny. Alignment of 711 DNA base pairs of mitochondrial cytochrome b gene was used to assess phylogenetic relationships of inquiline species to their hosts and to other members of the genus. We show that the inquiline social parasites of the North American seed harvester ants are monophyletic, descending from one of the known hosts (Pogonomyrmex barbatus) in the recent past and shifting hosts in a pattern similar to that observed in other Hymenopteran social parasites. In addition, the host populations unexpectedly were found to be polyphyletic. Populations of Pogonomyrmex rugosus from an area east of the Chiricahua Mountains in Southern Arizona belong to a mitochondrial clade separate from the more western clade of P. rugosus from the Sonoran and Chihuahuan Deserts. Evidence of mitochondrial DNA introgression between P. rugosus and P. barbatus was also observed. We conclude that Emery's rule does not strictly hold for this system, but that the hosts and parasites are very closely related, supporting a loose definition of Emery's rule. [source] PHYLOGENETIC RELATIONSHIPS AND MORPHOLOGICAL DIVERSITY IN DARWIN'S FINCHES AND THEIR RELATIVESEVOLUTION, Issue 6 2002Kevin J. Burns Abstract Despite the importance of Darwin's finches to the development of evolutionary theory, the origin of the group has only recently been examined using a rigorous, phylogenetic methodology that includes many potential outgroups. Knowing the evolutionary relationships of Darwin's finches to other birds is important for understanding the context from which this adaptive radiation arose. Here we show that analysis of mitochondrial DNA sequence data from the cytochrome b gene confirm that Darwin's finches are monophyletic. In addition, many taxa previously proposed as the sister taxon to Darwin's finches can be excluded as their closest living relative. Darwin's finches are part of a well-supported monophyletic group of species, all of which build a domed nest. All but two of the non-Darwin's finches included in this clade occur on Caribbean islands and most are Caribbean endemics. These close relatives of Darwin's finches show a diversity of bill types and feeding behaviors similar to that observed among Darwin's finches themselves. Recent studies have shown that adaptive evolution in Darwin's finches occurred relatively quickly. Our data show that among the relatives of Darwin's finches, the evolution of bill diversity was also rapid and extensive. [source] Genetic diversity and historical population structure in the New Zealand mayfly Acanthophlebia cruentataFRESHWATER BIOLOGY, Issue 1 2006PETER J. SMITH Summary 1. Nucleotide sequences of a 280 base pair region of the cytochrome b gene were used to assess genetic diversity and to infer population histories in the New Zealand mayfly Acanthophlebia cruentata. 2. A hierarchial examination of populations from 19 streams at different spatial scales in the central and northern North Island of New Zealand found 34 haplotypes. A common haplotype was found in all central region streams and unique haplotypes in northern streams. Several central streams had region specific haplotypes with genetically differentiated populations at the 70,100 km scale. 3. Haplotype diversity was high (0.53,0.8) at most sites, but low (0,0.22) in some central sites. amova analyses found significant genetic diversity among regions (69%) and among catchments (58%). Most population pairwise FST tests were significant, with non-significant pairwise tests among sites in the central region and pairs of sites between neighbouring streams. 4. The levels of sequence divergence are interpreted as the result of Pleistocene divergence in multiple refugia, leading to the evolution of regionally unique haplotypes. The low diversity in some central region populations may result from recent colonisation following local extinctions, associated with volcanic events. [source] Discovery of ten new specimens of large-billed reed warbler Acrocephalus orinus, and new insights into its distributional rangeJOURNAL OF AVIAN BIOLOGY, Issue 6 2008Lars Svensson We here report the finding of ten new specimens of the poorly known large-billed reed warbler Acrocephalus orinus. Preliminary identifications were made on the basis of bill, tarsus and claw measurements, and their specific identity was then confirmed by comparison of partial sequences of the cytochrome b gene with a large data set containing nearly all other species in the genus Acrocephalus, including the type specimen of A. orinus. Five of the new specimens were collected in summer in Afghanistan and Kazakhstan, indicating that the species probably breeds in Central Asia, and the data and moult of the others suggest that the species migrates along the Himalayas to winter in N India and SE Asia. The population structure suggests a stable or shrinking population. [source] Glacial survival or late glacial colonization?JOURNAL OF BIOGEOGRAPHY, Issue 12 2006Phylogeography of the root vole (Microtus oeconomus) in north-west Norway Abstract Aim, It has been proposed that the root vole subspecies, Microtus oeconomus finmarchicus, survived the last glacial period on islands on the north-west coast of Norway. The Norwegian island of Andøya may have constituted the only site with permanent ice-free conditions. Geological surveys and fossil finds from Andøya demonstrate that survival throughout the last glacial maximum was probably possible for some plants and animals. In this study we aim to infer the recent evolutionary history of Norwegian root vole populations and to evaluate the glacial survival hypothesis. Methods, DNA sequence variation in the mitochondrial cytochrome b gene was studied in 46 root voles from 19 localities. Location, Northern Fennoscandia and north-west Russia with a focus on islands on the north-west coast of Norway. Results The phylogeographical analyses revealed two North European phylogroups labelled ,Andøya' and ,Fennoscandia'. The Andøya phylogroup contained root voles from the Norwegian islands of Andøya, Ringvassøya and Reinøya and two localities in north-west Russia. The Fennoscandian phylogroup encompassed root voles from the three Norwegian islands of Kvaløya, Håkøya and Arnøya and the remaining specimens from Norway, northern Sweden and Finland. Nucleotide diversity within the Andøya and Fennoscandian phylogroups was similar, ranging from 0.5% to 0.7%. Main conclusions Both our genetic data and previously published morphological data are consistent with in situ glacial survival of root voles on Andøya during the last glacial maximum. However, the level of genetic diversity observed in the extant island populations, the past periods of severe climatic conditions on Andøya and the ecology of the root vole are somewhat difficult to reconcile with