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Different Genotypes (different + genotype)
Selected AbstractsVisual gene diagnosis of HBV and HCV based on nanoparticle probe amplification and silver staining enhancementJOURNAL OF MEDICAL VIROLOGY, Issue 2 2003Ye-Fu Wang Abstract A visual gene-detecting technique using nanoparticle-supported gene probes is described. With the aid of gold nanoparticle-supported 3,-end,mercapto-derivatized oligonucleotide serving as detection probe, and 5,-end ,amino-derivatized oligonucleotide immobilized on glass surface acting as capturing probe, target DNA was detected visually by sandwich hybridization based on highly sensitive "nano-amplification" and silver staining. Different genotypes of Hepatitis B and C viruses in the serum samples from infected patients were detected using home-made HBV, HCV, and HBV/HCV gene chips by the gold/silver nanoparticle staining amplification method. The present visual gene-detecting technique may avoid limitations with the reported methods, for its high sensitivity, good specificity, simplicity, speed, and cheapness. This technique has potential applications in many fields, especially in multi-gene detection gene chips coupled with the detection will find applications in clinic. Additionally, resonance Rayleigh light scattering (RLS) spectroscopy is used, for the first time, to judge and monitor the immobilization of gene probes on gold nanoparticle surfaces. J. Med. Virol. 70: 205,211, 2003. © 2003 Wiley-Liss, Inc. [source] Different genotypes are responsible for the normal Russell viper venom assays seen in some cases of congenital factor X deficiencyAMERICAN JOURNAL OF HEMATOLOGY, Issue 11 2008Antonio Girolami No abstract is available for this article. [source] Mutagenic induction of double-podding trait in different genotypes of chickpea and their characterization by STMS markerPLANT BREEDING, Issue 1 2010H. Ali With 1 figure and 2 tables Abstract A gene that confers double-podding in chickpea is considered to be important for breeding higher yielding cultivars. Double-podded mutants were produced from five desi- and four kabuli-type chickpea genotypes through induced mutations and stabilty was checked up to M13 generation. Desi-type produced higher number of mutants as compared with kabuli-type. The inheritance studies in induced mutants of six genotypes showed that the double-podded trait was governed by single recessive gene. Different genotypes and their double-podded mutants were also characterized through sequence-tagged microsatellite site marker, TA-80. Allelic variations were found in single-podded genotypes and eight different alleles were identified, while for double-poddedness no allelic variants were found in all the analysed mutants. Addition of bases in the double-podded mutants showed that there might be involvement of transposable elements in the production of double-podded mutants through mutagens. [source] Characterization of Genotypes of Enterocytozoon bieneusi in Immunosuppressed and Immunocompetent Patient GroupsTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 4 2009ROBERT J. TEN HOVE ABSTRACT. A retrospective phylogenetic analysis was performed on isolates of Enterocytozoon bieneusi to characterize the genotypes in different patient cohorts. Fifty-seven isolates, collected from patients living in Malawi and the Netherlands, were classified by age and immune status of the hosts. Sequence analysis of the internal transcribed spacer (ITS) region identified 16 genotypes; nine have not previously been described. Genotypes K and D were most prevalent among patient groups, whereas genotype C was restricted to transplantation patients receiving immunosupressives and genotype B showed a predisposition toward patients living with HIV/AIDS. Different genotypes showed more dispersion among isolates from Malawi compared with those from the Netherlands. A constructed map estimating the genealogy of the ITS region reveals a dynamic evolutionary process between the genotypes. [source] Genetic identity of interspecific neighbours mediates plant responses to competition and environmental variation in a species-rich grasslandJOURNAL OF ECOLOGY, Issue 5 2007JASON D. FRIDLEY Summary 1Although outbreeding populations of many grassland plants exhibit substantial genetic and phenotypic variation at fine spatial scales (< 100 m2), the implications of local genetic diversity for community structure are poorly understood. Genetic diversity could contribute to local species diversity by mediating the effects of competition between species and by enhancing species persistence in the face of environmental variation. 2We assayed the performance of three genotypes each of a dominant tussock grass (Koeleria macrantha [Ledeb.] J.A. Schultes) and dominant sedge (Carex caryophyllea Lat.) derived from a single 10 × 10 m quadrat within a limestone grassland in Derbyshire, UK. Genotypes were grown in monoculture and grass,sedge mixtures of different genetic composition in two environments of contrasting fertility. Species mixtures also included one genotype of the subordinate forb Campanula rotundifolia L. 3When grown without neighbours, intraspecific genotypes responded similarly to environmental treatments. One genotype of the sedge performed worse in both environments than the other two sedge genotypes. 4When grown in species mixtures, genotype performance was significantly influenced by the genetic identity of the neighbouring species for both the sedge and the grass. At high fertility, differential genotype performance was not sufficient to alter the expectation of competitive exclusion of the sedge by the grass. However, at low fertility, the competitive dominant depended on the genetic identity of both the grass and the sedge. In addition, each genotype of the grass performed best next to a different genotype of the sedge, and the identity of the best genotype pairings switched with environment. 