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Reference Strains (reference + strain)
Selected AbstractsVariation in gene content among geographically diverse Sulfolobus isolatesENVIRONMENTAL MICROBIOLOGY, Issue 1 2008Dennis W. Grogan Summary The ability of competitive (i.e., comparative) genomic hybridization (CGH) to assess similarity across entire microbial genomes suggests that it should reveal diversification within and between natural populations of free-living prokaryotes. We used CGH to measure relatedness of genomes drawn from Sulfolobus populations that had been shown in a previous study to be diversified along geographical lines. Eight isolates representing a wide range of spatial separation were compared with respect to gene-specific tags based on a closely related reference strain (Sulfolobus solfataricus P2). For the purpose of assessing genetic divergence, 232 loci identified as polymorphic were assigned one of two alleles based on the corresponding fluorescence intensities from the arrays. Clustering of these binary genotypes was stable with respect to changes in the threshold and similarity criteria, and most of the groupings were consistent with an isolation-by-distance model of diversification. These results indicate that increasing spatial separation of geothermal sites correlates not only with minor sequence polymorphisms in conserved genes of Sulfolobus (demonstrated in the previous study), but also with the regions of difference (RDs) that occur between genomes of conspecifics. In view of the abundance of RDs in prokaryotic genomes and the relevance that some RDs may have for ecological adaptation, the results further suggest that CGH on microarrays may have advantages for investigating patterns of diversification in other free-living archaea and bacteria. [source] The Helicobacter pylori plasticity region locus jhp0947,jhp0949 is associated with duodenal ulcer disease and interleukin-12 production in monocyte cellsFEMS IMMUNOLOGY & MEDICAL MICROBIOLOGY, Issue 2 2004Ramon De Jonge Abstract Colonization with Helicobacter pylori always results in chronic gastritis, which is controlled by infiltration of mononuclear cells and the subsequent release of cytokines like interleukin (IL)-12. To identify H. pylori factors involved in inducing cytokine production in mononuclear cells, a random H. pylori mutant library was screened for the inability to induce IL-12 production in monocyte THP-1 cells. Of the 231 random mutants screened, one mutant (M1) showed a consistent twofold decrease in the amount of IL-12 induction compared to the parental strain 1061 (P<0.01). Further characterization of mutant M1 revealed that the kanamycin resistance cassette had integrated in the jhp0945 gene, which is situated in an H. pylori strain-specific plasticity region. Three reference strains possessing this plasticity region induced significantly higher amounts of IL-12 when compared to the H. pylori 26695 reference strain, which does not possess this plasticity region. The role in disease outcome of jhp0945 as well as the neighbouring plasticity region genes jhp0947 and jhp049 was assessed in a Dutch population cohort. Firstly, the presence of jhp0947 was completely linked with that of jhp0949 and was roughly associated with jhp0945 (P=0.072), but not with the cag pathogenicity island (PAI) (P=0.464). The presence of the jhp0947 and jhp0949 genes, but not of jhp0945, was significantly associated with duodenal ulcer disease when compared to gastritis (P=0.027). Therefore, the jhp0947,jhp0949 locus may be a novel putative H. pylori marker for disease outcome independent of the cag PAI. [source] Elucidation of the role of Grr1p in glucose sensing by Saccharomyces cerevisiae through genome-wide transcription analysisFEMS YEAST RESEARCH, Issue 3 2004Steen L. Westergaard Abstract The role of Grr1p in glucose sensing in Saccharomyces cerevisiae was elucidated through genome-wide transcription analysis. From triplicate analysis of a strain with deletion of the GRR1 -gene from the genome and an isogenic reference strain, 68 genes were identified to have significantly altered expression using a Student's t -test with Bonferroni correction. These 68 genes were widely distributed across different parts of the cellular metabolism and GRR1 -deletion is therefore concluded to result in polytrophic effects, indicating multiple roles for Grr1p. Using a less conservative statistical test, namely the SAM test, 232 genes were identified as having significantly altered expression, and also these genes were widely distributed across different parts of the cellular metabolism. Promoter analyses on a genome-wide scale and on the genes with significant changes revealed an over-representation of DNA-binding motifs for the transcriptional regulators Mig1p and Rgt1p in the promoter region of the significantly altered genes, indicating that Grr1p plays an important role in the regulatory pathways that ultimately lead to transcriptional regulation by each of the components Mig1p and Rgt1p. [source] Characterization of Pantoea dispersa UQ68J: producer of a highly efficient sucrose isomerase for isomaltulose biosynthesisJOURNAL OF APPLIED MICROBIOLOGY, Issue 1 2004L. Wu Abstract Aims:, Isolation, identification and characterization of a highly efficient isomaltulose producer. Methods and Results:, After an enrichment procedure for bacteria likely to metabolize isomaltulose in sucrose-rich environments, 578 isolates were screened for efficient isomaltulose biosynthesis using an aniline/diphenylamine assay and capillary electrophoresis. An isolate designated UQ68J was exceptionally efficient in sucrose isomerase activity. Conversion of sucrose into isomaltulose by UQ68J (enzyme activity of 90,100 U mg,1 DW) was much faster than the current industrial strain Protaminobacter rubrum CBS574.77 (41,66 U mg,1 DW) or a reference strain of Erwinia rhapontici (0·3,0·9 U mg,1 DW). Maximum yield of isomaltulose at 78,80% of supplied sucrose was achieved in less than half the reaction time needed by CBS574.77, and the amount of contaminating trehalulose (4%) was the lowest recorded from an isomaltulose-producing microbe. UQ68J is a Gram negative, facultatively anaerobic, motile, noncapsulate, straight rod-shaped bacterium producing acid but no gas from glucose. Based on 16S rDNA analysis UQ68J is closest to Klebsiella