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  • 1
    Publication Date: 2012-11-16
    Description: For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars approximately 1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3566564/" 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/PMC3566564/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Groenen, Martien A M -- Archibald, Alan L -- Uenishi, Hirohide -- Tuggle, Christopher K -- Takeuchi, Yasuhiro -- Rothschild, Max F -- Rogel-Gaillard, Claire -- Park, Chankyu -- Milan, Denis -- Megens, Hendrik-Jan -- Li, Shengting -- Larkin, Denis M -- Kim, Heebal -- Frantz, Laurent A F -- Caccamo, Mario -- Ahn, Hyeonju -- Aken, Bronwen L -- Anselmo, Anna -- Anthon, Christian -- Auvil, Loretta -- Badaoui, Bouabid -- Beattie, Craig W -- Bendixen, Christian -- Berman, Daniel -- Blecha, Frank -- Blomberg, Jonas -- Bolund, Lars -- Bosse, Mirte -- Botti, Sara -- Bujie, Zhan -- Bystrom, Megan -- Capitanu, Boris -- Carvalho-Silva, Denise -- Chardon, Patrick -- Chen, Celine -- Cheng, Ryan -- Choi, Sang-Haeng -- Chow, William -- Clark, Richard C -- Clee, Christopher -- Crooijmans, Richard P M A -- Dawson, Harry D -- Dehais, Patrice -- De Sapio, Fioravante -- Dibbits, Bert -- Drou, Nizar -- Du, Zhi-Qiang -- Eversole, Kellye -- Fadista, Joao -- Fairley, Susan -- Faraut, Thomas -- Faulkner, Geoffrey J -- Fowler, Katie E -- Fredholm, Merete -- Fritz, Eric -- Gilbert, James G R -- Giuffra, Elisabetta -- Gorodkin, Jan -- Griffin, Darren K -- Harrow, Jennifer L -- Hayward, Alexander -- Howe, Kerstin -- Hu, Zhi-Liang -- Humphray, Sean J -- Hunt, Toby -- Hornshoj, Henrik -- Jeon, Jin-Tae -- Jern, Patric -- Jones, Matthew -- Jurka, Jerzy -- Kanamori, Hiroyuki -- Kapetanovic, Ronan -- Kim, Jaebum -- Kim, Jae-Hwan -- Kim, Kyu-Won -- Kim, Tae-Hun -- Larson, Greger -- Lee, Kyooyeol -- Lee, Kyung-Tai -- Leggett, Richard -- Lewin, Harris A -- Li, Yingrui -- Liu, Wansheng -- Loveland, Jane E -- Lu, Yao -- Lunney, Joan K -- Ma, Jian -- Madsen, Ole -- Mann, Katherine -- Matthews, Lucy -- McLaren, Stuart -- Morozumi, Takeya -- Murtaugh, Michael P -- Narayan, Jitendra -- Nguyen, Dinh Truong -- Ni, Peixiang -- Oh, Song-Jung -- Onteru, Suneel -- Panitz, Frank -- Park, Eung-Woo -- Park, Hong-Seog -- Pascal, Geraldine -- Paudel, Yogesh -- Perez-Enciso, Miguel -- Ramirez-Gonzalez, Ricardo -- Reecy, James M -- Rodriguez-Zas, Sandra -- Rohrer, Gary A -- Rund, Lauretta -- Sang, Yongming -- Schachtschneider, Kyle -- Schraiber, Joshua G -- Schwartz, John -- Scobie, Linda -- Scott, Carol -- Searle, Stephen -- Servin, Bertrand -- Southey, Bruce R -- Sperber, Goran -- Stadler, Peter -- Sweedler, Jonathan V -- Tafer, Hakim -- Thomsen, Bo -- Wali, Rashmi -- Wang, Jian -- Wang, Jun -- White, Simon -- Xu, Xun -- Yerle, Martine -- Zhang, Guojie -- Zhang, Jianguo -- Zhang, Jie -- Zhao, Shuhong -- Rogers, Jane -- Churcher, Carol -- Schook, Lawrence B -- 095908/Wellcome Trust/United Kingdom -- 249894/European Research Council/International -- 5 P41 LM006252/LM/NLM NIH HHS/ -- 5 P41LM006252/LM/NLM NIH HHS/ -- BB/E010520/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/E010520/2/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/E010768/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/E011640/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/G004013/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/H005935/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/I025328/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- G0900950/Medical Research Council/United Kingdom -- P20-RR017686/RR/NCRR NIH HHS/ -- P30 DA018310/DA/NIDA NIH HHS/ -- R13 RR020283A/RR/NCRR NIH HHS/ -- R13 RR032267A/RR/NCRR NIH HHS/ -- R21 DA027548/DA/NIDA NIH HHS/ -- R21 HG006464/HG/NHGRI NIH HHS/ -- T32 AI083196/AI/NIAID NIH HHS/ -- England -- Nature. 2012 Nov 15;491(7424):393-8. doi: 10.1038/nature11622.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708 WD, Wageningen, The Netherlands. martien.groenen@wur.nl〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23151582" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Demography ; Genome/*genetics ; Models, Animal ; Molecular Sequence Data ; *Phylogeny ; Population Dynamics ; Sus scrofa/*classification/*genetics
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    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2012-10-06
