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  • 1
    Publication Date: 2014-08-20
    Description: Fastidious anaerobic bacteria play critical roles in environmental bioremediation of halogenated compounds. However, their characterization and application have been largely impeded by difficulties in growing them in pure culture. Thus far, no pure culture has been reported to respire on the notorious polychlorinated biphenyls (PCBs), and functional genes responsible for...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 2
    Publication Date: 2009-08-29
    Description: A single-base pair resolution silkworm genetic variation map was constructed from 40 domesticated and wild silkworms, each sequenced to approximately threefold coverage, representing 99.88% of the genome. We identified ~16 million single-nucleotide polymorphisms, many indels, and structural variations. We find that the domesticated silkworms are clearly genetically differentiated from the wild ones, but they have maintained large levels of genetic variability, suggesting a short domestication event involving a large number of individuals. We also identified signals of selection at 354 candidate genes that may have been important during domestication, some of which have enriched expression in the silk gland, midgut, and testis. These data add to our understanding of the domestication processes and may have applications in devising pest control strategies and advancing the use of silkworms as efficient bioreactors.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3951477/" 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/PMC3951477/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xia, Qingyou -- Guo, Yiran -- Zhang, Ze -- Li, Dong -- Xuan, Zhaoling -- Li, Zhuo -- Dai, Fangyin -- Li, Yingrui -- Cheng, Daojun -- Li, Ruiqiang -- Cheng, Tingcai -- Jiang, Tao -- Becquet, Celine -- Xu, Xun -- Liu, Chun -- Zha, Xingfu -- Fan, Wei -- Lin, Ying -- Shen, Yihong -- Jiang, Lan -- Jensen, Jeffrey -- Hellmann, Ines -- Tang, Si -- Zhao, Ping -- Xu, Hanfu -- Yu, Chang -- Zhang, Guojie -- Li, Jun -- Cao, Jianjun -- Liu, Shiping -- He, Ningjia -- Zhou, Yan -- Liu, Hui -- Zhao, Jing -- Ye, Chen -- Du, Zhouhe -- Pan, Guoqing -- Zhao, Aichun -- Shao, Haojing -- Zeng, Wei -- Wu, Ping -- Li, Chunfeng -- Pan, Minhui -- Li, Jingjing -- Yin, Xuyang -- Li, Dawei -- Wang, Juan -- Zheng, Huisong -- Wang, Wen -- Zhang, Xiuqing -- Li, Songgang -- Yang, Huanming -- Lu, Cheng -- Nielsen, Rasmus -- Zhou, Zeyang -- Wang, Jian -- Xiang, Zhonghuai -- Wang, Jun -- R01 HG003229/HG/NHGRI NIH HHS/ -- R01 HG003229-05/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2009 Oct 16;326(5951):433-6. doi: 10.1126/science.1176620. Epub 2009 Aug 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Key Sericultural Laboratory of Agricultural Ministry, College of Biotechnology, Southwest University, Chongqing 400715, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19713493" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bombyx/classification/*genetics ; Digestive System/metabolism ; Exocrine Glands/metabolism ; Female ; Gene Expression ; *Genes, Insect ; *Genetic Variation ; *Genome, Insect ; INDEL Mutation ; Linkage Disequilibrium ; Male ; Phylogeny ; Polymorphism, Single Nucleotide ; Principal Component Analysis ; Selection, Genetic ; *Sequence Analysis, DNA ; Testis/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2018
    Description: 〈p〉Posttranslational modifications (PTMs) play critical roles in regulating protein functions and mediating protein-protein interactions. An important PTM is lysine methylation that orchestrates chromatin modifications and regulates functions of non-histone proteins. Methyllysine peptides are bound by modular domains, of which chromodomains are representative. Here, we conducted the first large-scale study of chromodomains in the human proteome interacting with both histone and non-histone methyllysine peptides. We observed significant degenerate binding between chromodomains and histone peptides, i.e., different histone sites can be recognized by the same set of chromodomains, and different chromodomains can share similar binding profiles to individual histone sites. Such degenerate binding is not dictated by amino acid sequence or PTM motif but rather rooted in the physiochemical properties defined by the PTMs on the histone peptides. This molecular mechanism is confirmed by the accurate prediction of the binding specificity using a computational model that captures the structural and energetic patterns of the domain-peptide interaction. To further illustrate the power and accuracy of our model, we used it to effectively engineer an exceptionally strong H3K9me3-binding chromodomain and to label H3K9me3 in live cells. This study presents a systematic approach to deciphering domain-peptide recognition and reveals a general principle by which histone modifications are interpreted by reader proteins, leading to dynamic regulation of gene expression and other biological processes.〈/p〉