5Performance of a single genotype of the subordinate Campanula was not predictable by fertility alone, but by how fertility interacted with different neighbouring genotypes of both the grass and the sedge. 6Results support the hypothesis that the genetic identity of interspecific neighbours influences plant performance in multispecies assemblages and mediates species' responses to environmental variation. Such interactions could be a key factor in the contribution of local intraspecific genetic diversity to species diversity. [source] A microsatellite-based estimation of clonal diversity and population subdivision in Zostera marina, a marine flowering plantMOLECULAR ECOLOGY, Issue 2 2000T. B. H. Reusch Abstract We examined the genetic population structure in eelgrass (Zostera marina L.), the dominant seagrass species of the northern hemisphere, over spatial scales from 12 km to 10 000 km using the polymorphism of DNA microsatellites. Twelve populations were genotyped for six loci representing a total of 67 alleles. Populations sampled included the North Sea (four), the Baltic Sea (three), the western Atlantic (two), the eastern Atlantic (one), the Mediterranean Sea (one) and the eastern Pacific (one). Microsatellites revealed substantial genetic variation in a plant group with low allozyme diversity. Average expected heterozygosities per population (monoclonal populations excluded) ranged from 0.32 to 0.61 (mean = 0.48) and allele numbers varied between 3.3 and 6.7 (mean = 4.7). Using the expected frequency of multilocus genotypes within populations, we distinguished ramets from genetic individuals (i.e. equivalent to clones). Differences in clonal diversity among populations varied widely and ranged from maximal diversity (i.e. all ramets with different genotype) to near or total monoclonality (two populations). All multiple sampled ramets were excluded from further analysis of genetic differentiation within and between populations. All but one population were in Hardy,Weinberg equilibrium, indicating that Zostera marina is predominantly outcrossing. From a regression of the pairwise population differentiation with distance, we obtained an effective population size Ne of 2440,5000. The overall genetic differentiation among eelgrass populations, assessed as , (a standardized estimate of Slatkin's RST) was 0.384 (95% CI 0.34,0.44, P < 0.001). Genetic differentiation was weak among three North Sea populations situated 12,42 km distant from one another, suggesting that tidal currents result in an efficient exchange of propagules. In the Baltic and in Nova Scotia, a small but statistically significant fraction of the genetic variance was distributed between populations (, = 0.029,0.053) at scales of 15,35 km. Pairwise genetic differentiation between European populations were correlated with distance between populations up to a distance of 4500 km (linear differentiation-by-distance model, R2 = 0.67). In contrast, both Nova Scotian populations were genetically much closer to North Sea and Baltic populations than expected from their geographical distance (pairwise , = 0.03,0.08, P < 0.01). A biogeographical cluster of Canadian with Baltic/North Sea populations was also supported using a neighbour-joining tree based on Cavalli,Sforza's chord distance. Relatedness between populations may be very different from predictions based on geographical vicinity. [source] Molecular epidemiology of measles virus in JapanPEDIATRICS INTERNATIONAL, Issue 2 2004Tetsuo Nakayama AbstractBackground:,Measles virus has been classified into 22 genotypes. The present report examines the molecular epidemiology of measles virus in Japan from 1984 to 2002, and the epidemiological link between imported cases in several foreign countries and Japanese strains was elucidated from the literature. Methods:,B95a or Vero cells was used to isolate the measles virus. The measles virus genome was amplified in the N and H genes by reverse transcriptase-polymerase chain reaction and were partially sequenced. Phylogenetic analysis of a partial sequence of the N gene, from position 1230 to 1685, of the recent measles strains was performed in comparison with the World Health Organization reference strains. Results:,There were large outbreaks of measles in Japan in 1984, 1987,1988, 1991,1993, and 2001,2002 and each outbreak was caused by a different genotype. Genotype C1 was an indigenous strain for a long period before 1985, while D3 was isolated in 1987,1988 and D5 in 1991,1993 outbreaks. In addition, the Chicago-type D3 caused sporadic regional outbreaks from 1998 to 1999. After 2000, H1 became the dominant circulating strain. It should be noted that the Japanese strains were detected as imported cases by epidemiological linkage in several countries. Conclusion:,Among the recent circulating strain of measles virus in Japan the genotype H1 was dominant after 2000 and the Japanese strains D3, D5, and H1 were exported to several countries. It is recommended that Japan should adopt a more extensive and active vaccination strategy for measles elimination in line with other countries in the world. [source] Changes in peroxisome proliferator-activated receptor gamma gene expression of chicken abdominal adipose tissue with different age, sex and genotypeANIMAL SCIENCE JOURNAL, Issue 3 2009Kan SATO ABSTRACT Peroxisome proliferatior-activated receptor gamma (PPAR,) is a transcription factor that regulates adipocyte differentiation, and the activation of PPAR, increases fat deposition in growing chickens. The aim of the present study was to investigate whether the levels of PPAR, gene expression were related to fat pad weight