oxytoca, but it differs from Klebsiella in defining characteristics and most closely resembles Pantoea dispersa in phenotype. Significance and Impact of Study:, This organism is likely to have substantial advantage over previously characterized sucrose isomerase producers for the industrial production of isomaltulose. [source] Mumps virus strains isolated in Croatia in 1998 and 2005: Genotyping and putative antigenic relatedness to vaccine strainsJOURNAL OF MEDICAL VIROLOGY, Issue 5 2006antak Abstract Two mumps virus strains 9218/Zg98 and Du/CRO05 were isolated in two locations in Croatia in 1998 and 2005, respectively. Genetic characterization of these temporally distinct mumps virus isolates was carried out in order to determine their genotype and putative antigenic relatedness to mumps virus vaccine strains. Sequence analysis of the small hydrophobic (SH) gene revealed that isolate 9218/Zg98 shows less than 95% of similarity to any reference strain, thus representing a potential reference strain for a new genotype. Isolate Du/CRO05 clearly belongs to genotype G with the 97% of homology to the reference strain Glouc1/UK96. When compared to each other, the two Croatian strains have extremely low level of homology of only 89% indicating no relatedness between them. Putative antigenic properties of the HN protein of these two isolates were compared to different vaccine strains. The results reveal a higher level of homology of antigenic determinants to non-A genotype vaccine strains than to A genotype vaccine strain. J. Med. Virol. 78:638,643, 2006. © 2006 Wiley-Liss, Inc. [source] A phylogenetic study of human respiratory syncytial viruses group A and B strains isolated in two cities in Japan from 1980,2002JOURNAL OF MEDICAL VIROLOGY, Issue 2 2005Yuki Kuroiwa Abstract The circulation pattern and genetic evolution of respiratory syncytial virus (RSV) in Japan were examined based on 109 RSV field strains isolated over 20 seasons (1980,2002) in two cities, Sapporo and Tokyo. The second hypervariable region of the large glycoprotein (G) gene was amplified by RT-PCR and the products sequenced directly. The nucleotide sequences were compared to those representatives of RSV genotypes identified previously. Japanese group A and B isolates clustered into five and four genotypes defined previously, respectively. Another one group A and one group B genotypes, which could not be assigned to previous genotypes, were also identified. Although different genotypes usually co-circulated in each season, the isolates in proximate seasons from two communities were usually located in the same branches. Moreover, the strains with genotypes defined previously were usually isolated at the same time as each reference strain of Western countries. Several mutant group B strains with 1,20 longer amino acid G proteins were newly identified in Sapporo. These findings suggest that Japanese RSV strains underwent geographical and also temporal clustering while participating in RSV genetic evolution in a global setting. In addition, Japanese strains, especially group B, might have evolved individually in each community, sometimes changing the length of the G protein. J. Med. Virol. 76:241,247, 2005. © 2005 Wiley-Liss, Inc. [source] Human laminin-332 degradation by Candida proteinasesJOURNAL OF ORAL PATHOLOGY & MEDICINE, Issue 6 2008P. Pärnänen Background:, Human laminin-332 (Lm-332) degradation by 12 Candida strains and effects of synthetic proteinase inhibitors [Ilomastat (ILM), EDTA, chemically modified tetracycline-3(CMT-3), CMT-308, synthetic peptide CTT-2, and Pefabloc] were studied. Materials and methods:, Laminin-332 was incubated with sonicated cell fractions and 10 times concentrated cell-free fractions of reference and clinical strains of C. albicans, C. dubliniensis, C. guilliermondii, C. glabrata, C. krusei, and C. tropicalis. Proteolysis, pH effects, and inhibitors were analyzed by fluorography and zymography. Results:, Cell fractions of all species except C. guilliermondii and cell-free fractions of C. albicans, and C. dubliniensis showed 20,70 kDa gelatinases at pH 5.0 and 6.0. At pH 7.6, C. glabrata, C. krusei, and C. tropicalis cell fractions and C. tropicalis cell-free fractions showed 55,70 kDa gelatinases. CMT-3, CMT-308, and CTT-2 inhibited Candida gelatinases slightly better than Pefabloc, ILM, and EDTA. No Candida fractions degraded Lm-332 at pH 7.6, but at pH 5.0, 100 kDa bands were generated by cell fractions of C. dubliniensis and C. tropicalis; C. albicans and C. glabrata clinical strains; and C. guilliermondii reference strain. C. krusei reference strain yielded three 100,130 kDa bands. C. albicans, C. dubliniensis, and C. tropicalis reference and clinical strain's cell-free fractions generated 100 kDa band. Conclusions:, Laminin-332 degradation is pH-dependent and differences exist between studied Candida strains. Lm-332 degradation can exert functional disturbances on basement membrane integrity, possibly aiding Candida cell invasion into tissues. Certain synthetic matrix metalloproteinase inhibitors (CMTs, CTT) can inhibit Candida proteinases and may be therapeutically useful in future. [source] HETEROGENEITY OF THE CYANOBACTERIAL GENUS SYNECHOCYSTIS AND DESCRIPTION OF A NEW GENUS, GEMINOCYSTIS,JOURNAL OF PHYCOLOGY, Issue 4 2009Jana Korelusová The study and revision of the unicellular cyanobacterial genus Synechocystis was based on the type species S. aquatilis Sauv. and strain PCC 6803, a reference strain for this species. Uniformity in rRNA gene sequence, morphology, and ultrastructure was observed in all available Synechocystis strains, with the exception of the strain PCC 6308, which has been considered by some to be a model strain for Synechocystis. This strain differs substantially from the typical Synechocystis cluster according to both molecular (<90% of similarity, differences in 16S,23S rRNA internal transcribed spacer [ITS] secondary structure) and phenotypic criteria (different ultrastructure of cells). This strain is herein classified into the new genus Geminocystis gen. nov., as a sister taxon to the genus Cyanobacterium. Geminocystis differs from Cyanobacterium by genetic position (<94.4% of similarity) and more importantly by its different type of cell division. Because strain PCC 6308 was designated as a reference strain of the Synechocystis cluster 1 in