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排序方式: 共有192条查询结果,搜索用时 15 毫秒
101.
Gitte Berkers Peter van Mourik Annelotte M. Vonk Evelien Kruisselbrink Johanna F. Dekkers Karin M. de Winter-de Groot Hubertus G.M. Arets Rozemarijn E.P. Marck-van der Wilt Jasper S. Dijkema Maaike M. Vanderschuren Roderick H.J. Houwen Harry G.M. Heijerman Eduard A. van de Graaf Sjoerd G. Elias Christof J. Majoor Gerard H. Koppelman Jolt Roukema Marleen Bakker Cornelis K. van der Ent 《Cell reports》2019,26(7):1701-1708.e3
102.
Martine Schroyen Juan P. Steibel James E. Koltes Igseo Choi Nancy E. Raney Christopher Eisley Eric Fritz-Waters James M. Reecy Jack C. M. Dekkers Robert R. R. Rowland Joan K. Lunney Catherine W. Ernst Christopher K. Tuggle 《BMC genomics》2015,16(1)
Background
The presence of variability in the response of pigs to Porcine Reproductive and Respiratory Syndrome virus (PRRSv) infection, and recent demonstration of significant genetic control of such responses, leads us to believe that selection towards more disease resistant pigs could be a valid strategy to reduce its economic impact on the swine industry. To find underlying molecular differences in PRRS susceptible versus more resistant pigs, 100 animals with extremely different growth rates and viremia levels after PRRSv infection were selected from a total of 600 infected pigs. A microarray experiment was conducted on whole blood RNA samples taken at 0, 4 and 7 days post infection (dpi) from these pigs. From these data, we examined associations of gene expression with weight gain and viral load phenotypes. The single nucleotide polymorphism (SNP) marker WUR10000125 (WUR) on the porcine 60 K SNP chip was shown to be associated with viral load and weight gain after PRRSv infection, and so the effect of the WUR10000125 (WUR) genotype on expression in whole blood was also examined.Results
Limited information was obtained through linear modeling of blood gene differential expression (DE) that contrasted pigs with extreme phenotypes, for growth or viral load or between animals with different WUR genotype. However, using network-based approaches, molecular pathway differences between extreme phenotypic classes could be identified. Several gene clusters of interest were found when Weighted Gene Co-expression Network Analysis (WGCNA) was applied to 4dpi contrasted with 0dpi data. The expression pattern of one such cluster of genes correlated with weight gain and WUR genotype, contained numerous immune response genes such as cytokines, chemokines, interferon type I stimulated genes, apoptotic genes and genes regulating complement activation. In addition, Partial Correlation and Information Theory (PCIT) identified differentially hubbed (DH) genes between the phenotypically divergent groups. GO enrichment revealed that the target genes of these DH genes are enriched in adaptive immune pathways.Conclusion
There are molecular differences in blood RNA patterns between pigs with extreme phenotypes or with a different WUR genotype in early responses to PRRSv infection, though they can be quite subtle and more difficult to discover with conventional DE expression analyses. Co-expression analyses such as WGCNA and PCIT can be used to reveal network differences between such extreme response groups.Electronic supplementary material
The online version of this article (doi:10.1186/s12864-015-1741-8) contains supplementary material, which is available to authorized users. 相似文献103.
Power and precision of alternate methods for linkage disequilibrium mapping of quantitative trait loci 总被引:1,自引:0,他引:1
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Linkage disequilibrium (LD) analysis in outbred populations uses historical recombinations to detect and fine map quantitative trait loci (QTL). Our objective was to evaluate the effect of various factors on power and precision of QTL detection and to compare LD mapping methods on the basis of regression and identity by descent (IBD) in populations of limited effective population size (N(e)). An 11-cM region with 6-38 segregating single-nucleotide polymorphisms (SNPs) and a central QTL was simulated. After 100 generations of random mating with N(e) of 50, 100, or 200, SNP genotypes and phenotypes were generated on 200, 500, or 1000 individuals with the QTL explaining 2 or 5% of phenotypic variance. To detect and map the QTL, phenotypes were regressed on genotypes or (assumed known) haplotypes, in comparison with the IBD method. Power and precision to detect QTL increased with sample size, marker density, and QTL effect. Power decreased with N(e), but precision was affected little by N(e). Single-marker regression had similar or greater power and precision than other regression models, and was comparable to the IBD method. Thus, for rapid initial screening of samples of adequate size in populations in which drift is the primary force that has created LD, QTL can be detected and mapped by regression on SNP genotypes without recovering haplotypes. 相似文献
104.