in abdominal adipose tissue in growing chickens with different genotype and sex. Body weight and abdominal adipose tissue weight in broiler chickens (Ross strain) were higher than the other genotypes (Road Island Red, White Leghorn, and Japanese native poultry (Tsushima)) at 3 and 5 weeks of age. PPAR, mRNA expression in abdominal adipose tissue tended to increase with age, as evidenced by higher expression levels at 5 weeks than at 1 week of age in all sex and genotype of chickens. In broiler chickens, the PPAR, expressions were significantly higher than the other genotypes. PPAR, mRNA expression levels in abdominal adipose tissue of female chickens rapidly increased at 3 weeks, and were unchanged until 5 weeks, while those in male chickens gradually increased until 5 weeks. In addition, abdominal adipose tissue weight was correlated with PPAR, expression levels. These results demonstrated that PPAR, gene expression is a useful marker of fat deposition in chickens, suggesting that PPAR, is a key factor of fat accumulation in chicken abdominal fat pad. [source] DIRECT AND CORRELATED RESPONSES TO SELECTION IN A HOST,PARASITE SYSTEM: TESTING FOR THE EMERGENCE OF GENOTYPE SPECIFICITYEVOLUTION, Issue 8 2007Thibault Nidelet Genotype × environment interactions can facilitate coexistence of locally adapted specialists. Interactions evolve if adaptation to one environment trades off with performance in others. We investigated whether evolution on one host genotype traded off with performance on others in long-term experimental populations of different genotypes of the protozoan Paramecium caudatum, infected with the bacterial parasite Holospora undulata. A total of nine parasite selection lines evolving on three host genotypes and the ancestral parasite were tested in a cross-infection experiment. We found that evolved parasites produced more infections than did the ancestral parasites, both on host genotypes they had evolved on (positive direct response to selection) and on genotypes they had not evolved on (positive correlated response to selection). On two host genotypes, a negative relationship between direct and correlated responses indicated pleiotropic costs of adaptation. On the third, a positive relationship suggested cost-free adaptation. Nonetheless, on all three hosts, resident parasites tended to be superior to the average nonresident parasite. Thus genotype specificity (i.e., patterns of local adaptation) may evolve without costs of adaptation, as long as direct responses to selection exceed correlated responses. [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] Haplotype analysis in the presence of informatively missing genotype dataGENETIC EPIDEMIOLOGY, Issue 4 2006Nianjun Liu Abstract It is common to have missing genotypes in practical genetic studies, but the exact underlying missing data mechanism is generally unknown to the investigators. Although some statistical methods can handle missing data, they usually assume that genotypes are missing at random, that is, at a given marker, different genotypes and different alleles are missing with the same probability. These include those methods on haplotype frequency estimation and haplotype association analysis. However, it is likely that this simple assumption does not hold in practice, yet few studies to date have examined the magnitude of the effects when this simplifying assumption is violated. In this study, we demonstrate that the violation of this assumption may lead to serious bias in haplotype frequency estimates, and haplotype association analysis based on this assumption can induce both false-positive and false-negative evidence of association. To address this limitation in the current methods, we propose a general missing data model to characterize missing data patterns across a set of two or more markers simultaneously. We prove that haplotype frequencies and missing data probabilities are identifiable if and only if there is linkage disequilibrium between these markers under our general missing data model. Simulation studies on the analysis of haplotypes consisting of two single nucleotide polymorphisms illustrate that our proposed model can reduce the bias both for haplotype frequency estimates and association analysis due to incorrect assumption on the missing data mechanism. Finally, we illustrate the utilities of our method through its application to a real data set. Genet. Epidemiol. 2006. © 2006 Wiley-Liss, Inc. [source] Optimization of culture conditions for plant regeneration of Panicum spp. through somatic embryogenesisGRASSLAND SCIENCE, Issue 1 2010Mi-Suk Seo Abstract We developed a rapid and efficient shoot regeneration system for Panicum spp. by adjusting the regeneration medium and studying the responses of different genotypes and the influence of explant types (mature seed, immature embryo and shoot apex). We used Panicum meyerianum (Nees) and Panicum longijubatum (Stapf) which were shown to perform well, to select the optimal medium for shoot regeneration. The highest frequency of shoot regeneration was obtained on Murashige and Skoog medium supplemented with 30 g L,1 maltose and 1 mg L,1 N-phenyl-N,-[(1,2,3-thidiazol-5-yl) urea]. The callus formed green spots after 1 week of culture and showed primary green shoots after 2 weeks. In this system, the calli derived from mature seed of nine Panicum genotypes showed large variation in shoot regeneration ability: from 0 to 69.9% in the frequency of shoot formation and from 0 to 8.4 in the number of shoots per callus. Guineagrass (Panicum maximum Jacq.) showed no ability and switchgrass (Panicum virgatum L.) showed low ability to regenerate from mature seed-derived calli; however, both were able to be regenerated from immature embryos and calli derived from shoot apices. We developed an