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Specific Genotypes (specific + genotype)
Selected AbstractsMixture model equations for marker-assisted genetic evaluationJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 4 2005Y. Liu Summary Marker-assisted genetic evaluation needs to infer genotypes at quantitative trait loci (QTL) based on the information of linked markers. As the inference usually provides the probability distribution of QTL genotypes rather than a specific genotype, marker-assisted genetic evaluation is characterized by the mixture model because of the uncertainty of QTL genotypes. It is, therefore, necessary to develop a statistical procedure useful for mixture model analyses. In this study, a set of mixture model equations was derived based on the normal mixture model and the EM algorithm for evaluating linear models with uncertain independent variables. The derived equations can be seen as an extension of Henderson's mixed model equations to mixture models and provide a general framework to deal with the issues of uncertain incidence matrices in linear models. The mixture model equations were applied to marker-assisted genetic evaluation with different parameterizations of QTL effects. A sire-QTL-effect model and a founder-QTL-effect model were used to illustrate the application of the mixture model equations. The potential advantages of the mixture model equations for marker-assisted genetic evaluation were discussed. The mixed-effect mixture model equations are flexible in modelling QTL effects and show desirable properties in estimating QTL effects, compared with Henderson's mixed model equations. [source] Are there predominant strains and toxins of Staphylococcus aureus in atopic dermatitis patients?THE JOURNAL OF DERMATOLOGY, Issue 2 2009Genotypic characterization, adult patients with atopic dermatitis, toxin determination of S. aureus isolated in adolescent ABSTRACT The colonization of Staphylococcus aureus is one of the most important aggravating factors of atopic dermatitis (AD). Until now, the importance of S. aureus in AD and a positive correlation between colonization with S. aureus and clinical severity/skin barrier function has been demonstrated. The aim of this study was to determine whether there are certain clones of S. aureus which colonize the skin of AD patients. For this purpose, the genotype of S. aureus isolated from AD patients was examined by newly-developed typing methods. With 36 strains of S. aureus isolated from 35 patients with AD, spa typing, multi-locus sequence typing (MLST), and staphylococcal toxin gene assay by multiplex polymerase chain reaction, were performed. Clinical severity and skin barrier function were evaluated with eczema area and severity index (EASI) and with transepidermal water loss (TEWL). Among 36 strains of S. aureus, 14 sequence types (ST) and 20 spa types were identified, suggesting a very heterogeneous genetic composition of S. aureus and the absence of a prevailing genotype in S. aureus colonized with AD patients. Furthermore, there was no specific genotype of S. aureus which was associated with the clinical severity of AD or skin barrier dysfunction. A toxin gene assay, however, showed the predominance of S. aureus strains carrying sea and/or tsst-1. To the best of our knowledge, this is the first report to show the genetic composition of S. aureus strains isolated from AD patients determined by sequence-based typing methods. [source] Genetic improvement in the presence of genotype by environment interactionANIMAL SCIENCE JOURNAL, Issue 1 2002Ching Y. LIN ABSTRACT Although the underlying mechanisms for triggering genotype,environment (GE) interaction are poorly understood, the potential impacts of GE interaction on genetic improvement are well recognized. Genotype,environment interaction may be classified into three levels: breed, individual and gene,environment interactions. Three measures of GE interaction (genetic correlation, interaction correlation, and commonality of individuals selected between environments) are discussed. Three options are currently available to deal with GE interaction: environmental, breeding and marker-assisted approaches. Three possible selection strategies for improving global net merit were outlined: (i) selection of a specific genotype for each environment; (ii) selection in a single environment alone for overall response across environments; and (iii) global optimum index selection for high stability and average performance across environments. Global optimum index should be the method of choice from the standpoint of global marketing. Because of the complexity of GE interaction, it is impossible