Prevalence of Helicobacter pylori vacA, cagA, cagE, iceA, babA2 genotypes and correlation with clinical outcome in Turkish patients with dyspepsia

BACKGROUND: Distinct virulence factors of Helicobacter pylori have been associated with clinical outcome of the infection; however, considerable variations have been reported from different geographic regions and data on genotypes of Turkish H. pylori isolates are sparse. AIM: To determine the prevalence of specific genotypes of H. pylori in Turkish patients with dyspepsia. MATERIALS AND METHODS: Ninety-three H. pylori-positive patients [30 with non-ulcer dyspepsia (NUD), 30 with duodenal ulcer (DU), and 33 with gastric cancer (GC)] who were admitted to our endoscopy unit due to dyspepsia were enrolled in the study. H. pylori infection was confirmed in all patients by histology and rapid urease test (RUT). The presence of vacA alleles, cagA, cagE, iceA, and babA2 genotypes were determined by polymerase chain reaction (PCR). Chi-squared test and Fisher's exact test were used for statistical comparisons and multivariate regression analysis was performed to find out independent predictors of different clinical outcomes. RESULTS: Turkish strains examined predominantly possessed the vacA s1,m2 (48.4%) and s1,m1 (40.7%) genotypes. The vacA s1a genotype was detected in 66.7, 96.4, and 87.9% of isolates from patients with NUD, DU, and GC, respectively, and its presence was significantly associated with that of DU (p = .004), GC (p = .043), and cagA gene (p = .021). None of the cases was found to harbor the s1c genotype. The frequencies of the cagA and cagE genes among studied isolates were 73.6 and 59.3%, respectively. The cagA gene was significantly associated with the presence of DU (p = .004) and GC (p = .003), and the cagE gene, too, was significantly associated with the presence of DU (p = .002) and GC (p = .000). All H. pylori isolates possessed the iceA gene. In all, 68 isolates (74.7%) were positive for iceA1 and 23 (25.3%) for iceA2. The frequency of icea1 gene was significantly higher in cases with GC (85%) than in cases with NUD (60%) (p = .026). The frequency of babA2 gene was 23.3, 46.4, and 87.9% in isolates of patients with NUD, DU, and GC, respectively. When compared to cases with NUD (p = .000) and DU (p = .000), the presence of babA2 gene was significantly higher in cases with GC. Multivariate regression analysis disclosed cagE (p = .006) and vacA s1a (p = .027) genotypes to be independent predictors of DU and babA2 (p = .000) and cagE (p = .013) genotypes to be independent predictors of GC. CONCLUSIONS: H. pylori vacA s1a, cagA, cagE genotypes have significant relations with the presence of DU and GC, and iceA1, babA2 with GC in Turkish patients with dyspepsia, whereas cagE and vacA s1a genotypes are independent predictors of DU, and babA2 and cagE genotypes are independent predictors of GC.     

Characterization of norovirus infections in Seoul,Korea

The present study has determined the detection rate of norovirus (NoV) with acute gastroenteritis (AGE) in hospitalized children and describes the molecular epidemiology of NoV circulating in Seoul, Korea. Six hundred and eighty‐three (9.8%) of samples were positive for NoV. Of these, the NoV GII genogroup was the most commonly found, with a prevalence of 96.2% (683 of 710). Only 27 samples were positive for the NoV GI genogroup. Ten kinds of GI genotype (GI/1, GI/2, GI/3, GI/4, GI/5, GI/6, GI/7, GI/9, GI/12, and GI/13) and eight kinds of GII genotype (GII/2, GII/3, GII/4, GII/8, GII/14, GII/15, GII/16, and GII/17) were identified in children with AGE during the years 2008–2011.     

Comparison of different imputation methods from low- to high-density panels using Chinese Holstein cattle

Imputation of high-density genotypes from low- or medium-density platforms is a promising way to enhance the efficiency of whole-genome selection programs at low cost. In this study, we compared the efficiency of three widely used imputation algorithms (fastPHASE, BEAGLE and findhap) using Chinese Holstein cattle with Illumina BovineSNP50 genotypes. A total of 2108 cattle were randomly divided into a reference population and a test population to evaluate the influence of the reference population size. Three bovine chromosomes, BTA1, 16 and 28, were used to represent large, medium and small chromosome size, respectively. We simulated different scenarios by randomly masking 20%, 40%, 80% and 95% single-nucleotide polymorphisms (SNPs) on each chromosome in the test population to mimic different SNP density panels. Illumina Bovine3K and Illumina BovineLD (6909 SNPs) information was also used. We found that the three methods showed comparable accuracy when the proportion of masked SNPs was low. However, the difference became larger when more SNPs were masked. BEAGLE performed the best and was most robust with imputation accuracies >90% in almost all situations. fastPHASE was affected by the proportion of masked SNPs, especially when the masked SNP rate was high. findhap ran the fastest, whereas its accuracies were lower than those of BEAGLE but higher than those of fastPHASE. In addition, enlarging the reference population improved the imputation accuracy for BEAGLE and findhap, but did not affect fastPHASE. Considering imputation accuracy and computational requirements, BEAGLE has been found to be more reliable for imputing genotypes from low- to high-density genotyping platforms.     

