Academic literature on the topic 'SNP candidati'
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Journal articles on the topic "SNP candidati"
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Seoane, José A., Vanessa Aguiar Pulido, Alba Cabarcos, Sonsoles Quintela, Juan Ramon Rabuñal, and Julián Dorado. "SNP locator: a candidate SNP selection tool." International Journal of Data Mining, Modelling and Management 5, no. 3 (2013): 193. http://dx.doi.org/10.1504/ijdmmm.2013.055863.
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Souche, E. L., B. Hellemans, J. K. J. Van Houdt, A. Canario, S. Klages, R. Reinhardt, and F. A. M. Volckaert. "Mining for Single Nucleotide Polymorphisms in Expressed Sequence Tags of European Sea Bass." Journal of Integrative Bioinformatics 4, no. 3 (December 1, 2007): 158–67. http://dx.doi.org/10.1515/jib-2007-73.
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Abstract As a multitude of sequence data are published, discovering polymorphisms bioinformatically becomes a valid option. In silico Single Nucleotide Polymorphism (SNP) detection is based on the analysis of multiple alignments. Each column of an alignment is considered a slice containing one base of every sequence aligned. If a mismatch is detected, the slice is further analysed and the mismatch may be reported as a candidate SNP.About 30,000 Expressed Sequence Tags (ESTs) of the fish European sea bass have been sequenced and processed. Since ESTs are redundant, they provide a resource for in silico SNP discovery. To prevent the detection of sequencing errors, a redundancy of two is chosen in order for a mismatch to be considered a candidate SNP. Among the various tools available to detect candidate SNPs, three software packages were tested: SNPServer, PolyBayes and PolyFreq. Candidate SNPs were validated in the laboratory by cloning and sequencing. From preliminary results PolyFreq outperforms both PolyBayes and SNPServer in terms of positive predictive value and SNPServer is the most sensitive tool. PolyFreq and SNPServer non-default identify respectively the fewest and highest number of candidates. Considering candidates detected by several tools seems to enhance both positive predictive value and sensitivity. Out of the 69 loci sequenced, only four were monomorphic, leading to a total of 91.3% polymorphic loci. Randomly chosen contigs will be sequenced to know whether SNP discovery tools tend to predict polymorphic fragments. Polymorphisms will be mapped, used for selection in aquaculture and the study of adaptation in natural populations.
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Um, Nam-Hyun. "Effectiveness of Celebrity Endorsement Of Political Candidates." Social Behavior and Personality: an international journal 46, no. 10 (October 4, 2018): 1585–96. http://dx.doi.org/10.2224/sbp.6757.
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I examined the effects of celebrity endorsement of political candidates, drawing on third-person effect theory, social identification theory, and political efficacy theory. Participants were 283 students at an American university who took part in a web-based survey that explored attitudes using actual presidential candidates and real celebrities. Study findings suggest that people view such endorsements as having no impact on their own voting behavior yet influencing that of others by encouraging them to vote for the endorsed candidate. In addition, people positively evaluate the endorsed political candidate when they hold a high level of identification with the celebrity endorser and are likely to vote for the candidate. Lastly, whereas political efficacy does influence people's intention to vote, it does not appear to influence their evaluation of the candidate. Limitations of the study and future research are discussed.
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Harlid, Sophia, Malin I. L. Ivarsson, Salma Butt, Shehnaz Hussain, Ewa Grzybowska, Jorunn Erla Eyfjörd, Per Lenner, et al. "A candidate CpG SNP approach identifies a breast cancer associated ESR1-SNP." International Journal of Cancer 129, no. 7 (March 11, 2011): 1689–98. http://dx.doi.org/10.1002/ijc.25786.
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Taylor, Jacquelyn Y., Deborah Sampson, Andre D. Taylor, Dennis Caldwell, and Yan V. Sun. "Genetic and BMI Risks for Predicting Blood Pressure in Three Generations of West African Dogon Women." Biological Research For Nursing 15, no. 1 (August 22, 2011): 105–11. http://dx.doi.org/10.1177/1099800411419026.
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The study of genetic polymorphisms and body mass index (BMI) among African women in Africa and in the United States contributes to our understanding of the genetic and environmental risk factors for hypertension. African American women have the highest prevalence of hypertension and obesity compared to other ethnic groups in the United States. Using a cross-sectional research design, we examined the effects of genetic and environmental risks of single nucleotide polymorphisms (SNPs) and BMI on blood pressure (BP) among three generations of West African Dogon women ( N = 199). We genotyped six SNPs located in the candidate genes known to be related to hypertension. We tested the associations between these SNPs and systolic BP (SBP) and diastolic BP (DBP) with Fisher’s exact tests, chi-square tests for independence, and multivariable linear mixed models. The SNP rs8179526 (SLC4A5) was significantly associated with SBP adjusted for age, age2, and BMI ( p = .02). The “C” allele variant of rs8179526 (allele frequency of 0.445) was associated with higher SBP. This SNP did not deviate from the Hardy–Weinberg equilibrium (HWE) with p value of .772. The SNP × BMI interaction effects associated with SBP and DBP were not significant. rs8179526 is located on the SLC4A5 gene on chromosome 2. SLC4A5 encodes a protein that transports sodium and bicarbonate across cell membranes while regulating cellular pH and contains several SNPs linked to elevated BP. Knowledge of the SNP’s effect on hypertension among West African women can help health practitioners educate their patients about genetic risks of developing hypertension.
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Stone, Brad, Scott Graves, Arnold Kas, Alexander Ford, Nathan Standifer, Crystal Rawlings, Steven Rosinski, Susan Masewicz, Maynard Olson, and Rainer F. Storb. "Direct Genotyping of Coding Non-Synonymous SNPs for Identification of Novel Minor Histocompatibility Antigens." Blood 108, no. 11 (November 16, 2006): 3237. http://dx.doi.org/10.1182/blood.v108.11.3237.3237.
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Abstract Traditional methods for identifying minor histocompatibility antigens (mHags) are technically challenging and biased against discovery of mHags not expressed in the peripheral blood. In this work, we propose a rapid, unbiased, genetic approach for identification minor antigens resulting from disparities in coding non-synonymous SNPs (“C SNPS”). This approach is capable of testing for responses to candidate minor antigens expressed in virtually any tissue, including those expressed exclusively in tissues targeted by GVHD. The first step in our approach begins with comparison of donor and recipient C SNP genotypes generated using C SNP microarrays. These arrays interrogate approximately 80% of human C SNPs predicted to occur in greater than 5% of the population. Comparison of C SNP genotypes directly identifies protein-altering alleles present in the recipient but not the donor (hereafter referred to as “recipient-restricted” alleles), thereby identifying a transplant-specific set of candidate minor antigens. The second step utilizes conventional HLA-class I epitope prediction performed on all linear peptides that include amino-acid residues defined by a recipient-restricted allele. This two step filtering process identifies a small, “testable” number candidate minor peptide epitopes for an individual expressed HLA-class I allele. Candidate epitopes can then be synthesized, pooled and tested at diagnosis of GVHD using a commercial Granzyme B ELISPOT assay. As proof-of-principal for a direct genotyping approach, we have analyzed C SNP genotypes, performed epitope prediction and generated T-cell lines specific for candidate minor antigens using DNA and PBL from a pair of disease-free HLA-identical siblings. Analysis of 10,000 C SNPs shows that approximately 2,000 C SNP alleles are restricted to one sibling within the pair. BIMAS epitope prediction of short unique peptide sequences determined by each sibling-restricted allele identifies approximately 100 candidate minor epitopes predicted to bind HLA-A*0201. These candidate minor epitopes were ranked using expression microarrays performed on EBV-transformed LCL derived from each sibling, with candidates derived from highly expressed genes ranked above those from genes with lower expression levels. A pool of 12 candidate minor epitopes that were both unique to sibling “A” and derived from genes highly expressed in LCL were synthesized and used to generate CD8+ T-cell lines from sibling “B”. Stimulation utilized autologous (sibling “B”-derived) mature dendritic cells loaded with candidate minor epitopes. After several rounds of in-vitro stimulation, each T-cell line was tested for responses to EBV-LCL from sibling “B” and sibling “A” using a Granzyme B ELISPOT kit. Five out of sixteen lines responded to LCL from sibling A while no line responded to autologous LCL. Thus we show that this approach frequently generates CD8+ T-cell lines specific for sibling-derived target cells, suggesting that this approach efficiently identifies genuine, novel, endogenously processed and presented minor epitopes. Deconvolution of the peptide pool suggests that at least two out of the twelve candidate minor epitopes are naturally processed and presented.
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Laird, Eamon, Aisling M. O’halloran, Artur Fedorowski, Olle Melander, Ann Hever, Marketa Sjögren, Daniel Carey, and Rose Anne Kenny. "Orthostatic Hypotension and Novel Blood Pressure Associated Gene Variants in Older Adults: Data From the TILDA Study." Journals of Gerontology: Series A 75, no. 11 (December 10, 2019): 2074–80. http://dx.doi.org/10.1093/gerona/glz286.
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Abstract Orthostatic hypotension (OH) is associated with increased risk of trauma and cardiovascular events. Recent studies have identified new genetic variants that influence orthostatic blood pressure (BP). The aim of this study was to investigate the associations of candidate gene loci with orthostatic BP responses in older adults. A total of 3,430 participants aged ≥50 years from The Irish Longitudinal Study on Ageing (TILDA) with BP measures and genetic data from 12 single-nucleotide polymorphism (SNP) linked to BP responses were analyzed. Orthostatic BP responses were recorded at each 10 s interval and were defined as OH (SBP drop ≥20 mmHg or DBP drop ≥10 mmHg) at the time-points 40, 90, and 110 s. We defined sustained OH (SOH) as a drop that exceeded consensus BP thresholds for OH at 40, 90, and 110 s after standing. Logistic regression analyses modeled associations between the candidate SNP alleles and OH. We report no significant associations between OH and measured SNPs after correction for multiple comparisons apart from the SNP rs5068 where proportion of the minor allele was significantly different between cases and controls for SOH 40 (p = .002). After adjustment for covariates in a logistic regression, those with the minor G allele (compared to the A allele) had a decreased incidence rate ratio (IRR) for SOH 40 (IRR 0.45, p = .001, 95% CI 0.29–0.72). Only one SNP linked with increased natriuretic peptide concentrations was associated with OH. These results suggest that genetic variants may have a weak impact on OH but needs verification in other population studies.
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Levin, Irwin P., Robert M. Rouwenhorst, and Heather M. Trisko. "SEPARATING GENDER BIASES IN SCREENING AND SELECTING CANDIDATES FOR HIRING AND FIRING." Social Behavior and Personality: an international journal 33, no. 8 (January 1, 2005): 793–804. http://dx.doi.org/10.2224/sbp.2005.33.8.793.
