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Information-theoretic identification of predictive SNPs and supervised visualization of genome-wide association studies 总被引:2,自引:0,他引:2
The size, dimensionality and the limited range of the data values makes visualization of single nucleotide polymorphism (SNP) datasets challenging. The purpose of this study is to evaluate the usefulness of 3D VizStruct, a novel multi-dimensional data visualization technique for SNP datasets capable of identifying informative SNPs in genome-wide association studies. VizStruct is an interactive visualization technique that reduces multi-dimensional data to three dimensions using a combination of the discrete Fourier transform and the Kullback–Leibler divergence. The performance of 3D VizStruct was challenged with several diverse, biologically relevant published datasets including the human lipoprotein lipase (LPL) gene locus, the human Y-chromosome in several populations and a multi-locus genotype dataset of coral samples from four populations. In every case, the SNPs and or polymorphic markers identified by the 3D VizStruct mapping were predictive of the underlying biology. 相似文献
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Salinity poses a major threat for agriculture worldwide. Rice is one of the major crops where most of the high-yielding cultivars are highly sensitive to salinity. Several studies on the genetic variability across rice cultivars suggest that the activity and composition of root plasma membrane transporters could underlie the observed cultivar-specific salinity tolerance in rice. In the current study, it was found that the salt-tolerant cultivar Pokkali maintains a higher K+/Na+ ratio compared with the salt-sensitive IR20 in roots as well as in shoots. Using Na+ reporter dyes, IR20 root protoplasts showed a much faster Na+ accumulation than Pokkali protoplasts. Membrane potential measurements showed that root cells exposed to Na+ in IR20 depolarized considerably further than those of Pokkali. These results suggest that IR20 has a larger plasma membrane Na+ conductance. To assess whether this could be due to different ion channel properties, root protoplasts from both Pokkali and IR20 rice cultivars were patch-clamped. Voltage-dependent K+ inward rectifiers, K+ outward rectifiers, and voltage-independent, non-selective channels with unitary conductances of around 35, 40, and 10 pS, respectively, were identified. Only the non-selective channel showed significant Na+ permeability. Intriguingly, in both cultivars, the activity of the K+ inward rectifier was drastically down-regulated after plant growth in salt but gating, conductance, and activity of all channel types were very similar for the two cultivars. 相似文献
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Yin W Carballo-Jane E McLaren DG Mendoza VH Gagen K Geoghagen NS McNamara LA Gorski JN Eiermann GJ Petrov A Wolff M Tong X Wilsie LC Akiyama TE Chen J Thankappan A Xue J Ping X Andrews G Wickham LA Gai CL Trinh T Kulick AA Donnelly MJ Voronin GO Rosa R Cumiskey AM Bekkari K Mitnaul LJ Puig O Chen F Raubertas R Wong PH Hansen BC Koblan KS Roddy TP Hubbard BK Strack AM 《Journal of lipid research》2012,53(1):51-65
In an attempt to understand the applicability of various animal models to dyslipidemia in humans and to identify improved preclinical models for target discovery and validation for dyslipidemia, we measured comprehensive plasma lipid profiles in 24 models. These included five mouse strains, six other nonprimate species, and four nonhuman primate (NHP) species, and both healthy animals and animals with metabolic disorders. Dyslipidemic humans were assessed by the same measures. Plasma lipoprotein profiles, eight major plasma lipid fractions, and FA compositions within these lipid fractions were compared both qualitatively and quantitatively across the species. Given the importance of statins in decreasing plasma low-density lipoprotein cholesterol for treatment of dyslipidemia in humans, the responses of these measures to simvastatin treatment were also assessed for each species and compared with dyslipidemic humans. NHPs, followed by dog, were the models that demonstrated closest overall match to dyslipidemic humans. For the subset of the dyslipidemic population with high plasma triglyceride levels, the data also pointed to hamster and db/db mouse as representative models for practical use in target validation. Most traditional models, including rabbit, Zucker diabetic fatty rat, and the majority of mouse models, did not demonstrate overall similarity to dyslipidemic humans in this study. 相似文献