Production of live offspring with predicted genotypes using PCR-RFLP analysis of polar bodies from mouse oocytes

Accurate identification of genotypes in gametes and early embryos could facilitate the efficient production of offspring with desirable traits. This study demonstrates the feasibility of producing offspring with predictable genotypes from micromanipulated mouse oocytes. The Polymerase Chain Reaction (PCR) was used to amplify genes in the IA subregion of the major histocompatibility complex of the mouse. The validity of the approach was demonstrated in experiment 1 with IA haplo-types of unfertilized mouse ova amplified via PCR and distinguished by restriction fragment length polymorphism (RFLP) analysis. In experiment 2, fertilized oocytes were micromanipulated to remove the first and second polar bodies, which were then genotyped by validated PCR-RFLP procedures. Primary oocytes of heterozygous females contain two copies of each of the different alleles. Following meiosis I and II, the genotype of the ovum was predicted by subtracting the alleles observed in micromanipulated polar body samples. Sixty-two fertilized ova were micromanipulated and transferred to recipient females resulting in 27 live offspring (44%). The correct maternal contribution to the embryonic genotype was predicted in 19 of 27 (71%) offspring as confirmed by PCR-RFLP analysis of DNA from pup tails. Predicted genotypes of two pups were not confirmed (7%), whereas no prediction could be made in six cases (22%). © 1995 Wiley-Liss, Inc.     

A comparison of genome modifications leading to genetic and epigenetic tumorous transformation in Nicotiana spp. tissue cultures

A single system is presented, where both genetic and epigenetic control of tumor induction can be studied at the same time. This system is offered by the amphidiploid tumorous hybrid Nicotiana glauca × N. langsdorffii, a nontumorous mutant of it and the nontumorous parent species N. glauca and N. langsdorffii. The aim of the present paper is to compare long-term in vitro cultures of tumorous (genetic and habituated), and nontumorous strains, through the characterization of their genomes according to several physico-chemical parameters. The data reported show that both qualitative and quantitative differences in DNA complexity are correlated with the tumorous transformation. Particularly, a high degree of mismatching between the DNAs of the tumorous and nontumorous hybrids and the lack, in the second genotype (nontumorous), of three DNA peaks in Ag⁺?Cs²SO⁴ analytical ultracentrifugation profile seem to support the hypothesis, suggested in a previous paper, of the presence, in the nontumorous mutant, of a gross chromosomal rearrangement, probably a deletion. Amplification and underreplication of specific sequences also seemed to be correlated with changes from the normal to the tumorous state, highly repetitive sequences being present in higher amounts in the normal strains and in the habituated N. glauca than in the case of the tumorous hybrid. Finally, DNA bound ion contents were found to be strikingly higher in tumorous than in nontumorous tissues. The results are discussed in the frame of the general hypothesis of high somatic genomic plasticity in plants.     

苜蓿属3种不同花色基因型的染色体核型分析

基于形态学的显著差异,对紫花苜蓿(Medicago sativa L.)、黄花苜蓿(Medicago falcata L.)和白花苜蓿(Alfalfa with Cream flower)进行染色体核型分析,结果表明,3种类型的苜蓿材料在染色体核型方面有显著差别,白花苜蓿和黄花苜蓿都是随体染色体,其中,黄花苜蓿有2条为端部着丝点染色体,其核型公式分别为:紫花苜蓿2n=4x=24m+8sm、黄花苜蓿2n=4x=24m+6sm+2T(SAT)、白花苜蓿2n=4x=24m+8sm(SAT)。紫花苜蓿与白花苜蓿的染色体具有89%的相似性,只是在紫花苜蓿7号染色体和白花苜蓿15号染色体存在随体有无的区别;黄花苜蓿染色体具有独特性,显著区别于紫花苜蓿和白花苜蓿,但从其19号染色体来看,参与了紫花苜蓿或白花苜蓿的构建;白花苜蓿15号随体染色体与黄花苜蓿25号随体染色体和紫花苜蓿7号染色体有高度的相似性,但也存在随体有无的区别。     

Abnormal segregation of alkaline ribonuclease genes in cattle1

Polymorphism of alkaline ribonuclease in the leucocytes of 76 bulls, 554 cows and their progeny of 556 calves was investigated. All possible genotype matings were examined. Observed offspring genotypes were compared with the expected ratios. Abnormal genotype distribution was noticed: homozygous calves of RNase^B/RNase^B genotype were significantly fewer than expected.     