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A two-stage procedure (consideration set formation and final choice) was used to track the emergence of gender biases in hiring and firing decisions. Participants were allowed to select their own strategy for narrowing choice options (which candidates to retain or which candidates to delete). Each of the two experiments included a condition where job candidates were considered for hiring and a condition where current employees were considered for firing. Candidate features varied across experiments but the initial set always included 18 females and 18 males with comparable credentials. In both experiments male and female respondents selected candidates of their own sex for hiring and both males and females selected mostly male candidates for firing. In each experiment the bias showed up only in the final-choice stage.
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Pun, F., C. Zhao, W. Lo, S. Ng, S. Tsang, V. Nimgaonkar, W. Chung, G. Ungvari, and H. Xue. "Imprinting in the schizophrenia candidate gene GABRB2." European Psychiatry 26, S2 (March 2011): 823. http://dx.doi.org/10.1016/s0924-9338(11)72528-7.
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Imprinting, characterized by unequal expression of the offspring's genes in a parent-of-origin dependent manner, has been functionally implicated in brain development and in psychiatric disorders. In this study, unambiguous distortion in paternal but not maternal transmission of the disease-associated single-nucleotide polymorphism (SNP) rs6556547 (T/G) clearly indicated the presence of parent-of-origin effect (POE) in the GABAA receptor β2 subunit gene (GABRB2). ‘Flipping’ of allelic mRNA expression in heterozygotes of SNP rs2229944 (C/T) and the observed two-tiered distribution of mRNA expression levels in heterozygotes of the disease-associated SNP rs1816071 (G/A) furnished important support for the occurrence of imprinting at GABRB2. Imprinting in effect introduced heterozygotes from different parents-of-origin endowed with dissimilar mRNA expression capabilities. The deficit of upper-tiered expressions accounted for the lowered mRNA expression levels in the schizophrenic heterozygotes. This pointed to the necessity of differentiating between two kinds of heterozygotes of different parental origins in disease association studies on GABRB2. Bisulfite sequencing revealed hypermethylation in the neighborhood of SNP rs1816071, and methylation differences between controls and schizophrenia patients. Notably, allele-specific methylation was observed at the disease-associated SNPs rs6556547 and rs1816071. These findings raised the possibility that CpG methylation status of these sites could have an impact on the expression of GABRB2 and the risk of schizophrenia. Furthermore, the occurrence of imprinting and allele-specific methylation in the schizophrenia candidate gene GABRB2 was compatible with the epigenetic hypothesis for schizophrenia pathophysiology, thereby calling for the need to explore the role of epigenetic factors in mediating susceptibility to schizophrenia.
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Song, Long, Jing Qin Wu, Chong Mei Dong, and Robert F. Park. "Integrated Analysis of Gene Expression, SNP, InDel, and CNV Identifies Candidate Avirulence Genes in Australian Isolates of the Wheat Leaf Rust Pathogen Puccinia triticina." Genes 11, no. 9 (September 21, 2020): 1107. http://dx.doi.org/10.3390/genes11091107.
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The leaf rust pathogen, Puccinia triticina (Pt), threatens global wheat production. The deployment of leaf rust (Lr) resistance (R) genes in wheat varieties is often followed by the development of matching virulence in Pt due to presumed changes in avirulence (Avr) genes in Pt. Identifying such Avr genes is a crucial step to understand the mechanisms of wheat-rust interactions. This study is the first to develop and apply an integrated framework of gene expression, single nucleotide polymorphism (SNP), insertion/deletion (InDel), and copy number variation (CNV) analysis in a rust fungus and identify candidate avirulence genes. Using a long-read based de novo genome assembly of an isolate of Pt (‘Pt104’) as the reference, whole-genome resequencing data of 12 Pt pathotypes derived from three lineages Pt104, Pt53, and Pt76 were analyzed. Candidate avirulence genes were identified by correlating virulence profiles with small variants (SNP and InDel) and CNV, and RNA-seq data of an additional three Pt isolates to validate expression of genes encoding secreted proteins (SPs). Out of the annotated 29,043 genes, 2392 genes were selected as SP genes with detectable expression levels. Small variant comparisons between the isolates identified 27–40 candidates and CNV analysis identified 14–31 candidates for each Avr gene, which when combined, yielded the final 40, 64, and 69 candidates for AvrLr1, AvrLr15, and AvrLr24, respectively. Taken together, our results will facilitate future work on experimental validation and cloning of Avr genes. In addition, the integrated framework of data analysis that we have developed and reported provides a more comprehensive approach for Avr gene mining than is currently available.
Dissertations / Theses on the topic "SNP candidati"
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Raschetti, M. "RICERCA E VALIDAZIONE DI SNP IN GENI CANDIDATI PER LA QUALITÀ DELLA CARNE E APPLICAZIONE DELL'ANALISI GENOMICA ALLA SPECIE SUINA." Doctoral thesis, Università degli Studi di Milano, 2010. http://hdl.handle.net/2434/150123.
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An important aim of pig selection in Italy is to obtain animals having a high aptitude for the PDO dry-cured ham production, such as Parma or S. Daniele ham. Over the past years, advances in the porcine genetic map have led to valuable gene and trait information being discovered. Since that time, sequences for the pig genome have been generated from various tissues, the sequencing of candidate genes, and more recently large scale genomic sequencing projects. These efforts are also being directed to SNPs identification for future large scale association studies. In the next years, the efficiency and accuracy of the traditional pig selection schemes could be improved by the implementation of molecular data into breeding programs. In this work, seven swine candidate genes for meat quality were investigated in order to identify informative SNPs. Molecular analyses were performed on twenty-two animals representing the extreme tails of the Gaussian distribution for three selected phenotypes (muscle compactness, fat thickness and the principal component 1) of 231 Large White x Landrace individuals. Among the nine identified SNPs, only two SNPs in the CRADD gene, two SNPs in the PTPRD gene and one SNP in the PIK3R2 gene showed a MAF (Minor Allele Frequency) more than 5% in the animals tested and therefore were considered for the subsequent association analysis.
Association analysis between these five SNPs and the three phenotypes considered in this study was carried out using the GML procedure. The SNP CRADD g343 [A/G] showed a good association with the compactness of the muscles (P = 0,0498), the SNP PTPRD g30194 [G/T] showed a good association with the compactness of the muscles (P = 0,0195) and fat thickness dorsal (P = 0,0265), the SNP PIK3R2 g.3008 [C/T] showed a very good association with the compactness of muscle mass (P = 00,0014) and thickness of backfat (P = 0,0087). Therefore, the PIK3R2SNP g.3008 [C / T] was genotyped on all 231 animals of the population. The analysis showed a significant effect of this SNP on the following variables: marbling (P < 0.0001), fat cover (P < 0.05), fat thickness (P < 0.05), Prin1 (P < 0.05), Prin3 (P < 0.01); Prin4 (P < 0.01). In particular, the CC genotype was positively associated with marbling and fat cover. Moreover, the SNP in PIK3R2 gene was tested on 600 samples of three different Italian breeds (Large White, Duroc, Landrace) obtained from the National Association of Pig Breeders of Italy. Within each breed, the 100 individuals with the highest and the 100 individuals with the lowest values for EBVs (Estimated Breeding Values) for average daily weight gain were analyzed, resulting this SNP polymorphic in each breed. The association analyses between this SNP and these extreme EBVs showed a good association with backfat thikness, average daily gain, feed conversion rate and thigh weight in Landrace individuals. The two SNPs identified in CRADD gene and the two SNPs identified in the PTPRD gene were tested in another group of 560 Italian Large White animals with extreme EBVs for fat thickness. Three of the four SNPs resulted polymorphic also in this population. Then, association analysis between these three SNPs and EBVs for fat thickness were performed, showing the association of the SNP g29962[A/G ] of PTPRD gene with thigh weight. Another aim of this PhD thesis is the genetic characterization of a swine genetic type, the “Nero di Garlasco”, expressing both ancient and recent biodiversity. Although in the last years admirable efforts have been made to recover pig biodiversity, extremely endangered, today only few Italian local breeds can withstand the competition with commercial foreign breeds (i.e. the Large White, Landrace and Duroc) and with the commercial crosses today more and more widespread in the market. To date, at the national Herd Book only few breeds are registered as the Cinta senese, Mora Romagnola, Nero Siciliano, Casertana, Apulo-Calabrese and the Sarda. A very limited number with respect to the tens of breeds and lines cited in the textbooks of agronomy of the second postwar period. The majority of the extinct pig breeds were adapted to free range breeding, and were characterized by dark coat color (to defend themselves form the sun), slow growth and extensive fat deposits. In recent years, an ancient genetic type barely still existing (Razza di Garlasco) is reconstructing in the province of Pavia (Lomellina). In this case, pig phenotypes consisted of dark coat color and, surprisingly, high growth rates, similar to the commercial breeds. These two characteristics made these animals well adapted for the non-industrial production, where animals can be bred in free range, because the dark color protects them from the sun. To achieve this goal, a genetic characterization of the model population should be conducted. The tight bottleneck, through which this small population has passed, allows the fixation of genetic markers that enable precise traceability of the fresh and transformed products. This can give an added value to the breeding of theses animals that responds to the request for security and sustainability of the animal production system. Thanks to innovative technologies, a population of 96 animals, belonging to the Nero di Garlasco breed, was analyzed using the PorcineSNP60 BeadChip, in order to screen about 60,000 SNPs. The obtained data allowed a first description of the genetic structure of this population, but further studies are required to characterize this swine genetic type.
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Abou-Khater, Charbel. "Caractérisation de nouveaux gènes et polymorphismes potentiellement impliqués dans les interactions hôtes-pathogènes." Thesis, Aix-Marseille, 2017. http://www.theses.fr/2017AIXM0196/document.