Bergey's Manual, the members of this genetic cluster have to be revised and reclassified into Geminocystis gen. nov. Only the members of the Synechocystis cluster 2 allied with PCC 6803 correspond both genetically and phenotypically to the type species of the genus Synechocystis (S. aquatilis). [source] Detection of Phytoplasma Infection in Rose, with Degeneration SymptomsJOURNAL OF PHYTOPATHOLOGY, Issue 1 2001M. Kami In 1998 a severe disease was observed on rose cvs. ,Patina', ,Papillon' and ,Mercedes' cultivated in a commercial greenhouse in Poland. The symptoms included stunted growth, bud proliferation, leaf malformation and deficiency of flower buds. Sporadically some plants yielded flower buds transformed into big-bud structures and degenerated flowers. The presence of phytoplasma in roses with severe symptoms as well as in recovered plants and Catharanthus roseus experimentally infected by grafting and via dodder was demonstrated by nested polymerase chain reaction assay with primers pair R16F2/R2 or R16F1/R0 and R16(I)F1/R1 amplifying phytoplasma 16S rDNA fragment. The polymerase chain reaction products (1.1 kb) used for restriction fragment length polymorphism analysis after digestion with endonuclease enzymes AluI and MseI produced the same restriction profiles for all samples. The restriction profiles of phytoplasma DNA from these plants corresponded to those of an aster yellows phytoplasma reference strain. Electron microscope examination of the ultra-thin sections of the stem showed wall thickenings of many sieve tubes of the diseased roses and single phytoplasma cells within a sieve element of the phloem of experimentally infected periwinkles. This paper is the first report on aster yellows phytoplasma in rose identified at a molecular level. Detektion einer Phytoplasma-Infektion bei Rosen mit Degenerationserscheinungen Im Jahr 1998 wurde eine schwere Krankheit bei Rosen der Sorten ,Patina', ,Papillon' und ,Mercedes' festgestellt, die in einem polnischen Gewächshaus für kommerzielle Zwecke kultiviert wurden. Zu den Symptomen gehörten Kümmerwuchs, durchwachsene Knospen, Blattmißbildungen und ein Mangel an Blütenknospen. Einige wenige Pflanzen trugen übergroße Blütenknospen, die degenerierte Blüten hervorbrachten. Die Anwesenheit von Phytoplasmen in Rosen mit starken Symptomen, in erholten Pflanzen und in Catharanthus roseus, der durch Pfropfen und durch Teufelszwirn (Cuscuta) experimentell infiziert worden war, wurde mittels einer genesteten Polymerase-Kettenreaktion mit den Primerpaaren R16F2/R2 oder R16F1/R0 und R16(1)F1/R1 zur Amplifikation des Phytoplasma-16S rDNA-Fragments demonstriert. Die für die Analyse der Restriktionsfragmentlängenpolymorphismen nach Verdau mit den Endonucleasen AluI und MseI verwendeten PCR-Produkte (1,1 kb) produzierten bei allen Proben die gleichen Restriktionsprofile. Die Restriktionsprofile der Phytoplasma-DNA aus diesen Pflanzen entsprachen denjenigen eines Typenstamms eines Asternvergilbung auslösenden Phytoplasmas. Elektronenmikroskopische Untersuchungen ultradünner Schnitte des Stamms zeigten Wandverdickungen bei zahlreichen Siebröhren der erkrankten Rosen und einzelne Phytoplasmazellen innerhalb eines Siebelements des Phloems experimentell infizierter Immergrün-Pflanzen. Dies ist der erste Bericht über ein auf molekularer Ebene identifiziertes Asternvergilbungs-Phytoplasma bei Rosen. [source] Pyrethroid resistance/susceptibility and differential urban/rural distribution of Anopheles arabiensis and An. gambiae s.s. malaria vectors in Nigeria and GhanaMEDICAL AND VETERINARY ENTOMOLOGY, Issue 3 2003M. Kristan Abstract., Resistance to pyrethroid insecticides and DDT caused by the kdr gene in the malaria vector Anopheles gambiae Giles s.s. (Diptera: Culicidae) has been reported in several West African countries. To test for pyrethroid resistance in two more countries, we sampled populations of the An. gambiae complex from south-western Ghana and from urban and rural localities in Ogun State, south-west Nigeria. Adult mosquitoes, reared from field-collected larvae, were exposed to the WHO-recommended discriminating dosage of exposure for 1 h to DDT 4%, deltamethrin 0.05% or permethrin 0.75% and mortality was recorded 24 h post-exposure. Susceptibility of An. gambiae s.l. to DDT was 94,100% in Ghana and 72,100% in Nigeria, indicating low levels of DDT resistance. Deltamethrin gave the highest mortality rates: 97,100% in Ghana, 95,100% in Nigeria. Ghanaian samples of An. gambiae s.l. were fully susceptible to permethrin, whereas some resistance to permethrin was detected at 4/5 Nigerian localities (percentage mortalities 75, 82, 88, 90 and 100%), with survivors including both An. arabiensis Patton and An. gambiae s.s. identified by PCR assay. Even so, the mean knockdown time was not significantly different from a susceptible reference strain, indicating absence or low frequency of kdr -type resistance. Such low levels of pyrethroid resistance are unlikely to impair the effectiveness of pyrethroid-impregnated bednets against malaria transmission. Among Nigerian samples of An. gambiae s.l., the majority from two urban localities were identified as An. arabiensis, whereas the majority from rural localities were An. gambiae s.s. These findings are consistent with those of M. Coluzzi et al. (1979). Differences of ecological distribution between molecular forms of An. gambiae s.s. were also found, with rural samples almost exclusively of the S-form, whereas the M-form predominated in urban samples. It is suggested that ,urban island' populations of An. arabiensis and of An. gambiae s.s. M-form in the rainforest belt of West Africa might be appropriate targets for elimination of these malaria vectors by the sterile insect technique. [source] The identification of circular extrachromosomal DNA in the nuclear genome of Trypanosoma bruceiMOLECULAR MICROBIOLOGY, Issue 2 2003N. S. Alsford Summary Nuclear extrachromosomal DNA elements have been identified in several kinetoplastids such as Leishmania and Trypanosoma cruzi, but never in Trypanosoma brucei. They can occur naturally or arise spontaneously as the result of sublethal drug exposure of parasites. In most cases, they are represented as circular elements and are mitotically unstable. In this study we describe the presence of circular DNA in the nucleus of Trypanosoma brucei. This novel type of