efficient protocol for high shoot regeneration of various Panicum genotypes which provides a foundation for efficient tissue culture and genetic improvement of Panicum. [source] Different Helicobacter pylori Strains Colonize the Antral and Duodenal Mucosa of Duodenal Ulcer PatientsHELICOBACTER, Issue 2 2000Ann-Catrin E. Thoreson Background. We have investigated the possibility that the same patients may be colonized by Helicobacter pylori strains of different genotypes or phenotypes in the antrum as compared to in the duodenum. The strains were typed for DNA fingerprints, different lipopolysaccharides (LPS), and Lewis antigen expression on the O,side chains of LPS. Materials and Methods. Polymerase chain reaction (PCR) amplifications using primer sequences (i.e., the Enterobacterial Repetitive Intergenic Consensus [ERIC]) and randomly amplified polymorphic DNA (RAPD) elements were performed to asses chromosomal DNA diversity between H. pylori strains. The expression of different LPS types and Lewis antigens in the various H. pylori isolates were determined by whole bacterial enzyme-linked immunosorbent assays using monoclonal antibodies. Results. Duodenal ulcer patients had different H. pylori genotypes in the duodenum as compared to in the antrum as shown by ERIC-PCR (44%) and by RAPD-PCR (75%). Different DNA patterns were found among the strains that were isolated from various regions of the duodenum in 4 of 16 patients (25%) as shown by ERIC-PCR and in 8 of 16 patients (50%) as shown by RAPD-PCR. Sixty-three percent of the duodenal ulcer patients had H. pylori strains with a different Lewis antigen phenotype in the duodenum as compared to in the antrum, and 3 of 16 patients (19%) had strains with different Lewis antigens expressed by strains from different duodenal biopsies from the same patient. Conclusion. The results suggest that a mixed population of different H. pylori strains with marked variation, both genotypically and phenotypically, colonize the same patient. [source] A self-adjuvanting multiepitope immunogen that induces a broadly cross-reactive antibody to hepatitis C virus,HEPATOLOGY, Issue 4 2007Joseph Torresi We describe a peptide-based strategy for HCV vaccine design that addresses the problem of variability in hypervariable region 1 (HVR1). Peptides representing antibody epitopes of HVR1 from genotype 1a were synthesized and incorporated into multideterminant immunogens that also included lipid moieties and helper T (Th) cell epitopes. Mice inoculated with these polyepitopes generated strong antibody responses. Antibody titers were highest in mice inoculated with polyepitope immunogens which contained the lipid moiety dipalmitoyl- S -glyceryl cysteine (Pam2Cys). Antisera were tested for their potential to neutralize HCV by 3 currently available assays. Antibodies elicited in mice by the polyepitope-based vaccine candidates were able to (1) bind to E2 expressed on the surface of E1/E2-transfected human embryonic kidney (HEK) 293T cells, (2) capture HCV of different genotypes (1, 2, and 3) from the serum of chronically infected humans in an immune capture RT-PCR assay and (3) inhibit HCVpp entry into Huh7 cells. Antibody present in the sera of patients chronically infected with HCV genotypes 1, 2, 3, and 4 also bound to the HVR1-based polyepitope. Conclusion: These results demonstrate the potential of self-adjuvanting epitope-based constructs in the development and delivery of cross-reactive immunogens that incorporate potential neutralizing epitopes present within the viral envelope of HCV. (HEPATOLOGY 2007;45:911,920.) [source] Impact of the hepatitis B virus genotype and genotype mixtures on the course of liver disease in Vietnam,HEPATOLOGY, Issue 6 2006Nguyen L. Toan Eight genotypes (A-H) of hepatitis B virus (HBV) have been identified. However, the impact of different genotypes on the clinical course of hepatitis B infection remains controversial. We investigated the frequency and clinical outcome of HBV genotypes and genotype mixtures in HBV-infected patients from Vietnam, Europe, and Africa. In addition, we analyzed the effects of genotype mixtures on alterations in in vitro viral replication. In Asian patients, seven genotypes (A-G) were detected, with A, C, and D predominating. In European and African patients, only genotypes A, C, D, and G were identified. Genotype mixtures were more frequently encountered in African than in Asian (P = .01) and European patients (P = .06). In Asian patients, the predominant genotype mixtures included A/C and C/D, compared to C/D in European and A/D in African patients. Genotype A was more frequent in asymptomatic compared with symptomatic patients (P < .0001). Genotype C was more frequent in patients with hepatocellular carcinoma (HCC; P = .02). Genotype mixtures were more frequently encountered in patients with chronic hepatitis in comparison to patients with acute hepatitis B (P = .015), liver cirrhosis (P = .013), and HCC (P = .002). Viral loads in patients infected with genotype mixtures were significantly higher in comparison to patients with a single genotype (P = .019). Genotype mixtures were also associated with increased in vitro HBV replication. In conclusion, infection with mixtures of HBV genotypes is frequent in Asia, Africa, and Europe. Differences in the replication-phenotype of single genotypes compared to genotype-mixtures suggest that co-infection with different HBV-genotypes is associated with altered pathogenesis and clinical outcome. (HEPATOLOGY 2006;43:1375,1384.) [source] Characterization of host-range and cell entry properties of the major genotypes and subtypes of hepatitis C virus,HEPATOLOGY, Issue 2 2005Dimitri Lavillette Because of the lack of a robust cell culture system, relatively little is known about the molecular details of