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La coévolution ainsi que les différentes interactions entre hôte et pathogène contribuent à former la diversité génétique de ces deux organismes. Dans le cadre de cette thèse, nous nous sommes intéressés à l’étude de la variabilité génétique de 1760 gènes immunitaires choisis suivant des critères définis, pour essayer d’expliquer pourquoi il existe une variation individuelle face aux infections. L’objectif principal de ce projet était alors de caractériser et d'analyser de nouveaux gènes et polymorphismes immunitaires pouvant expliquer le contrôle ou la susceptibilité à certaines infections. Deux études pilotes nous ont permis de développer le pipeline de détection de polymorphismes. Pour la première, le polymorphisme des 3 gènes CD28, CTLA4, et ICOS a été caractérisé. Dans la deuxième, nous avons caractérisé le polymorphisme de 10 gènes impliqués dans la réponse immunitaire contre M. tuberculosis. Ces gènes ne sont pas très polymorphes et trois d’entre eux sont très conservés. Ces deux études nous ont aidés à préparer l’analyse à grande échelle avec les mises au point et l’amélioration du pipeline. Nous avons sélectionné 1760 gènes en se basant sur des critères définis. La variabilité génétique a été étudiée dans les populations humaines par une analyse minutieuse in silico de données de séquençage d’exomes générées par différents projets et consortiums pour plus de 700 individus représentant 20 populations à travers le monde. 30 gènes les plus polymorphes ont été ainsi identifiés. Ces gènes pourront être entièrement caractérisés et les données produites pourraient être comparées avec des données de résistance/sensibilité de certaines maladies infectieusesHost-pathogen co-evolution and interactions contribute in shaping the genetic diversity of both organisms. The objective of this thesis is to define the genetic basis of variability in disease resistance/susceptibility through the development of large-scale in silico screens to identify novel gene candidates implicated in host-pathogen interactions (such as tuberculosis).A pilot study was conducted on CD28, CTLA4, and ICOS to investigate their polymorphism. As a first step in our study based on data available in the literature, we selected a set of ten genes relevant for the immune response against M. tuberculosis. Seven of these genes were moderately polymorphic, while three of them were highly conserved. This analysis was used to prepare and setup the large scale analysis using the same developed pipeline for polymorphism detection and allele reconstruction. For our in silico, we used sequence data from several projects and consortiums to isolate most polymorphic human genes amongst a list of over 1760 candidates selected based on already established relevance for infections and on evolutionary considerations. A first screen of 64 individuals from eight different populations from several regions of the world was performed and most variable genes were selected for further extensive analyses on a larger panel (715 individuals). 30 most polymorphic genes were thus identified. The extent of polymorphism and the allelic worldwide variants of each of these 30 genes are ready to be fully characterized. The data generated could be compared against infectious disease resistance/susceptibility data to identify potentially relevant gene variation
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Feuk, Lars. "SNP based strategies to study candidate genes for Alzheimer's disease /." Stockholm, 2002. http://diss.kib.ki.se/2002/91-7349-334-1.
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Lalagüe, Hadrien. "Genetic response of tree population to spatial climatic variation : an experimental genomic and simulation approach in Fagus sylvatica populations along altitudinal gradients." Thesis, Montpellier 2, 2013. http://www.theses.fr/2013MON20042/document.
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Un enjeu majeur de la génétique évolutive est de comprendre comment l'adaptation locale se développe en population naturelle, et comment les différentes forces évolutives y contribuent. Les études expérimentales d'adaptation locale utilisent couramment les gradients altitudinaux présentant une variation spatiale marquée des conditions environnementales. Dans ces conditions, on s'attend à ce que la différentiation génétique pour les caractères (traditionnellement mesurée par QST) et pour les gènes déterminant ces caractères (traditionnellement mesurée par FSTq) le long du gradient soit gouvernée de façon prédominante par la sélection et les flux de gènes, et peu influencée en revanche par la dérive génétique et la mutation. En particulier, des études théoriques ont montré un découplage entre QST et FST lorsque que les flux de gènes sont forts et/ou que la sélection est récente. Dans cette étude, nous avons testé cette hypothèse en combinant une approche de génomique expérimentale et des simulations dans des populations naturelles de hêtre commun (F. sylvatica) séparées de ~trois kilomètres et soumis à des environnements contrastés.Pour l'approche expérimentale, nous avons échantillonné 4 populations sur deux gradients altitudinaux sur le Mont Ventoux (avec une population à haute altitude et une à basse altitude sur chaque gradient). Cinquante huit gènes potentiellement impliqué dans la réponse aux stress abiotiques et dans le débourrement ont été séquencés sur un total de quatre-vingt seize individus, révélant 581 SNPs (Single Nucleotide Polymorphisms). Différentes approches ont été utilisées pour identifier les SNP outlier, présentant une différentiation plus forte qu'attendu sous un modèle neutre sans sélection. Le nombre de SNPs outlier identifié comme étant sous sélection s'est révélé être grandement dépendant de la méthode utilisé. La méthode fréquentiste a détecté de nombreux outliers alors que l'approche bayésienne n'a pu permettre de détecter des SNPs sous sélection. Par ailleurs, nous avons utilisé un modèle mécaniste individu-centré pour simuler les patrons de diversité phénotypique et génétique attendus le long du gradient pour la phénologie du débourrement végétatif, un caractère généralement adaptatif dans la réponse aux variations de température. Les résultats des simulations confirment que la différentiation génétique observée pour le caractère (QST) est généralement plus forte que celle observée au gène (FSTq), et que cette différentiation génétique au trait intervient dès la première génération. Toutefois, les tests d'outlier conduits sur le le modèle simulé ont révélé que plus de 95% des SNPs outlier sont des faux positifs. Comme dans l'approche expérimentale, l'approche Bayésienne ne s'est pas révélé suffisamment fiable pour détecter des QTLs dans des populations spatialement proche et génétiquement faiblement différentiée. Néanmoins une approche multi-locus basée sur un estimateur peu utilisé en génétique (le Zg) a révélé la forte corrélation inter-populations inter-gènes des QTLs confirmant les attendus théoriques. Toutefois, cette approche ne permet pas de détecter précisément les QTLs sans connaissance a priori sur les QTLs. En conclusion, les travaux de cette thèse mettent en évidence la rapidité des changements génétique qui interviennent en moins de 5 générations pendant la modification du climat, et la difficulté de détecter les gènes codant pour des traits complexesA major challenge in population genetics is to understand the local adaptation process in natural population and so to disentangle the various evolution forces contributing to local adaptation. The experimental studies on local adaption generally resort to altitudinal gradients that are characterized by strong environmental changes across short spatial scales. Under such condition, the genetic differentiation of the functional trait (measured by the Qst) as well as the genes coding for trait (measured by Fstq) are expected to be mainly driven by selection and gene flow. Genetic drift and mutation are expected to have minor effect. Theoretic studies showed a decoupling between Qst and Fst under strong gene flow and / or recent selection. In this study, I tested this hypothesis by combining experimental and modelling genomic approach in natural population of Fagus sylvatica separated by ~3 kilometres and under contrasted environments.Sampling was conducted in south-eastern France, a region known to have been recently colonised by F.sylvatica. Four naturally-originated populations were sampled at both high and low elevations along two altitudinal gradients. Populations along the altitudinal gradients are expected to be subjected to contrasting climatic conditions. Fifty eight candidate genes were chosen from a databank of 35,000 ESTs according to their putative functional roles in response to drought, cold stress and leaf phenology and sequenced for 96 individuals from four populations that revealed 581 SNPs. Classical tests of departure of site frequency spectra from expectation and outlier detection tests that accounted for the complex demographic history of the populations were used. In contrast with the mono-locus tests, an approach for detecting selection at the multi-locus scale have been tested.The results from experimental approaches were highly contrasted according the method highlighting the limits of those method for population loosely differentiated and spatially close. The modelling approach confirmed the results from the experimental data but revealed that up to 95% of the SNPs detected as outliers were false positive. The multi-locus approach revealed that the markers coding for the trait are differentially correlated compared to the neutral SNPs. But this approach failed to detect accurately the markers coding for the trait if no a priori knowledge is known about them. The modelling approach revealed that genetic changes may occur across very few generation. But while this genetic adaptation is measurable at the trait level, the available method for detecting genetic adaptation at the molecular level appeared to be greatly inaccurate. However, the multi-locus approach provided much more promise for understanding the genetic basis of local adaptation from standing genetic variation of forest trees in response to climate change
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Costa, ?rica Cristina Xisto da. "Polimorfismo do gene MSTN e do SNP BIEC2-808543 e sua rela??o com crescimento de potros da ra?a brasileiro de hipismo." Universidade Federal Rural do Rio de Janeiro, 2015. https://tede.ufrrj.br/jspui/handle/jspui/1392.
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The gene encoding myostatin (MSTN), located on chromosome 18 (ECA 18) and the SNP BIEC2-808543 located in the intergenic region, which precedes the gene encoding the protein similar to the nuclear corepressor receptor dependent binder (LCORL), located on chromosome 3 (ACE 3) in horses, both positioned in regions that are associated with conformational traits of these animals. In view of this, we aimed to identify if the variations described in MSTN and LCORL loci exist in the study population; and to identify the effects of these polymorphisms on the growth profiles of these animals. For this purpose, the characteristics measured were weight, height at withers and hip height of foals at different ages, belonging to the Coudelaria e Campo de Instru??o de Rinc?o do Ex?rcito Brasileiro. Nonlinear mixed models were adjusted resulting from the combination of six nonlinear simple models, Brody (1945), Gompertz (Winsor, 1932), Logistics (Ratkowski, 1983), Von Bertalanffy (1957), generalized Michaelis- Menten (Lopez et al., 2000) and Richards (1959) associated with four types of variance functions for each model, homogeneous, exponential, asymptotic and staggered. The polymorphism described in the promoter region of the MSTN gene was not found in the studied population, in which there has been only the T allele, however the BIEC2-808543 polymorphism, located in the region prior to the LCORL gene is significantly associated (P <0, 05) to the characteristics evaluated, in which the animals who presented the genotype TT were smaller and lighter when compared to the other genotypes. There was no significant difference between animals with CT and CC genotype. The model that best describes the growth curve for body mass variance is the model of Brody (1945) associated with the scaled variance for the variable height at the withers the model that best fit was the Von Bertalanffy (1957) (adjusted without polymorphism effect in b) parameter associated with the asymptotic variance and the characteristic hip height the model that best described was that of Brody (1945) associated with the asymptotic variance, explaining that the nonlinear mixed models are indeed promising to describe equine growth curves, for the simple models did not differ much among themselves what defined in fact the selection of the model was the variance, being for body mass staggered variance and the height at the withers and on the back, the asymptotic variance. This polymorphism can be used as molecular markers for early selection of foals as to the characteristics evaluated
O gene que codifica a miostatina (MSTN), localizado no cromossomo 18 (ECA 18) e o SNP BIEC2-808543 localizado na regi?o interg?nica que antecede o gene que codifica a prote?na semelhante a correpressor de receptor nuclear dependente de ligante (LCORL), localizado no cromossomo 3 (ECA 3) de cavalos, ambos posicionados em regi?es que est?o associadas ?s caracter?sticas conformacionais destes animais. Diante disto, objetivamos identificar se as varia??es descritas nos loci MSTN e LCORL, existem na popula??o em estudo; al?m de verificar os efeitos desses polimorfismos sobre os perfis de crescimento desses animais. Com este intuito foram mensuradas as caracter?sticas massa corporal, altura na cernelha e altura na garupa de potros em diversas faixas et?rias, pertencentes ? Coudelaria e Campo de Instru??o de Rinc?o do Ex?rcito Brasileiro. Foram ajustados modelos n?o lineares mistos que resultaram da combina??o de seis modelos n?o lineares simples, Brody (1945), Gompertz (Winsor, 1932), Log?stico (Ratkowski, 1983), Von Bertalanffy (1957), Michaelis-Menten generalizado (L?pez et al., 2000) e Richards (1959), associados a quatro tipos de fun??es de vari?ncia para cada modelo, homog?nea, exponencial, assint?tica e escalonada. O polimorfismo descrito na regi?o promotora do gene MSTN n?o foi encontrado na popula??o estudada, na qual observa-se apenas o alelo T, entretanto o polimorfismo BIEC2-808543, localizado na regi?o que antecede o gene LCORL, est? significativamente associado (P<0,05) ?s caracter?sticas avaliadas, sendo os animais que apresentaram o gen?tipo TT menores e mais leves quando comparado com os demais gen?tipos. N?o foi observada diferen?a significativa entre os animais com gen?tipo TC e CC. O modelo que melhor descreve a curva de crescimento para a vari?vel massa corporal ? o modelo de Brody (1945) associado com a vari?ncia escalonada, para a vari?vel altura na cernelha o modelo que melhor se ajustou foi o de Von Bertalanffy (1957) (ajustado sem efeito de polimorfismo no par?metro b) associado com a vari?ncia assint?tica e para a caracter?stica altura na garupa o modelo que melhor a descreveu foi o de Brody (1945) associado ? vari?ncia assint?tica, elucidando que os modelos n?o-lineares mistos s?o de fato promissores para a descri??o de curvas de crescimento de equinos, pois os modelos simples n?o diferiram muito entre si o que definiu de fato a sele??o do modelo foi a vari?ncia, sendo para massa corporal a vari?ncia escalonada e para as alturas, na cernelha e na garupa, a vari?ncia assint?tica. Este polimorfismo pode ser utilizado como marcador molecular para sele??o precoce de potros quanto ?s caracter?sticas avaliadas
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Alves, Fernanda Aparecida Vargas de Brito e. "ANÁLISE DO POLIMORFISMO T102C DO RECEPTOR DE SEROTONINA (HTR2A) EM PACIENTES COM FIBROMIALGIA E CONTROLES." Pontifícia Universidade Católica de Goiás, 2012. http://localhost:8080/tede/handle/tede/2360.