Livant EJ Avendano S McLeod S Ye X Lamont SJ Dekkers JC Ewald SJ 《Animal genetics》2007,38(2):177-179
The Mx1 gene in mice is induced by type I interferons and is the major determinant of resistance to influenza virus and related orthomyxoviruses. It has been previously shown that a SNP in exon 13 of the chicken MX1 gene determines differential antiviral activity of the protein. We evaluated this SNP and two additional SNPs in elite broiler lines by PCR amplification and sequence analysis. Associations between MX1 exon 13 SNPs and several traits of economic interest were evaluated. Significant associations were found between the SNP determining antiviral activity and mortality in one line and leg defects in another line. 相似文献
105.
Xianghai Ye Stewart R Brown Kátia Nones Luiz L Coutinho Jack CM Dekkers Susan J Lamont 《遗传、选种与进化》2007,39(1):73-89
Myostatin is a negative regulator of skeletal muscle growth. We evaluated effects of myostatin polymorphisms in three elite commercial broiler chicken lines on mortality, growth, feed conversion efficiency, ultrasound breast depth, breast percentage, eviscerated carcass weight, leg defects, blood oxygen level, and hen antibody titer to infectious bursal disease virus vaccine. Progeny mean data adjusted for fixed and mate effects and DNA from 100 sires per line were used. Single nucleotide polymorphisms (SNPs) of the myostatin gene segregating in these lines were identified by designing specific primers, amplifying individual DNA in each line by polymerase chain reaction, cloning, sequencing and aligning the corresponding products. Individual sires were genotyped for five identified SNPs which contributed to eight haplotypes. Frequencies of SNP alleles and haplotypes differed between lines. Using the allele substitution effect model, the myostatin SNPs were found to have significant (P < 0.031) associations with growth, mortality, blood oxygen and hen antibody titer to infectious bursal disease virus vaccine, although the associations were not often consistent across lines. These results suggest that the myostatin gene has pleiotropic effects on broiler performance. 相似文献
106.
Anja Konietzny Jasper Grendel Alan Kadek Michael Bucher Yuhao Han Nathalie Hertrich Dick H W Dekkers Jeroen A A Demmers Kay Grünewald Charlotte Uetrecht Marina Mikhaylova 《The EMBO journal》2022,41(4)
Excitatory synapses of principal hippocampal neurons are frequently located on dendritic spines. The dynamic strengthening or weakening of individual inputs results in structural and molecular diversity of dendritic spines. Active spines with large calcium ion (Ca2+) transients are frequently invaded by a single protrusion from the endoplasmic reticulum (ER), which is dynamically transported into spines via the actin‐based motor myosin V. An increase in synaptic strength correlates with stable anchoring of the ER, followed by the formation of an organelle referred to as the spine apparatus. Here, we show that myosin V binds the Ca2+ sensor caldendrin, a brain‐specific homolog of the well‐known myosin V interactor calmodulin. While calmodulin is an essential activator of myosin V motor function, we found that caldendrin acts as an inhibitor of processive myosin V movement. In mouse and rat hippocampal neurons, caldendrin regulates spine apparatus localization to a subset of dendritic spines through a myosin V‐dependent pathway. We propose that caldendrin transforms myosin into a stationary F‐actin tether that enables the localization of ER tubules and formation of the spine apparatus in dendritic spines. 相似文献
107.
