ALBERT

Description: The 2008 Mw 7.9 Wenchuan earthquake occurred along the middle and northern segments of the Longmen Shan fault zone at the eastern margin of the Tibetan Plateau. Five years later, the 2013 Mw 6.6 Lushan earthquake ruptured a section of the southern segment of the Longmen Shan fault zone, leaving a 50-km-long seismic gap between the seismogenic structures of the two earthquakes. In our study, we use trenching and calibrated radiocarbon age models to assess the rupture behavior of the gap over multiple earthquakes. At least two paleoseismic events were identified with age constraints between A.D. 1350–1830 and 525–760 B.C., respectively. Trench stratigraphy suggests the presence of another possible event with an age constraint of A.D. 590–1210. Using cumulative vertical displacement of ~1.5 m for the lowest unit exposed in the trench (U1) and its age of ca. 2500 yr B.P., we estimate the vertical slip rate of the Dachuan-Shuangshi fault, the primary fault along the southern segment, to be ~0.6 mm/yr. The lack of correlation of events between multiple paleoseismic sites along the Dachuan-Shuangshi fault suggests that the seismic gap has a low possibility of rupturing completely during paleoearthquakes. A comparison of the rupture behavior of the southern segment with the middle segment of the Longmen Shan fault zone indicates that the likelihood of cascading ruptures between the two segments is low.

Description: Inhibition of human mitochondrial peptide deformylase causes apoptosis in c-myc-overexpressing hematopoietic cancers Cell Death and Disease 5, e1152 (March 2014). doi:10.1038/cddis.2014.112 Authors: A Sheth, S Escobar-Alvarez, J Gardner, L Ran, M L Heaney & D A Scheinberg

Description: Activation of oncogenes by mechanisms other than genetic aberrations such as mutations, translocations, or amplifications is largely undefined. Here we report a novel isoform of the anaplastic lymphoma kinase (ALK) that is expressed in approximately 11% of melanomas and sporadically in other human cancer types, but not in normal tissues. The novel ALK transcript initiates from a de novo alternative transcription initiation (ATI) site in ALK intron 19, and was termed ALK(ATI). In ALK(ATI)-expressing tumours, the ATI site is enriched for H3K4me3 and RNA polymerase II, chromatin marks characteristic of active transcription initiation sites. ALK(ATI) is expressed from both ALK alleles, and no recurrent genetic aberrations are found at the ALK locus, indicating that the transcriptional activation is independent of genetic aberrations at the ALK locus. The ALK(ATI) transcript encodes three proteins with molecular weights of 61.1, 60.8 and 58.7 kilodaltons, consisting primarily of the intracellular tyrosine kinase domain. ALK(ATI) stimulates multiple oncogenic signalling pathways, drives growth-factor-independent cell proliferation in vitro, and promotes tumorigenesis in vivo in mouse models. ALK inhibitors can suppress the kinase activity of ALK(ATI), suggesting that patients with ALK(ATI)-expressing tumours may benefit from ALK inhibitors. Our findings suggest a novel mechanism of oncogene activation in cancer through de novo alternative transcription initiation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wiesner, Thomas -- Lee, William -- Obenauf, Anna C -- Ran, Leili -- Murali, Rajmohan -- Zhang, Qi Fan -- Wong, Elissa W P -- Hu, Wenhuo -- Scott, Sasinya N -- Shah, Ronak H -- Landa, Inigo -- Button, Julia -- Lailler, Nathalie -- Sboner, Andrea -- Gao, Dong -- Murphy, Devan A -- Cao, Zhen -- Shukla, Shipra -- Hollmann, Travis J -- Wang, Lu -- Borsu, Laetitia -- Merghoub, Taha -- Schwartz, Gary K -- Postow, Michael A -- Ariyan, Charlotte E -- Fagin, James A -- Zheng, Deyou -- Ladanyi, Marc -- Busam, Klaus J -- Berger, Michael F -- Chen, Yu -- Chi, Ping -- DP2 CA174499/CA/NCI NIH HHS/ -- DP2CA174499/CA/NCI NIH HHS/ -- K08 CA151660/CA/NCI NIH HHS/ -- K08CA140946/CA/NCI NIH HHS/ -- K08CA151660/CA/NCI NIH HHS/ -- P01 CA129243/CA/NCI NIH HHS/ -- P01CA12943/CA/NCI NIH HHS/ -- P30 CA008748/CA/NCI NIH HHS/ -- P50 CA172012/CA/NCI NIH HHS/ -- P50CA172012/CA/NCI NIH HHS/ -- England -- Nature. 2015 Oct 15;526(7573):453-7. doi: 10.1038/nature15258. Epub 2015 Oct 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York 10065, USA. ; Department of Dermatology, Medical University of Graz, 8010 Graz, Austria. ; Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York 10065, USA. ; Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York 10065, USA. ; Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York 10065, USA. ; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York 10065, USA. ; Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York 10065, USA. ; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College/New York Presbyterian Hospital, New York 10065, USA. ; Institute for Computational Biomedicine, Weill Cornell Medical College/New York Presbyterian Hospital, New York 10065, USA. ; Institute for Precision Medicine, Weill Cornell Medical College/New York Presbyterian Hospital, New York, USA. ; Immunology Program, Memorial Sloan Kettering Cancer Center 10065, New York, USA. ; Herbert Irving Comprehensive Cancer Center, Columbia University Cancer Center, New York 10032, USA. ; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York 10065, USA. ; Department of Medicine, Weill Cornell Medical College, New York 10065, USA. ; Department of Surgery, Memorial Sloan Kettering Cancer Center, New York 10065, USA. ; Department of Neurology, Albert Einstein College of Medicine, New York 10461, USA. ; Department of Genetics, Albert Einstein College of Medicine, New York 10461, USA. ; Department of Neuroscience, Albert Einstein College of Medicine, New York 10461, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26444240" target="_blank"〉PubMed〈/a〉

Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ran, Lishan -- Lu, X X -- England -- Nature. 2011 May 26;473(7348):452. doi: 10.1038/473452c.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21614065" target="_blank"〉PubMed〈/a〉

Description: Protein acetylation emerged as a key regulatory mechanism for many cellular processes. We used genetic analysis of Saccharomyces cerevisiae to identify Esa1 as a histone acetyltransferase required for autophagy. We further identified the autophagy signaling component Atg3 as a substrate for Esa1. Specifically, acetylation of K19 and K48 of Atg3 regulated autophagy by controlling Atg3 and Atg8 interaction and lipidation of Atg8. Starvation induced transient K19-K48 acetylation through spatial and temporal regulation of the localization of acetylase Esa1 and the deacetylase Rpd3 on pre-autophagosomal structures (PASs) and their interaction with Atg3. Attenuation of K19-K48 acetylation was associated with attenuation of autophagy. Increased K19-K48 acetylation after deletion of the deacetylase Rpd3 caused increased autophagy. Thus, protein acetylation contributes to control of autophagy.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yi, Cong -- Ma, Meisheng -- Ran, Leili -- Zheng, Jingxiang -- Tong, Jingjing -- Zhu, Jing -- Ma, Chengying -- Sun, Yufen -- Zhang, Shaojin -- Feng, Wenzhi -- Zhu, Liyuan -- Le, Yan -- Gong, Xingqi -- Yan, Xianghua -- Hong, Bing -- Jiang, Fen-Jun -- Xie, Zhiping -- Miao, Di -- Deng, Haiteng -- Yu, Li -- New York, N.Y. -- Science. 2012 Apr 27;336(6080):474-7. doi: 10.1126/science.1216990.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉State Key Laboratory of Biomembrane and Membrane Biotechnology, School of Life Sciences, Tsinghua University, Beijing, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22539722" target="_blank"〉PubMed〈/a〉