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FERNANDA APARECIDA VARGAS DE BRITO E ALVES.pdf: 1009586 bytes, checksum: 8dc12edf912fed637ebefe39ffdd52d4 (MD5)
Previous issue date: 2012-06-30Introduction: Fibromyalgia is a syndrome characterized by widespread chronic pain. The syndrome is chronic with dubious possibility of healing. The prevalence in the world population varies from 0,66 to 4,4 %. It is believed that fibromyalgia is the result of abnormal changes in sensory processing of pain. In this context, are inserted gene polymorphisms T102C gene HTR2A serotonin receptor. The HTR2A gene T102C polymorphism is the presence of a thymine (T) or cytosine (C), defined by a transition from T to C at nucleotide position 102. It is a silent polymorphism receptor gene HTR2A, which determine the different levels of gene expression. Objectives: To determine and compare the allele frequency and genotype of the T102C polymorphism of the serotonin receptor gene HTR2A in a group of 48 women diagnosed with fibromyalgia and 50 healthy controls. Methodology: For this we used the PCR- RFLP , from DNA extracted from peripheral blood samples obtained from control and testing. The comparison of allele and genotype frequencies was performed by Chi -square test. Results: The results showed allele frequencies obtained for both groups were: T (46,9%) and C (53,1%). The TT genotype frequencies were found (22,9%), TC (47,9%) and CC (29,2%) for patients with fibromyalgia and TT (16%), TC (70%) and CC (14%) for controls. Conclusions: The FMS is composed of multiple characteristics that reflect a diversity of causes. Our results showed a significantly higher frequency for the CC genotype in patients with FMS, partially explaining the reduced serotoninergic response observed in such patients.
Introdução: A Fibromialgia é uma síndrome reumática caracterizada por dor difusa e crônica. A síndrome é crônica com duvidosa possibilidade de cura. A prevalência na população mundial varia de 0,66 a 4,4%. Acredita-se que a fibromialgia seja o resultado de mudanças anormais no processamento sensorial da dor. Neste contexto, inserem-se os polimorfismos do gene T102C do gene do receptor de serotonina HTR2A. O polimorfismo T102C do gene HTR2A consiste na presença de uma timina (T) ou citosina (C), definida por uma transição de um T para C na posição nucleotídica 102. Trata-se de um polimorfismo silencioso do gene do receptor HTR2A, que determinam níveis de expressão gênica diferentes. Objetivos: Determinar e comparar a freqüência alélica e genotípica do polimorfismo T102C do gene do receptor de serotonina HTR2A em um grupo de 48 mulheres diagnosticadas com fibromialgia e 50 controles saudáveis. Metodologia: Para isso foi utilizada a técnica de PCR-RFLP, a partir de DNA extraído de amostras de sangue periférico obtidas do grupo controle e testes. A comparação das freqüências alélicas e genotípicas foi feita por meio de teste Chi-quadrado. Resultados: Os resultados demonstraram as freqüências alélicas obtidas para os dois grupos foram: T (46,9%) e C (53,1%). As freqüências genotípicas encontradas foram TT (22,9%); TC (47,9%) e CC (29,2%) para os pacientes com fibromialgia e TT (16%); TC (70%) e CC (14%) para os controles. Conclusões: A SFM é composta por múltiplas características que refletem em uma diversidade de causas. Nossos resultados demonstraram que o genótipo CC foi significativamente mais comum nas pacientes com a SFM, justificando parcialmente a menor resposta serotononérgica observada nesse grupo.
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Donatoni, Flavia Aline Bressani. "Prospecção de SNPs por eletroforese capilar e sua identificação em genes candidatos relacionados à resistência de caprinos a nematóides gastrintestinais." Universidade de São Paulo, 2012. http://www.teses.usp.br/teses/disponiveis/75/75135/tde-24072012-163708/.
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Citocinas são pequenas moléculas de sinalização celular que desempenham um papel muito importante no sistema imunológico e atuam na comunicação intracelular. Escolheu-se cinco genes pertencentes a essa família com o objetivo de se estudar SNPs que possam estar associados com a resistência à verminose gastrintestinal em caprinos. São eles: IL2, IL4, IL13, IFNg e TNFa. Para isso foi estudada uma população de 229 caprinos. Estes animais foram produzidos na Embrapa Caprinos e Ovinos (Sobral, CE) a partir de animais das Raças Saanen, raça considerada susceptível a endoparasitas gastrintestinais e Anglo-nubiana, raça considerada resistente aos mesmos endoparasitas. Após dois cruzamentos a terceira geração de animais, considerada F2, possuía 229 animais. Foram coletadas amostras de sangue para posteriores etapas de extração de DNA e quantificação; foram coletadas também amostras de fezes para contagem de ovos por grama de fezes (OPG). Os dados foram transformados em log10(n+1), onde n é número de ovos por grama de fezes, e analisados usando o procedimento dos modelos mistos do SAS (2002/2003). Os efeitos fixos incluídos no modelo foram sexo, coleta e idade a coleta e a variável animal foi utilizada como efeito aleatório. Com base no resultado dessa análise escolheu-se 44 animais com fenótipos extremos para resistência. Visando a prospecção de SNPs foram sequenciadas duas regiões do gene IL2, uma região do gene IL4, duas regiões do gene IL13, três regiões do gene IFNg e quatro regiões do gene TNFa. Foram encontrados dois SNPs no gene IL2 (intron 1 e intron 2), um SNP no gene IL4 (intron 3), um SNP no gene IL13 (intron 1), seis SNPs no gene IFNg (dois no exon 1, um no intron 1, um no intron 2, um no exon 3 e um no exon 4) e dez SNPs no gene TNFa (dois deles na região promotora do gene, dois no intron 2 e seis no exon 4). Verificou-se que há alteração de aminoácido na sequência de apenas um dos SNPs encontrados em regiões codificadoras de proteínas. A troca ocorre no segundo SNP localizado no exon 1 do gene IFNg (A/C), onde há alteração do aminoácido asparagina (considerando o alelo A) para treonina (alelo C). O estudo da associação entre as amostras extremos para resistência e os marcadores tipo SNP foi realizado com o teste de Fisher e observou-se que, dentre os vinte SNPs encontrados, oito deles apresentaram um valor de P ≤0,05, o que indica que os SNPs são potenciais marcadores moleculadores para resistência à verminose gastrintestinal, ou seja, provavelmente associados ao fenótipo estudado. Para essa associação ser validada é necessário estudar o efeito desses SNPs na população completa e em outras populações.The cytokines are small cell-signaling proteins that play important role in immunologic system acting in intracellular communication. Five genes from cytokine family, i.e., IL2, IL4, IL13, IFNg, and TNFa were selected to search for SNPs, which may be associated with goat gastrointestinal endoparasites resistance. A population of 229 goats was produced in Embrapa Caprinos (Sobral, CE, Brazil). This population was an F2 offspring from a F1 intercross, which was in turn produced by crossing Saanen pure breed considered to be susceptible to gastrointestinal endoparasites with Anglo-nubiana pure breed considered to be resistant. Blood samples were collected for DNA extraction and fecal samples were collected for parasite egg counting. The data were transformed in log10(n+1), where n is the number of eggs per gram of feces, and analyzed by using the mixed model procedure of SAS (2002/2003). The fixed effects included were sex, sampling and age at sampling. The animal variable was used as random effect. After data analyses, forty four phenotypic extremes for endoparasite resistance were selected. Two regions of the gene IL2, one region of each gene IL4 and IL13, three regions of IFNg, and four regions of TNFa were sequenced in the search for SNPs. Two SNPs were found in the gene IL2 (intron 1 and intron 2), one SNP was found in IL4 (intron 3) one SNP in IL13 (intron 1) six SNPs in IFNg (two in the exon 1, one in the intron 1, one in the intron 2, one in the exon 3, and one in the exon 4) and ten SNPs were found in the gene TNFa (two in the promoter region, two in the intron 2 and six in the exon 4). Among all the SNPs found within exons only the second SNP of the IFNg exon 1 changes the amino acid. This SNP replaces an asparagine (allele A) by a threonin (allele C). The association study between the extremes and SNPs was performed using the Fisher exact test. A number of eight of the twenty described SNPs presented significant P value (P ≤0.05) indicating association with gastrointestinal endoparasite resistance and thus, the potential applicability as molecular markers for genetic improvement efforts involving this disease. To validate the associations, however, is necessary to study the effect of SNPs in a great number of animals and also in a variety of breeds.
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Carolino, Maria Inês Alves de Carvalho Martins. "Influências genéticas nas características da carcaça e carne em bovinos." Doctoral thesis, Universidade de Lisboa. Faculdade de Medicina Veterinária, 2015. http://hdl.handle.net/10400.5/11653.