Carolyn J. Lawrence-Dill Robyn L. Allscheid Albert Boaitey Todd Bauman Edward S. Buckler IV Jennifer L. Clarke Christopher Cullis Jack Dekkers Cassandra J. Dorius Shawn F. Dorius David Ertl Matthew Homann Guiping Hu Mary Losch Eric Lyons Brenda Murdoch Zahra-Katy Navabi Somashekhar Punnuri Fahad Rafiq James M. Reecy Patrick S. Schnable Nicole M. Scott Moira Sheehan Xavier Sirault Margaret Staton Christopher K. Tuggle Alison Van Eenennaam Rachael Voas 《PLoS computational biology》2022,18(4)
108.
109.
Roger Ros-Freixedes Sofia Gol Ramona N. Pena Marc Tor Noelia Ibá?ez-Escriche Jack C. M. Dekkers Joan Estany 《PloS one》2016,11(3)
Intramuscular fat (IMF) content and fatty acid composition affect the organoleptic quality and nutritional value of pork. A genome-wide association study was performed on 138 Duroc pigs genotyped with a 60k SNP chip to detect biologically relevant genomic variants influencing fat content and composition. Despite the limited sample size, the genome-wide association study was powerful enough to detect the association between fatty acid composition and a known haplotypic variant in SCD (SSC14) and to reveal an association of IMF and fatty acid composition in the LEPR region (SSC6). The association of LEPR was later validated with an independent set of 853 pigs using a candidate quantitative trait nucleotide. The SCD gene is responsible for the biosynthesis of oleic acid (C18:1) from stearic acid. This locus affected the stearic to oleic desaturation index (C18:1/C18:0), C18:1, and saturated (SFA) and monounsaturated (MUFA) fatty acids content. These effects were consistently detected in gluteus medius, longissimus dorsi, and subcutaneous fat. The association of LEPR with fatty acid composition was detected only in muscle and was, at least in part, a consequence of its effect on IMF content, with increased IMF resulting in more SFA, less polyunsaturated fatty acids (PUFA), and greater SFA/PUFA ratio. Marker substitution effects estimated with a subset of 65 animals were used to predict the genomic estimated breeding values of 70 animals born 7 years later. Although predictions with the whole SNP chip information were in relatively high correlation with observed SFA, MUFA, and C18:1/C18:0 (0.48–0.60), IMF content and composition were in general better predicted by using only SNPs at the SCD and LEPR loci, in which case the correlation between predicted and observed values was in the range of 0.36 to 0.54 for all traits. Results indicate that markers in the SCD and LEPR genes can be useful to select for optimum fatty acid profiles of pork. 相似文献
110.
C.M. Köhler D. Heslop W. Krijgsman M.J. Dekkers 《Palaeogeography, Palaeoclimatology, Palaeoecology》2010,285(1-2):66-73
The astronomically tuned marls of the Monte Gibliscemi section, Sicily, constitute an archive to trace the late Miocene palaeoenvironmental conditions (~ 9.7–7.0 Ma) in North Africa. Here we have utilised carbonate content and Al-normalised geochemical proxies to trace changes in terrigenous source area and bottom-water ventilation. The terrigenous input into the section is dominated by North African river systems draining into the Eastern Mediterranean. The proxy parameters indicate that the palaeoenvironmental conditions in North Africa were humid from 9.5 Ma onward with high fluvial input to the Mediterranean. Increases in the Si/Al and Mg/Al ratios occurred from 8.4 to 8.2 Ma and from 8.05 to 7.75 Ma, with maximum values similar to those of Messinian diatomites. These peaks indicate conditions of enhanced biosiliceous productivity and the presence of authigenic clay formation. Sluggish water circulation in the Mediterranean during those times is inferred from the Mn/Al and V/Al behaviour. Late Miocene changes of the Betic (southern Spain) and Rifian (Morocco) Mediterranean–Atlantic gateways are interpreted as the driving force for the changes in water circulation and the transgression associated with the opening of the Rifian corridor is interpreted to occur at 7.8 Ma. 相似文献