Phenylalanine ammonia-lyase activity in alfalfa suspension cultures treated with conidia and elicitors of Verticillium albo-atrum

Alfalfa (Medicago sativa L.) cell suspension cultures of Verticillium albo-atrum resistant and susceptible genotypes were established from leaf callus tissues. Treatment of cultures with conidia and heat-released elicitors of V. albo-atrum induced a large increase in the activity of phenylalanine ammonia-lyase, only in the cells of the resistant genotypes with a maximum after 12 h. In co-cultivation with the fungal conidia and resistant cell lines, the production of spores were inhibited. This revised version was published online in July 2006 with corrections to the Cover Date.     

樱桃品种S基因型及自交不亲和性分子机制研究进展

系统介绍了樱桃S基因型鉴定的主要方法,全面列出上百个已知甜樱桃品种的S基因型,其中共涉及16个S基因;着重讨论了樱桃S基因座内S-RNase和SFB基因的研究概况、结构特点及位置关系,并提出该领域善待解决的问题。     

Dynamics of toxic genotypes of Microcystis aeruginosa complex (MAC) through a wide freshwater to marine environmental gradient

Bloom-forming species belonging to Microcystis aeruginosa complex (MAC) are the most commonly reported worldwide. MAC blooms are composed by toxic and non-toxic genotypes and the environmental conditions favouring the dominance of toxic genotypes are still a matter of debate among the scientific community. In this study, we evaluated the distribution of toxic MAC genotypes along a seasonal cycle and over an environmental gradient spanning 800 km, from a eutrophic freshwater reservoir in Río Uruguay to marine water in the outer limit of Río de la Plata. Abundance of four mcy genes, mcyB, mcyD, mcyE and mcyJ was determined by qPCR and used as a proxy of abundance of toxic MAC genotypes. All the mcy genes were detected through the seasonal cycle at all sampling sites, being systematically higher in the freshwater reservoir and decreasing towards the marine site. The highest toxic genotype abundance was found during the austral summer months. According to generalized linear regressions and random forest models, temperature and conductivity were the most relevant explanatory variables. This suggests that although toxic MAC genotypes grow optimally in freshwater, they are also able to tolerate the high-salinity and low temperature conditions found in estuarine and marine waters. This ability to resist harsh conditions impose a health risk and a management challenge. To our knowledge, this is the first report addressing several mcy genes in a broad gradient that includes a wide array of different environmental conditions.     

Putrescine-enhanced somatic embryos and plant numbers from elite oat (Avena spp. L.) and reciprocal crosses

Summary Mature embryos from hulled, regenerable GP-1 (A. sativa L.), hull-less, recalcitrant Tibor (A. nuda L.) and reciprocal crosses were cultured in vitro on a putrescine- (Put) containing medium. Hormone-free Murashige and Skoog medium (MS-0) or shoot proliferation medium (SPM) [2.0 mgl⁻¹ (9.0 μM) 2,4-dichlorophenoxyacetic acid (2,4-D)], with and without 0.5 mM Put or 1 mM Put, were tested for effects on somatic embryogenesis and plant regeneration. Put/SPM (0.5mM) was the best medium for both somatic embryos (SEs) and plant numbers per gram of callus, regardless of genotype. This effect was most evident in Tibor, which produced no somatic embryos or plants on SPM, a previously published regeneration medium, and in Tibor ×GP-1, which produced reduced numbers of SE and plants on the remaining media. The number of SEs per gram of callus for GP-1 and GP-1× Tibor showed little significant differences between the different media. Put treatments produced plants from the four genotypes but the regeneration efficiency on Put-containing medium was similar or even better than on SPM for explants containing maternal GP-1 germplasm. This suggests that Put-containing MS-0 medium can be used for testing regeneration of other oat lines. In addition, SPM containing 0.5 mM Put can be used to induce significant regeneration of plants from normally recalcitrant genotypes. This improvement greatly increases the number of potential germplasms for further transformation efforts.     

Evidence for multiple paternity in the school shark Galeorhinus galeus found in New Zealand waters

This study assessed the levels of relatedness of Galeorhinus galeus of progeny arrays using six microsatellite DNA markers. A parentage analysis from five families (mother and litter) from the North Island of New Zealand suggested the occurrence of genetic polyandry in G. galeus with two of the five litters showing multiple sires involved in the progeny arrays. This finding may be consistent with the reproductive characteristics of G. galeus, in which females can potentially store sperm for long periods of time after the mating season.     