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Tese de Doutoramento em Ciências Veterinárias - Especialidade de Produção AnimalA seleção das características da carcaça e da qualidade da carne, que são normalmente avaliadas post-mortem, é complicada, pelo que a utilização de marcadores moleculares pode constituir uma estratégia alternativa no melhoramento genético animal. Neste trabalho utilizaram-se 273 amostras de bovinos de 9 raças/populações provenientes do Brasil (Angus, Holstein, Simental, cruzados Pardo Suíço x Holstein, Montana, cruzados Guzerá x Holstein, Gir, Nelore e Tabapuã) e de 211 amostras de animais das raças Blanc Bleu Belge (BBB), Alentejana e Mertolenga explorados em Portugal, com o objetivo de proceder à sua caracterização genética em 20 SNP’s (CAPN316, CAPN530, CAPN4751, CAPN4753, CAPN5331, CAST257, CAST2959, LEP140, LEP252, LEP305, UASMS1, UASMS2, UASMS3, nt414, nt419, Q204X, E226X, nt821, E291X, C313Y) pertencentes aos genes da calpaína, calpastatina, leptina e miostatina. As frequências genotípicas e alélicas dos SNP’s localizados nos genes codificadores da calpaína (μ-calpaína) e calpastatina mostraram distribuições muito semelhantes às encontradas por outros autores. No gene da Leptina, as diferenças observadas entre os animais provenientes do Brasil e de Portugal, sugere que estes grupos de animais têm influências genéticas distintas (Bos indicus e Bos taurus) e que, possivelmente, possam ter sido sujeitos a processos de seleção diferentes. Na raça Mertolenga o genótipo ++ do SNP nt821 do GDF8 está associado com melhores valores genéticos para a capacidade maternal, capacidade de crescimento e longevidade produtiva, mas com piores valores genéticos para o intervalo entre parto. Os resultados obtidos demonstraram que há um efeito da congelação nas características físicas da carne (cor, força de corte, capacidade de retenção de água e pH). A tenrura da carne é influenciada pelos genótipos dos marcadores CAPN316, CAPN4751, CAST2 e LEP140, com diferenças máximas do valor da FC de 2,35Kgf, 4,96Kgf, 5,24kgF, e 9,04Kgf, respetivamente. O marcador UASMS3 tem influência na percentagem de AGM trans da carne de animais da raça Alentejana, enquanto os marcadores CAPN530 e LEP252 têm influência na percentagem de AGS C16:0 e AGCL n3 da carne de animais da raça Mertolenga. Os resultados obtidos confirmam a utilidade dos marcadores estudados no melhoramento genético e que as raças bovinas Alentejana e Mertolenga têm condições para incorporar marcadores genéticos para a qualidade da carne e da carcaça nos seus programas de seleção
ABSTRACT - The selection of the carcass characteristics and meat quality, which are normally evaluated postmortem is complicated, hence the use of molecular markers can provide an alternative strategy in animal breeding. This work was performed using a total sampling of 273 animals from 9 cattle breeds/populations from Brazil (Angus, Holstein, Simental, Pardo Suíço x Holstein crossbreed, Montana, Guzerá x Holstein crossbreed, Gir, Nelore and Tabapuã) and 211 animals from Blanc Bleu Belge (BBB) and to Portuguese - Alentejana and Mertolenga - breeds, in order to assess its genetic characterization in 20 SNP (CAPN316; CAPN530; CAPN4751; CAPN4753; CAPN5331; CAST257; CAST2959; LEP140; LEP252; LEP305; UASMS1; UASMS2; UASMS3; nt414; nt419; Q204X; E226X; nt821; E291X; C313Y) located within the calpain, calpastatin, leptin and myostatin genes. The genotypic and allelic frequencies of SNP's located within the genes coding for calpain (μ-calpain) and calpastatin showed very similar distributions to those found by other authors. In the leptin gene, the differences observed between the animals from Brazil and Portugal, suggested that these groups of animals have distinct genetic influences (Bos indicus and Bos taurus), and possibly may have been subject to different selection processes. In the breed Mertolenga the ++ genotype in SNP nt821 within GDF8 gene is associated with better genetic maternal ability, growth capacity and productive longevity values, but with worse breeding values for calving interval. The results have shown that freezing caused an effect on the physical characteristics of the meat (color, shear force, water holding capacity and pH), but with some differences among breeds. The meat tenderness is influenced by genotypes of markers CAPN316, CAPN4751, CAST2 and LEP140, with maximum differences of the FC value of 2.35 Kgf, 4.96 Kgf, 5.24 kgF and 9,04 Kgf, respectively. The UASMS3 marker influences the percentage of trans AGM of the meat of Alentejana breed, while CAPN530 and LEP252 markers influence the percentage of SFA C16: 0 and n3 LCFA of the Mertolenga meet. The results confirm the usefulness of genetic markers for genetic improvement, and show that breeds Alentejana and Mertolenga may be amenable to incorporate genetic conditions for meat and carcass quality in their programs of selection markers.
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Keren, Boris. "La déficience intellectuelle : du diagnostic en puces ADN à l'identification de gènes candidats." Phd thesis, Université René Descartes - Paris V, 2013. http://tel.archives-ouvertes.fr/tel-00918306.
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L'analyse chromosomique sur puce ADN (ACPA) tend à devenir le principal examen diagnostique dans la déficience intellectuelle (DI). Parmi les techniques d'ACPA, les puces SNP ont l'intérêt de pouvoir détecter les pertes d'hétérozygotie, et par conséquent d'identifier les isodisomies uniparentales (iUPD) et les zones d'identité liées à la consanguinité. Nous avons étudié une cohorte de 1 187 patients atteints de DI, dans un cadre diagnostique, sur puces SNP. Nous avons réalisé, par cette étude, 145 diagnostics (12%) dont 2 iUPD et 6 délétions n'incluant qu'un seul gène. De plus, nous avons détecté 639 CNV rares non décrits chez des sujets contrôles et incluant des séquences codantes, ce qui nous a permis d'identifier 11 gènes candidats dans la DI : CAMTA1, SP3, CNTNAP4, NUDT12, STXBP6, DOCK8, DOCK10, SMARCA2, NYAP2, ATAD3A et ATAD3B. Nous avons tenté de valider l'implication de ces gènes par séquençage, mais n'avons trouvé de seconde mutation pour aucun d'entre eux. Toutefois, des réarrangements de CAMTA1 ont été retrouvés dans 2 autres familles avec un phénotype homogène (DI et ataxie congénitale) ce qui nous a permis d'affirmer qu'il s'agit d'un gène de DI. Par ailleurs, l'homozygosity mapping, réalisé avec puces SNP, a identifié, par séquençage whole exome, une mutation non-sens homozygote du gène BUD13 dans une famille de DI syndromique. Enfin, de façon fortuite, nous avons caractérisé en ACPA une translocation familiale entraînant une disruption d'un gène d'ataxie spino-cérébelleuse, ATXN10, ce qui a permis de mieux comprendre la physiopathologie de cette maladie. Au total, notre étude démontre l'intérêt des puces SNP dans la DI, d'une part en diagnostic et d'autre part pour l'identification de nouveaux gènes responsables de DI.
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Lin, Kuan-chin. "Candidate Gene Expression and SNP Analyses of Toxin-Induced Dilated Cardiomyopathy in the Turkey(Meleagris gallopavo)." Thesis, Virginia Tech, 2006. http://hdl.handle.net/10919/42012.
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Dilated cardiomyopathy (DCM), a heart disease, affects many vertebrates including humans and poultry. The disease can be either idiopathic (IDCM) or toxin-induced. Idiopathic DCM often occurs without a consensus cause. Though genetic and other studies of IDCM are extensive, the specific etiology of toxin-induced is still unknown. Here, our objective was to compare the level of mRNA expression of two candidate genes including troponin T (cTnT) and phospholamban (PLN) using quantitative reverse transcription polymerase chain reaction (RT-PCR) in toxin-induced DCM affected and unaffected turkeys. Cardiac TnT and PLN were chosen because their spontaneous expression has been reported to be associated with IDCM. We also scanned these genes for single nucleotide polymorphisms (SNPs) that could be useful in evaluating their functions in the incidence and severity of toxin-induced DCM in turkeys. There were no significant differences between affected and unaffected birds in the expression of both cTnT and PLN. A total of 12 SNPs were detected in cTnT and PLN DNA sequences. One of the seven haplotypes detected in cTnT was the most frequent. Linkage analysis showed that cTnT gene was unlinked on the current turkey genetic map. Resources developed here, including SNPs, haplotypes, cDNA sequences, and the PCR-RFLP genotype procedure will be used for future investigations involving cTnT and PLN and toxin-induced DCM.Master of Science
Books on the topic "SNP candidati"
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Sobel, Jack D. Genito-urinary fungal infections. Edited by Christopher C. Kibbler, Richard Barton, Neil A. R. Gow, Susan Howell, Donna M. MacCallum, and Rohini J. Manuel. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780198755388.003.0027.
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The predominant fungal causes of genitourinary disease are Candida spp.; other fungal genera are uncommon pathogens in both sexes. Vulvovaginal candidiasis affects millions of women worldwide—and includes acute sporadic, recurrent, and chronic syndromes—and considerable progress has been made in understanding its pathophysiology and hence the best therapy. Therapeutic options are still limited, however, and misdiagnosis is common. In contrast, urinary tract candidiasis reflects an entirely different pathogenesis and clinical expression affecting a predominantly hospital-based older population. Candida organisms are extremely difficult to eradicate from often complicated urinary tract infections. Non-Candida fungal species reach the kidney and prostate by the bloodstream rather than the ascending route taken by Candida spp. In women, not infrequently, there is simultaneous lower genital tract and urinary tract infection, requiring attention to both systems.
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Drake, Sarah, and Jonathan Sandoe. Fungal cardiovascular infections. Edited by Christopher C. Kibbler, Richard Barton, Neil A. R. Gow, Susan Howell, Donna M. MacCallum, and Rohini J. Manuel. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780198755388.003.0021.
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Fungal cardiovascular disease can broadly be divided into four groups: infective endocarditis (including implantable cardiac electronic devices), mycotic aneurysms, vascular graft infections, and intravascular catheter-related infections. These conditions are rare but are associated with significant morbidity and mortality, which may be in excess of 80% in certain groups of patients. Candida spp. and Aspergillus spp. account for the majority of these infections, but rare fungi may also be involved, particularly in infective endocarditis, where they are responsible for approximately 25% of cases. This chapter will cover the epidemiology, causative fungi, clinical features, diagnosis, management, and prevention of these four fungal cardiovascular conditions.
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Chakrabarti, Arunaloke. Fungal diseases of the ear, nose, and throat. Edited by Christopher C. Kibbler, Richard Barton, Neil A. R. Gow, Susan Howell, Donna M. MacCallum, and Rohini J. Manuel. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780198755388.003.0024.
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Fungal infection of the ear (otomycosis), nose (fungal rhinosinusitis), and throat (oropharyngeal candidiasis) are common diseases. Fungal laryngeal diseases and invasive otomycosis & acute fungal rhinosinusitis are much less common and occur in immunosuppressed hosts, including those with diabetes. Aspergillus and Candida spp. are the commonest causes of otomycosis, whilst Aspergillus spp. predominate in sinus disease, with members of the Mucorales also causing serious invasive infections. Management of the non-invasive conditions can be difficult, and otomycosis and rhinosinusitis often become chronic. Invasive disease usually requires surgical intervention along with appropriate antifungal therapy. Acute invasive fungal rhinosinusitis has a mortality of approximately 50%.
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Levinson, Douglas F., and Walter E. Nichols. Genetics of Depression. Edited by Dennis S. Charney, Eric J. Nestler, Pamela Sklar, and Joseph D. Buxbaum. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780190681425.003.0024.
