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51.
Russell L Legg Jessica R Tolman Cameron T Lovinger Edwin D Lephart Kenneth DR Setchell Merrill J Christensen 《Reproductive biology and endocrinology : RB&E》2008,6(1):57
Background
High dietary intake of selenium or soybean isoflavones reduces prostate cancer risk. These components each affect androgen-regulated gene expression. The objective of this work was to determine the combined effects of selenium and isoflavones on androgen-regulated gene expression in rat prostate. 相似文献52.
Lihong?BuEmail author Kenneth?DR?Setchell Edwin?D?Lephart 《Reproductive biology and endocrinology : RB&E》2005,3(1):58
Background
Isoflavones, the most abundant phytoestrogens in soy foods, are structurally similar to 17beta-estradiol. Few studies have examined the nociception and stress hormone responses after consumption of soy isoflavones. 相似文献53.
Alexander T Xue Daniel R Schrider Andrew D Kern Agg Consortium 《Molecular biology and evolution》2021,38(3):1168
Identification of partial sweeps, which include both hard and soft sweeps that have not currently reached fixation, provides crucial information about ongoing evolutionary responses. To this end, we introduce partialS/HIC, a deep learning method to discover selective sweeps from population genomic data. partialS/HIC uses a convolutional neural network for image processing, which is trained with a large suite of summary statistics derived from coalescent simulations incorporating population-specific history, to distinguish between completed versus partial sweeps, hard versus soft sweeps, and regions directly affected by selection versus those merely linked to nearby selective sweeps. We perform several simulation experiments under various demographic scenarios to demonstrate partialS/HIC’s performance, which exhibits excellent resolution for detecting partial sweeps. We also apply our classifier to whole genomes from eight mosquito populations sampled across sub-Saharan Africa by the Anopheles gambiae 1000 Genomes Consortium, elucidating both continent-wide patterns as well as sweeps unique to specific geographic regions. These populations have experienced intense insecticide exposure over the past two decades, and we observe a strong overrepresentation of sweeps at insecticide resistance loci. Our analysis thus provides a list of candidate adaptive loci that may be relevant to mosquito control efforts. More broadly, our supervised machine learning approach introduces a method to distinguish between completed and partial sweeps, as well as between hard and soft sweeps, under a variety of demographic scenarios. As whole-genome data rapidly accumulate for a greater diversity of organisms, partialS/HIC addresses an increasing demand for useful selection scan tools that can track in-progress evolutionary dynamics. 相似文献
54.
James F. Denton Jose Lugo-Martinez Abraham E. Tucker Daniel R. Schrider Wesley C. Warren Matthew W. Hahn 《PLoS computational biology》2014,10(12)
Current sequencing methods produce large amounts of data, but genome assemblies based on these data are often woefully incomplete. These incomplete and error-filled assemblies result in many annotation errors, especially in the number of genes present in a genome. In this paper we investigate the magnitude of the problem, both in terms of total gene number and the number of copies of genes in specific families. To do this, we compare multiple draft assemblies against higher-quality versions of the same genomes, using several new assemblies of the chicken genome based on both traditional and next-generation sequencing technologies, as well as published draft assemblies of chimpanzee. We find that upwards of 40% of all gene families are inferred to have the wrong number of genes in draft assemblies, and that these incorrect assemblies both add and subtract genes. Using simulated genome assemblies of Drosophila melanogaster, we find that the major cause of increased gene numbers in draft genomes is the fragmentation of genes onto multiple individual contigs. Finally, we demonstrate the usefulness of RNA-Seq in improving the gene annotation of draft assemblies, largely by connecting genes that have been fragmented in the assembly process. 相似文献
55.
Thirty-four cytochrome P-450 sequences from one bacterial and six
vertebrate species have been aligned with the aid of a computer alignment
algorithm. Phylogenetic trees were constructed using the
unweighted-pair-group and neighbor-joining methods. The two trees differed
at only a single branch point near the base of the tree. The cytochrome
P-450 superfamily of proteins clustered into eight families and contained
16 gene-duplication events. The first gene duplication occurred
approximately 1,360 Myr before the present (Mybp) and gave rise to
cytochrome P-450s found in two different cellular organelles, the
mitochondria and the endoplasmic reticulum. Both groups utilize cholesterol
or its metabolites as substrates, implying that cholesterol existed greater
than 1,360 Mybp. The fourth gene duplication (approximately 900 Mybp) gave
rise to the drug-metabolizing P-450s. These proteins aid in the
detoxification of foreign chemicals, as opposed to the metabolism of
endogenous compounds. The importance of the capacity to metabolize drugs is
reflected in 11 further gene duplications occurring in this lineage. The
first occurred approximately 800 Mybp and gave rise to the two major P-450
families, the phenobarbital and 3-methylcholanthrene families. An apparent
increase in the rate of cytochrome P-450 evolution is noted between the
bird-mammal divergence (300 Mybp) and the mammalian radiation (75 Mybp).
相似文献
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