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  • 1
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    Investigating the Path of Plastid Genome Degradation in an Early-Transitional Clade of Heterotrophic Orchids, and Implications for Heterotrophic Angiosperms (2014)
    Oxford University Press
    Details
    Publication Date: 2014-11-28
    Description: Parasitic organisms exemplify morphological and genomic reduction. Some heterotrophic, parasitic plants harbor drastically reduced and degraded plastid genomes resulting from relaxed selective pressure on photosynthetic function. However, few studies have addressed the initial stages of plastome degradation in groups containing both photosynthetic and nonphotosynthetic species. Corallorhiza is a genus of leafless, heterotrophic orchids that contains both green, photosynthetic species and nongreen, putatively nonphotosynthetic species, and represents an ideal system in which to assess the beginning of the transition to a "minimal plastome." Complete plastomes were generated for nine taxa of Corallorhiza using Illumina paired-end sequencing of genomic DNA to assess the degree of degradation among taxa, and for comparison with a general model of degradation among angiosperms. Quantification of total chlorophyll suggests that nongreen Corallorhiza still produce chlorophyll, but at 10-fold lower concentrations than green congeners. Complete plastomes and partial nuclear rDNA cistrons yielded a fully resolved tree for Corallorhiza , with at least two independent losses of photosynthesis, evidenced by gene deletions and pseudogenes in Co. striata and nongreen Co. maculata . All Corallorhiza show some evidence of degradation in genes of the NAD(P)H dehydrogenase complex. Among genes with open reading frames, photosynthesis-related genes displayed evidence of neutral evolution in nongreen Corallorhiza , whereas genes of the ATP synthase complex displayed some evidence of positive selection in these same groups, though for reasons unknown. Corallorhiza spans the early stages of a general model of plastome degradation and has added critical insight for understanding the process of plastome evolution in heterotrophic angiosperms.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Gut microbiomes of Malawian twin pairs discordant for kwashiorkor (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-02-01
    Description: Kwashiorkor, an enigmatic form of severe acute malnutrition, is the consequence of inadequate nutrient intake plus additional environmental insults. To investigate the role of the gut microbiome, we studied 317 Malawian twin pairs during the first 3 years of life. During this time, half of the twin pairs remained well nourished, whereas 43% became discordant, and 7% manifested concordance for acute malnutrition. Both children in twin pairs discordant for kwashiorkor were treated with a peanut-based, ready-to-use therapeutic food (RUTF). Time-series metagenomic studies revealed that RUTF produced a transient maturation of metabolic functions in kwashiorkor gut microbiomes that regressed when administration of RUTF was stopped. Previously frozen fecal communities from several discordant pairs were each transplanted into gnotobiotic mice. The combination of Malawian diet and kwashiorkor microbiome produced marked weight loss in recipient mice, accompanied by perturbations in amino acid, carbohydrate, and intermediary metabolism that were only transiently ameliorated with RUTF. These findings implicate the gut microbiome as a causal factor in kwashiorkor.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3667500/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3667500/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Smith, Michelle I -- Yatsunenko, Tanya -- Manary, Mark J -- Trehan, Indi -- Mkakosya, Rajhab -- Cheng, Jiye -- Kau, Andrew L -- Rich, Stephen S -- Concannon, Patrick -- Mychaleckyj, Josyf C -- Liu, Jie -- Houpt, Eric -- Li, Jia V -- Holmes, Elaine -- Nicholson, Jeremy -- Knights, Dan -- Ursell, Luke K -- Knight, Rob -- Gordon, Jeffrey I -- DK078669/DK/NIDDK NIH HHS/ -- DK30292/DK/NIDDK NIH HHS/ -- F32 DK091044/DK/NIDDK NIH HHS/ -- P01 DK078669/DK/NIDDK NIH HHS/ -- P30 DK056341/DK/NIDDK NIH HHS/ -- R37 DK030292/DK/NIDDK NIH HHS/ -- T32 HD049338/HD/NICHD NIH HHS/ -- T32-HD049338/HD/NICHD NIH HHS/ -- T35 DK074375/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 2013 Feb 1;339(6119):548-54. doi: 10.1126/science.1229000. Epub 2013 Jan 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, MO 63110, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23363771" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acids/metabolism ; Animals ; Arachis ; Carbohydrate Metabolism ; Child, Preschool ; Diseases in Twins/*microbiology ; Feces/microbiology ; Female ; Gastrointestinal Tract/*microbiology ; Germ-Free Life ; Humans ; Infant ; Kwashiorkor/diet therapy/epidemiology/*microbiology ; Longitudinal Studies ; Malawi/epidemiology ; Male ; *Metagenome ; Mice ; Mice, Inbred C57BL