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
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  • 4
    Publication Date: 2018-11-08
    Description: Posttranslational modifications (PTMs) play critical roles in regulating protein functions and mediating protein-protein interactions. An important PTM is lysine methylation that orchestrates chromatin modifications and regulates functions of non-histone proteins. Methyllysine peptides are bound by modular domains, of which chromodomains are representative. Here, we conducted the first large-scale study of chromodomains in the human proteome interacting with both histone and non-histone methyllysine peptides. We observed significant degenerate binding between chromodomains and histone peptides, i.e., different histone sites can be recognized by the same set of chromodomains, and different chromodomains can share similar binding profiles to individual histone sites. Such degenerate binding is not dictated by amino acid sequence or PTM motif but rather rooted in the physiochemical properties defined by the PTMs on the histone peptides. This molecular mechanism is confirmed by the accurate prediction of the binding specificity using a computational model that captures the structural and energetic patterns of the domain-peptide interaction. To further illustrate the power and accuracy of our model, we used it to effectively engineer an exceptionally strong H3K9me3-binding chromodomain and to label H3K9me3 in live cells. This study presents a systematic approach to deciphering domain-peptide recognition and reveals a general principle by which histone modifications are interpreted by reader proteins, leading to dynamic regulation of gene expression and other biological processes.
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
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  • 5
    Publication Date: 2013-07-03
    Description: For decades, scholars have been trying to determine whether small or large groups are more likely to cooperate for collective action and successfully manage common-pool resources. Using data gathered from the Wolong Nature Reserve since 1995, we examined the effects of group size (i.e., number of households monitoring a single...
    Keywords: Sustainability Science
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 6
    Publication Date: 2013-11-22
    Description: Amyloid-β1–42 oligomer accelerates senescence in adult hippocampal neural stem/progenitor cells via formylpeptide receptor 2 Cell Death and Disease 4, e924 (November 2013). doi:10.1038/cddis.2013.437 Authors: N He, W-L Jin, K-H Lok, Y Wang, M Yin & Z-J Wang
    Keywords: Aβ42adult hippocampal neural stem/progenitor cellssenescenceFPR2ROSp38 MAPK
    Electronic ISSN: 2041-4889
    Topics: Biology , Medicine
    Published by Springer Nature
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  • 7
    Publication Date: 2017-10-13
    Description: The selective oxidation of methane, the primary component of natural gas, remains an important challenge in catalysis. We used colloidal gold-palladium nanoparticles, rather than the same nanoparticles supported on titanium oxide, to oxidize methane to methanol with high selectivity (92%) in aqueous solution at mild temperatures. Then, using isotopically labeled oxygen (O 2 ) as an oxidant in the presence of hydrogen peroxide (H 2 O 2 ) , we demonstrated that the resulting methanol incorporated a substantial fraction (70%) of gas-phase O 2 . More oxygenated products were formed than the amount of H 2 O 2 consumed, suggesting that the controlled breakdown of H 2 O 2 activates methane, which subsequently incorporates molecular oxygen through a radical process. If a source of methyl radicals can be established, then the selective oxidation of methane to methanol using molecular oxygen is possible.