DNA was termed NR-element (NlaIII repeat element). In contrast to drug-induced episomes in other kinetoplastids, the T. brucei extrachromosomal NR-element is not generated by drug selection. Furthermore, the element is stable during mitosis over many generations. Restriction analysis of tagged NR-element DNA, unusual migration patterns during pulsed field gel electrophoresis (PFGE) and CsCl/ethidium bromide equilibrium centrifugation demonstrates that the NR-element represents circular DNA. Whereas it has been found in all field isolates of the parasites we analysed, it is not detectable in some laboratory strains notably the genome reference strain 927. The DNA sequence of this element is related to a 29 bp repeat present in the subtelomeric region of VSG-bearing chromosomes of T. brucei. It has been suggested that this subtelomeric region is part of a transition zone on chromosomes separating the relatively stable telomeric repeats from the recombinationaly active region downstream of VSG genes. Therefore, we discuss a functional connection between the occurrence of this circular DNA and subtelomeric recombination events in T. brucei. [source] Distribution of Bacteroides forsythus genotypes in a Japanese periodontitis populationMOLECULAR ORAL MICROBIOLOGY, Issue 4 2003Y. Huang Bacteroides forsythus is an important pathogen in periodontal diseases and has been associated with advanced and refractory periodontitis. The difficulties associated with culturing this species have meant that the distribution and pathogenic mechanisms of B. forsythus remain unclear. In this study, the arbitrarily primed polymerase chain reaction (AP-PCR) method was used to investigate the genotype distribution of B. forsythus in a Japanese periodontitis population, as well as the relationship between AP-PCR genotypes and periodontal status. B. forsythus reference strain, ATCC 43037T and 137 clinical bacterial isolates from 64 subjects were separated into 11 distinct AP-PCR genotypes using a single randomly-sequenced primer, 5,-CCGGCGGCG-3, (A-05). The majority (80.9%) of B. forsythus strains examined belonged to AP-PCR genotypes I, II, III and IV (accounting for 39.7%, 20.6%, 10.3% and 10.3%, respectively). Types I and III primarily consisted of isolates from chronic periodontitis subjects (80.8% and 85.7%, respectively), while Types II and IV consisted mainly of isolates from aggressive periodontitis subjects (85.7% and 100%, respectively). Except for three subjects who harbored two different B. forsythus genotypes in the oral cavity, all subjects only infected with one genotype intraindividually. These results demonstrate that the AP-PCR method is useful for genotypic analysis of B. forsythus. This species showed a genetic diversity among the investigated population. A clonal nature of B. forsythus infection is suggested. Furthermore, different AP-PCR genotypes of B. forsythus appear to be associated with different types of periodontitis. [source] Relationship between esterase activity and acrinathrin and methiocarb resistance in field populations of western flower thrips, Frankliniella occidentalis,PEST MANAGEMENT SCIENCE (FORMERLY: PESTICIDE SCIENCE), Issue 12 2006Ana C Maymó Abstract The western flower thrips, Frankliniella occidentalis (Pergande), is a serious pest in the south-east of Spain owing to its direct feeding on crops, transmission of the tomato spotted wilt virus and its very high level of resistance to insecticides. Mechanisms of resistance were examined using field populations of F. occidentalis with different susceptibilities to acrinathrin, methiocarb (selective insecticides), endosulfan, metamidophos and deltamethrin (broad-spectrum insecticides). Esterase activity towards ,-naphthyl acetate and p -nitrophenyl acetate in resistant strains was significantly higher than in the reference strain (MLFOM) for both model substrates. This higher activity was significantly correlated with acrinathrin and methiocarb resistance. Copyright © 2006 Society of Chemical Industry [source] Impact of spray application methodology on the development of resistance to cypermethrin and spinosad by fall armyworm Spodoptera frugiperda (JE Smith)PEST MANAGEMENT SCIENCE (FORMERLY: PESTICIDE SCIENCE), Issue 11 2006Ali Al-Sarar Abstract The development of resistance to an insecticide under various types of application method has yet to be reported in the literature. Five fall armyworm Spodoptera armigera (JE Smith) colonies were reared in a chamber for ten generations before starting topical application bioassays. From each colony, 200,500 third,fourth-instar larvae were fed for 72 h on corn plants sprayed with cypermethrin or spinosad at minimum application rate (20 g ha,1) using a small droplet size nozzle XR8001VS (volume median diameter Dv0.5 = 163 µm) or a large droplet size nozzle XR8008VS (Dv0.5 = 519 µm). Surviving larvae were transferred to untreated corn leaves to complete their life cycle. Next-generation third-instar larvae of each colony were topically dosed with technical cypermethrin or spinosad at 1 µL per larva, and mortality was recorded 24 h post-treatment. The results indicated that cypermethrin demonstrated an insecticidal activity greater than that of spinosad, and the cypermethrin regression lines moved to the right faster than those for spinosad, indicating an increased tolerance of cypermethrin. Generally, larvae from all generations (F1,F7) under the XR8008VS treatments were less susceptible to cypermethrin and developed resistance faster and to higher levels than larvae from the XR8001VS treatments. The confidence limits (95%) of LD50 for all spinosad treatments indicated that there was no significant difference from the LD50 value of the susceptible reference strain. The results are a first indication that application technology/insecticide reaction may affect the rapidity of resistance development in certain pest/plant scenarios, but field studies are needed to confirm this conclusion. Copyright © 2006 Society of Chemical Industry [source] Upper susceptibility threshold limits with confidence intervals: a method to identify normal and abnormal population values for laboratory toxicological parameters, based on acetylcholinesterase activities in sea licePEST MANAGEMENT SCIENCE (FORMERLY: PESTICIDE SCIENCE), Issue 3 2006Anders Fallang Abstract The interpretation and importance