the cell entry mechanism for hepatitis C virus (HCV). Recently, we described infectious HCV pseudo-particles (HCVpp) that were generated by incorporating unmodified HCV E1E2 glycoproteins into the membrane of retroviral core particles. These initial studies, performed with E1E2 glycoproteins of genotype 1, noted that HCVpp closely mimic the cell entry and neutralization properties of parental HCV. Because sequence variations in E1 and E2 may account for differences in tropism, replication properties, neutralization, and response to treatment in patients infected with different genotypes, we investigated the functional properties of HCV envelope glycoproteins from different genotypes/subtypes. Our studies indicate that hepatocytes were preferential targets of infection in vitro, although HCV replication in extrahepatic sites has been reported in vivo. Receptor competition assays using antibodies against the CD81 ectodomain as well as ectopic expression of CD81 in CD81-deficient HepG2 cells indicated that CD81 is used by all the different genotypes/subtypes analyzed to enter the cells. However, by silencing RNA (siRNA) interference assays, our results show that the level of Scavenger Receptor Class-B Type-I (SR-BI) needed for efficient infection varies between genotypes and subtypes. Finally, sera from chronic HCV carriers were found to exhibit broadly reactive activities that inhibited HCVpp cell entry, but failed to neutralize all the different genotypes. In conclusion, we characterize common steps in the cell entry pathways of the major HCV genotypes that should provide clues for the development of cell entry inhibitors and vaccines. (HEPATOLOGY 2005;41:265,274.) [source] Position of nonmuscle myosin heavy chain IIA (NMMHC-IIA) mutations predicts the natural history of MYH9 -related disease,HUMAN MUTATION, Issue 3 2008Alessandro Pecci Abstract MYH9 -related disease (MYH9 -RD) is a rare autosomal-dominant disorder caused by mutations in MYH9, the gene for the heavy chain of nonmuscle myosin IIA (NMMHC-IIA). All patients present from birth with macrothrombocytopenia, but in infancy or adult life, some of them develop sensorineural deafness, presenile cataracts, and/or progressive nephritis leading to end-stage renal failure. No consistent correlations have been identified between the 27 different MYH9 mutations identified so far and the variable clinical evolution of the disease. We have evaluated 108 consecutive MYH9 -RD patients belonging to 50 unrelated pedigrees. The risk of noncongenital manifestations associated with different genotypes was estimated over time by event-free survival analysis. We demonstrated that all subjects with mutations in the motor domain of NMMHC-IIA present with severe thrombocytopenia and develop nephritis and deafness before the age of 40 years, while those with mutations in the tail domain have a much lower risk of noncongenital complications and significantly higher platelet counts. We also evaluated the clinical course of patients with mutations in the four most frequently affected residues of NMMHC-IIA (responsible for 70% of MYH9 -RD cases). We concluded that mutations at residue 1933 do not induce kidney damage or cataracts and cause deafness only in the elderly, those in position 702 result in severe thrombocytopenia and produce nephritis and deafness at a juvenile age, while alterations at residue 1424 or 1841 result in intermediate clinical pictures. These findings are relevant not only to patients' clinical management but also to the elucidation of the pathogenesis of the disease. Hum Mutat 29(3), 409,417, 2008. © 2007 Wiley-Liss, Inc. [source] Interleukin-6 gene polymorphism is an age-dependent risk factor for myocardial infarction in menINTERNATIONAL JOURNAL OF IMMUNOGENETICS, Issue 6 2005M. Chiappelli Summary Several studies show that inflammatory components may contribute to atherosclerosis and increase the risk for myocardial infarction (MI). Interleukin-6 (IL-6) is a key pro-inflammatory and immune-modulatory cytokine of relevance for cardiovascular diseases. In this case-control study, 200 patients with MI and 257 healthy controls were genotyped for the polymorphism present in ,174 promoter region of the IL-6 gene. Plasma concentrations of IL-6 and C-reactive protein (CRP) in a group of patients and controls were measured. The ,174 C allele was associated with an increased risk of developing MI (OR = 2.886, c.i. = 1.801,4.624, P = 0.0001) in older patients, while no association was found in younger ones. The IL-6 plasma levels were higher in patients with MI carrying the CC genotype than in GG patients (CC carriers, IL-6 = 2.97 pg mL,1 vs. GG carriers = 1.81 pg mL,1, P = 0.016). A positive correlation of IL-6 levels with those of CRP in serum from patients with MI was also found. Data from this study suggest that the C allele of the promoter polymorphism in the IL-6 gene is a risk factor for MI in the elderly, and the production of the IL-6 is differentially affected by different genotypes of the IL-6 ,174 promoter polymorphism. [source] Hematological features and molecular lesions of hemoglobin gene disorders in Taiwanese patientsINTERNATIONAL JOURNAL OF LABORATORY HEMATOLOGY, Issue 1p2 2010H.