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  • 1
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    ter Steege, H., Pitman, N. C. A., Killeen, T. J., Laurance, W. F., Peres, C. A., Guevara, J. E., Salomao, R. P., Castilho, C. V., Amaral, I. L., de Almeida Matos, F. D., de Souza Coelho, L., Magnusson, W. E., Phillips, O. L., de Andrade Lima Filho, D., de Jesus Veiga Carim, M., Irume, M. V., Martins, M. P., Molino, J.-F., Sabatier, D., Wittmann, F., Lopez, D. C., da Silva Guimaraes, J. R., Mendoza, A. M., Vargas, P. N., Manzatto, A. G., Reis, N. F. C., Terborgh, J., Casula, K. R., Montero, J. C., Feldpausch, T. R., Honorio Coronado, E. N., Montoya, A. J. D., Zartman, C. E., Mostacedo, B., Vasquez, R., Assis, R. L., Medeiros, M. B., Simon, M. F., Andrade, A., Camargo, J. L., Laurance, S. G. W., Nascimento, H. E. M., Marimon, B. S., Marimon, B.-H., Costa, F., Targhetta, N., Vieira, I. C. G., Brienen, R., Castellanos, H., Duivenvoorden, J. F., Mogollon, H. F., Piedade, M. T. F., Aymard C., G. A., Comiskey, J. A., Damasco, G., Davila, N., Garcia-Villacorta, R., Diaz, P. R. S., Vincentini, A., Emilio, T., Levis, C., Schietti, J., Souza, P., Alonso, A., Dallmeier, F., Ferreira, L. V., Neill, D., Araujo-Murakami, A., Arroyo, L., Carvalho, F. A., Souza, F. C., Amaral, D. D. d., Gribel, R., Luize, B. G., Pansonato, M. P., Venticinque, E., Fine, P., Toledo, M., Baraloto, C., Ceron, C., Engel, J., Henkel, T. W., Jimenez, E. M., Maas, P., Mora, M. C. P., Petronelli, P., Revilla, J. D. C., Silveira, M., Stropp, J., Thomas-Caesar, R., Baker, T. R., Daly, D., Paredes, M. R., da Silva, N. F., Fuentes, A., Jorgensen, P. M., Schöngart, J., Silman, M. R., Arboleda, N. C., Cintra, B. B. L., Valverde, F. C., Di Fiore, A., Phillips, J. F., van Andel, T. R., von Hildebrand, P., Barbosa, E. M., de Matos Bonates, L. C., de Castro, D., de Sousa Farias, E., Gonzales, T., Guillaumet, J.-L., Hoffman, B., Malhi, Y., de Andrade Miranda, I. P., Prieto, A., Rudas, A., Ruschell, A. R., Silva, N., Vela, C. I. A., Vos, V. A., Zent, E. L., Zent, S., Cano, A., Nascimento, M. T., Oliveira, A. A., Ramirez-Angulo, H., Ramos, J. F., Sierra, R., Tirado, M., Medina, M. N. U., van der Heijden, G., Torre, E. V., Vriesendorp, C., Wang, O., Young, K. R., Baider, C., Balslev, H., de Castro, N., Farfan-Rios, W., Ferreira, C., Mendoza, C., Mesones, I., Torres-Lezama, A., Giraldo, L. E. U., Villarroel, D., Zagt, R., Alexiades, M. N., Garcia-Cabrera, K., Hernandez, L., Huamantupa-Chuquimaco, I., Milliken, W., Cuenca, W. P., Pansini, S., Pauletto, D., Arevalo, F. R., Sampaio, A. F., Valderrama Sandoval, E. H., Gamarra, L. V.
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2015-11-22
    Description: Estimates of extinction risk for Amazonian plant and animal species are rare and not often incorporated into land-use policy and conservation planning. We overlay spatial distribution models with historical and projected deforestation to show that at least 36% and up to 57% of all Amazonian tree species are likely to qualify as globally threatened under International Union for Conservation of Nature (IUCN) Red List criteria. If confirmed, these results would increase the number of threatened plant species on Earth by 22%. We show that the trends observed in Amazonia apply to trees throughout the tropics, and we predict that most of the world’s 〉40,000 tropical tree species now qualify as globally threatened. A gap analysis suggests that existing Amazonian protected areas and indigenous territories will protect viable populations of most threatened species if these areas suffer no further degradation, highlighting the key roles that protected areas, indigenous peoples, and improved governance can play in preventing large-scale extinctions in the tropics in this century.