of comparing field values of susceptibility to pesticides with a laboratory reference strain that might bear little resemblance to the actual situation in the field are problematic and a continuing subject of debate. In this paper a procedure for defining a ,normal sensitive' population from a field study of 383 individuals to provide a basis for analysing and interpreting in vitro results is described and examined. Instead of using only the 95th percentile, the upper and lower confidence limits for the 95th percentile were also compared to select the best estimation of the limit for the normal material. A field population constrained by the upper confidence limit for the 95th percentile provides appropriate descriptions of the normal material in this study. This approach should prove useful in studies of pesticide resistance in field populations. Copyright © 2006 Society of Chemical Industry [source] Synergism and stability of acetamiprid resistance in a laboratory colony of Plutella xylostellaPEST MANAGEMENT SCIENCE (FORMERLY: PESTICIDE SCIENCE), Issue 8 2005Kodwo D Ninsin Abstract The involvement of metabolic enzymes in the resistance of a laboratory colony of diamondback moth, Plutella xylostella (L), to the neonicotinoid insecticide acetamiprid was determined with the synergists piperonyl butoxide (PBO), which suppresses the activity of cytochrome P-450 monooxygenases, and S,S,S -tributyl phosphorotrithioate (DEF), an inhibitor of esterases, using the leaf-dipping method. Both PBO and DEF enhanced the insecticidal activity of acetamiprid significantly in the resistant P xylostella strain but not in a reference strain, suggesting that cytochrome P-450 monooxygenases and esterases play an important role in the resistance of P xylostella to acetamiprid. The resistant P xylostella strain was also reared without further exposure to acetamiprid to determine the stability of resistance. Maintaining the resistant strain for seven generations in the absence of selection pressure resulted in a drop in resistance ratio from 110 to 2.42, indicating that acetamiprid resistance in P xylostella is not stable. Copyright © 2005 Society of Chemical Industry [source] Proteomic analysis of exoproteins expressed by enterotoxigenic Staphylococcus aureus strainsPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 12 2008Gabriella Pocsfalvi Dr. Abstract Pathogenic bacteria excrete a variety of virulence factors into extracellular medium and to the cell surface which have essential roles in the colonization and insurrection of the host cells, and thus reflect the degree of bacterial pathogenicity. For the exploration of virulence factors expressed in the secreted proteome fraction, different Staphylococcus aureus strains were analyzed using gel-based bottom-up proteomic approach. A total of 119 distinct proteins were identified for the enterotoxin gene cluster (egc) negative and seb gene positive S. aureus American Type Culture Collection (ATCC) 14458 strain by the use of one- and 2-DE based proteomics. Detailed analysis of enterotoxin region of the 2-D map confirmed, beside the highly expressed staphylococcal enterotoxin B (SEB), the presence of enterotoxin-like proteins SElK and SElQ previously predicted by genotyping (Sergeev et al.., J. Clin. Microbiol. 2004, 42, 2134,2143). Exoprotein patterns at the late-exponential (7,h) and stationary (24,h) phases of cellular growth show a high-level similarity in this region. Comparative analysis of enterotoxin region of five S. aureus strains including two clinical isolates (RIMD 31092 and A900322), a food derived strain (AB-8802) with highly prevalent egc positive operon and a nonenterotoxigenic reference strain (ROS) revealed the presence of different known enterotoxins and other virulence factors along with a number of core exoproteins. In addition, production of SElL (RIMD 31092) and SElP (A900322) was demonstrated for the first time at the protein level. Under the experimental conditions applied none of the enterotoxins encoded by the genes of egc operon was identified. [source] Growth response of Nile tilapia fry to salinity stress in the presence of an ,internal reference' fishAQUACULTURE RESEARCH, Issue 7 2005Zubaida U Basiao Abstract Growth of three strains of Oreochromis niloticus L. fry exposed to salinity stress in the presence of an internal reference fish were compared. The Central Luzon State University (CLSU) strain was obtained from the Freshwater Aquaculture Center, CLSU, Philippines. The ISRAEL strain was acquired from the Philippine government's Bureau of Fisheries and Aquatic Resources National Freshwater Fisheries Technology Center (BFAR-NFFTC), Munoz, Nueva Ecija. The National Inland Fisheries Institute (NIFI) strain was obtained from the NIFI, Bangkok, Thailand. Eight to nine full-sib families (replicates) per strain were split into two groups. One group was grown in freshwater for 2 weeks, acclimated to 32 ppt and reared for 2 weeks and finally grown in freshwater for another 2 weeks. Another group was contemporaneously grown in freshwater polyethylene tanks for 6 weeks. Each replicate family included a size-matched internal reference population of red tilapia strain. Two-way analysis of variance (anova) revealed no significant strain differences (P=0.081; r2=0.106). However, analysis of covariance with the internal reference strain used as a covariate showed significant (P=0.049; r2=0.638) strain effects on specific growth (based on standard length measurements). The ISRAEL strain showed consistently better growth rate in both saline and freshwater environments than the NIFI and CLSU strains. We estimated the statistical power of the two-way anova (,=,(k,,1)(factor MS,s2)/(k,s2); Zar 1984) to be ,0.30. There was a 70% probability of a Type II error and no true difference in the growth of the three strains was detected. The use of internal reference strain as a covariate improved the r2 from 0.106 to 0.638 and increased the efficiency of the test in detecting a true difference. Other strain comparison studies in our laboratory at the Southeast Asian Fisheries Development Center Aquaculture Department showed that the ISRAEL strain shows better growth than the NIFI and CLSU strains in a crowding stress tolerance experiment, when fed only with rice bran and under restrictive feeding regimes. [source] Comparison of one-tube multiplex PCR, automated ribotyping and intergenic spacer (ITS) sequencing for rapid identification of Acinetobacter baumanniiCLINICAL MICROBIOLOGY AND INFECTION, Issue 8 2007T.