    Description: Some planetary systems harbour debris disks containing planetesimals such as asteroids and comets. Collisions between such bodies produce small dust particles, the spectral features of which reveal their composition and, hence, that of their parent bodies. A measurement of the composition of olivine crystals (Mg(2-2x)Fe(2x)SiO(4)) has been done for the protoplanetary disk HD 100546 (refs 3, 4) and for olivine crystals in the warm inner parts of planetary systems. The latter compares well with the iron-rich olivine in asteroids (x approximately 0.29). In the cold outskirts of the beta Pictoris system, an analogue to the young Solar System, olivine crystals were detected but their composition remained undetermined, leaving unknown how the composition of the bulk of Solar System cometary olivine grains compares with that of extrasolar comets. Here we report the detection of the 69-micrometre-wavelength band of olivine crystals in the spectrum of beta Pictoris. Because the disk is optically thin, we can associate the crystals with an extrasolar proto-Kuiper belt a distance of 15-45 astronomical units from the star (one astronomical unit is the Sun-Earth distance), determine their magnesium-rich composition (x = 0.01 +/- 0.001) and show that they make up 3.6 +/- 1.0 per cent of the total dust mass. These values are strikingly similar to those for the dust emitted by the most primitive comets in the Solar System, even though beta Pictoris is more massive and more luminous and has a different planetary system architecture.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉de Vries, B L -- Acke, B -- Blommaert, J A D L -- Waelkens, C -- Waters, L B F M -- Vandenbussche, B -- Min, M -- Olofsson, G -- Dominik, C -- Decin, L -- Barlow, M J -- Brandeker, A -- Di Francesco, J -- Glauser, A M -- Greaves, J -- Harvey, P M -- Holland, W S -- Ivison, R J -- Liseau, R -- Pantin, E E -- Pilbratt, G L -- Royer, P -- Sibthorpe, B -- England -- Nature. 2012 Oct 4;490(7418):74-6. doi: 10.1038/nature11469.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Instituut voor Sterrenkunde, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium. bldevries.science@gmail.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23038467" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2016-03-17
    Description: CD8(+) T cells have a central role in antitumour immunity, but their activity is suppressed in the tumour microenvironment. Reactivating the cytotoxicity of CD8(+) T cells is of great clinical interest in cancer immunotherapy. Here we report a new mechanism by which the antitumour response of mouse CD8(+) T cells can be potentiated by modulating cholesterol metabolism. Inhibiting cholesterol esterification in T cells by genetic ablation or pharmacological inhibition of ACAT1, a key cholesterol esterification enzyme, led to potentiated effector function and enhanced proliferation of CD8(+) but not CD4(+) T cells. This is due to the increase in the plasma membrane cholesterol level of CD8(+) T cells, which causes enhanced T-cell receptor clustering and signalling as well as more efficient formation of the immunological synapse. ACAT1-deficient CD8(+) T cells were better than wild-type CD8(+) T cells at controlling melanoma growth and metastasis in mice. We used the ACAT inhibitor avasimibe, which was previously tested in clinical trials for treating atherosclerosis and showed a good human safety profile, to treat melanoma in mice and observed a good antitumour effect. A combined therapy of avasimibe plus an anti-PD-1 antibody showed better efficacy than monotherapies in controlling tumour progression. ACAT1, an established target for atherosclerosis, is therefore also a potential target for cancer immunotherapy.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4851431/" 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/PMC4851431/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yang, Wei -- Bai, Yibing -- Xiong, Ying -- Zhang, Jin -- Chen, Shuokai -- Zheng, Xiaojun -- Meng, Xiangbo -- Li, Lunyi -- Wang, Jing -- Xu, Chenguang -- Yan, Chengsong -- Wang, Lijuan -- Chang, Catharine C Y -- Chang, Ta-Yuan -- Zhang, Ti -- Zhou, Penghui -- Song, Bao-Liang -- Liu, Wanli -- Sun, Shao-cong -- Liu, Xiaolong -- Li, Bo-liang -- Xu, Chenqi -- HL 60306./HL/NHLBI NIH HHS/ -- R01 HL060306/HL/NHLBI NIH HHS/ -- England -- Nature. 