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
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  • 2
    Publication Date: 2015-10-31
    Description: Observations from the Gravity Recovery and Interior Laboratory (GRAIL) mission indicate a marked change in the gravitational signature of lunar impact structures at the morphological transition, with increasing diameter, from complex craters to peak-ring basins. At crater diameters larger than ~200 km, a central positive Bouguer anomaly is seen within the innermost peak ring, and an annular negative Bouguer anomaly extends outward from this ring to the outer topographic rim crest. These observations demonstrate that basin-forming impacts remove crustal materials from within the peak ring and thicken the crust between the peak ring and the outer rim crest. A correlation between the diameter of the central Bouguer gravity high and the outer topographic ring diameter for well-preserved basins enables the identification and characterization of basins for which topographic signatures have been obscured by superposed cratering and volcanism. The GRAIL inventory of lunar basins improves upon earlier lists that differed in their totals by more than a factor of 2. The size-frequency distributions of basins on the nearside and farside hemispheres of the Moon differ substantially; the nearside hosts more basins larger than 350 km in diameter, whereas the farside has more smaller basins. Hemispherical differences in target properties, including temperature and porosity, are likely to have contributed to these different distributions. Better understanding of the factors that control basin size will help to constrain models of the original impactor population.
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
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  • 3
    Publication Date: 2015-11-07
    Description: The Mars Atmosphere and Volatile Evolution (MAVEN) mission, during the second of its Deep Dip campaigns, made comprehensive measurements of martian thermosphere and ionosphere composition, structure, and variability at altitudes down to ~130 kilometers in the subsolar region. This altitude range contains the diffusively separated upper atmosphere just above the well-mixed atmosphere, the layer of peak extreme ultraviolet heating and primary reservoir for atmospheric escape. In situ measurements of the upper atmosphere reveal previously unmeasured populations of neutral and charged particles, the homopause altitude at approximately 130 kilometers, and an unexpected level of variability both on an orbit-to-orbit basis and within individual orbits. These observations help constrain volatile escape processes controlled by thermosphere and ionosphere structure and variability.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bougher, S -- Jakosky, B -- Halekas, J -- Grebowsky, J -- Luhmann, J -- Mahaffy, P -- Connerney, J -- Eparvier, F -- Ergun, R -- Larson, D -- McFadden, J -- Mitchell, D -- Schneider, N -- Zurek, R -- Mazelle, C -- Andersson, L -- Andrews, D -- Baird, D -- Baker, D N -- Bell, J M -- Benna, M -- Brain, D -- Chaffin, M -- Chamberlin, P -- Chaufray, J-Y -- Clarke, J -- Collinson, G -- Combi, M -- Crary, F -- Cravens, T -- Crismani, M -- Curry, S -- Curtis, D -- Deighan, J -- Delory, G -- Dewey, R -- DiBraccio, G -- Dong, C -- Dong, Y -- Dunn, P -- Elrod, M -- England, S -- Eriksson, A -- Espley, J -- Evans, S -- Fang, X -- Fillingim, M -- Fortier, K -- Fowler, C M -- Fox, J -- Groller, H -- Guzewich, S -- Hara, T -- Harada, Y -- Holsclaw, G -- Jain, S K -- Jolitz, R -- Leblanc, F -- Lee, C O -- Lee, Y -- Lefevre, F -- Lillis, R -- Livi, R -- Lo, D -- Ma, Y -- Mayyasi, M -- McClintock, W -- McEnulty, T -- Modolo, R -- Montmessin, F -- Morooka, M -- Nagy, A -- Olsen, K -- Peterson, W -- Rahmati, A -- Ruhunusiri, S -- Russell, C T -- Sakai, S -- Sauvaud, J-A -- Seki, K -- Steckiewicz, M -- Stevens, M -- Stewart, A I F -- Stiepen, A -- Stone, S -- Tenishev, V -- Thiemann, E -- Tolson, R -- Toublanc, D -- Vogt, M -- Weber, T -- Withers, P -- Woods, T -- Yelle, R -- New York, N.Y. -- Science. 