-L. Chen Abstract Acinetobacter baumannii has emerged as a serious cause of nosocomial infections. Rapid identification of this pathogen is required so that appropriate therapy can be given and outbreaks controlled. This study evaluated a multiplex PCR and an automated ribotyping system for the rapid identification of Acinetobacter baumannii. In total, 22 different reference strains and 138 clinical isolates of Acinetobacter spp., identified by 16S,23S rRNA intergenic spacer (ITS) sequence analysis, were evaluated. All A. baumannii isolates (82 clinical isolates and one reference strain) were identified by the multiplex PCR method (specificity 100%). The sensitivity and specificity of the ribotyping system for identification of A. baumannii were 85.5% (71/83) and 93.5% (72/77), respectively. An additional 100 clinical isolates belonging to the Acinetobacter calcoaceticus,A. baumannii complex were used to compare these two methods for identification of A. baumannii, and this comparison revealed a level of disagreement of 14% (14 isolates). The accuracy of the multiplex PCR was 100%, which was confirmed by sequence analysis of the ITS and recA gene of these isolates. Thus, the multiplex PCR method dramatically increased the efficiency and speed of A. baumannii identification. [source] The Helicobacter pylori plasticity region locus jhp0947,jhp0949 is associated with duodenal ulcer disease and interleukin-12 production in monocyte cellsFEMS IMMUNOLOGY & MEDICAL MICROBIOLOGY, Issue 2 2004Ramon De Jonge Abstract Colonization with Helicobacter pylori always results in chronic gastritis, which is controlled by infiltration of mononuclear cells and the subsequent release of cytokines like interleukin (IL)-12. To identify H. pylori factors involved in inducing cytokine production in mononuclear cells, a random H. pylori mutant library was screened for the inability to induce IL-12 production in monocyte THP-1 cells. Of the 231 random mutants screened, one mutant (M1) showed a consistent twofold decrease in the amount of IL-12 induction compared to the parental strain 1061 (P<0.01). Further characterization of mutant M1 revealed that the kanamycin resistance cassette had integrated in the jhp0945 gene, which is situated in an H. pylori strain-specific plasticity region. Three reference strains possessing this plasticity region induced significantly higher amounts of IL-12 when compared to the H. pylori 26695 reference strain, which does not possess this plasticity region. The role in disease outcome of jhp0945 as well as the neighbouring plasticity region genes jhp0947 and jhp049 was assessed in a Dutch population cohort. Firstly, the presence of jhp0947 was completely linked with that of jhp0949 and was roughly associated with jhp0945 (P=0.072), but not with the cag pathogenicity island (PAI) (P=0.464). The presence of the jhp0947 and jhp0949 genes, but not of jhp0945, was significantly associated with duodenal ulcer disease when compared to gastritis (P=0.027). Therefore, the jhp0947,jhp0949 locus may be a novel putative H. pylori marker for disease outcome independent of the cag PAI. [source] Genomic and phenotypic heterogeneity of Acidithiobacillus spp. strains isolated from diverse habitats in ChinaFEMS MICROBIOLOGY ECOLOGY, Issue 2 2008Yong-Qing Ni Abstract The genetic variability among 32 Chinese Acidithiobacillus spp. environmental isolates and four reference strains representing three recognized species of the genus Acidithiobacillus was characterized by using a combination of molecular methods, namely restriction fragment length polymorphisms of PCR-amplified 16S rRNA genes and 16S,23S rRNA gene intergenic spacers, repetitive element PCR, arbitrarily primed PCR and 16S rRNA gene sequence analyses. 16S rRNA gene sequences revealed that all Acidithiobacillus spp. strains could be assigned to seven groups, three of which encompassed the Acidithiobacillus ferrooxidans strains from various parts of the world. A comparative analysis of the phylogenetic Group 1 and 2 was undertaken. Restriction fragment length polymorphism results allowed us to separate the 35 Acidithiobacillus strains into 15 different genotypes. An integrated phenotypic and genotypic analysis indicated that the distribution of A. ferrooxidans strains among the physiological groups were in agreement with their distribution among the genomic groups, and that no clear correlation was found between the genetic polymorphism of the Acidithiobacillus spp. strains and either the geographic location or type of habitats from which the strains were isolated. In addition, five unidentified sulfur-oxidizing isolates may represent one or two novel species of the genus Acidithiobacillus. The results showed that the Chinese Acidithiobacillus spp. isolates exhibited a high degree of genomic and phenotypic heterogeneity. [source] Loop-mediated isothermal amplification targeting the apxIVA gene for detection of Actinobacillus pleuropneumoniaeFEMS MICROBIOLOGY LETTERS, Issue 1 2009Wang Yang Abstract Loop-mediated isothermal amplification (LAMP) is a novel nucleic acid amplification method performed under isothermal conditions with high specificity and efficiency. We developed a diagnostic method based on LAMP for detection of Actinobacillus pleuropneumoniae. Using six specific primers targeting the apxIVA gene, the LAMP assay rapidly amplified the target gene within 30 min, requiring only a laboratory water bath for the reaction to occur. The resulting amplificon was visualized by adding SYBR Green I to the mixture. The results obtained from testing 15 A. pleuropneumoniae reference strains and other seven bacterial species strains showed that the LAMP was as specific as and 10 times more sensitive than nested PCR. Sixty-five tonsil samples were collected from 65 healthy pigs. All the samples were negative for A. pleuropneumoniae by immunomagnetic separation-based (IMS) bacterial isolation, nested PCR and LAMP, respectively. Meanwhile, 115 tonsil samples were also collected from 115 pigs with apparent respiratory problems. Twenty-two were positive by IMS bacterial isolation. All the samples that were positive by IMS bacterial isolation were also positive by nested