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Major depressive disorder (MDD) is a common and heterogeneous complex trait. Twin heritability is 35%–40%, perhaps higher in severe/recurrent cases. Adverse life events (particularly during childhood) increase risk. Current evidence suggests some overlap in genetic factors among MDD, bipolar disorder, and schizophrenia. Large genome-wide association studies (GWAS) are now proving successful. Polygenic effects of common SNPs are substantial. Findings implicate genes with effects on synaptic development and function, including two obesity-associated genes (NEGR1 and OLFM4), but not previous “candidate genes.” It can now be expected that larger GWAS samples will produce additional associations that shed new light on MDD genetics.
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Todd, Stacy, and Nick Beeching. Fungal infection. Edited by Patrick Davey and David Sprigings. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780199568741.003.0315.
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Fungi, comprising yeasts, moulds, and higher fungi, have a worldwide distribution and are uncommon causes of disease in healthy individuals. However, over the last 20 years, invasive fungal disease (IFD) has become an increasing cause of morbidity and mortality. This is probably due to the increasing numbers of patients with underlying host conditions, which predispose to opportunistic IFD (e.g. transplant and anti-tumour necrosis factor immunosuppression, HIV, or chronic lung disease), and to increased recognition of endemic IFD (e.g. histoplasmosis), which cause disease in both immunocompetent and immunocompromised hosts in selected geographic locations. Diagnosis of IFD remains a challenge. Symptoms are often non-specific, and a definite diagnosis requires invasive sampling with appropriate laboratory testing of these samples. Non-invasive tests are being developed, but their positive and negative predictive values still need validation. Diagnostic criteria (‘proven, probable, and possible’) established primarily for use in research and clinical trials can also prove useful in clinical environments. However, the most important step in identifying patients with IFD is to consider the diagnosis in those at risk. This chapter will focus on the commonest causes of IFD (Candida spp., Aspergillus spp., Cryptococcus spp., and histoplasmosis).
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Schelenz, Silke. Fungal diseases of the gastrointestinal tract. Edited by Christopher C. Kibbler, Richard Barton, Neil A. R. Gow, Susan Howell, Donna M. MacCallum, and Rohini J. Manuel. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780198755388.003.0026.
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Fungal diseases of the gastrointestinal (GI) tract can occur because of an overgrowth of yeast in the gut, exposure to contaminated food and water, or as part of disseminated invasive fungal infections from other sites. The extent of the disease depends on the underlying risk factors, such as diabetes or immunosuppression, and ranges from colonization, localized infection, or fungaemia, to aggressive life-threatening GI tract infections. Candida spp. are the commonest cause of mucosal infection, although mould infections are increasingly reported. Serious invasive mould infections are difficult to diagnose as symptoms are often non-specific. Early recognition, prompt antifungal treatment, and surgical intervention can be lifesaving.
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Maziarz, Eileen K., and John R. Perfect. Fungal infections of the kidney and those associated with renal failure, dialysis, and renal transplantation. Edited by Christopher C. Kibbler, Richard Barton, Neil A. R. Gow, Susan Howell, Donna M. MacCallum, and Rohini J. Manuel. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780198755388.003.0029.
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Fungal infections involving the kidney are often a manifestation of disseminated fungal infection, although primary renal fungal infections do occur, usually from a lower urinary tract source or in the setting of renal transplantation. Candida spp. cause the vast majority of these infections and are the representative pathogen for understanding the pathogenesis of these types of infections. The risk factors and mycology of acute renal candidiasis reflect those of invasive candidiasis. Unique risk factors are observed in chronic renal candidiasis, which manifests differently and requires distinct management approaches. This chapter discusses the spectrum of invasive mycoses involving the kidney, as well as those associated with chronic renal failure, dialysis, and renal transplantation.
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Clark, Heather L., and Eric Pearlman. Fungal eye infections. Edited by Christopher C. Kibbler, Richard Barton, Neil A. R. Gow, Susan Howell, Donna M. MacCallum, and Rohini J. Manuel. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780198755388.003.0028.
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Mycotic keratitis is a fungal infection of the cornea that leads to severe, painful ulceration and loss of vision, and is a major cause of blindness worldwide, particularly in the developing world. Major risk factors for mycotic keratitis include ocular trauma and contact lens use. Both yeasts and moulds can cause mycotic keratitis, with the filamentous moulds of the Fusarium and Aspergillus genera the most common aetiological agents worldwide. Fungi, particularly Candida spp. yeasts, can also cause endophthalmitis—a painful, blinding infection of the posterior eye. Treatment of these infections is challenging owing to a limited arsenal of antifungal agents and highly variable susceptibility among causative fungi. Furthermore, associated inflammation contributes greatly to tissue damage and permanent blindness. Studies using experimental models of mycotic keratitis have revealed new targets for novel antifungal agents and anti-inflammatory therapies that have the potential to reduce the impact of these devastating infections.
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Roby, Ferny. The Secret to Lose Weight, Stop Your Cravings and Flatten Your Belly in a Snap: The Sugar-candidas-yeast link and the know how to beat obesity. CreateSpace Independent Publishing Platform, 2012.
Find full textBook chapters on the topic "SNP candidati"
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Athanur, Anand ‘Andy’, Mark Ingram, and Michael A. Wellens. "Candidate Attraction." In Innovative SAP SuccessFactors Recruiting, 75–100. Berkeley, CA: Apress, 2021. http://dx.doi.org/10.1007/978-1-4842-7425-5_4.
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Athanur, Anand ‘Andy’, Mark Ingram, and Michael A. Wellens. "Enhancing Candidate Engagement." In Innovative SAP SuccessFactors Recruiting, 101–29. Berkeley, CA: Apress, 2021. http://dx.doi.org/10.1007/978-1-4842-7425-5_5.
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Lam, Ching-Wan, and Kin-Chong Lau. "Candidate Screening through High-Density SNP Array." In Gene Discovery for Disease Models, 195–214. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2012. http://dx.doi.org/10.1002/9780470933947.ch10.
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Reames, Donald V. "A Turbulent History." In Solar Energetic Particles, 19–48. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-66402-2_2.
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AbstractLarge solar energetic-particle (SEP) events are clearly associated in time with eruptive phenomena on the Sun, but how? When large SEP events were first observed, flares were the only visible candidate, and diffusion theory was stretched to explain how the particles could spread through space, as widely as observed. The observation of coronal mass ejections (CMEs), and the wide, fast shock waves they can drive, provided better candidates later. Then small events were found with 1000-fold enhancements in 3He/4He that required a different kind of source—should we reconsider flares, or their open-field cousins, solar jets? The 3He-rich events were soon associated with the electron beams that produce type III radio bursts. It seems the radio astronomers knew of both SEP sources all along. Sometimes the distinction between the sources is blurred when shocks reaccelerate residual 3He-rich impulsive suprathermal ions. Eventually, however, we would even begin to measure the source-plasma temperature that helps to better distinguish the SEP sources.
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Athanur, Anand ‘Andy’, Mark Ingram, and Michael A. Wellens. "Candidate Offer Automation Using Business Rules." In Innovative SAP SuccessFactors Recruiting, 281–99. Berkeley, CA: Apress, 2021. http://dx.doi.org/10.1007/978-1-4842-7425-5_11.
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Mooney, Sean D., Vidhya G. Krishnan, and Uday S. Evani. "Bioinformatic Tools for Identifying Disease Gene and SNP Candidates." In Methods in Molecular Biology, 307–19. Totowa, NJ: Humana Press, 2010. http://dx.doi.org/10.1007/978-1-60327-367-1_17.
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McNally, Kenneth L., Ma Elizabeth Naredo, and Jill Cairns. "SNP discovery at candidate genes for drought responsiveness in rice." In Drought Frontiers in Rice, 311–24. WORLD SCIENTIFIC, 2009. http://dx.doi.org/10.1142/9789814280013_0017.
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Jackson, Jami, and Alison Motsinger-Reif. "Current Study Designs, Methods, and Future Directions of Genetic Association Mapping." In Big Data Analytics in Bioinformatics and Healthcare, 323–58. IGI Global, 2015. http://dx.doi.org/10.4018/978-1-4666-6611-5.ch014.
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Rapid progress in genotyping technologies, including the scaling up of assay technologies to genome-wide levels and next generation sequencing, has motivated a burst in methods development and application to detect genotype-phenotype associations in a wide array of diseases and other phenotypes. In this chapter, the authors review the study design and genotyping options that are used in association mapping, along with the appropriate methods to perform mapping within these study designs. The authors discuss both candidate gene and genome-wide studies, focused on DNA level variation. Quality control, genotyping technologies, and single-SNP and multiple-SNP analyses have facilitated the successes in identifying numerous loci influence disease risk. However, variants identified have generally explained only a small fraction of the heritable component of disease risk. The authors discuss emerging trends and future directions in performing analysis for rare variants to detect these variants that predict these traits with more complex etiologies.
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Endo, Shiho, Kenta Motomura, Masakazu Tsuhako, Yuki Kakazu, Morikazu Nakamura, and Joji M. Otaki. "Search for Human-Specific Proteins Based on Availability Scores of Short Constituent Sequences: Identification of a WRWSH Protein in Human Testis." In Computational Biology and Chemistry. IntechOpen, 2020. http://dx.doi.org/10.5772/intechopen.89653.
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Little is known about protein sequences unique in humans. Here, we performed alignment-free sequence comparisons based on the availability (frequency bias) of short constituent amino acid (aa) sequences (SCSs) in proteins to search for human-specific proteins. Focusing on 5-aa SCSs (pentats), exhaustive comparisons of availability scores among the human proteome and other nine mammalian proteomes in the nonredundant (nr) database identified a candidate protein containing WRWSH, here called FAM75, as human-specific. Examination of various human genome sequences revealed that FAM75 had genomic DNA sequences for either WRWSH or WRWSR due to a single nucleotide polymorphism (SNP). FAM75 and its related protein FAM205A were found to be produced through alternative splicing. The FAM75 transcript was found only in humans, but the FAM205A transcript was also present in other mammals. In humans, both FAM75 and FAM205A were expressed specifically in testis at the mRNA level, and they were immunohistochemically located in cells in seminiferous ducts and in acrosomes in spermatids at the protein level, suggesting their possible function in sperm development and fertilization. This study highlights a practical application of SCS-based methods for protein searches and suggests possible contributions of SNP variants and alternative splicing of FAM75 to human evolution.
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Ding, Jupeng, Chih-Lin I, and Lili Wang. "Visible Light Wireless Data Center Links with Distinct Beam Configurations." In Proceedings of CECNet 2021. IOS Press, 2021. http://dx.doi.org/10.3233/faia210439.