-J. LIN Summary Hemoglobin (Hb) gene disorders are one of the most common inherited diseases in Taiwan, which include ,-thalassemia, ,-thalassemia, and Hb variants. In this study, we collected and analyzed mutations found in 930 patients with Hb gene disorders except Hb Bart's Hydrops and ,-thalassemia major. The patients included 650 cases of ,-thalassemia, 225 cases of ,-thalassemia, 9 cases of ,-thalassemia combined with ,-thalassemia, and 46 cases of Hb variants or Hb variants combined with ,-thalassemia or ,-thalassemia. The most common type of ,0 -thalassemia and ,++ -thalassemia mutations in our study were the SEA type deletion and the ,3.7 deletion, respectively; the most common ,-thalassemia mutation was the IVS-2 nt 654 C,T mutation; and the most common Hb variant was the HbE. We compared the relationships between genotype and hematological phenotypes of various Hb gene disorders and found that different genotypes of ,0 -thalassemia have similar hematological features. In conclusion, the results of our study provide data of the complex interaction of thalassemias and Hb variants which might be useful for other researchers in this field. [source] The impact of nutrient density in terms of energy and/or protein on live performance, metabolism and carcass composition of female and male broiler chickens of two commercial broiler strainsJOURNAL OF ANIMAL PHYSIOLOGY AND NUTRITION, Issue 4 2010E. Delezie Summary The objective of this study was to investigate the effects of diet composition on performance, slaughter yield and plasma metabolites, as different modern broiler strains show different responses to feed intake. Broilers of two commercial strains and of both sexes received one of three diets being different in energy and/or protein level [control diet, low energy/low protein diet (LM/LP) and low protein diet (LP)]. Low energy/low protein diet chickens were characterized by significantly lower body weights and feed intake compared with their LP and control counterparts. Broilers of the Cobb strain or broilers that were fed the control diet were most efficient in converting energy to body weight. No significant differences in plasma metabolites were detected due to diet composition or genotype. The diet with the lower energy and crude protein levels reached the lowest slaughter yield but the highest drumstick and wing percentages. The lowest mortality percentages were observed for broilers fed the LM/LP diet, and Cobb birds appeared to be more sensitive for metabolic disorders resulting in death. It is obvious from this study that different genotypes respond differently to changes in diet composition and therefore have adjusted nutritional requirements. [source] Genetic diversity and technological properties of Streptococcus thermophilus strains isolated from dairy productsJOURNAL OF APPLIED MICROBIOLOGY, Issue 2 2002D. Mora Aims: To evaluate the genetic diversity and the technological properties of 44 strains of Streptococcus thermophilus isolated from dairy products. Methods and Results: Strains were analysed for some relevant technological properties, i.e. exopolysaccharide (EPS) production, growth kinetic in skim milk medium, urease activity and galactose fermentation. The EPS production, determined by evaluating the colour of the colonies grown in ruthenium red milk agar, was observed in 50% of the analysed strains. Urease activity, determined by colorimetric and conductimetric methods, showed that 91% of the isolates, all except four, could hydrolyse urea. A conductimetric approach was also used for the evaluation of the overall metabolic behaviour in milk of Strep. thermophilus strains and the differences observed allowed grouping of the strains in seven different clusters. A total of 11 strains were able to produce acid in presence of galactose. Genetic diversity of Streptococcus thermophilus strains, evaluated by Random Amplified Polymorphic DNA fingerprinting (RAPD) and amplified epsC,D restriction analysis, allowed the identification of 21 different genotypes. Conclusions: Comparison between the genotypic and phenotypic data highlights an interesting correlation between some important technological properties and well-defined genotypes. Significance and Impact of the Study: The genetic and technological characterization carried out on several Strep. thermophilus strains of dairy origin should expand the knowledge on this important lactic acid bacteria species and lead to a simple, rapid, and reliable identification of strains on the basis of well-defined biotechnological properties. [source] Genotypic and phenotypic heterogeneity among lactococci isolated from traditional Pecorino Sardo cheeseJOURNAL OF APPLIED MICROBIOLOGY, Issue 2 2000L. Mannu Twenty-nine Lactococcus lactis isolates from one traditional 24 h-old Pecorino Sardo cheese were characterized phenotypically, technologically and genotypically in order to assess the biodiversity within this wild microbial population. Two DNA-based techniques, plasmid profiling and PFGE, were used for the genetic typing of the isolates. All 29 isolates were characterized at strain level and eight different genotypes were recognized. In addition, by combining the results from plasmid profile analysis and PFGE, it was possible to identify closely related isolates probably belonging to the same clonal lineage. The dominant biotype was identified in the 24 h-old cheese, as were the strains believed to act as starters for the curd. Atypical lactococci, able to grow in 6·5% NaCl, were isolated. The results suggest that wild bacterial populations should be preserved in order to protect the traditional raw milk cheeses, and to select new starter strains for the dairy industry. [source] TLR4 and IL-18 gene variants in aggressive periodontitisJOURNAL OF CLINICAL PERIODONTOLOGY, Issue 12 2008Barbara Noack Abstract Aim: We aimed to assess the association of different genotypes with increased aggressive periodontitis susceptibility by studying functional relevant variants in the pathogen-recognition receptor Toll-like receptor 4 (TLR4) and variants in the promoter region of the pro-inflammatory cytokine interleukin-18 (IL-18). Material and Methods: One hundred and eleven patients with aggressive periodontitis and 80 periodontally healthy controls were genotyped for four functional variants in the TLR4 gene (c.896A>G and c.1196C>T) and in the IL-18 promoter (c.,368G>C and c.,838C>A). The genotype and allele frequencies, as well as the frequency of combined genotypes were compared between study groups. Results: There were no statistical differences in genotype and allele frequencies within the four variants between the groups. All study subjects were further classified into carriers and non-carriers of at least one variant of both genes. The logistic regression analysis adjusted for gender and smoking showed no association between carrier status of at least one variant of both genes and periodontal status (OR=1.41, 95% CI: 0.43,4.70). Conclusions: Our results reject the hypothesis that functionally relevant IL-18 and TLR4 gene mutations have a major effect on aggressive periodontitis susceptibility alone or in combination. [source] Consistency of resistance to attack by the green spruce aphid (Elatobium abietinum Walker) in different ontogenetic stages of Sitka spruceAGRICULTURAL AND FOREST ENTOMOLOGY, Issue 2 2003S. Harding Abstract 1,The susceptibility of different genotypes of 29-year-old Sitka spruce to damage by the green spruce aphid, Elatobium abietinum, was investigated in a progeny trial where aphid damage on individual trees had previously been assessed twice in an earlier stage of ontogenetic development. The progeny trial comprised 14 open-pollinated families originating from a clonal seed orchard that had been established using mature spruce trees selected for aphid resistance. 2,Previous investigations had demonstrated that resistance was inherited by the offspring, and that differences in resistance between progenies of the individual orchard clones were highly significant. 3,Susceptibility to aphid attack was recorded as the percentage loss of previous year's needles. Differences in susceptibility recorded between the juvenile trees were found to persist after the trees had developed into the closed-canopy, sexually reproducing stage. Needle loss of the families was significantly less than that of the reference population of Sitka spruce. 4,Hybrids between Sitka spruce and white spruce were defoliated more heavily than pure Sitka spruce, and the difference increased with age. 5,Family heritability of resistance was estimated as 0.60 compared to 0.73 when the trees were assessed in the juvenile stage. The genetic correlation based on family means between damage in the juvenile and sexually reproducing stand was high (0.83), indicating a high consistency of resistance to the aphid over years and ontogenetic stages. 6,A skewed distribution of defoliation indicated that major genes are involved in the expression of resistance, and that the genetics behind resistance has a nonadditive component. [source] Drought Stress and Preharvest Aflatoxin Contamination in Agricultural Commodity: Genetics, Genomics and ProteomicsJOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 10 2008Baozhu Guo Abstract Throughout the world, aflatoxin contamination is considered one of the most serious food safety issues concerning health. Chronic problems with preharvest aflatoxin contamination occur in the southern US, and are particularly troublesome in corn, peanut, cottonseed, and tree nuts. Drought stress is a major factor to contribute to preharvest aflatoxin contamination. Recent studies have demonstrated higher concentration of defense or stress-related proteins in corn kernels of resistant genotypes compared with susceptible genotypes, suggesting that preharvest field condition (drought or not drought) influences gene expression differently in different genotypes resulting in different levels of "end products": PR(pathogenesis-related) proteins in the mature kernels. Because of the complexity of Aspergillus -plant interactions, better understanding of the mechanisms of genetic resistance will be needed using genomics and proteomics for crop improvement. Genetic improvement of crop resistance to drought stress is one component and will provide a good perspective on the efficacy of control strategy. Proteomic comparisons of corn kernel proteins between resistant or susceptible genotypes to Aspergillus flavus infection have identified stress-related proteins along with antifungal proteins as associated with kernel resistance. Gene expression studies in developing corn kernels are in agreement with the proteomic studies that defense-related genes could be upregulated or downregulated by abiotic stresses. [source] Analysis of intracellular short organic acid-coenzyme A esters from actinomycetes using liquid chromatography-electrospray ionization-mass spectrometryJOURNAL OF MASS SPECTROMETRY (INCORP BIOLOGICAL MASS SPECTROMETRY), Issue 9 2007Je Won Park Abstract A method employing silicone oil density centrifugation, solid-phase extraction (SPE) cleanup, and LC-ESI-MS/MS analysis was developed for the rapid, selective, sensitive, and quantitative detection of an intracellular pool of short organic acid-CoA esters in actinomycetes. The detection limit was determined to be approximately 0.8 pmol (1.2 ng/ml) for each standard CoA-ester analyzed by the present LC-ESI-MS/MS method. A selected ion chromatogram for a typical fragment ion (m/z 428) specific to CoA-esters enabled the detection of eight intracellular CoA-esters involved in both primary and secondary metabolisms. The application of this method to bacterial metabolomic study is demonstrated by the profiling of the intracellular CoA-ester pools in the wild-type Streptomyces venezuelae strain producing polyketide antibiotics (methymycin and pikromycin), a polyketide synthase (PKS)-deleted S. venezuelae mutant, and a S. venezuelae mutant expressing the heterologous PKS genes. By quantifying the individual CoA-esterlevel in three different genotypes of the S. venezuela e strain, further insight could be gained into the role of