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Ravi V Mural Marcin Grzybowski Chenyong Miao Alyssa Damke Sirjan Sapkota Richard E Boyles Maria G Salas Fernandez Patrick S Schnable Brandi Sigmon Stephen Kresovich James C Schnable 《Genetics》2021,218(3)
Community association populations are composed of phenotypically and genetically diverse accessions. Once these populations are genotyped, the resulting marker data can be reused by different groups investigating the genetic basis of different traits. Because the same genotypes are observed and scored for a wide range of traits in different environments, these populations represent a unique resource to investigate pleiotropy. Here, we assembled a set of 234 separate trait datasets for the Sorghum Association Panel, a group of 406 sorghum genotypes widely employed by the sorghum genetics community. Comparison of genome-wide association studies (GWAS) conducted with two independently generated marker sets for this population demonstrate that existing genetic marker sets do not saturate the genome and likely capture only 35–43% of potentially detectable loci controlling variation for traits scored in this population. While limited evidence for pleiotropy was apparent in cross-GWAS comparisons, a multivariate adaptive shrinkage approach recovered both known pleiotropic effects of existing loci and new pleiotropic effects, particularly significant impacts of known dwarfing genes on root architecture. In addition, we identified new loci with pleiotropic effects consistent with known trade-offs in sorghum development. These results demonstrate the potential for mining existing trait datasets from widely used community association populations to enable new discoveries from existing trait datasets as new, denser genetic marker datasets are generated for existing community association populations. 相似文献
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Processing of viral envelope glycoprotein by the endomannosidase pathway: evaluation of host cell specificity 总被引:4,自引:2,他引:2
Endo-alpha-D-mannosidase is an enzyme involved in N-linked oligosaccharide
processing which through its capacity to cleave the internal linkage
between the glucose-substituted mannose and the remainder of the
polymannose carbohydrate unit can provide an alternate pathway for
achieving deglucosylation and thereby make possible the continued formation
of complex oligosaccharides during a glucosidase blockade. In view of the
important role which has been attributed to glucose on nascent
glycoproteins as a regulator of a number of biological events, we chose to
further define the in vivo action of endomannosidase by focusing on the
well characterized VSV envelope glycoprotein (G protein) which can be
formed by the large array of cell lines susceptible to infection by this
pathogen. Through an assessment of the extent to which the G protein was
converted to an endo-beta-N- acetylglucosaminidase (endo H)-resistant form
during a castanospermine imposed glucosidase blockade, we found that
utilization of the endomannosidase-mediated deglucosylation route was
clearly host cell specific, ranging from greater than 90% in HepG2 and PtK1
cells to complete absence in CHO, MDCK, and MDBK cells, with intermediate
values in BHK, BW5147.3, LLC-PK1, BRL, and NRK cell lines. In some of the
latter group the electrophoretic pattern after endo H treatment suggested
that only one of the two N-linked oligosaccharides of the G protein was
processed by endomannosidase. In the presence of the specific
endomannosidase inhibitor, Glcalpha1-->3(1- deoxy)mannojirimycin, the
conversion of the G protein into an endo H- resistant form was completely
arrested. While the lack of G protein processing by CHO cells was
consistent with the absence of in vitro measured endomannosidase activity
in this cell line, the failure of MDBK and MDCK cells to convert the G
protein into an endo H-resistant form was surprising since these cell lines
have substantial levels of the enzyme. Similarly, we observed that
influenza virus hemagglutinin was not processed in castanospermine-treated
MDCK cells. Our findings suggest that studies which rely on glucosidase
inhibition to explore the function of glucose in controlling such critical
biological phenomena as intracellular movement or quality control should be
carried out in cell lines in which the glycoprotein under study is not a
substrate for endomannosidase action.