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Equalization of X linked gene expression is necessary in mammalian cells due to the presence of two X chromosomes in females and one in males. To achieve this, all female cells inactivate one of the two X chromosomes during development. This process, termed X chromosome inactivation (XCI), is a quintessential epigenetic phenomenon and involves a complex interplay between noncoding RNAs and protein factors. Progress in this area of study has consequently resulted in new approaches to study epigenetics and regulatory RNA function. Here we will discuss recent developments in the field that have advanced our understanding of XCI and its regulatory mechanisms. 相似文献
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Semi-synthesis and bio-evaluation of polybrominated diphenyl ethers from the sponge Dysidea herbacea
Srikanth Reddy T Suryakiran N Narasimhulu M Ramesh D Chinni Mahesh K Sai Krishna A Kavitha P Venkateswara Rao J Venkateswarlu Y 《Bioorganic & medicinal chemistry letters》2012,22(14):4900-4906
The sponge Dysidea herbacea was collected from the Mandapam Coast, Tamilnadu, India. Isolated gram quantities of hydroxylated polybrominated diphenyl ether (HO-PBDE) and semi-synthesized a series of new PBDEs derivatives and tested them for antibacterial and cytotoxic activities. 相似文献
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In this study, we characterized a putative peroxidase Prx1 of Candida albicans by: 1) demonstrating the thioredoxin-linked peroxidase activity with purified proteins, 2) examining the sensitivity to several
oxidants and the accumulation of intracellular reactive oxygen species with a null mutant (prx1Δ), a mutant (C69S) with a point mutation at Cys69, and a revertant, and 3) subcelluar localization. Enzymatic assays showed
that Prx1 is a thioredoxin-linked peroxidase which reduces both hydrogen peroxide (H2O2) and tert-butyl hydroperoxide (t-BOOH). Compared with two other strong H2O2 scavenger mutants for TSA1 and CAT1, prx1Δ and C69S were less sensitive to H2O2, menadione and diamide at all concentrations tested, but were more sensitive to low concentration of t-BOOH. Intracellular reactive oxygen species accumulated in prx1Δ and C69S cells treated with t-BOOH but not H2O2. These results suggest that peroxidase activity of Prx1 is specified to t-BOOH in cells. In both biochemical and physiological cases, the evolutionarily conserved Cys69 was found to be essential
for the function. Immunocytochemical staining revealed Prx1 is localized in the cytosol of yeast cells, but is translocated
to the nucleus during the hyphal transition, though the significances of this observation are unclear. Our data suggest that
PRX1 has a thioredoxin peroxidase activity reducing both t-BOOH and H2O2, but its cellular function is specified to t-BOOH. 相似文献
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Rahul R Nair Manivasagam B Nandhini Elango Monalisha Kavitha Murugan Thilaga Sethuraman Sangeetha Nagarajan Nayani Surya Prakash Rao Doss Ganesh 《Bioinformation》2012,8(22):1096-1104
Synonymous codon usage of 53 protein coding genes in chloroplast genome of Coffea arabica was analyzed for the first time to find
out the possible factors contributing codon bias. All preferred synonymous codons were found to use A/T ending codons as
chloroplast genomes are rich in AT. No difference in preference for preferred codons was observed in any of the two strands, viz.,
leading and lagging strands. Complex correlations between total base compositions (A, T, G, C, GC) and silent base contents (A3, T3,
G3, C3, GC3) revealed that compositional constraints played crucial role in shaping the codon usage pattern of C. arabica chloroplast
genome. ENC Vs GC3 plot grouped majority of the analyzed genes on or just below the left side of the expected GC3 curve
indicating the influence of base compositional constraints in regulating codon usage. But some of the genes lie distantly below the
continuous curve confirmed the influence of some other factors on the codon usage across those genes. Influence of compositional
constraints was further confirmed by correspondence analysis as axis 1 and 3 had significant correlations with silent base contents.
Correlation of ENC with axis 1, 4 and CAI with 1, 2 prognosticated the minor influence of selection in nature but exact separation
of highly and lowly expressed genes could not be seen. From the present study, we concluded that mutational pressure combined
with weak selection influenced the pattern of synonymous codon usage across the genes in the chloroplast genomes of C. arabica. 相似文献
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