CoA-estersin polyketide biosynthesis. This analytical approach can be extended to the quantification of the size and composition of in vivo CoA-ester pools in various microbes, and can provide a detailed understanding of the relationship between the in vivo CoA-ester pool and the production of pharmaceutically important polyketides. Copyright © 2007 John Wiley & Sons, Ltd. [source] A serological and molecular survey of hepatitis B in children 15 years after inception of the national hepatitis B vaccination program in eastern China,JOURNAL OF MEDICAL VIROLOGY, Issue 9 2009Ying Dong Abstract The emergence of mutations in the hepatitis B virus (HBV) S gene has threatened the long-term success of vaccination programs since the worldwide introduction of effective vaccines against hepatitis B. This study was conducted on 5,407 children (0,8 years old) in eastern China in 2007. We analyzed the prevalence of HBsAg, anti-HBs, and "a"-determinant mutations in the HBV S gene by microparticle enzyme immunoassays, PCR, and DNASTAR software. The total HBsAg prevalence was 1.52% (82/5,407) in the children and increased with age. In contrast, the positive rate (65.42%, 2,374/3,629) and the titers of anti-HBs decreased with age. The predominant infection was HBV of genotype C and serotype adr (45/51; 88% of cases). Mutations of I126T, amino acid 137 (nt553T deletion mutation), G145A, G145R, and F158S were found in the children; the mutations of amino acid 137 and F158S have not been reported previously. The total prevalence of mutant strains was 14% (7/51). To investigate whether the infection resulted from maternal transmission, we compared the S gene sequences in 16 mother,child pairs. Fourteen mother,child pairs exhibited the same HBV genotype, with 99.5,100% sequence homology in the S gene, while two pairs exhibited different genotypes. This study suggested that the hepatitis B vaccination strategies in eastern China have been successful. Although the emergence of "a"-determinant mutations in the HBV S gene have resulted in HBV infection in immunized children, this does not pose a threat to the vaccination strategies. The HBV-infected children had contracted the infection via vertical transmission. J. Med. Virol. 81:1517,1524, 2009. © 2009 Wiley-Liss, Inc. [source] HHV8 a subtype is associated with rapidly evolving classic Kaposi's sarcomaJOURNAL OF MEDICAL VIROLOGY, Issue 12 2008Roberta Mancuso Abstract The link between human herpesvirus 8 (KSHV) and Kaposi's sarcoma (KS) has been proven, but many important aspects including risk factors, genetic predisposition to tumor development, transmission of KSHV, and the pathogenic potential of different genotypes remain to be elucidated. Possible associations between clinical parameters and antibody levels, viral load fluctuations, and viral genotype were analyzed by quantitative real-time PCR, an in-house developed IFA assay, and sequence analysis of ORF K1-VR1 in blood, serum and saliva of 38 subjects with classic KS (cKS). KSHV lytic antibodies were significantly increased in stage IV compared to stage I and II patients (p,=,0.006 and p,=,0.041, respectively). KSHV blood, serum, and saliva viral load was comparable in all stages. The highest viral loads were detected in saliva, and they decreased in stages III,IV compared to stages I,II patients. Higher concentrations of lytic antibodies and higher viral loads were observed in fast progressing cKS patients, in whom KSHV detection from blood was also more frequent. Type A KSHV strain was almost exclusively present in rapid progressors (12/17 cases), while C type was mainly present in slow progressing patients (6/7 cases). Finally, detection of type A KSHV strain associated with higher blood viral loads. KSHV lytic antibody levels and viral load can be used to monitor clinical evolution of cKS. Infection supported by KSHV A subtype is associated with more rapid progressive disease. Careful monitoring and aggressive therapeutic protocols should be considered in patients with KSHV A-supported infection. J. Med. Virol. 80:2153,2160, 2008. © 2008 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] Hepatitis in Albanian children: Molecular analysis of hepatitis A virus isolatesJOURNAL OF MEDICAL VIROLOGY, Issue 4 2004Rosanna Gabrieli Abstract Hepatitis A is a common disease in developing countries and Albania has a high prevalence of this disease associated to young age. In spite of the occurrence of a unique serotype there are different genotypes classified from I to VII. Genotype characterisation of HAV isolates circulating in Albania has been undertaken, as well as the study of the occurrence of antigenic variants in the proteins VP3 and VP1. To evaluate the genetic variability of the Albanian hepatitis A virus (HAV) isolates, samples were collected from 12 different cities, and the VP1/2A junction amplified and sequenced. These sequences were aligned and a phylogenetic analysis performed. Additionally, the amino half sequence of the protein VP3 and the complete sequence of the VP1 was determined. Anti-HAV IgM were present in 66.2% of all the sera. Fifty HAV isolates were amplified and the analysis revealed that all the isolates were sub-genotype IA with only limited mutations. When the deduced amino acid sequences were obtained, the alignment showed only two amino acids substitutions at positions 22 and 34 of the 2A protein. A higher genomic stability of the VP1/2A region, in contrast with what occurs in other parts of the world could be observed, indicating high endemicity of HAV in Albania. In addition, two potential antigenic variants were detected. The first at position 46 of VP3 in seven isolates and the second at position 23 of VP1 in six isolates. J. Med. Virol. 72:533,537, 2004. © 2004 Wiley-Liss, Inc. [source] | ||||||||||||||||