2015 Nov 6;350(6261):aad0459. doi: 10.1126/science.aad0459.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉CLaSP Department, University of Michigan, Ann Arbor, MI, USA. bougher@umich.edu. ; Laboratory for Atmospheric and Space Physics, University. of Colorado, Boulder, CO, USA. ; Department of Physics and Astronomy, University of Iowa, Iowa City, IA, USA. ; NASA/Goddard Space Flight Center, Greenbelt, MD, USA. ; Space Sciences Laboratory, University of California at Berkeley, Berkeley, CA, USA. ; Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA. ; CNRS/Institut de Recherche en Astrophysique et Planetologie, Toulouse, France. University Paul Sabatier, Toulouse, France. ; Swedish Institute of Space Physics, Kiruna, Sweden. ; NASA/Johnson Space Center, Houston, TX, USA. ; National Institute of Aerospace, Hampton, VA, USA. ; Laboratoire Atmospheres, Milieux, Observations Spatiales /CNRS, Verrieres-le-Buisson, France. ; Department of Astronomy, Boston University, Boston, MA, USA. ; CLaSP Department, University of Michigan, Ann Arbor, MI, USA. ; Department of Physics and Astronomy, University of Kansas, Lawrence, KS, USA. ; Computational Physics, Springfield, VA, USA. ; Department of Physics, Wright State University, Fairborn, OH, USA. ; Lunar and Planetary Laboratory, University of Arizona, Tucson, AZ, USA. ; Institute of Geophysics and Planetary Physics, University of California, Los Angeles, Los Angeles, CA, USA. ; Solar-Terrestrial Environment Laboratory, Nagoya University, Nagoya, Aichi, Japan. ; Naval Research Laboratory, Washington, DC, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26542579" target="_blank"〉PubMed〈/a〉
    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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  • 4
    Publication Date: 2015-01-31
    Description: The mechanistic basis of eukaryotic circadian oscillators in model systems as diverse as Neurospora, Drosophila, and mammalian cells is thought to be a transcription-and-translation-based negative feedback loop, wherein progressive and controlled phosphorylation of one or more negative elements ultimately elicits their own proteasome-mediated degradation, thereby releasing negative feedback and determining circadian period length. The Neurospora crassa circadian negative element FREQUENCY (FRQ) exemplifies such proteins; it is progressively phosphorylated at more than 100 sites, and strains bearing alleles of frq with anomalous phosphorylation display abnormal stability of FRQ that is well correlated with altered periods or apparent arrhythmicity. Unexpectedly, we unveiled normal circadian oscillations that reflect the allelic state of frq but that persist in the absence of typical degradation of FRQ. This manifest uncoupling of negative element turnover from circadian period length determination is not consistent with the consensus eukaryotic circadian model.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4432837/" 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/PMC4432837/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Larrondo, Luis F -- Olivares-Yanez, Consuelo -- Baker, Christopher L -- Loros, Jennifer J -- Dunlap, Jay C -- P01 GM68087/GM/NIGMS NIH HHS/ -- R01 GM034985/GM/NIGMS NIH HHS/ -- R01 GM083336/GM/NIGMS NIH HHS/ -- R01 GM34985/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2015 Jan 30;347(6221):1257277. doi: 10.1126/science.1257277.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Millennium Nucleus for Fungal Integrative and Synthetic Biology, Departamento de Genetica Molecular y Microbiologia, Facultad de Ciencias Biologicas, Pontificia Universidad Catolica de Chile, Casilla 114-D, Santiago, Chile. Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA. jay.c.dunlap@dartmouth.edu llarrondo@bio.puc.cl. ; Millennium Nucleus for Fungal Integrative and Synthetic Biology, Departamento de Genetica Molecular y Microbiologia, Facultad de Ciencias Biologicas, Pontificia Universidad Catolica de Chile, Casilla 114-D, Santiago, Chile. ; Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA. ; Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA. Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA. ; Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA. jay.c.dunlap@dartmouth.edu llarrondo@bio.puc.cl.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25635104" target="_blank"〉PubMed〈/a〉