相似文献
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Background
Although cystic fibrosis is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, the severity of disease is highly variable indicating the influence of modifier genes. The intestines of Cftr deficient mice (CF mice: Cftr tm1Unc ) are prone to obstruction by excessive mucus accumulation and are used as a model of meconium ileus and distal intestinal obstruction syndrome. This phenotype is strongly dependent on the genetic background of the mice. On the C57Bl/6 background, the majority of CF mice cannot survive on solid mouse chow, have inflammation of the small intestine, and are about 30% smaller than wild type littermates. In this work potential modifier loci of the CF intestinal phenotype were identified.Results
CF mice on a mixed genetic background (95% C57Bl/6 and 5% 129Sv) were compared to CF mice congenic on the C57Bl/6 background for several parameters of the intestinal CF phenotype. CF mice on the mixed background exhibit significantly greater survival when fed dry mouse chow, have reduced intestinal inflammation as measured by quantitative RT-PCR for marker genes, have near normal body weight gain, and have reduced mucus accumulation in the intestinal crypts. There was an indication of a gender effect for body weight gain: males did not show a significant improvement at 4 weeks of age, but were of normal weight at 8 weeks, while females showed improvement at both 4 and 8 weeks. By a preliminary genome-wide PCR allele scanning, three regions were found to be potentially associated with the milder phenotype. One on chr.1, defined by marker D1Mit36, one on chr. 9 defined by marker D9Mit90, and one on chr. 10, defined by marker D10Mit14.Conclusion
Potential modifier regions were found that have a positive impact on the inflammatory phenotype of the CF mouse small intestine and animal survival. Identification of polymorphisms in specific genes in these regions should provide important new information about genetic modifiers of the CF intestinal phenotype. 相似文献6.
Lora Sigmon Sarah Hoopes Morgan Booker Catherine Waters Kara Salpeter Brant Touchette 《Wetlands Ecology and Management》2013,21(1):45-54
Bioretention basins are man-made topographic depressions designed to collect and retain surface water runoff. In most cases these basins are used to prevent flooding and/or remove environmentally harmful pollutants and sediments from entering natural aquatic systems. To maximize environmental benefits, these systems are often planted with flood-tolerant wetland hydrophytes that are capable of withstanding extended periods of drought. Unfortunately, little is known about how these plants respond to extreme hydrologies while breaking seasonal dormancy. The purpose of this study was to better understand the morphological and physiological responses of three wetland species (Pontederia cordata L., Saururus cernuus L., and Schoenoplectus tabernaemontani C.C. Gmel. Palla) often used in bioretention basins while emerging from dormancy in either flooded or drought conditions. Results indicate that only S. tabernaemontani was affected morphologically by drought with lower leaf area and aboveground biomass. While significant reductions in stomatal surface indices were also observed in drought-treated S. tabernaemontani, all three species had reductions in stomatal conductance (g) when grown in drier soils. Moreover, drought conditions promoted decreases in leaf water potential (Ψ leaf) for all three species, and reductions in tissue water content (θ) for P. cordata and S. tabernaemontani. Based on the overall morphological and physiological responses, S. cernuus maintained the lowest productivity, and appeared to be the best suited for tolerating sustained soil water deficits. If high plant productivity is desired, however, S. tabernaemontani was able to maintain high plant growth while making necessary modifications that facilitated greater drought-resistance. 相似文献
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Phylogeny of the M superhaplogroup inferred from complete mitochondrial genome sequence of Indian specific lineages
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Revathi Rajkumar Jheelam Banerjee Hima Bindu Gunturi R Trivedi VK Kashyap 《Genome biology》2004,6(2):P3
Background
Phylogenetic analysis of human complete mitochondrial DNA sequences has largely contributed to resolving phylogenies and antiquity of different lineages belonging to the majorhaplogroups L, N and M (East-Asian lineages). In the absence of whole mtDNA sequence information of M lineages reported in India that exhibits highest diversity within the sub-continent, the present study was undertaken to provide a detailed analysis of this haplogroup to precisely characterize the lineages and unravel their intricate phylogeny. 相似文献9.
A Puri R Sethi B Singh SK Dwivedi VS Narain RK Saran VK Puri 《Indian pacing and electrophysiology journal》2009,9(3):186-189
A 25-year-old previously asymptomatic pregnant woman at 36 weeks'' gestation was noticed to have repetitive monomorphic ventricular tachycardia. A dilated left ventricle with moderately reduced systolic function was found on echocardiographic examination. This is a very rare presentation of peripartum cardiomyopathy (PPCMP) presenting with repetitive monomorphic ventricular tachycardia. 相似文献
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A Rajor R Sharma VK Sood Dr V Ramamurthy 《Journal of industrial microbiology & biotechnology》1996,16(4):237-240
Sawdust, a bulky waste generated by wood processing industries, has very few profitable and ecofriendly uses and poses a problem of proper disposal. Treatment with the fungusVolvariella volvaceae and a dilute solution of urea converted sawdust from a phytoinhibitory material to a phytostimulatory soil conditioner. In different types of soils, the soil conditioner increased the moisture retention and facilitated the cohesive interaction of particles. Analyses of the major biopolymers of sawdust after fungal treatment indicated that levels of cellulose, hemicellulose and lignin decreased; however, these changes did not account for the plant growth stimulatory property attained by this material. 相似文献