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Visible light communication (VLC) is being explored as one promising approach to enable wireless data centers (WDC). Up to now, the visible light wireless data center links are still limited to the conventional Lambertian beam paradigm. The potential coverage gain relevant to the optical beam space is waiting for sufficient investigation. For addressing this issue, in this paper, the dynamic optical beam based WDC coverage enhancement scheme is introduced, and for each transmitter, the best candidate asymmetrical optical beam is selected to load the data signal. Numerical evaluation shows that, compared with the conventional static beam configuration, up to 6.76 dB peak signal to noise ratio (SNR) gain and 4.46 dB average SNR gain could be provided by the proposed dynamic beam scheme. Moreover, this SNR dynamic range is reduced to 36.65 dB while the counterpart of the static non-Lambertian beam configuration is up to 44.78 dB.
Conference papers on the topic "SNP candidati"
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Hapsari, Niken, and Sri Wardani. "Women Candidates in Indonesia: Experience in Candidate Selection within Political Parties." In Proceedings of the 1st International Symposium on Indonesian Politics, SIP 2019, 26-27 June 2019, Central Java, Indonesia. EAI, 2019. http://dx.doi.org/10.4108/eai.25-6-2019.2288008.
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COMERON, JOSEP M., MARTIN KREITMAN, and FRANCISCO M. DE LA VEGA. "ON THE POWER TO DETECT SNP/PHENOTYPE ASSOCIATION IN CANDIDATE QUANTITATIVE TRAIT LOCI GENOMIC REGIONS: A SIMULATION STUDY." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 2002. http://dx.doi.org/10.1142/9789812776303_0045.
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Xu, Nuo, Hideki Takeuchi, Nattapol Damrongplasit, Robert J. Stephenson, Marek Hytha, Nyles Cody, Robert J. Mears, and Tsu-Jae King Liu. "Oxygen-inserted SegFET: A candidate for 10-nm node system-on-chip applications." In 2014 Silicon Nanoelectronics Workshop (SNW). IEEE, 2014. http://dx.doi.org/10.1109/snw.2014.7348549.
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Malik, Aisha, Arshad Aziz, and Abdul Qadeer. "Implementation of SHA-3 candidate skein on two unexplored multiprocessor platforms." In 2013 International Conference on Sensor Network Security Technology and Privacy Communication System (SNS & PCS). IEEE, 2013. http://dx.doi.org/10.1109/sns-pcs.2013.6553863.
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Li, Xinyu, Jing Xu, Zhenfeng Zhang, Dengguo Feng, and Honggang Hu. "Multiple Handshakes Security of TLS 1.3 Candidates." In 2016 IEEE Symposium on Security and Privacy (SP). IEEE, 2016. http://dx.doi.org/10.1109/sp.2016.36.
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Bhargavan, Karthikeyan, Bruno Blanchet, and Nadim Kobeissi. "Verified Models and Reference Implementations for the TLS 1.3 Standard Candidate." In 2017 IEEE Symposium on Security and Privacy (SP). IEEE, 2017. http://dx.doi.org/10.1109/sp.2017.26.
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Gross, Korey, and Lisa Weiland. "Flexural Testing of Shape Memory Polymers for Morphing Aircraft Applications." In ASME 2007 International Mechanical Engineering Congress and Exposition. ASMEDC, 2007. http://dx.doi.org/10.1115/imece2007-43219.
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Shape memory polymers (SMPs) have garnered significant attention in recent years for their potential to return to a “memorized” state when warmed above their glass transition temperature Tg. However, they also have potential in morphing aircraft applications because of their significant modulus change above and below Tg. Much less energy is required to deform this material when in its soft state, but when the material returns to the hard state, it is able to support significant loads. In the proposed effort, SMP is experimentally considered as a candidate material for morphing aircraft applications where the material’s ability to support out of plane loads above and below the Tg is of primary importance. The SMP of study in the work is Veriflex®.
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Alli, Kolapo, and Haniph Latchman. "METHODS OF SOLVING MULTI-AREA ECONOMIC DISPATCH PROBLEMS- A SURVEY AND PROPOSED CANDIDATE SDP APPROACH." In International Conference on Emerging Trends in Engineering & Technology (IConETech-2020). Faculty of Engineering, The University of the West Indies, St. Augustine, 2020. http://dx.doi.org/10.47412/dsqg6925.
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Computational intelligence methods may be effectively used to control power system settings automatically to achieve optimal operating power systems objective functions and ensure optimal load flows while fulfilling system constraints. Economic dispatch of power systems involving large interconnected areas or zones require optimum and efficient allocation of the power to ensure efficient transferred output power to the systems in the various zones. One approach in achieving optimum dispatch of the power generated is to model the system as a Multi Area Emission Economic Dispatch (MAEED) optimization problem. One such formulation could be the minimization the running cost and emission objective functions subject to generator power limits, power balance and tie-line capacity constraints. This paper provides a survey of some of the existing research on both single area and multi area economic dispatch problems respectively and discusses the associated methods used in solving these different problems. Based on this study, we propose a candidate approach to address multi area economic dispatch problems using a semidefinite programming (SDP) method and we outline the associated computational and performance advantages.
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Farouk, Issame, Fatima Gaboun, Zakaria Kehel, Ahmad Alsaleh, Bouchra Belkadi, Ismahane Elouafi, Jihan Motowaj, Abdelkarim Filali maltouf, and M. Miloudi Nachit. "Dissection of QTL linked to grain yield and identification of candidate genes involved in grain yield formation using comparative SNP sequences analysis." In 2020 1st International Conference on Innovative Research in Applied Science, Engineering and Technology (IRASET). IEEE, 2020. http://dx.doi.org/10.1109/iraset48871.2020.9091989.
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Kusmayadi, Edi, Akhmad Satori, and Subhan Agung. "Cartel Politics Model in Single Candidate Election in Tasikmalaya Regency." In Proceedings of the 1st International Symposium on Indonesian Politics, SIP 2019, 26-27 June 2019, Central Java, Indonesia. EAI, 2019. http://dx.doi.org/10.4108/eai.25-6-2019.2287977.
Full textReports on the topic "SNP candidati"
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Medrano, Juan, Adam Friedmann, Moshe (Morris) Soller, Ehud Lipkin, and Abraham Korol. High resolution linkage disequilibrium mapping of QTL affecting milk production traits in Israel Holstein dairy cattle. United States Department of Agriculture, March 2008. http://dx.doi.org/10.32747/2008.7696509.bard.
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Original objectives: To create BAC contigs covering two QTL containing chromosomal regions (QTLR) and obtain BAC end sequence information as a platform for SNP identification. Use the SNPs to search for marker-QTL linkage disequilibrium (LD) in the test populations (US and Israel Holstein cattle). Identify candidate genes, test for association with dairy cattle production and functional traits, and confirm any associations in a secondary test population. Revisions in the course of the project: The selective recombinant genotyping (SRG) methodology which we implemented to provide moderate resolution QTL mapping turned out to be less effective than expected, due to problems introduced by incomplete marker informativity. This required a no-cost one-year extension of the project. Aside from this, the project was implemented essentially as envisaged, but only with respect to a single QTLR and single population association-test. Background to the topic. Dairy cattle breeders are looking to marker-assisted selection (MAS) as a means of identifying genetically superior sires and dams. MAS based on population-wide LD can be many times more effective than MAS based on within-family linkage mapping. In this proposal we developed a protocol leading from family based QTL mapping to population-wide LD between markers and the QTL Major conclusions, solutions, achievements. The critical importance of marker informativity for application of the SRG design in outcrossing random mating populations was identified, and an alternative Fractioned Pool Design (FPD) based on selective DNA pooling was developed. We demonstrated the feasibility of constructing a BAC contig across a targeted chromosomal region flanking the marker RM188 on bovine chromosome BTA4, which was shown in previous work to contain a QTL affecting milk production traits. BAC end sequences were obtained and successfully screened for SNPs. LD studies of these SNPs in the Israel population, and of an independent set of SNPs taken across the entire proximal region of BTA4 in the USA population, showed a much lower degree of LD than previously reported in the literature. Only at distances in the sub-cM level did an appreciable fraction of SNP marker-pairs show levels of LD useful for MAS. In contrast, studies in the Israel population using microsatellite markers, presented an equivalent degree of LD at a 1-5 separation distance. SNP LD appeared to reflect historical population size of Bostaurus (Ne=5000- 10,000), while microsatellite LD appeared to be in proportion to more recent effective population size of the Holstein breed (Ne=50-100). An appreciable fraction of the observed LD was due to Family admixture structure of the Holstein population. The SNPs MEOX2/IF2G (found within the gene SETMAR at 23,000 bp from RM188) and SNP23 were significantly associated with PTA protein, Cheese dollars and Net Merit Protein in the Davis bull resource population, and were also associated with protein and casein percentages in the Davis cow resource population. Implications. These studies document a major difference in degree of LD presented by SNPs as compared to microsatellites, and raise questions as to the source of this difference and its implications for QTL mapping and MAS. The study lends significant support to the targeted approach to fine map a previously identified QTL. Using high density genotyping with SNP discovered in flanking genes to the QTL, we have identified important markers associated with milk protein percentage that can be tested in markers assisted selection programs.
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Weller, Joel I., Harris A. Lewin, and Micha Ron. Determination of Allele Frequencies for Quantitative Trait Loci in Commercial Animal Populations. United States Department of Agriculture, February 2005. http://dx.doi.org/10.32747/2005.7586473.bard.
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Individual loci affecting economic traits in dairy cattle (ETL) have been detected via linkage to genetic markers by application of the granddaughter design in the US population and the daughter design in the Israeli population. From these analyses it is not possible to determine allelic frequencies in the population at large, or whether the same alleles are segregating in different families. We proposed to answer this question by application of the "modified granddaughter design", in which granddaughters with a common maternal grandsire are both genotyped and analyzed for the economic traits. The objectives of the proposal were: 1) to fine map three segregating ETL previously detected by a daughter design analysis of the Israeli dairy cattle population; 2) to determine the effects of ETL alleles in different families relative to the population mean; 3) for each ETL, to determine the number of alleles and allele frequencies. The ETL on Bostaurusautosome (BT A) 6 chiefly affecting protein concentration was localized to a 4 cM chromosomal segment centered on the microsatellite BM143 by the daughter design. The modified granddaughter design was applied to a single family. The frequency of the allele increasing protein percent was estimated at 0.63+0.06. The hypothesis of equal allelic frequencies was rejected at p<0.05. Segregation of this ETL in the Israeli population was confirmed. The genes IBSP, SPP1, and LAP3 located adjacent to BM143 in the whole genome cattle- human comparative map were used as anchors for the human genome sequence and bovine BAC clones. Fifteen genes within 2 cM upstream of BM143 were located in the orthologous syntenic groups on HSA4q22 and HSA4p15. Only a single gene, SLIT2, was located within 2 cM downstream of BM143 in the orthologous HSA4p15 region. The order of these genes, as derived from physical mapping of BAC end sequences, was identical to the order within the orthologous syntenic groups on HSA4: FAM13A1, HERC3. CEB1, FLJ20637, PP2C-like, ABCG2, PKD2. SPP, MEP, IBSP, LAP3, EG1. KIAA1276, HCAPG, MLR1, BM143, and SLIT2. Four hundred and twenty AI bulls with genetic evaluations were genotyped for 12 SNPs identified in 10 of these genes, and for BM143. Seven SNPs displayed highly significant linkage disequilibrium effects on protein percentage (P<0.000l) with the greatest effect for SPP1. None of SNP genotypes for two sires heterozygous for the ETL, and six sires homozygous for the ETL completely corresponded to the causative mutation. The expression of SPP 1 and ABCG2 in the mammary gland corresponded to the lactation curve, as determined by microarray and QPCR assays, but not in the liver. Anti-sense SPP1 transgenic mice displayed abnormal mammary gland differentiation and milk secretion. Thus SPP 1 is a prime candidate gene for this ETL. We confirmed that DGAT1 is the ETL segregating on BTA 14 that chiefly effects fat concentration, and that the polymorphism is due to a missense mutation in an exon. Four hundred Israeli Holstein bulls were genotyped for this polymorphism, and the change in allelic frequency over the last 20 years was monitored.