PCR and LAMP. The LAMP assay demonstrated exceptionally higher sensitivity than nested PCR by picking up 14 additional positive cases (,2 test, P<0.0001); we concluded that LAMP was a highly sensitive and reliable method for detection of A. pleuropneumoniae infection. [source] Characterisation of symbionts of entomopathogenic nematodes by universally primed-PCR (UP-PCR) and UP-PCR product cross-hybridisationFEMS MICROBIOLOGY LETTERS, Issue 1 2002O. Nielsen Abstract This work introduces and demonstrates the applicability of universally primed-PCR (UP-PCR) for differentiating bacterial symbionts of entomopathogenic nematodes. Furthermore, typing by UP-PCR product cross-hybridisation was successfully introduced to cluster the bacterial strains. The work was initiated by isolating 10 isolates of Photorhabdus temperata (S172) from the nematode host Heterorhabditis sp. (DK172) and 12 isolates of Xenorhabdus bovienii (S1) from the nematode Steinernema feltiae (DK1). The isolates were compared by UP-PCR using different primers. The two bacterial species (P. temperata and X. bovienii) could be distinguished on the basis of the banding pattern whereas isolates isolated from the same nematode host had identical banding patterns. Three isolates obtained from DK172 and DK1, respectively, were then selected along with a number of reference strains (Hb, HP88, C1, K122, HSH2, HL81, T228, 61, AN6, Q58) and further characterised by UP-PCR product cross-hybridisation. The Xenorhabdus strains (Q58, AN6, 61, T228, S1) represented three species and these species were separated by the hybridisation technique. The Photorhabdus strains (Hb, HP88, C1, K122, HSH2, HL81, S172) represented two species and were also separated according to this in the cross-hybridisation. Within each species of Photorhabdus, two subgroups were formed as a result of intensity of the hybridisation signals. This grouping was in agreement with previous studies in other laboratories. [source] Identification of Trichoderma strains by image analysis of HPLC chromatogramsFEMS MICROBIOLOGY LETTERS, Issue 2 2001Ulf Thrane Abstract Forty-four Trichoderma strains from water-damaged building materials or indoor dust were classified with chromatographic image analysis on full chromatographic matrices obtained by high performance liquid chromatography with UV detection of culture extracts. The classes were compared with morphological identification and rDNA sequence data, and for each class all strains were of the same identity. With all three techniques each strain , except one , was identified as the same species. These strains belonged to Trichoderma atroviride (nine strains), Trichoderma viride (three strains), Trichoderma harzianum (10 strains), Trichoderma citrinoviride (12 strains), and Trichoderma longibrachiatum (nine strains). The odd strain was identified as Trichoderma hamatum by morphology and rDNA sequencing, but not by image analysis as no reference strains of this species were included. It is concluded that the secondary metabolite profile contains sufficient information for classification and species identification. [source] Anaerobic homolactate fermentation with Saccharomyces cerevisiae results in depletion of ATP and impaired metabolic activityFEMS YEAST RESEARCH, Issue 3 2009Derek A. Abbott Abstract Conversion of glucose to lactic acid is stoichiometrically equivalent to ethanol formation with respect to ATP formation from substrate-level phosphorylation, redox equivalents and product yield. However, anaerobic growth cannot be sustained in homolactate fermenting Saccharomyces cerevisiae. ATP-dependent export of the lactate anion and/or proton, resulting in net zero ATP formation, is suspected as the underlying cause. In an effort to understand the mechanisms behind the decreased lactic acid production rate in anaerobic homolactate cultures of S. cerevisiae, aerobic carbon-limited chemostats were performed and subjected to anaerobic perturbations in the presence of high glucose concentrations. Intracellular measurements of adenosine phosphates confirmed ATP depletion and decreased energy charge immediately upon anaerobicity. Unexpectedly, readily available sources of carbon and energy, trehalose and glycogen, were not activated in homolactate strains as they were in reference strains that produce ethanol. Finally, the anticipated increase in maximal velocity (Vmax) of glycolytic enzymes was not observed in homolactate fermentation suggesting the absence of protein synthesis that may be attributed to decreased energy availability. Essentially, anaerobic homolactate fermentation results in energy depletion, which, in turn, hinders protein synthesis, central carbon metabolism and subsequent energy generation. [source] Visualization of Helicobacter Species Within the Murine Cecal Mucosa Using Specific Fluorescence In Situ HybridizationHELICOBACTER, Issue 2 2005Vivian Chan ABSTRACT Background., Members of the genus Helicobacter have been associated with colitis development in a number of immunodeficient animal models. While it is known that these organisms can initiate colitis development, the location and spatial distribution of these bacteria within the intestinal tract is currently unknown. In this study, we developed and optimized fluorescence in situ hybridization (FISH) probes specifically for Helicobacter species. Materials and Methods., Based on 16S-RNA gene alignments, two probes specific for the entire family Helicobacteraceae and two probes specific for Helicobacter ganmani and Helicobacter hepaticus were designed. Evaluation of these probes was determined using ATCC reference strains and cecum samples from ten IL-10 knockout mice. The presence of Helicobacter species was determined using FISH and verified using PCR-DGGE and microscopic examination of silver stained sections. Results., Analysis of the ATCC reference strains revealed that the probes HEL274/HEL717 were specific for the family Helicobacteraceae, while HEP642 was specific for H. hepaticus and GAN1237 for H. ganmani. Using these probes, a pattern of spatial localization of the two different Helicobacter species was observed in the cecum tissues of IL-10 knockout mice. This consistently showed that H. ganmani was localized to the lower regions and H. hepaticus to the mid-upper regions of the crypts. Conclusion., We have developed FISH probes specific