Description: The massless solutions to the Dirac equation are described by the so-called Weyl Hamiltonian. The Weyl equation requires a particle to have linear dispersion in all three dimensions while being doubly degenerate at a single momentum point. These Weyl points are topological monopoles of quantized Berry flux exhibiting numerous unusual properties. We performed angle-resolved microwave transmission measurements through a double-gyroid photonic crystal with inversion-breaking where Weyl points have been theoretically predicted to occur. The excited bulk states show two linear dispersion bands touching at four isolated points in the three-dimensional Brillouin zone, indicating the observation of Weyl points. This work paves the way to a variety of photonic topological phenomena in three dimensions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lu, Ling -- Wang, Zhiyu -- Ye, Dexin -- Ran, Lixin -- Fu, Liang -- Joannopoulos, John D -- Soljacic, Marin -- New York, N.Y. -- Science. 2015 Aug 7;349(6248):622-4. doi: 10.1126/science.aaa9273. Epub 2015 Jul 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA. linglu@mit.edu. ; Laboratory of Applied Research on Electromagnetics (ARE), Zhejiang University, Hangzhou, Zhejiang 310027, China. ; Department of Physics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26184914" target="_blank"〉PubMed〈/a〉

Description: Several types of pediatric cancers reportedly contain high-frequency missense mutations in histone H3, yet the underlying oncogenic mechanism remains poorly characterized. Here we report that the H3 lysine 36-to-methionine (H3K36M) mutation impairs the differentiation of mesenchymal progenitor cells and generates undifferentiated sarcoma in vivo. H3K36M mutant nucleosomes inhibit the enzymatic activities of several H3K36 methyltransferases. Depleting H3K36 methyltransferases, or expressing an H3K36I mutant that similarly inhibits H3K36 methylation, is sufficient to phenocopy the H3K36M mutation. After the loss of H3K36 methylation, a genome-wide gain in H3K27 methylation leads to a redistribution of polycomb repressive complex 1 and de-repression of its target genes known to block mesenchymal differentiation. Our findings are mirrored in human undifferentiated sarcomas in which novel K36M/I mutations in H3.1 are identified.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lu, Chao -- Jain, Siddhant U -- Hoelper, Dominik -- Bechet, Denise -- Molden, Rosalynn C -- Ran, Leili -- Murphy, Devan -- Venneti, Sriram -- Hameed, Meera -- Pawel, Bruce R -- Wunder, Jay S -- Dickson, Brendan C -- Lundgren, Stefan M -- Jani, Krupa S -- De Jay, Nicolas -- Papillon-Cavanagh, Simon -- Andrulis, Irene L -- Sawyer, Sarah L -- Grynspan, David -- Turcotte, Robert E -- Nadaf, Javad -- Fahiminiyah, Somayyeh -- Muir, Tom W -- Majewski, Jacek -- Thompson, Craig B -- Chi, Ping -- Garcia, Benjamin A -- Allis, C David -- Jabado, Nada -- Lewis, Peter W -- DP2CA174499/CA/NCI NIH HHS/ -- DP2OD007447/OD/NIH HHS/ -- K08CA151660/CA/NCI NIH HHS/ -- K08CA181475/CA/NCI NIH HHS/ -- P01CA196539/CA/NCI NIH HHS/ -- P30CA008748/CA/NCI NIH HHS/ -- R01GM110174/GM/NIGMS NIH HHS/ -- Canadian Institutes of Health Research/Canada -- New York, N.Y. -- Science. 2016 May 13;352(6287):844-9. doi: 10.1126/science.aac7272.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA. ; Epigenetics Theme, Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI 53715, USA. Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53715, USA. ; Department of Human Genetics, McGill University, Montreal, Quebec H3Z 2Z3, Canada. ; Epigenetics Program and Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA. Department of Chemistry, Princeton University, Princeton, NJ 08544, USA. ; Human Oncology and Pathogenesis Program and Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. ; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA. ; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. ; Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA. ; University Musculoskeletal Oncology Unit, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada. Department of Surgical Oncology and Division of Orthopedic Surgery, Princess Margaret Hospital, University of Toronto, Toronto, Ontario M5T 2M9, Canada. ; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada. Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada. ; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA. ; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada. Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada. Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada. The Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario M5G 1X5, Canada. ; Department of Medical Genetics and Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada. ; Division of Orthopaedic Surgery, Montreal General Hospital, McGill University Health Centre, Montreal, Quebec H3G 1A4, Canada. ; Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. ; Human Oncology and Pathogenesis Program and Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA. ; Epigenetics Program and Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA. ; Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA. plewis@discovery.wisc.edu nada.jabado@mcgill.ca alliscd@rockefeller.edu. ; Department of Human Genetics, McGill University, Montreal, Quebec H3Z 2Z3, Canada. Department of Pediatrics, McGill University, Montreal, Quebec H3Z 2Z3, Canada. plewis@discovery.wisc.edu nada.jabado@mcgill.ca alliscd@rockefeller.edu. ; Epigenetics Theme, Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI 53715, USA. Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53715, USA. plewis@discovery.wisc.edu nada.jabado@mcgill.ca alliscd@rockefeller.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/27174990" target="_blank"〉PubMed〈/a〉