2016 Mar 31;531(7596):651-5. doi: 10.1038/nature17412. Epub 2016 Mar 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China. ; State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China. ; Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China. ; MOE Key Laboratory of Protein Science, School of Life Sciences, Collaborative Innovation Center for Infectious Diseases, Tsinghua University, Beijing 100084, China. ; Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, New Haven 03755, USA. ; Rheumatology and Immunology Department of ChangZheng Hospital, Second Military Medical University, Shanghai 200433, China. ; Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China. ; College of Life Sciences, Wuhan University, Wuhan, Hubei Province 430072, China. ; Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA. ; State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China. ; School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26982734" target="_blank"〉PubMed〈/a〉
    Keywords: Acetates/*pharmacology/therapeutic use ; Acetyl-CoA C-Acetyltransferase/antagonists & ; inhibitors/deficiency/genetics/metabolism ; Animals ; Atherosclerosis/drug therapy ; CD8-Positive T-Lymphocytes/*drug effects/*immunology/metabolism ; Cell Membrane/drug effects/metabolism ; Cholesterol/*metabolism ; Esterification/drug effects ; Female ; Immunological Synapses/drug effects/immunology/metabolism ; Immunotherapy/*methods ; Male ; Melanoma/*drug therapy/*immunology/metabolism/pathology ; Mice ; Programmed Cell Death 1 Receptor/antagonists & inhibitors/immunology ; Receptors, Antigen, T-Cell/immunology/metabolism ; Signal Transduction/drug effects ; Sulfonic Acids/*pharmacology/therapeutic use
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2012-05-19
    Description: Members of the opioid receptor family of G-protein-coupled receptors (GPCRs) are found throughout the peripheral and central nervous system, where they have key roles in nociception and analgesia. Unlike the 'classical' opioid receptors, delta, kappa and mu (delta-OR, kappa-OR and mu-OR), which were delineated by pharmacological criteria in the 1970s and 1980s, the nociceptin/orphanin FQ (N/OFQ) peptide receptor (NOP, also known as ORL-1) was discovered relatively recently by molecular cloning and characterization of an orphan GPCR. Although it shares high sequence similarity with classical opioid GPCR subtypes ( approximately 60%), NOP has a markedly distinct pharmacology, featuring activation by the endogenous peptide N/OFQ, and unique selectivity for exogenous ligands. Here we report the crystal structure of human NOP, solved in complex with the peptide mimetic antagonist compound-24 (C-24) (ref. 4), revealing atomic details of ligand-receptor recognition and selectivity. Compound-24 mimics the first four amino-terminal residues of the NOP-selective peptide antagonist UFP-101, a close derivative of N/OFQ, and provides important clues to the binding of these peptides. The X-ray structure also shows substantial conformational differences in the pocket regions between NOP and the classical opioid receptors kappa (ref. 5) and mu (ref. 6), and these are probably due to a small number of residues that vary between these receptors. The NOP-compound-24 structure explains the divergent selectivity profile of NOP and provides a new structural template for the design of NOP ligands.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3356928/" 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/PMC3356928/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Thompson, Aaron A -- Liu, Wei -- Chun, Eugene -- Katritch, Vsevolod -- Wu, Huixian -- Vardy, Eyal -- Huang, Xi-Ping -- Trapella, Claudio -- Guerrini, Remo -- Calo, Girolamo -- Roth, Bryan L -- Cherezov, Vadim -- Stevens, Raymond C -- P50 GM073197/GM/NIGMS NIH HHS/ -- P50 GM073197-08/GM/NIGMS NIH HHS/ -- R01 DA017204/DA/NIDA NIH HHS/ -- R01 DA017204-08/DA/NIDA NIH HHS/ -- R01 DA027170/DA/NIDA NIH HHS/ -- R01 DA027170-03/DA/NIDA NIH HHS/ -- R01 DA27170/DA/NIDA NIH HHS/ -- U54 GM094618/GM/NIGMS NIH HHS/ -- U54 GM094618-02/GM/NIGMS NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- England -- Nature. 2012 May 16;485(7398):395-9. doi: 10.1038/nature11085.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22596163" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Biomimetic Materials/*chemistry/metabolism/pharmacology ; Crystallography, X-Ray ; HEK293 Cells ; Humans ; Ligands ; Models, Molecular ; Narcotic Antagonists ; Opioid Peptides/*chemistry/metabolism/pharmacology ; Piperidines/*chemistry/*metabolism/pharmacology ; Protein Conformation ; Receptors, Opioid/*chemistry/*metabolism ; Receptors, Opioid, kappa/chemistry/metabolism ; Spiro Compounds/*chemistry/*metabolism/pharmacology ; Substrate Specificity