    Keywords: Chemistry
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Geosciences , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
    Publication Date: 2016-02-26
    Description: Controlling dropwise condensation is fundamental to water-harvesting systems, desalination, thermal power generation, air conditioning, distillation towers, and numerous other applications. For any of these, it is essential to design surfaces that enable droplets to grow rapidly and to be shed as quickly as possible. However, approaches based on microscale, nanoscale or molecular-scale textures suffer from intrinsic trade-offs that make it difficult to optimize both growth and transport at once. Here we present a conceptually different design approach--based on principles derived from Namib desert beetles, cacti, and pitcher plants--that synergistically combines these aspects of condensation and substantially outperforms other synthetic surfaces. Inspired by an unconventional interpretation of the role of the beetle's bumpy surface geometry in promoting condensation, and using theoretical modelling, we show how to maximize vapour diffusion fluxat the apex of convex millimetric bumps by optimizing the radius of curvature and cross-sectional shape. Integrating this apex geometry with a widening slope, analogous to cactus spines, directly couples facilitated droplet growth with fast directional transport, by creating a free-energy profile that drives the droplet down the slope before its growth rate can decrease. This coupling is further enhanced by a slippery, pitcher-plant-inspired nanocoating that facilitates feedback between coalescence-driven growth and capillary-driven motion on the way down. Bumps that are rationally designed to integrate these mechanisms are able to grow and transport large droplets even against gravity and overcome the effect of an unfavourable temperature gradient. We further observe an unprecedented sixfold-higher exponent of growth rate, faster onset, higher steady-state turnover rate, and a greater volume of water collected compared to other surfaces. We envision that this fundamental understanding and rational design strategy can be applied to a wide range of water-harvesting and phase-change heat-transfer applications.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Park, Kyoo-Chul -- Kim, Philseok -- Grinthal, Alison -- He, Neil -- Fox, David -- Weaver, James C -- Aizenberg, Joanna -- England -- Nature. 2016 Mar 3;531(7592):78-82. doi: 10.1038/nature16956. Epub 2016 Feb 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, USA. ; Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA. ; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26909575" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Beetles/anatomy & histology/metabolism ; Biomimetics ; Cactaceae/anatomy & histology/metabolism ; Diffusion ; Distillation ; Gravitropism ; *Motion ; *Phase Transition ; Plants/anatomy & histology/metabolism ; Surface Properties ; Temperature ; Time Factors ; Volatilization ; Water/*chemistry/*metabolism ; Water Supply
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 9
    Publication Date: 2018-05-11
    Description: Materials, Vol. 11, Pages 765: Finite Element Analysis of Interaction of Laser Beam with Material in Laser Metal Powder Bed Fusion Process Materials doi: 10.3390/ma11050765 Authors: Guang Fu David Z. Zhang Allen N. He Zhongfa Mao Kaifei Zhang A deep understanding of the laser-material interaction mechanism, characterized by laser absorption, is very important in simulating the laser metal powder bed fusion (PBF) process. This is because the laser absorption of material affects the temperature distribution, which influences the thermal stress development and the final quality of parts. In this paper, a three-dimensional finite element analysis model of heat transfer taking into account the effect of material state and phase changes on laser absorption is presented to gain insight into the absorption mechanism, and the evolution of instantaneous absorptance in the laser metal PBF process. The results showed that the instantaneous absorptance was significantly affected by the time of laser radiation, as well as process parameters, such as hatch space, scanning velocity, and laser power, which were consistent with the experiment-based findings. The applicability of this model to temperature simulation was demonstrated by a comparative study, wherein the peak temperature in fusion process was simulated in two scenarios, with and without considering the effect of material state and phase changes on laser absorption, and the simulated results in the two scenarios were then compared with experimental data respectively.
    Electronic ISSN: 1996-1944
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Published by MDPI Publishing
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  • 10
    Publication Date: 2014-06-25
    Description: The selective autophagy substrate p62 serves as a molecular link between autophagy and cancer. Suppression of autophagy causes p62 accumulation and thereby contributes to tumorigenesis. Here we demonstrate that autophagy deficiency promotes cell proliferation and migration through p62-dependent stabilization of the oncogenic transcription factor Twist1. p62 binds to Twist1 and...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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