Multi-criteria clustering in genotype-environment interaction problems

Summary Significant genotype-environment interactions in an ANOVA can be found for a number of reasons: one is the differences in the among-environments variances for each genotype, another is the differences in the ordering of the environments by each genotype. Using conditional clustering, groups may be formed in which the means, variances and patterns are used simultaneously but separately to decide on group homogeneity. Contribution No. I-685 from the Engineering and Statistical Research Institute     

大豆基因型对根癌农杆菌菌株敏感性的研究

以栽培大豆［Glycine max (L.) Mer］吉林30、吉林43、绥农8、黑农35和东农42等的下胚轴为外植体,用EHA105和LBA4404 2个根癌农杆菌菌株（分别含有pGBI121S4ABC和pGBI4A2B质粒）研究大豆基因型对根癌农杆菌的敏感性,以及根癌农杆菌对大豆的侵染能力。结果表明,大豆基因型对根癌农杆菌的敏感性存在显著差异,以吉林43最敏感。根癌农杆菌菌株对大豆下胚轴侵染能力不同,含有pGBI121S4ABC质粒的LBA4404侵染能力较强,但差异未达显著水平。 Abstract:The sensitivity of genotypes in soybean to lines of Agrobacterium tumefaciens and the ability of A.tumefaciens infecting to soybean were investigated with hypocotyls of soybean (Jilin30,Jilin43,Suinong8,Heinong35 and Dongnong42) and lines of A.tumefaciens LBA4404 and EHA105 which including plasmid pGBI121S4ABC and pGBI4A2B respectively.The results showed that the sensitivity of genotypes in soybean to A.tumefaciens was significantly different.Jilin43 was the most sensitive materials to A.tumefaciens.The ability of A.tumefaciens infecting hypocotyls in soybean was different.LBA4404 including plasmid pGBI121S4ABC was easier to infect hypocotyls of soybean.     

Entry into midgut epithelial cells is a key step in the selection of genotypes in a nucleopolyhedrovirus

An isolate of the Spodoptera frugiperda multiple nucleopolyhedrovirus comprises a stable proportion of deletion genotypes (e.g., SfNIC-C), that lack pif1 and pif2 rendering them noninfectious per os, and that survive by complementation with a complete genotype (SfNIC-B) in coinfected cells. To determine whether selection for particular ratios of complete and deletion genotypes occurs mainly during the establishment of the primary infection in insect midgut cells or during subsequent systemic infection, we examined genotype frequencies in insects that fed on OBs comprising different co-occluded mixtures of genotypes. Dramatic changes in genotype frequencies were observed between the OB inoculum and budded virus (BV) samples taken from larvae inoculated with OBs comprising 10% SfNIC-B + 90% SfNIC-C indicating that a marked reduction of SfNIC-C genotype had occurred in the insect midgut due to the immediate elimination of all OBs that originated from cells that had been infected only by SfNIC-C. In contrast, immediate changes were not observed in OBs comprising mixtures of 50% SfNIC-B + 50% SfNIC-C or those comprising 10% SfNIC-B + 90% SfNIC-C as most of the OBs in these mixtures originated from cells that had been infected by both genotypes. Subsequent changes in genotypic frequencies during five days of systemic infection were fairly small in magnitude for all genotypic mixtures. We conclude that the prevalence of defective genotypes in the SfNIC population is likely determined by a balance between host selection against OBs produced in cells infected by SfNIC-C alone and within-host selection for fast-replicating deletion genotypes. The strength of intra-host selection is likely modulated by changes in MOI during the infection period.     

Grouping genotypes by a cluster method directly related to genotype-environment interaction mean square

Summary To facilitate the interpretation of data from a genotype by environment (GE) experiment when the GE interaction is large, a cluster method is proposed to group genotypics according to their response to the environments. The dissimilarity index between a pair of genotypes is defined in terms of distance adjusted for the average effects of genotypes, and Sokal and Michener's (1958) unweighted pair-group method is used in the clustering algorithm. The new index, constructed in each cluster cycle for any group, is shown to be equivalent to within group GE interaction mean square under 2-way ANOVA. Thus, if the F-value is used as an empirical stopping criterion for clustering, there will be no significant GE interaction within groups and the genotypes within the groups can be compared by their average effects. The method of analysis is illustrated by an example.Contribution no. I-348 from the Engineering and Statistical Research Institute     