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2013-06-25
    Description: In the mammalian neocortex, segregated processing streams are thought to be important for forming sensory representations of the environment, but how local information in primary sensory cortex is transmitted to other distant cortical areas during behaviour is unclear. Here we show task-dependent activation of distinct, largely non-overlapping long-range projection neurons in the whisker region of primary somatosensory cortex (S1) in awake, behaving mice. Using two-photon calcium imaging, we monitored neuronal activity in anatomically identified S1 neurons projecting to secondary somatosensory (S2) or primary motor (M1) cortex in mice using their whiskers to perform a texture-discrimination task or a task that required them to detect the presence of an object at a certain location. Whisking-related cells were found among S2-projecting (S2P) but not M1-projecting (M1P) neurons. A higher fraction of S2P than M1P neurons showed touch-related responses during texture discrimination, whereas a higher fraction of M1P than S2P neurons showed touch-related responses during the detection task. In both tasks, S2P and M1P neurons could discriminate similarly between trials producing different behavioural decisions. However, in trials producing the same decision, S2P neurons performed better at discriminating texture, whereas M1P neurons were better at discriminating location. Sensory stimulus features alone were not sufficient to elicit these differences, suggesting that selective transmission of S1 information to S2 and M1 is driven by behaviour.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Jerry L -- Carta, Stefano -- Soldado-Magraner, Joana -- Schneider, Bernard L -- Helmchen, Fritjof -- England -- Nature. 2013 Jul 18;499(7458):336-40. doi: 10.1038/nature12236. Epub 2013 Jun 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Brain Research Institute, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23792559" target="_blank"〉PubMed〈/a〉
    Keywords: Afferent Pathways ; Animals ; Behavior, Animal ; Calcium/analysis ; Discrimination (Psychology)/*physiology ; Mice ; Neurons/chemistry/*physiology ; Somatosensory Cortex/cytology/*physiology ; Vibrissae/innervation
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 6
    Publication Date: 2013-09-06
    Description: The ability to design proteins with high affinity and selectivity for any given small molecule is a rigorous test of our understanding of the physiochemical principles that govern molecular recognition. Attempts to rationally design ligand-binding proteins have met with little success, however, and the computational design of protein-small-molecule interfaces remains an unsolved problem. Current approaches for designing ligand-binding proteins for medical and biotechnological uses rely on raising antibodies against a target antigen in immunized animals and/or performing laboratory-directed evolution of proteins with an existing low affinity for the desired ligand, neither of which allows complete control over the interactions involved in binding. Here we describe a general computational method for designing pre-organized and shape complementary small-molecule-binding sites, and use it to generate protein binders to the steroid digoxigenin (DIG). Of seventeen experimentally characterized designs, two bind DIG; the model of the higher affinity binder has the most energetically favourable and pre-organized interface in the design set. A comprehensive binding-fitness landscape of this design, generated by library selections and deep sequencing, was used to optimize its binding affinity to a picomolar level, and X-ray co-crystal structures of two variants show atomic-level agreement with the corresponding computational models. The optimized binder is selective for DIG over the related steroids digitoxigenin, progesterone and beta-oestradiol, and this steroid binding preference can be reprogrammed by manipulation of explicitly designed hydrogen-bonding interactions. The computational design method presented here should enable the development of a new generation of biosensors, therapeutics and diagnostics.