    Keywords: Adenine/analogs & derivatives/pharmacology ; Alleles ; *Circadian Clocks ; *Circadian Rhythm ; Feedback, Physiological ; Fungal Proteins/biosynthesis/*genetics/*metabolism ; Half-Life ; Neurospora crassa/*physiology ; Phosphorylation ; Proteasome Endopeptidase Complex/metabolism ; Protein Kinase Inhibitors/pharmacology ; Protein Stability ; Proteolysis ; Signal Transduction
    Print ISSN: 0036-8075
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  • 5
    Publication Date: 2015-11-07
    Description: Coupling between the lower and upper atmosphere, combined with loss of gas from the upper atmosphere to space, likely contributed to the thin, cold, dry atmosphere of modern Mars. To help understand ongoing ion loss to space, the Mars Atmosphere and Volatile Evolution (MAVEN) spacecraft made comprehensive measurements of the Mars upper atmosphere, ionosphere, and interactions with the Sun and solar wind during an interplanetary coronal mass ejection impact in March 2015. Responses include changes in the bow shock and magnetosheath, formation of widespread diffuse aurora, and enhancement of pick-up ions. Observations and models both show an enhancement in escape rate of ions to space during the event. Ion loss during solar events early in Mars history may have been a major contributor to the long-term evolution of the Mars atmosphere.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jakosky, B M -- Grebowsky, J M -- Luhmann, J G -- Connerney, J -- Eparvier, F -- Ergun, R -- Halekas, J -- Larson, D -- Mahaffy, P -- McFadden, J -- Mitchell, D F -- Schneider, N -- Zurek, R -- Bougher, S -- Brain, D -- Ma, Y J -- Mazelle, C -- Andersson, L -- Andrews, D -- Baird, D -- Baker, D -- Bell, J M -- Benna, M -- Chaffin, M -- Chamberlin, P -- Chaufray, Y-Y -- Clarke, J -- Collinson, G -- Combi, M -- Crary, F -- Cravens, T -- Crismani, M -- Curry, S -- Curtis, D -- Deighan, J -- Delory, G -- Dewey, R -- DiBraccio, G -- Dong, C -- Dong, Y -- Dunn, P -- Elrod, M -- England, S -- Eriksson, A -- Espley, J -- Evans, S -- Fang, X -- Fillingim, M -- Fortier, K -- Fowler, C M -- Fox, J -- Groller, H -- Guzewich, S -- Hara, T -- Harada, Y -- Holsclaw, G -- Jain, S K -- Jolitz, R -- Leblanc, F -- Lee, C O -- Lee, Y -- Lefevre, F -- Lillis, R -- Livi, R -- Lo, D -- Mayyasi, M -- McClintock, W -- McEnulty, T -- Modolo, R -- Montmessin, F -- Morooka, M -- Nagy, A -- Olsen, K -- Peterson, W -- Rahmati, A -- Ruhunusiri, S -- Russell, C T -- Sakai, S -- Sauvaud, J-A -- Seki, K -- Steckiewicz, M -- Stevens, M -- Stewart, A I F -- Stiepen, A -- Stone, S -- Tenishev, V -- Thiemann, E -- Tolson, R -- Toublanc, D -- Vogt, M -- Weber, T -- Withers, P -- Woods, T -- Yelle, R -- New York, N.Y. -- Science. 2015 Nov 6;350(6261):aad0210. doi: 10.1126/science.aad0210.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Colorado, Boulder, CO, USA. bruce.jakosky@lasp.colorado.edu. ; NASA/Goddard Space Flight Center, Greenbelt, MD, USA. ; University of California at Berkeley, Berkeley, CA, USA. ; University of Colorado, Boulder, CO, USA. ; University of Iowa, Iowa City, IA, USA. ; Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA. ; University of Michigan, Ann Arbor, MI, USA. ; University of California at Los Angeles, Los Angeles, CA, USA. ; CNRS-Institut de Recherche en Astrophysique et Planetologie (IRAP), Toulouse, France. University Paul Sabatier, Toulouse, France. ; Swedish Institute of Space Physics, Uppsala, Sweden. ; NASA/Johnson Space Center, Houston, TX, USA. ; National Institute of Aerospace, Hampton, VA, USA. ; Laboratoire atmospheres, milieux et observations spatiales (LATMOS)-CNRS, Paris, France. ; Boston University, Boston, MA, USA. ; University of Kansas, Lawrence, KS, USA. ; Computational Physics, Inc., Boulder, CO, USA. ; Wright State University, Dayton, OH, USA. ; University of Arizona, Tucson, AZ, USA. ; Nagoya University, Nagoya, Japan. ; Naval Research Laboratory, Washington, DC, USA. ; North Carolina State University, Raleigh, NC, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26542576" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