this model. A biogeographical scenario involving late glacial recolonization along the northern coasts of Russia and Norway therefore represents a viable alternative. Our results demonstrate that complex recolonization and extinction histories can generate intricate phylogeographical patterns and relatively high levels of genetic variation in northern populations. [source] Weak phylogenetic effects on ecological niches of Sylvia warblersJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 5 2003K. Böhning-Gaese Abstract To understand the evolution of ecological niches it is important to know whether niche evolution is constrained by phylogeny. We approached this question for Sylvia warblers by testing if closely related species are more similar in 20 ecologically relevant morphological traits than distantly related species. Phylogenetic relatedness was quantified using a molecular phylogeny based on the mitochondrial cytochrome b gene. By Principal Component Analysis (PCA) two major niche axes were extracted. We tested the individual ecomorphological traits and the positions of the species on the PCA axes for phylogenetic effects using Mantel tests. The results demonstrated small but significant phylogenetic effects only for the length of the middle toe, a trait probably correlated with locomotion. In general, however, phylogenetic effects were very weak. This suggests that ecological niches in passerine birds have the potential to evolve rapidly and are not subject to major phylogenetic constraints. [source] Morphometric convergence and molecular divergence: the taxonomic status and evolutionary history of Gymnura crebripunctata and Gymnura marmorata in the eastern Pacific OceanJOURNAL OF FISH BIOLOGY, Issue 4 2009W.D. Smith To clarify the taxonomic status of Gymnura crebripunctata and Gymnura marmorata, the extent of morphological and nucleotide variation between these nominal species was examined using multivariate morphological and mitochondrial DNA comparisons of the same characters with congeneric species. Discriminant analysis of 21 morphometric variables from four species (G. crebripunctata, G. marmorata, Gymnura micrura and Gymnura poecilura) successfully distinguished species groupings. Classification success of eastern Pacific species improved further when specimens were grouped by species and sex. Discriminant analysis of size-corrected data generated species assignments that were consistently accurate in separating the two species (100% jackknifed assignment success). Nasal curtain length was identified as the character which contributed the most to discrimination of the two species. Sexual dimorphism was evident in several characters that have previously been relied upon to distinguish G. crebripunctata from G. marmorata. A previously unreported feature, the absence of a tail spine in G. crebripunctata, provides an improved method of field identification between these species. Phylogenetic and genetic distance analyses based on 698 base pairs of the mitochondrial cytochrome b gene indicate that G. crebripunctata and G. marmorata form highly divergent lineages, supporting their validity as distinct species. The closely related batoid Aetoplatea zonura clustered within the Gymnura clade, indicating that it may not represent a valid genus. Strong population structuring (overall ,ST = 0·81,P < 0·01) was evident between G. marmorata from the Pacific coast of the Baja California peninsula and the Gulf of California, supporting the designation of distinct management units in these regions. [source] Phylogeography of the bigeye chub Hybopsis amblops (Teleostei: Cypriniformes): early Pleistocene diversification and post-glacial range expansionJOURNAL OF FISH BIOLOGY, Issue 8 2008P. B. Berendzen The bigeye chub, Hybopsis amblops, is a member of the Central Highlands ichthyofauna of eastern North America. Phylogenetic analyses of the H. amblops species group based on a 1059 bp fragment of the mitochondrial DNA cytochrome b gene did not recover a monophyletic group. The inclusion of Hybopsis hypsinotus in the species complex is questionable. Within H. amblops, five strongly supported clades were identified; two clades containing haplotypes from the Ozark Highlands and three clades containing haplotypes from the Eastern Highlands and previously glaciated regions of the Ohio and Wabash River drainages. Estimates of the timing of divergence indicated that prior to the onset of glaciation, vicariant events separated populations east and west of the Mississippi River. East of the Mississippi River glacial cycles associated with the blocking and rerouting of the Teays River system caused populations to be pushed southward into refugia of the upper Ohio River. Following the most recent Wisconsinan glaciation, populations expanded northward into previously glaciated regions and southward into the Cumberland River drainage. In the Ozarks, west of the Mississippi River, isolation of clades appears to be maintained by the lack of stream capture events between the upper Arkansas and the White River systems and a barrier formed by the Arkansas River. [source] Mitochondrial DNA in Atherina (Teleostei, Atheriniformes): differential distribution of an intergenic spacer in lagoon and marine forms of Atherina boyeriJOURNAL OF FISH BIOLOGY, Issue 5 2008V. MILANA The big-scale sand smelt Atherina boyeri lives in fresh water, brackish water and sea water of the western Atlantic Ocean and Mediterranean Sea. Previous studies concerning distribution, biometric characters and genetic molecular markers have suggested the possible existence of two or even three different groups or species of sand smelt, one ,lagoon' type and one (or two , punctuated and non-punctuated on the flanks) ,marine' type. In this study, the presence and the localization of an insertion was described, c. 200 bp in length, in the mtDNA of the lagoon and marine punctuated specimens of A. boyeri and its absence in the marine non-punctuated specimens, as well as in other two congeneric species, Atherina hepsetus and Atherina presbyter, and in the atheriniform Menidia menidia. The intergenic spacer is located between the tRNAGlu and cytochrome b (cyt b) genes and shares a c. 50% sequence similarity with cyt b. The distribution and the features of the intergenic spacer suggest that it might have originated from an event of gene duplication, which involved the cyt b gene (or, more likely, a part of it) and which took place in the common ancestor of the lagoon and the marine punctuated specimens. The data obtained therefore support the hypothesis of the existence of three cryptic and, or sibling species within the A. boyeri taxon and provide a genetic molecular marker to distinguish them. 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