    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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  • 3
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    Beneficial effect of post-deposition treatment in high-efficiency Cu(In,Ga)Se2 solar cells through reduced potential fluctuations (2016)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2016-08-13
    Description: World-record power conversion efficiencies for Cu(In,Ga)Se 2 (CIGS) solar cells have been achieved via a post-deposition treatment with alkaline metals, which increases the open-circuit voltage and fill factor. We explore the role of the potassium fluoride (KF) post-deposition treatment in CIGS by employing energy- and time-resolved photoluminescence spectroscopy and electrical characterization combined with numerical modeling. The bulk carrier lifetime is found to increase with post-deposition treatment from 255 ns to 388 ns, which is the longest charge carrier lifetime reported for CIGS, and within ∼40% of the radiative limit. We find evidence that the post-deposition treatment causes a decrease in the electronic potential fluctuations. These potential fluctuations have previously been shown to reduce the open-circuit voltage and the device efficiency in CIGS. Additionally, numerical simulations based on the measured carrier lifetimes and mobilities show a diffusion length of ∼10  μ m, which is ∼4 times larger than the film thickness. Thus, carrier collection in the bulk is not a limiting factor for device efficiency. By considering differences in doping, bandgap, and potential fluctuations, we present a possible explanation for the voltage difference between KF-treated and untreated samples.
    Print ISSN: 0021-8979
    Electronic ISSN: 1089-7550
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 4
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    Measuring long-range carrier diffusion across multiple grains in polycrystalline semiconductors by photoluminescence imaging (2013)
    Springer Nature
    Details
    Publication Date: 2013-10-27
    Description: Article Understanding the role of defects on semiconductor carrier transport should help improve their performance in devices. Using photoluminescence techniques, Alberi et al . image the carrier diffusion in polycrystalline CdTe and find that long-range transport is mediated by the distribution of defect states. Nature Communications doi: 10.1038/ncomms3699 Authors: K. Alberi, B. Fluegel, H. Moutinho, R. G. Dhere, J. V. Li, A. Mascarenhas
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 5
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    Global metabolic responses of mice to Trypanosoma brucei brucei infection (2008)
    National Academy of Sciences
    Details
    Publication Date: 2008-04-14
    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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  • 6
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    Beneficial effect of post-deposition treatment in high-efficiency Cu(In,Ga)Se2 solar cells through reduced potential fluctuations (2016)
    American Institute of Physics
    Details
    Publication Date: 2016-08-12
    Print ISSN: 0021-8979
    Electronic ISSN: 1089-7550
    Topics: Physics
    Published by American Institute of Physics
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  • 7
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    Methylation of histone H3 lysine 9 occurs during translation (2015)
    Oxford University Press
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    Publication Date: 2015-10-31
    Description: Histone post-translational modifications are key contributors to chromatin structure and function, and participate in the maintenance of genome stability. Understanding the establishment and maintenance of these marks, along with their misregulation in pathologies is thus a major focus in the field. While we have learned a great deal about the enzymes regulating histone modifications on nucleosomal histones, much less is known about the mechanisms establishing modifications on soluble newly synthesized histones. This includes methylation of lysine 9 on histone H3 (H3K9), a mark that primes the formation of heterochromatin, a critical chromatin landmark for genome stability. Here, we report that H3K9 mono- and dimethylation is imposed during translation by the methyltransferase SetDB1. We discuss the importance of these results in the context of heterochromatin establishment and maintenance and new therapeutic opportunities in pathologies where heterochromatin is perturbed.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    Engineering material structure by fractal cut [Engineering] (2014)
    National Academy of Sciences
    Details
    Publication Date: 2014-12-10
    Description: In this paper we discuss the transformation of a sheet of material into a wide range of desired shapes and patterns by introducing a set of simple cuts in a multilevel hierarchy with different motifs. Each choice of hierarchical cut motif and cut level allows the material to expand into...