Genotypic comparison of five isolates of Rickettsia prowazekii by multilocus sequence typing

Genetic traits of five Rickettsia prowazekii isolates, including the first from Africa and North America, and representatives from human and flying squirrels were compared using multilocus sequence typing. Four rickettsial genes encoding 17 kDa genus-common antigen (17 kDa gene), citrate synthase (gltA), OmpB immunodominant antigen (ompB) and 120 kDa cytoplasmic antigen (sca4) were examined. Sequence identities of 17 kDa gene and gltA were 100% among the isolates. Limited sequence diversity of ompB (0.02-0.11%) and sca4 (0.03-0.20%) was enough to distinguish the isolates, and evaluation of the combined four genes provided a method to easily differentiate R. prowazekii from other rickettsiae.     

Genetic differentiation and phenotypic plasticity in Plantago major ssp. major. II. The effect of differences in level of irradiance on Mg2+- and Ca2+-stimulated ATPase activity from roots and shoot

Ca²⁺- and Mg²⁺-stimulated ATPase activity of the microsomal fraction of shoots and roots and the temperature dependence of the Ca²⁺-stimulated ATPase activity of the shoot of plants of two genotypes of Plantago major ssp. major L., one originating from an exposed and the other from a shaded habitat, were followed at two levels of irradiance. In addition the responses of these parameters were studied after transfer of the plants from one light condition to the other. The capacity and the optimum temperature of shoot ATPase activity were affected by irradiance during growth, in contrast to the root ATPase activity. Generally, no plastic adaptive response of the measured characteristics was observed after transfer of the plants. The remaining plasticity or stability of plant characteristics could not be interpreted as adaptive; the adaptive plastic responses were confined to the seedling stage of individuals of both genotypes. Possible mechanisms involved in plastic and adaptive responses and including phytochrome are discussed.     

Adipocyte cellularity in different adipose depots in bulls of seven Spanish breeds slaughtered at two body weights

The influence of body weight (BW) at slaughter and genotype on adipocyte size and number in the omental (OM), perirenal (PR), subcutaneous (SC) and intermuscular (IM) adipose tissues was studied in 168 bulls of Spain's local Asturiana, Avileña, Morucha, Parda Alpina, Pirenaica, Retinta, and Rubia Gallega cattle breeds. The young bulls were slaughtered at two BWs, 320 and 540 kg. The results obtained showed the higher amounts of lipids that accumulated between 320 and 540 kg BW (P < 0.001) to be ascribable primarily to adipose cell hypertrophy, i.e. larger adipocyte size, in the OM and PR depots (P < 0.001). In addition to hypertrophy, there was also an increase (P < 0.001) in the number of adipose cells, i.e. hyperplasia, in the SC and IM adipose depots. Significant differences were observed when comparing the different genotypes, with the Morucha, Retinta and Avileña breeds having the highest amount of adipose tissue and the largest adipocytes. The Asturiana and Rubia Gallega breeds had the lowest amount of adipose tissue and the smallest adipocytes. The Pirenaica and Parda Alpina breeds had intermediate values in between the two groups identified above. In short, the results were indicative of different lipid deposition patterns in the different breeds depending on the individual growth and maturation rates in each. Similar findings were made when comparing the different adipose tissue depots, with adipocyte hypertrophy being the main factor responsible for lipid accumulation in the OM and PR depots, as opposed to adipocyte hyperplasia in the SC and IM depots.     

EB病毒相关胃癌中病毒分型的研究

收集236例胃癌组织标本及135份健康人群咽漱液(throat washings,TWs)标本,采用原位杂交、PCR-Southern blot筛选出17例EB病毒相关胃癌(EBVaGC)(7.2%)和33例EBV阳性的TWs标本(24.4%);应用PCR-RFLP、巢式PCR及DNA测序等方法,检测EBV阳性标本病毒1/2分型、F/f分型、I/i分型及LMP1XhoI(+)/(-)等四种基因变异。EBVaGC及健康对照均为F型变异,未检测到f型变异。EBVaGC中1/2型、I/i型及LMP1XhoI(+)/(-)型的例数及比例分别为:17(100%)/0(0)、1(5.9%)/16(94.1%)及0(0)/15(88.2%);而TWs中上述分型的相应数据为25(75.8%)/8(24.2%)、11(33.3%)/19(57.6%)及12(36.4%)/18(54.5%),各位点两种基因型在EBVaGC和健康人中的分布不同(1/2:P=0.047;I/i:P=0.048;XhoI(+)/(-):P=0.012)。综合分析表明在3种基因多态性均能确定的标本中,EBVaGC均为1/i/XhoI(-)亚型(15/1...