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  • 1
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    Genome-Wide Patterns of Genetic Variation in Two Domestic Chickens (2013)
    Oxford University Press
    Details
    Publication Date: 2013-08-02
    Description: Domestic chickens are excellent models for investigating the genetic basis of phenotypic diversity, as numerous phenotypic changes in physiology, morphology, and behavior in chickens have been artificially selected. Genomic study is required to study genome-wide patterns of DNA variation for dissecting the genetic basis of phenotypic traits. We sequenced the genomes of the Silkie and the Taiwanese native chicken L2 at ~23- and 25-fold average coverage depth, respectively, using Illumina sequencing. The reads were mapped onto the chicken reference genome (including 5.1% Ns) to 92.32% genome coverage for the two breeds. Using a stringent filter, we identified ~7.6 million single-nucleotide polymorphisms (SNPs) and 8,839 copy number variations (CNVs) in the mapped regions; 42% of the SNPs have not found in other chickens before. Among the 68,906 SNPs annotated in the chicken sequence assembly, 27,852 were nonsynonymous SNPs located in 13,537 genes. We also identified hundreds of shared and divergent structural and copy number variants in intronic and intergenic regions and in coding regions in the two breeds. Functional enrichments of identified genetic variants were discussed. Radical nsSNP-containing immunity genes were enriched in the QTL regions associated with some economic traits for both breeds. Moreover, genetic changes involved in selective sweeps were detected. From the selective sweeps identified in our two breeds, several genes associated with growth, appetite, and metabolic regulation were identified. Our study provides a framework for genetic and genomic research of domestic chickens and facilitates the domestic chicken as an avian model for genomic, biomedical, and evolutionary studies.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Maize cis elements and their cognate regulators [Genetics] (2015)
    National Academy of Sciences
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    Publication Date: 2015-05-13
    Description: Maize is a major crop and a model plant for studying C4 photosynthesis and leaf development. However, a genomewide regulatory network of leaf development is not yet available. This knowledge is useful for developing C3 crops to perform C4 photosynthesis for enhanced yields. Here, using 22 transcriptomes of developing maize...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 3
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    Evolutionary Conservation of Histone Modifications in Mammals (2012)
    Oxford University Press
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    Publication Date: 2012-06-16
    Description: Histone modification is an important mechanism of gene regulation in eukaryotes. Why many histone modifications can be stably maintained in the midst of genetic and environmental changes is a fundamental question in evolutionary biology. We obtained genome-wide profiles of three histone marks, H3 lysine 4 tri-methylation (H3K4me3), H3 lysine 4 mono-methylation (H3K4me1), and H3 lysine 27 acetylation (H3K27ac), for several cell types from human and mouse. We identified histone modifications that were stable among different cell types in human and histone modifications that were evolutionarily conserved between mouse and human in the same cell type. We found that histone modifications that were stable among cell types were also likely to be conserved between species. This trend was consistently observed in promoter, intronic, and intergenic regions for all of the histone marks tested. Importantly, the trend was observed regardless of the expression breadth of the nearby gene, indicating that slow evolution of housekeeping genes was not the major reason for the correlation. These regions showed distinct genetic and epigenetic properties, such as clustered transcription factor binding sites (TFBSs), high GC content, and CTCF binding at flanking sides. Based on our observations, we proposed that TFBS clustering in or near a histone modification plays a significant role in stabilizing and conserving the histone modification because TFBS clustering promotes TFBS conservation, which in turn promotes histone modification conservation. In summary, the results of this study support the view that in mammalian genomes a common mechanism maintains histone modifications against both genetic and environmental (cellular) changes.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    Gene clustering pattern, promoter architecture, and gene expression stability in eukaryotic genomes [Evolution] (2011)
    National Academy of Sciences
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    Publication Date: 2011-02-23
    Description: A balance between gene expression stability and evolvability is essential for the long-term maintenance of a living system. In this paper, we studied whether the genetic and epigenetic properties of the promoter affect gene expression variability. We hypothesized that upstream distance and orientation (head-to-head or head-to-tail) are important for the promoter architecture and gene expression variability. We found that in budding yeast genes with a short upstream distance tend to have low gene expression variability, and their promoter is flanked by strongly positioned nucleosomes and tends to have low nucleosome occupancy. These observations suggest that in vivo positioning of the flanking nucleosomes facilitates stable nucleosome depletion at the core promoter region and enhances gene expression stability. Head-to-head genes have, on average, lower gene expression variability, greater nucleosome depletion at the core promoter region, and more strongly positioned nucleosomes that flank the core promoter than do head-to-tail genes. These observations hold for diverse eukaryotes. In complex organisms such as mammals, only a small fraction of head-to-tail genes have retained a short upstream distance, probably because the promoter may not be flanked by a strongly positioned nucleosome on the upstream side.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 5
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    Reversed two-cell convection in the Northern and Southern hemispheres during northward interplanetary magnetic field (2011)
    Wiley
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    Publication Date: 2011-12-31