    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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  • 9
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    MGAS: a powerful tool for multivariate gene-based genome-wide association analysis (2015)
    Oxford University Press
    Details
    Publication Date: 2015-04-03
    Description: Motivation : Standard genome-wide association studies, testing the association between one phenotype and a large number of single nucleotide polymorphisms (SNPs), are limited in two ways: (i) traits are often multivariate, and analysis of composite scores entails loss in statistical power and (ii) gene-based analyses may be preferred, e.g. to decrease the multiple testing problem. Results : Here we present a new method, multivariate gene-based association test by extended Simes procedure (MGAS), that allows gene-based testing of multivariate phenotypes in unrelated individuals. Through extensive simulation, we show that under most trait-generating genotype–phenotype models MGAS has superior statistical power to detect associated genes compared with gene-based analyses of univariate phenotypic composite scores (i.e. GATES, multiple regression), and multivariate analysis of variance (MANOVA). Re-analysis of metabolic data revealed 32 False Discovery Rate controlled genome-wide significant genes, and 12 regions harboring multiple genes; of these 44 regions, 30 were not reported in the original analysis. Conclusion : MGAS allows researchers to conduct their multivariate gene-based analyses efficiently, and without the loss of power that is often associated with an incorrectly specified genotype–phenotype models. Availability and implementation : MGAS is freely available in KGG v3.0 ( http://statgenpro.psychiatry.hku.hk/limx/kgg/download.php ). Access to the metabolic dataset can be requested at dbGaP ( https://dbgap.ncbi.nlm.nih.gov/ ). The R-simulation code is available from http://ctglab.nl/people/sophie_van_der_sluis . Contact : mxli@hku.hk Supplementary information : Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 10
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    Modern pollen assemblages from cultivated rice fields and rice pollen morphology: Application to a study of ancient land use and agriculture in the Pearl River Delta, China (2012)
    Sage
    In: Holocene
    Details
    Publication Date: 2012-11-23
    Description: Pollen from a series of surface soil samples collected along a transect spanning southeast China was investigated to better understand palynological signals of ancient agriculture and other human activity. The transect surface samples consist of pairs taken inside and outside rice paddy fields. Pollen assemblages from these samples are valuable as modern analogs of human-altered environments and rice agriculture. Our measurements of Poaceae pollen grains from inside the modern rice fields discovered that 34–40 µm is the statistically significant size range for identifying domesticated rice in fossil pollen samples. This conclusion is also based on a size comparison of raw and chemically treated modern pollen grains from the plants. Pollen measurements for local wild grasses show that most native weeds have pollen grains less than 30 µm in size. The modern analogs and our study of the influence of chemical treatment on pollen grain size made it possible to examine a sediment core from the Pearl River delta for evidence of anthropogenic influence, including rice farming. Pollen assemblages from around 2200 cal. yr BP are highly similar to those of our modern analogs representing disturbed landscapes outside modern rice fields. The pollen spectra reveal abrupt increases in Poaceae, Dicranopteris, Artemisia and Pinus indicative of rice farming and forest clearance, at around 2200 cal. yr BP. Major factors associated with this abrupt transition were the rapid formation of the deltaic flood plain and massive increases in the Pearl River delta area population during the Qin Dynasty.
    Print ISSN: 0959-6836
    Electronic ISSN: 1477-0911
    Topics: Geography , Geosciences
    Published by Sage
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