to develop a general strategy to deal with different types of GE interaction. Each type of interaction requires its own solution, depending upon a combination of the following six factors: (i) the intensity of GE interaction; (ii) relative economic weights among environments; (iii) the size of environments; (iv) the nature of environments; (v) the nature of GE interaction; and (vi) selection intensity. Profitability is a major concern in animal production. Extra genetic gain does not necessarily mean extra profit. Does additional genetic gain justify the associated costs of dealing with GE interaction? This is a fundamental issue that needs to be considered before a specific breeding strategy for GE interaction is developed. [source] NEW ERA: PROPHYLACTIC SURGERY FOR PATIENTS WITH MULTIPLE ENDOCRINE NEOPLASIA-2AANZ JOURNAL OF SURGERY, Issue 7 2006Jessica E. Gosnell Background: The surgical management of patients with multiple endocrine neoplasia-2A (MEN-2A) continues to evolve with specific genotype,phenotype correlations allowing for a more tailored approach. In this study, we report the surgical management of one of the largest MEN-2A families with a rearranged during transfection (RET) codon 804 mutation. Method: This is a cohort study comprising all at-risk kindred within a single known MEN-2A family. Prophylactic total thyroidectomy with lymph node dissection was recommended to all mutation carriers aged 5 years and older. Results: There were a total of 48 at-risk individuals in the MEN-2A kindred, with 22 patients undergoing thyroidectomy after appropriate preoperative evaluation. A total of 9 patients had medullary thyroid cancer including 5 with a normal preoperative calcitonin level. A total of 11 patients had C-cell hyperplasia and 7 showed histological evidence of parathyroid disease. Only the index case had a phaeochromocytoma. Conclusion: Genetic testing for germline mutations in the RET proto-oncogene has allowed precise identification of affected RET carriers and provided the opportunity for prophylactic or ,preclinical' surgery to treat and in fact to prevent medullary thyroid cancer. This concept of prophylactic surgery based on a genetic test is likely to be applied more widely as the tools of molecular biology advance. [source] Importance of species interactions to community heritability: a genetic basis to trophic-level interactionsECOLOGY LETTERS, Issue 1 2006Joseph K. Bailey Abstract Recent community genetics studies have shown that specific genotypes of a host plant support distinct arthropod communities. Building upon these findings, we examined the hypothesis that a trophic community consisting of cottonwood trees, a galling herbivore and avian predators could also be related to the genetics of the host tree. We found genetic correlations among phytochemistry of individual tree genotypes, the density of a galling herbivore, and the intensity of avian predation on these herbivores. We detected significant broad-sense heritability of these interactions that range from H = 0.70 to 0.83. The genetic basis of these interactions tended to increase across trophic levels suggesting that small genetic changes in the cottonwood phenotype could have major consequences at higher trophic levels affecting species interactions and energy flow. These findings show a heritable basis to trophic-level interactions indicating that there is a significant genetic basis to community composition and energy flow that is predictable by plant genotype. Our data clearly link plant genetics to patterns of avian foraging and show that species interactions are important components of community heritability and ecosystem processes. Overall, these data support the hypothesis that evolution of plant traits can alter trophic-level interactions and community composition. [source] Direct amplification of nodD from community DNA reveals the genetic diversity of Rhizobium leguminosarum in soilENVIRONMENTAL MICROBIOLOGY, Issue 6 2001Adolphe Zézé Sequences of nodD, a gene found only in rhizobia, were amplified from total community DNA isolated from a pasture soil. The polymerase chain reaction (PCR) primers used, Y5 and Y6, match nodD from Rhizobium leguminosarum biovar trifolii, R. leguminosarum biovar viciae and Sinorhizobium meliloti. The PCR product was cloned and yielded 68 clones that were identified by restriction pattern as derived from biovar trifolii[11 restriction fragment length polymorphism (RFLP) types] and 15 clones identified as viciae (seven RFLP types). These identifications were confirmed by sequencing. There were no clones related to S. meliloti nodD. For comparison, 122 strains were isolated from nodules of white