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3898436/" 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/PMC3898436/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tinberg, Christine E -- Khare, Sagar D -- Dou, Jiayi -- Doyle, Lindsey -- Nelson, Jorgen W -- Schena, Alberto -- Jankowski, Wojciech -- Kalodimos, Charalampos G -- Johnsson, Kai -- Stoddard, Barry L -- Baker, David -- P41 GM103533/GM/NIGMS NIH HHS/ -- R01 GM049857/GM/NIGMS NIH HHS/ -- T32 HG000035/HG/NHGRI NIH HHS/ -- T32 HG00035/HG/NHGRI NIH HHS/ -- England -- Nature. 2013 Sep 12;501(7466):212-6. doi: 10.1038/nature12443. Epub 2013 Sep 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24005320" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Biotechnology ; *Computer Simulation ; Crystallography, X-Ray ; Digoxigenin/chemistry/*metabolism ; *Drug Design ; Estradiol/chemistry/metabolism ; Ligands ; Models, Molecular ; Progesterone/chemistry/metabolism ; Protein Binding ; Proteins/*chemistry/*metabolism ; Reproducibility of Results ; Substrate Specificity
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 2012-11-28
    Description: A remarkable feature of regenerative processes is their ability to halt proliferation once an organ's structure has been restored. The Wnt signalling pathway is the major driving force for homeostatic self-renewal and regeneration in the mammalian intestine. However, the mechanisms that counterbalance Wnt-driven proliferation are poorly understood. Here we demonstrate in mice and humans that yes-associated protein 1 (YAP; also known as YAP1)--a protein known for its powerful growth-inducing and oncogenic properties--has an unexpected growth-suppressive function, restricting Wnt signals during intestinal regeneration. Transgenic expression of YAP reduces Wnt target gene expression and results in the rapid loss of intestinal crypts. In addition, loss of YAP results in Wnt hypersensitivity during regeneration, leading to hyperplasia, expansion of intestinal stem cells and niche cells, and formation of ectopic crypts and microadenomas. We find that cytoplasmic YAP restricts elevated Wnt signalling independently of the AXIN-APC-GSK-3beta complex partly by limiting the activity of dishevelled (DVL). DVL signals in the nucleus of intestinal stem cells, and its forced expression leads to enhanced Wnt signalling in crypts. YAP dampens Wnt signals by restricting DVL nuclear translocation during regenerative growth. Finally, we provide evidence that YAP is silenced in a subset of highly aggressive and undifferentiated human colorectal carcinomas, and that its expression can restrict the growth of colorectal carcinoma xenografts. Collectively, our work describes a novel mechanistic paradigm for how proliferative signals are counterbalanced in regenerating tissues. Additionally, our findings have important implications for the targeting of YAP in human malignancies.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3536889/" 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/PMC3536889/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Barry, Evan R -- Morikawa, Teppei -- Butler, Brian L -- Shrestha, Kriti -- de la Rosa, Rosemarie -- Yan, Kelley S -- Fuchs, Charles S -- Magness, Scott T -- Smits, Ron -- Ogino, Shuji -- Kuo, Calvin J -- Camargo, Fernando D -- 1K08DK096048/DK/NIDDK NIH HHS/ -- 1U01DK085527/DK/NIDDK NIH HHS/ -- AR064036/AR/NIAMS NIH HHS/ -- K08 DK096048/DK/NIDDK NIH HHS/ -- P01CA87969/CA/NCI NIH HHS/ -- P30 DK049216/DK/NIDDK NIH HHS/ -- P50CA127003/CA/NCI NIH HHS/ -- R01 AR064036/AR/NIAMS NIH HHS/ -- R01 CA131426/CA/NCI NIH HHS/ -- R01 CA151993/CA/NCI NIH HHS/ -- R01 DK091427/DK/NIDDK NIH HHS/ -- U01 DK085527/DK/NIDDK NIH HHS/ -- England -- Nature. 2013 Jan 3;493(7430):106-10. doi: 10.1038/nature11693. Epub 2012 Nov 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Stem Cell Program and Department of Hematology/Oncology, Children's Hospital, Boston, Massachusetts 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23178811" target="_blank"〉PubMed〈/a〉
    Keywords: Active Transport, Cell Nucleus ; Adaptor Proteins, Signal Transducing/deficiency/genetics/*metabolism ; Animals ; *Cell Proliferation ; Colorectal Neoplasms/genetics/metabolism/pathology ; Genes, Tumor Suppressor ; Humans ; Intestines/*cytology/physiology ; Mice ; Mice, Knockout ; Neoplasm Transplantation ; Phosphoproteins/deficiency/genetics/*metabolism ; Regeneration/*physiology ; Stem Cell Niche ; Stem Cells/*cytology/*metabolism ; Thrombospondins/genetics/metabolism ; Tumor Suppressor Proteins/genetics/metabolism ; Wnt Proteins/metabolism ; Wnt Signaling Pathway