for the family Helicobacteraceae as well as two individual Helicobacter species. This study will allow the future use of the FISH to better understand host-pathogen interactions in vitro. [source] Preparation, antimicrobial activity, and toxicity of 2-amino-4-arylthiazole derivativesHETEROATOM CHEMISTRY, Issue 4 2006Pedro Morales-Bonilla Seven 2-amino-4-aryl-1,3-thiazoles (1a,g) and their corresponding 2-aminoacetyl (2a,g) and 2-aminoacetyl-5-bromo (3a,g) derivatives were synthesized and tested in vitro against 11 reference strains, three Gram-positive and four Gram-negative bacteria, two yeasts, and two moulds. Toxicity of the compounds was also evaluated using the brine shrimp test. Compounds 1a, 1b, 1e,g, and 3b showed moderate antimicrobial activity at different concentrations. The results indicated that acetylation of the amino group and bromination at position 5 of the thiazole moiety cause lost of activity. Compounds 1a, 1e, and 1f showed toxicity to brine shrimp nauplii below 10 ppm. Most other compounds showed moderate toxicity, LD50 above 100 ppm. Structures of all compounds were confirmed by NMR and MS data. © 2006 Wiley Periodicals, Inc. Heteroatom Chem 17:254,260, 2006; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/hc.20182 [source] Identification of surface protective antigen (spa) types in Erysipelothrix reference strains and diagnostic samples by spa multiplex real-time and conventional PCR assaysJOURNAL OF APPLIED MICROBIOLOGY, Issue 4 2010H.G. Shen Abstract Aim:, To develop spa multiplex real-time and conventional PCR assays to detect and differentiate between spaA, spaB and spaC genes within Erysipelothrix spp. Methods and Results:, For evaluation of the assays, 28 Erysipelothrix spp. reference strains, 25 tissues from pigs inoculated with reference strains of serotypes 1, 2, 5, 10 or 18, and 15 diagnostic samples were used. SpaA was found to be present in Erysipelothrix rhusiopathiae serotypes 1a, 1b, 2, 5, 9, 12, 15, 16, 17, 23 and N; spaB was detected in E. rhusiopathiae serotypes 4, 6, 8, 11, 19 and 21 and spaC was detected in E. sp. strain 2 serotype 18. Spa-related genes were not detected in E. tonsillarum strains (serotypes 3, 7, 10, 14, 20, 22, 24, 25, 26) or E. sp. strain 1 (serotype 13). With the spa multiplex real-time PCR assay, it was also possible to further differentiate spaB into spaB1 (serotypes 4, 6, 8, 19 and 21) and spaB2 (serotype 11). Overall, spaA was detected in seven experimental tissue samples and six diagnostic tissue samples, and spaC in two experimental tissue samples. The detection limits were determined to be five colony-forming units (CFU) per reaction for the spa multiplex real-time PCR assay and 4000 CFU per reaction for the conventional PCR assay. Conclusions:, Both spa PCR assays were specific and reproducible in the identification of spa types in Erysipelothrix spp. Significance and Impact of the Study:, The described spa PCR assays may be useful tools for investigating spa prevalence among strains isolated from field tissues and to determine the role of the Spa proteins in vaccine protection and pathogenesis. [source] Characterization of Pasteurellaceae-like bacteria isolated from clinically affected psittacine birdsJOURNAL OF APPLIED MICROBIOLOGY, Issue 4 2010R.H. Gregersen Abstract Aims:, The aim of the present investigation was to identify and characterize Pasteurella -like isolates obtained from clinically affected psittacine birds. Methods and Results:, A total of 37 isolates from psittacine birds tentatively classified with the family Pasteurellaceae were characterized phenotypically. The genetic relationship was investigated by sequencing of partial rpoB and 16S rRNA genes for selected isolates. The results obtained were compared with the data from 16 reference strains. Nine isolates were identified as Gallibacterium spp., 16 as Volucribacter spp. or Volucribacter- like, while 11 isolates were classified as taxon 44 of Bisgaard. A single isolate was identified as Pasteurella multocida. Conclusions:, Characterization of Pasteurellaceae by traditional methods is often inconclusive because of inconsistent reactions and phenotypic diversity. For the same reason, genotyping is essential to allow proper classification as demonstrated in the present study. Significance and Impact of the Study:, Limited information exists on the isolation and significance of Pasteurellaceae associated with clinically affected psittacine birds showing signs of digestive and/or respiratory disorders. The present investigations demonstrated that these organisms are widely distributed among clinically affected birds, but isolation of these taxa cannot be unambiguously correlated with the symptoms observed. [source] Application of recA and rpoB sequence analysis on phylogeny and molecular identification of Geobacillus speciesJOURNAL OF APPLIED MICROBIOLOGY, Issue 2 2009F.Y. Weng Abstract Aims:, Some Geobacillus species have highly similar 16S rRNA gene sequences, making 16S rDNA sequence analysis-based identification problematic. To overcome this limitation, recA and rpoB sequence analysis was evaluated as an alternative for distinguishing Geobacillus species. Methods and Results:, The phylogram of 16S rRNA gene sequences inferred from the neighbour-joining method showed that nine clusters of Geobacillus species were characterized with bootstrap values >90%. The recA and rpoB sequences of 10 reference strains in clusters V, VIb and VIc were amplified and sequenced using consensus primers. Alignment of recA sequences in clusters V, VIb and VIc revealed three types of recA genes, consistent with the putative amino acid sequences and in vivo recA splicing analysis. The phylogram constructed from rpoB sequences showed more divergence than that constructed from 16S rRNA gene sequences. Conclusions:,recA and rpoB sequence analysis differentiated closely-related Geobacillus species and provided direct evidence for reclassifying some species dubiously categorized as Geobacilli. Additionally, this study revealed three types of recA genes in the different Geobacillus species. Significance and Impact of the Study:, This study highlights the advantage of recA and rpoB sequence analysis to supplement 16S rRNA gene sequence analysis for efficient and convenient determination of Geobacillus species. [source] | |||||||||||||||||||||||||||||||||||||