clover (Trifolium repens) growing at the field site, and 134 from nodules on trap plants of T. repens inoculated with the soil. The nodule isolates were of four nodD RFLP types, with 77% being of a single type. All four of these patterns were also found among the clones from soil DNA, and the same type was the most abundant, although it made up only 34% of the trifolii -like clones. We conclude that clover selects specific genotypes from the available soil population, and that R. leguminosarum biovar trifolii was approximately five times more abundant than biovar viciae in this pasture soil, whereas S. meliloti was rare. [source] Gaucher disease: mutation and polymorphism spectrum in the glucocerebrosidase gene (GBA),,HUMAN MUTATION, Issue 5 2008Kathleen S. Hruska Abstract Gaucher disease (GD) is an autosomal recessive disorder caused by the deficiency of glucocerebrosidase, a lysosomal enzyme that catalyses the hydrolysis of the glycolipid glucocerebroside to ceramide and glucose. Lysosomal storage of the substrate in cells of the reticuloendothelial system leads to multisystemic manifestations, including involvement of the liver, spleen, bone marrow, lungs, and nervous system. Patients with GD have highly variable presentations and symptoms that, in many cases, do not correlate well with specific genotypes. Almost 300 unique mutations have been reported in the glucocerebrosidase gene (GBA), with a distribution that spans the gene. These include 203 missense mutations, 18 nonsense mutations, 36 small insertions or deletions that lead to either frameshifts or in-frame alterations, 14 splice junction mutations, and 13 complex alleles carrying two or more mutations in cis. Recombination events with a highly homologous pseudogene downstream of the GBA locus also have been identified, resulting from gene conversion, fusion, or duplication. In this review we discuss the spectrum of GBA mutations and their distribution in the patient population, evolutionary conservation, clinical presentations, and how they may affect the structure and function of glucocerebrosidase. Hum Mutat 29(5), 567,583, 2008. Published 2008 Wiley-Liss, Inc. [source] Human papillomavirus frequency in oral epithelial lesionsJOURNAL OF ORAL PATHOLOGY & MEDICINE, Issue 5 2004Carmen Maria Lazzari Background:, Oral human papillomavirus (HPV) prevalence varies according to geographical occurrence, the type of lesion, and the method of diagnosis. The polymerase chain reaction method (PCR) appears to be more sensitive and can be easily applicable to epidemiologic studies. Objectives:, To determine the frequency of HPV and its genotypes in oral lesions among patients attending a reference clinic of a university hospital. Methods:, PCR was performed to identify HPV DNA from samples of oral epithelial lesions in 80 patients. For HPV DNA amplification, MY09/MY11 consensus primers were used and specific genotypes were identified through restriction fragment of length polymorphism (RFLP) pattern. Results:, HPV DNA was present in 11.3% of patients, and the identified genotypes were 6b, MM4 (W13B), and MM9 (PAP238A). Conclusions:, HPV DNA frequency in patients with oral epithelial lesions was 11.3%. The genotypes MM4 and MM9 are uncommon in oral lesions, and they are characterized as high-risk HPV types in those types of lesions. [source] HBV core sequence: definition of genotype-specific variability and correlation with geographical originJOURNAL OF VIRAL HEPATITIS, Issue 6 2004M. Jazayeri Summary., There are eight genotypes and nine subtypes of HBV. Small differences in geographical origin are associated with sequence changes in the surface gene. Here, we compared core gene sequences from different genotypes and geographical regions. Specific combinations of 24 amino acid substitutions at nine residues allowed allocation of a sequence to a subtype. Six of these nine residues were located in different T cell epitopes depending on HBV geographical area and/or genotype. Thirty-seven nucleotide changes were associated uniquely with specific genotypes and subtypes. Unique amino acid and nucleotide variants were found in a majority of sequences from specific countries as well as within subtype ayw2 and adr. Specific nucleotide motifs were defined for Korean, Indian, Chinese, Italian and Pacific region isolates. Finally, we observed amino acid motifs that were common to either South-east Asian or Western populations, irrespective of subtype. We believe that HBV strains spread within constrained ethnic groups, result in selection pressures that define sequence variability within each subtype. It suggests that particular T cell epitopes are specific for geographical regions, and