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Blau, P. Transient Scuffing of Candidate Diesel Engine Materials at Temperatures up to 600oC. Office of Scientific and Technical Information (OSTI), June 2003. http://dx.doi.org/10.2172/885740.
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Coleman, Jonathan P. Searches for the θ5(1540)+ Strange-Pentaquark Candidate in e+e- Annihilation, Hadroproduction and Electroproduction with the BaBar Detector. Office of Scientific and Technical Information (OSTI), May 2009. http://dx.doi.org/10.2172/970450.
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Joel, Daniel M., Steven J. Knapp, and Yaakov Tadmor. Genomic Approaches for Understanding Virulence and Resistance in the Sunflower-Orobanche Host-Parasite Interaction. United States Department of Agriculture, August 2011. http://dx.doi.org/10.32747/2011.7592655.bard.
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Oroginal Objectives: (i) identify DNA markers linked to the avirulence (Avr) locus and locate the Avr locus through genetic mapping with an inter-race Orobanche cumana population; (ii) develop high-throughput fingerprint DNA markers for genotypingO. cumana races; (iii) identify nucleotide binding domain leucine rich repeat (NB-LRR) genes encoding R proteins conferring resistance to O. cumana in sunflower; (iv) increase the resolution of the chromosomal segment harboring Or₅ and related R genes through genetic and physical mapping in previously and newly developed mapping populations of sunflower; and (v) develop high-throughput DNA markers for rapidly and efficiently identifying and transferring sunflower R genes through marker-assisted selection. Revisions made during the course of project: Following changes in O. cumana race distribution in Israel, the newly arrived virulent race H was chosen for further analysis. HA412-HO, which was primarily chosen as a susceptible sunflower cultivar, was more resistant to the new parasite populations than var. Shemesh, thus we shifted sunflower research into analyzing the resistance of HA412-HO. We exceeded the deliverables for Objectives #3-5 by securing funding for complete physical and high-density genetic mapping of the sunflower genome, in addition to producing a complete draft sequence of the sunflower genome. We discovered limited diversity between the parents of the O. cumana population developed for the mapping study. Hence, the developed DNA marker resources were insufficient to support genetic map construction. This objective was beyond the scale and scope of the funding. This objective is challenging enough to be the entire focus of follow up studies. Background to the topic: O. cumana, an obligate parasitic weed, is one of the most economically important and damaging diseases of sunflower, causes significant yield losses in susceptible genotypes, and threatens production in Israel and many other countries. Breeding for resistance has been crucial for protecting sunflower from O. cumana, and problematic because new races of the pathogen continually emerge, necessitating discovery and deployment of new R genes. The process is challenging because of the uncertainty in identifying races in a genetically diverse parasite. Major conclusions, solutions, achievements: We developed a small collection of SSR markers for genetic mapping in O. cumana and completed a diversity study to lay the ground for objective #1. Because DNA sequencing and SNPgenotyping technology dramatically advanced during the course of the study, we recommend shifting future work to SNP discovery and mapping using array-based approaches, instead of SSR markers. We completed a pilot study using a 96-SNP array, but it was not large enough to support genetic mapping in O.cumana. The development of further SNPs was beyond the scope of the grant. However, the collection of SSR markers was ideal for genetic diversity analysis, which indicated that O. cumanapopulations in Israel considerably differ frompopulations in other Mediterranean countries. We supplied physical and genetic mapping resources for identifying R-genes in sunflower responsible for resistance to O. cumana. Several thousand mapped SNP markers and a complete draft of the sunflower genome sequence are powerful tools for identifying additional candidate genes and understanding the genomic architecture of O. cumana-resistanceanddisease-resistance genes. Implications: The OrobancheSSR markers have utility in sunflower breeding and genetics programs, as well as a tool for understanding the heterogeneity of races in the field and for geographically mapping of pathotypes.The segregating populations of both Orobanche and sunflower hybrids are now available for QTL analyses.
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David, Lior, Yaniv Palti, Moshe Kotler, Gideon Hulata, and Eric M. Hallerman. Genetic Basis of Cyprinid Herpes Virus-3 Resistance in Common Carp. United States Department of Agriculture, January 2011. http://dx.doi.org/10.32747/2011.7592645.bard.
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The goal of this project was to provide scientific and technical basis for initiating the development of breeding protocols using marker assisted selection for viral disease resistance in common carp. The specific objectives were: 1) Establishing families and characterizing the phenotypic and genetic variation of viral resistance; 2) Measuring the dynamics of immune response and developing a method to measure the long term immune memory; 3) Developing markers and generating a new genetic linkage map, which will enable initial QTL mapping; and, 4) Identifying genetic linkage of markers and candidate genes (like MHC and TLRs) with resistance to CyHV-3. The common carp is an important farmed freshwater fish species in the world. Edible carp is second only to tilapia in Israeli aquaculture production and ornamental carp (koi) is an important product in both the US and Israel. Carp industries worldwide have recently suffered enormous economic damage due to a viral disease caused by Cyprinid herpes virus 3 (CyHV-3). Aside from preventative measures, a sustainable solution to this problem will be to establish a genetic improvement program of the resistance of fish to the pathogen. The aims of the project was to take the necessary first steps towards that. The differences in survival rates after infection with CyHV-3 virus among 20 families from six types of crosses between three carp lines (two commercial lines and one wild-type carp) revealed that the wild-type carp and its crosses had a much-improved survival over the crosses of the commercial lines themselves. These crosses set the starting point for breeding of commercial strains with improved resistance. Resistant fish had lower antibody titer against the virus suggesting that resistance might depend more on the innate immunity. A set of 500 microsateliite markers was developed and the markers are currently being used for generating a genetic linkage map for carp and for identifying disease resistance QTL. Fourteen candidate immune genes, some of which were duplicated, were cloned from the carp and SNP markers were identified in them. The expression of these genes varied between tissues and suggested functional divergence of some duplicated genes. Initial association between CyHV-3 resistance and one of the genes was found when SNP alleles in these genes were tested for their segregation between susceptible and resistant progeny. The results of this project have implications to the development of viral resistant commercial carp strains and effective immunization against this aggressive disease. The genetic and immunological knowledge accumulated in this project will not only promote carp and koi production but will also contribute to a broader understanding of fish immunogenetics.
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Setser, D. Reactions of N sub 2 (A sup 3. Sigma. sub u sup + ) and candidates for short wavelengths lasers. Office of Scientific and Technical Information (OSTI), January 1990. http://dx.doi.org/10.2172/7029996.
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Byun, T. S. Temperature Effects on the Mechanical Properties of Candidate SNS Target Container Materials after Proton and Neutron Irradiation. Office of Scientific and Technical Information (OSTI), November 2001. http://dx.doi.org/10.2172/814075.
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Dubcovsky, Jorge, Tzion Fahima, Ann Blechl, and Phillip San Miguel. Validation of a candidate gene for increased grain protein content in wheat. United States Department of Agriculture, January 2007. http://dx.doi.org/10.32747/2007.7695857.bard.
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High Grain Protein Content (GPC) of wheat is important for improved nutritional value and industrial quality. However, selection for this trait is limited by our poor understanding of the genes involved in the accumulation of protein in the grain. A gene with a large effect on GPC was detected on the short arm of chromosome 6B in a Triticum turgidum ssp. dicoccoides accession from Israel (DIC, hereafter). During the previous BARD project we constructed a half-million clones Bacterial Artificial Chromosome (BAC) library of tetraploid wheat including the high GPC allele from DIC and mapped the GPC-B1 locus within a 0.3-cM interval. Our long-term goal is to provide a better understanding of the genes controlling grain protein content in wheat. The specific objectives of the current project were to: (1) complete the positional cloning of the GPC-B1 candidate gene; (2) characterize the allelic variation and (3) expression profile of the candidate gene; and (4) validate this gene by using a transgenic RNAi approach to reduce the GPC transcript levels. To achieve these goals we constructed a 245-kb physical map of the GPC-B1 region. Tetraploid and hexaploid wheat lines carrying this 245-kb DIC segment showed delayed senescence and increased GPC and grain micronutrients. The complete sequencing of this region revealed five genes. A high-resolution genetic map, based on approximately 9,000 gametes and new molecular markers enabled us to delimit the GPC-B1 locus to a 7.4-kb region. Complete linkage of the 7.4-kb region with earlier senescence and increase in GPC, Zn, and Fe concentrations in the grain suggested that GPC-B1 is a single gene with multiple pleiotropic effects. The annotation of this 7.4-kb region identified a single gene, encoding a NAC transcription factor, designated as NAM-B1. Allelic variation studies demonstrated that the ancestral wild wheat allele encodes a functional NAC transcription factor whereas modern wheat varieties carry a non-functional NAM-B1 allele. Quantitative PCR showed that transcript levels for the multiple NAMhomologues were low in flag leaves prior to anthesis, after which their levels increased significantly towards grain maturity. Reduction in RNA levels of the multiple NAMhomologues by RNA interference delayed senescence by over three weeks and reduced wheat grain protein, Zn, and Fe content by over 30%. In the transgenic RNAi plants, residual N, Zn and Fe in the dry leaves was significantly higher than in the control plants, confirming a more efficient nutrient remobilization in the presence of higher levels of GPC. The multiple pleiotropic effects of NAM genes suggest a central role for these genes as transcriptional regulators of multiple processes during leaf senescence, including nutrient remobilization to the developing grain. The cloning of GPC-B1 provides a direct link between the regulation of senescence and nutrient remobilization and an entry point to characterize the genes regulating these two processes. This may contribute to their more efficient manipulation in crops and translate into food with enhanced nutritional value. The characterization of the GPC-B1 gene will have a significant impact on wheat production in many regions of the world and will open the door for the identification of additional genes involved in the accumulation of protein in the grain.
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Setser, D. W. Reactions of N/sub 2/(A/sup 3/SIGMA/sub u//sup +/) and candidates for short wavelength lasers, March 1, 1984-February 28, 1985. Office of Scientific and Technical Information (OSTI), December 1987. http://dx.doi.org/10.2172/5545397.
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