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 8
    Publication Date: 2013-09-03
    Description: Topoisomerases are expressed throughout the developing and adult brain and are mutated in some individuals with autism spectrum disorder (ASD). However, how topoisomerases are mechanistically connected to ASD is unknown. Here we find that topotecan, a topoisomerase 1 (TOP1) inhibitor, dose-dependently reduces the expression of extremely long genes in mouse and human neurons, including nearly all genes that are longer than 200 kilobases. Expression of long genes is also reduced after knockdown of Top1 or Top2b in neurons, highlighting that both enzymes are required for full expression of long genes. By mapping RNA polymerase II density genome-wide in neurons, we found that this length-dependent effect on gene expression was due to impaired transcription elongation. Interestingly, many high-confidence ASD candidate genes are exceptionally long and were reduced in expression after TOP1 inhibition. Our findings suggest that chemicals and genetic mutations that impair topoisomerases could commonly contribute to ASD and other neurodevelopmental disorders.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3767287/" 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/PMC3767287/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉King, Ian F -- Yandava, Chandri N -- Mabb, Angela M -- Hsiao, Jack S -- Huang, Hsien-Sung -- Pearson, Brandon L -- Calabrese, J Mauro -- Starmer, Joshua -- Parker, Joel S -- Magnuson, Terry -- Chamberlain, Stormy J -- Philpot, Benjamin D -- Zylka, Mark J -- P30 NS045892/NS/NINDS NIH HHS/ -- P30HD03110/HD/NICHD NIH HHS/ -- P30NS045892/NS/NINDS NIH HHS/ -- R01 GM101974/GM/NIGMS NIH HHS/ -- R01 HD068730/HD/NICHD NIH HHS/ -- R01 MH093372/MH/NIMH NIH HHS/ -- R01GM101974/GM/NIGMS NIH HHS/ -- R01HD068730/HD/NICHD NIH HHS/ -- R01MH093372/MH/NIMH NIH HHS/ -- T32 HD040127/HD/NICHD NIH HHS/ -- T32HD040127/HD/NICHD NIH HHS/ -- England -- Nature. 2013 Sep 5;501(7465):58-62. doi: 10.1038/nature12504. Epub 2013 Aug 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23995680" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Autistic Disorder/*genetics ; DNA Topoisomerases, Type I/deficiency/*metabolism ; DNA Topoisomerases, Type II/deficiency/metabolism ; DNA-Binding Proteins/antagonists & inhibitors/deficiency/metabolism ; Gene Knockdown Techniques ; Genomic Imprinting/genetics ; Humans ; Mice ; Mutation/genetics ; RNA Polymerase II/metabolism ; Synapses/metabolism ; Topoisomerase Inhibitors/pharmacology ; Topotecan/pharmacology ; *Transcription Elongation, Genetic/drug effects
    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: 2014-06-27
    Description: Varying levels of boreal summer insolation and associated Earth system feedbacks led to differing climate and ice-sheet states during late-Quaternary interglaciations. In particular, Marine Isotope Stage (MIS) 11 was an exceptionally long interglaciation and potentially had a global mean sea level 6 to 13 metres above the present level around 410,000 to 400,000 years ago, implying substantial mass loss from the Greenland ice sheet (GIS). There are, however, no model simulations and only limited proxy data to constrain the magnitude of the GIS response to climate change during this 'super interglacial', thus confounding efforts to assess climate/ice-sheet threshold behaviour and associated sea-level rise. Here we show that the south GIS was drastically smaller during MIS 11 than it is now, with only a small residual ice dome over southernmost Greenland. We use the strontium-neodymium-lead isotopic composition of proglacial sediment discharged from south Greenland to constrain the provenance of terrigenous silt deposited on the Eirik Drift, a sedimentary deposit off the south Greenland margin. We identify a major reduction in sediment input derived from south Greenland's Precambrian bedrock terranes, probably reflecting the cessation of subglacial erosion and sediment transport as a result of near-complete deglaciation of south Greenland. Comparison with ice-sheet configurations from numerical models suggests that the GIS lost about 4.5 to 6 metres of sea-level-equivalent volume during MIS 11. This is evidence for late-Quaternary GIS collapse after it crossed a climate/ice-sheet stability threshold that may have been no more than several degrees above pre-industrial temperatures.