thus ethnic groups; this may affect the design of immunomodulatory therapies. [source] Genotypic characterization of hospital Enterococcus faecalis strains using multiple-locus variable-number tandem-repeat analysisLETTERS IN APPLIED MICROBIOLOGY, Issue 1 2009E. Wa, ecka Abstract Aims:, The level of genetic diversity and relationships between the specific genotypes and the distribution of virulence determinants among Enterococcus faecalis strains isolated from patients hospitalized in different wards of two hospitals were investigated. Methods and Results:, Fifty-six clinical strains of E. faecalis, isolated from patients hospitalized in the period of 1999,2004 in several wards in Wroc,aw (Poland), were analysed by multiple-locus variable-number tandem-repeat analysis (MLVA). Analysis of seven genomic loci identified 40 novel genotypes among the analysed E. faecalis strains, with two major genomic groups, designated I and II, distinguished at a cut-off of 35%. With a similarity cut-off of 85ˇ7%, the genotypes could be combined into 12 clusters (C1,C12), containing at least two isolates. The remaining 18 MLVA types were represented by a single isolate. Conclusions:, Based on the data obtained by MLVA, it was found that (i) many E. faecalis isolates recovered from patients from the wards whose location allowed the potential transmission of micro-organisms, belonged to closely related MLVA types and (ii) possible relationships between specific E. faecalis genotype and the virulence factors lipase, haemolysin and esp gene can exist. Significance and Impact of the Study:, Our study confirms that MLVA is a suitable method for the epidemiological study of E. faecalis and for the first time shows possible relationships between specific genotypes and such virulence determinants, i.e. lipase, haemolysin and esp gene. [source] GSTM1 and GSTT1 null genotypes as possible heritable factors of rosaceaPHOTODERMATOLOGY, PHOTOIMMUNOLOGY & PHOTOMEDICINE, Issue 4 2006Ayca Cordan Yazici Purpose: Rosacea might be related to an increased activity of reactive oxygen species (ROS) and deficient function of the antioxidant system. Glutathione S-transferases (GSTs) play a primer role in cellular defense against electrophilic chemical species and radical oxygen species. We hypothesized that increased ROS activity or decreased antioxidant potential, possibly induced by GST gene polymorphism, might have a pathogenic role in rosacea. Methods: The study group consisted of 45 patients with rosacea and 100 control subjects. DNA samples were isolated from blood samples using high pure polymerase chain reaction (PCR) Template preparation Kit. The GSTM1, GSTT1, and P1 polymorphisms were detected using a real-time PCR and fluorescence resonance energy transfer with a Light-Cycler Instrument. Associations between specific genotypes and the development of rosacea were examined using logistic regression analyses to calculate odds ratios (OR) and 95% confidence intervals (CI). Results: GSTM1 and GSTT1 null genotypes were found to be statistically different from control (P=0.005, P=0.009, respectively), and associated with an increased risk of rosacea (OR [95% CI]: 2.84 [1.37,5.89]; OR [95% CI]: 2.68 [1.27,5.67], respectively). There was a statistically significant relationship between both null combination of the GSTM1 and GSTT1 genotype polymorphisms and rosacea (P=0.003, OR [95% CI]: 4.18 [1.57,11.13]). There were no statistically significant differences between patient and control groups for the GSTP1 Ile/Ile, Ile/Val, and Val/Val genotypes (P>0.05). Conclusion: We demonstrated a significant association between the GSTT1 and/or GSTM1 null genotypes and rosacea. However, the potential role of GSTs as markers of susceptibility to rosacea needs further studies in larger patient groups. [source] Climate and genotypes of Pneumocystis jiroveciiCLINICAL MICROBIOLOGY AND INFECTION, Issue 4 2007R. F. Miller Abstract This study explored whether seasonal and/or climatic factors influenced detection of specific genotypes of Pneumocystis jirovecii. Between 1989 and 2001, 155 isolates of P. jirovecii were obtained from patients undergoing bronchoscopic alveolar lavage. For each isolate, the month and climatic conditions were noted. Genotypes of P. jirovecii were distinguished by polymorphisms in the mitochondrial large-subunit rRNA gene. There were monthly and seasonal variations in the frequency of detection of mixed genotypes (p 0.018 and p 0.031, respectively) and genotype 2 (p 0.029 and p 0.086, respectively). There was no association between month/season and genotypes 1, 3 and 4, or between monthly temperature or rainfall and any genotype. [source] | |||||||||||||