Description: A new windblown dust emission treatment was incorporated in the Community Multiscale Air Quality (CMAQ) modeling system. This new model treatment has been built upon previously developed physics-based parameterization schemes from the literature. A distinct and novel feature of this scheme, however, is the incorporation of a newly developed dynamic relation for the surface roughness length relevant to small-scale dust generation processes. Through this implementation, the effect of non-erodible elements on the local flow acceleration, drag partitioning, and surface coverage protection is modeled in a physically based and consistent manner. Careful attention is paid in integrating the new windblown dust treatment in the CMAQ model to ensure that the required input parameters are correctly configured. To test the performance of the new dust module in CMAQ, the entire year 2011 is simulated for the continental United States, with particular emphasis on the southwestern United States (SWUS) where windblown dust concentrations are relatively large. Overall, the model shows good performance with the daily mean bias of soil concentrations fluctuating in the range of ±1 µgm −3 for the entire year. Springtime soil concentrations are in quite good agreement (normalized mean bias of 8.3%) with observations, while moderate to high underestimation of soil concentration is seen in the summertime. The latter is attributed to the issue of representing the convective dust storms in summertime. Evaluations against observations for seven elevated dust events in the SWUS indicate that the new windblown dust treatment is capable of capturing spatial and temporal characteristics of dust outbreaks. This article is protected by copyright. All rights reserved.

Description: The element silicon (Si) is required for the growth of silicified organisms in marine environments, such as diatoms. These organisms consume vast amounts of Si together with N, P, and C, connecting the biogeochemical cycles of these elements. Thus, understanding the Si cycle in the ocean is critical for understanding wider issues such as carbon sequestration by the ocean's biological pump. In this review, we show that recent advances in process studies indicate that total Si inputs and outputs, to and from the world ocean, are 57 % and 37 % higher, respectively, than previous estimates. We also update the total ocean silicic acid inventory value, which is about 24 % higher than previously estimated. These changes are significant, modifying factors such as the geochemical residence time of Si, which is now about 8000 years, 2 times faster than previously assumed. In addition, we present an updated value of the global annual pelagic biogenic silica production (255 Tmol Si yr−1) based on new data from 49 field studies and 18 model outputs, and we provide a first estimate of the global annual benthic biogenic silica production due to sponges (6 Tmol Si yr−1). Given these important modifications, we hypothesize that the modern ocean Si cycle is at approximately steady state with inputs =14.8(±2.6) Tmol Si yr−1 and outputs =15.6(±2.4) Tmol Si yr−1. Potential impacts of global change on the marine Si cycle are discussed.