    Description: This article presents a case study of large-scale ionospheric convection in the Northern and Southern Hemispheres under strongly northward interplanetary magnetic field (IMF) conditions on 9 November 2004. Using a comprehensive data set from both ground- and space-based instruments, the study shows the formation of reversed two-cell convection in both the Northern and Southern Hemispheres that lasted for nearly 2 hours. Examination of the concurrent satellite energy-time spectrograms of precipitating particles reveals that reverse convection occurs in the region filled mostly with the boundary plasma sheet (BPS) type precipitating electrons except that the electron number flux is much smaller than that in the normal BPS. We have named this region the northward Bz boundary layer (NBZBL), which we interpret as a consequence of double-lobe reconnection. This interpretation is corroborated by the global MHD simulations, which show that the NBZBL consists of mostly closed field lines, resulting from double-lobe reconnection in both the hemispheres, together with intermittent presence of overdraped open field lines, resulting from single-lobe reconnection in one of the hemispheres. In addition to reversed two-cell convection, the distribution of field-aligned currents (FACs) shows clearly the presence of a pair of the northward Bz (NBZ) currents near the central polar region in both the hemispheres. Intense downward Poynting flux with a peak value around 100 mW/m2 is also seen in the high-latitude polar region, which tends to surround the upward leg of the NBZ currents. Finally, the potential drop between the two reverse-convection cells exceeds 100 kV, which is far larger than the values reported in any previous studies of reverse convection under northward IMF conditions. The unusually large reverse potential drop in this case is attributed in part to the strong NBZ component of 35–40 nT and in part to the unusually large solar wind dynamic pressure that is about five times its nominal value.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 6
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    Magnetic phase diagram of the antiferromagnetic cobalt tellurate Co_{3}TeO_{6} (2011)
    American Physical Society (APS)
    Details
    Publication Date: 2011-12-17
    Description: Author(s): J. L. Her, C. C. Chou, Y. H. Matsuda, K. Kindo, H. Berger, K. F. Tseng, C. W. Wang, W. H. Li, and H. D. Yang [Phys. Rev. B 84, 235123] Published Fri Dec 16, 2011
    Keywords: Electronic structure and strongly correlated systems
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society (APS)
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  • 7
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    Chromosomal location and evolutionary rate variation in enterobacterial genes (1989)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1989-11-10
    Description: The basal rate of DNA sequence evolution in enterobacteria, as seen in the extent of divergence between Escherichia coli and Salmonella typhimurium, varies greatly among genes, even when only "silent" sites are considered. The degree of divergence is clearly related to the level of gene expression, reflecting constraints on synonymous codon choice. However, where this constraint is weak, among genes not expressed at high levels, divergence is also related to the chromosomal location of the gene; it appears that genes furthest away from oriC, the origin of replication, have a mutation rate approximately two times that of genes near oriC.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sharp, P M -- Shields, D C -- Wolfe, K H -- Li, W H -- New York, N.Y. -- Science. 1989 Nov 10;246(4931):808-10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Trinity College, Dublin, Ireland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/2683084" target="_blank"〉PubMed〈/a〉
    Keywords: Bias (Epidemiology) ; *Biological Evolution ; *Chromosomes, Bacterial ; Codon/genetics ; DNA Repair ; DNA Replication ; DNA, Bacterial/genetics ; Enterobacteriaceae/*genetics/ultrastructure ; Escherichia coli/genetics/ultrastructure ; Gene Expression Regulation, Bacterial ; Genes, Bacterial ; *Mutation ; Regression Analysis ; Salmonella typhimurium/genetics/ultrastructure
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 8
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    Comment on "Chromosomal speciation and molecular divergence-accelerated evolution in rearranged chromosomes" (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-11-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lu, Jian -- Li, Wen-Hsiung -- Wu, Chung-I -- New York, N.Y. -- Science. 2003 Nov 7;302(5647):988; author reply 988.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA. ciwu@uchicago.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14605352" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Animals ; Biological Evolution ; Cercopithecidae/*genetics/physiology ; Chromosome Inversion ; Chromosomes, Human/genetics ; Chromosomes, Mammalian/*genetics ; *Evolution, Molecular ; Genes ; Genetics, Population ; Hominidae/*genetics/physiology ; Humans ; Models, Biological ; Pan troglodytes/*genetics/physiology ; *Recombination, Genetic ; Species Specificity
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 9
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    Nutrients Release from a Novel Gel-Based Slow/Controlled Release Fertilizer (2016)
    Hindawi
    Details
    Publication Date: 2016-05-18
    Description: A novel gel-based slow/controlled release fertilizer (G-CRF) was developed, which was produced by combining various natural, seminatural, and/or synthetic organic macromolecule materials and natural inorganic mineral with conventional NPK fertilizers. Its nutrient release characteristics were studied to compare with conventional fertilizers through the soil column leaching method. The influences of soil factors, including temperature, pH, water, and nutrient contents in the G-CRF on nutrient release, were also investigated through soil-water incubation method. These results indicated that the G-CRF had better effect on controlling release of N, P, and K nutrients, and the effect was more efficient when soil-water content was lower than 45% (w/w), temperature was below 35°C, and soil pH was in the range from weak acid to neutral. In addition, considering the effect of controlling nutrient release and cost of the materials in the G-CRF, it is recommended that the most feasible NPK nutrient contents in the G-CRF ranged from 30 to 35%.
    Print ISSN: 1687-7667
    Electronic ISSN: 1687-7675
    Topics: Geosciences , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Hindawi
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  • 10
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    Revealing the pseudogap in ${\mathrm{Sr}}_{3}{({\mathrm{Ru}}_{0.985}{\mathrm{Fe}}_{0.015})}_{2}{\mathrm{O}}_{7}$ by optical spectroscopy (2018)
    American Physical Society (APS)
    Details
    Publication Date: 2018-11-07
    Description: Author(s): W. J. Ban, B. Xu, W. H. Li, Y. Wang, J. J. Ge, P. G. Li, R. Yang, Y. M. Dai, Z. Q. Mao, and H. Xiao We report resistivity, magnetization, and optical spectroscopy study on single-crystal sample of Sr 3 ( Ru 0.985 Fe 0.015 ) 2 O 7 . An upturn is observed in resistivity at about 30 K. Below 30 K, the dip in resistivity R ( ω ), the suppression in scattering rate 1 / τ ( ω ) , the peaklike feature in optical conductivit... [Phys. Rev. B 98, 205111] Published Tue Nov 06, 2018
    Keywords: Electronic structure and strongly correlated systems
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society (APS)
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