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reyes, Alberto V -- Carlson, Anders E -- Beard, Brian L -- Hatfield, Robert G -- Stoner, Joseph S -- Winsor, Kelsey -- Welke, Bethany -- Ullman, David J -- England -- Nature. 2014 Jun 26;510(7506):525-8. doi: 10.1038/nature13456.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Department of Geoscience, University of Wisconsin-Madison, 1215 West Dayton Street, Madison, Wisconsin 53706, USA [2] School of Geography, Archaeology and Palaeoecology, Queen's University Belfast, Elmwood Avenue, Belfast BT7 1NN, UK [3] Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Alberta T6G 2E3, Canada (A.V.R); Department of Geosciences, University of Arizona, 1040 East 4th Street, Tucson, Arizona 85721, USA (B.W.). ; 1] Department of Geoscience, University of Wisconsin-Madison, 1215 West Dayton Street, Madison, Wisconsin 53706, USA [2] College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, 104 CEOAS Administration Building, Corvallis, Oregon 97331, USA. ; Department of Geoscience, University of Wisconsin-Madison, 1215 West Dayton Street, Madison, Wisconsin 53706, USA. ; College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, 104 CEOAS Administration Building, Corvallis, Oregon 97331, USA. ; 1] Department of Geoscience, University of Wisconsin-Madison, 1215 West Dayton Street, Madison, Wisconsin 53706, USA [2] Department of Earth and Atmospheric Sciences, University of Alberta, Edmonton, Alberta T6G 2E3, Canada (A.V.R); Department of Geosciences, University of Arizona, 1040 East 4th Street, Tucson, Arizona 85721, USA (B.W.).〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24965655" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 10
    Publication Date: 2014-01-10
    Description: Soil contains more carbon than the atmosphere and vegetation combined. Understanding the mechanisms controlling the accumulation and stability of soil carbon is critical to predicting the Earth's future climate. Recent studies suggest that decomposition of soil organic matter is often limited by nitrogen availability to microbes and that plants, via their fungal symbionts, compete directly with free-living decomposers for nitrogen. Ectomycorrhizal and ericoid mycorrhizal (EEM) fungi produce nitrogen-degrading enzymes, allowing them greater access to organic nitrogen sources than arbuscular mycorrhizal (AM) fungi. This leads to the theoretical prediction that soil carbon storage is greater in ecosystems dominated by EEM fungi than in those dominated by AM fungi. Using global data sets, we show that soil in ecosystems dominated by EEM-associated plants contains 70% more carbon per unit nitrogen than soil in ecosystems dominated by AM-associated plants. The effect of mycorrhizal type on soil carbon is independent of, and of far larger consequence than, the effects of net primary production, temperature, precipitation and soil clay content. Hence the effect of mycorrhizal type on soil carbon content holds at the global scale. This finding links the functional traits of mycorrhizal fungi to carbon storage at ecosystem-to-global scales, suggesting that plant-decomposer competition for nutrients exerts a fundamental control over the terrestrial carbon cycle.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Averill, Colin -- Turner, Benjamin L -- Finzi, Adrien C -- England -- Nature. 2014 Jan 23;505(7484):543-5. doi: 10.1038/nature12901. Epub 2014 Jan 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Integrative Biology, Graduate Program in Ecology, Evolution and Behavior, University of Texas at Austin, Austin, Texas 78712, USA. ; Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Republic of Panama. ; Department of Biology, Boston University, Boston, Masachusetts 02215, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24402225" target="_blank"〉PubMed〈/a〉
    Keywords: Aluminum Silicates/analysis ; Biota/genetics ; Carbon/analysis/*metabolism ; *Carbon Cycle ; *Ecosystem ; Mycorrhizae/classification/enzymology/*metabolism ; Nitrogen/analysis/metabolism ; Plants/*metabolism/*microbiology ; Soil/*chemistry ; Soil Microbiology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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