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  • 6
    Publication Date: 2015-02-24
    Description: The fleeting lifetimes of the transition states (TSs) of chemical reactions make determination of their three-dimensional structures by diffraction methods a challenge. Here, we used packing interactions within the core of a protein to stabilize the planar TS conformation for rotation around the central carbon-carbon bond of biphenyl so that it could be directly observed by x-ray crystallography. The computational protein design software Rosetta was used to design a pocket within threonyl-transfer RNA synthetase from the thermophile Pyrococcus abyssi that forms complementary van der Waals interactions with a planar biphenyl. This latter moiety was introduced biosynthetically as the side chain of the noncanonical amino acid p-biphenylalanine. Through iterative rounds of computational design and structural analysis, we identified a protein in which the side chain of p-biphenylalanine is trapped in the energetically disfavored, coplanar conformation of the TS of the bond rotation reaction.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4581533/" 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/PMC4581533/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pearson, Aaron D -- Mills, Jeremy H -- Song, Yifan -- Nasertorabi, Fariborz -- Han, Gye Won -- Baker, David -- Stevens, Raymond C -- Schultz, Peter G -- 2 R01 GM097206-05/GM/NIGMS NIH HHS/ -- F32 GM099210/GM/NIGMS NIH HHS/ -- F32GM099210/GM/NIGMS NIH HHS/ -- R01 GM097206/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2015 Feb 20;347(6224):863-7. doi: 10.1126/science.aaa2424.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. ; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. ; Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA. ; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Howard Hughes Medical Institute (HHMI), University of Washington, Seattle, WA 98195, USA. ; Department of Chemistry and Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. schultz@scripps.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25700516" target="_blank"〉PubMed〈/a〉
    Keywords: Alanine/*analogs & derivatives/chemistry ; Archaeal Proteins/*chemistry ; Biphenyl Compounds/*chemistry ; Computer Simulation ; Computer-Aided Design ; Crystallography, X-Ray ; Entropy ; Models, Chemical ; Protein Structure, Secondary ; Pyrococcus abyssi/*enzymology ; Software ; Threonine-tRNA Ligase/*chemistry
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  • 7
    Publication Date: 2015-12-19
    Description: Speciation, the process by which new biological species arise, involves the evolution of reproductive barriers, such as hybrid sterility or inviability between populations. However, identifying hybrid incompatibility genes remains a key obstacle in understanding the molecular basis of reproductive isolation. We devised a genomic screen, which identified a cell cycle-regulation gene as the cause of male inviability in hybrids resulting from a cross between Drosophila melanogaster and D. simulans. Ablation of the D. simulans allele of this gene is sufficient to rescue the adult viability of hybrid males. This dominantly acting cell cycle regulator causes mitotic arrest and, thereby, inviability of male hybrid larvae. Our genomic method provides a facile means to accelerate the identification of hybrid incompatibility genes in other model and nonmodel systems.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4703311/" 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/PMC4703311/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Phadnis, Nitin -- Baker, EmilyClare P -- Cooper, Jacob C -- Frizzell, Kimberly A -- Hsieh, Emily -- de la Cruz, Aida Flor A -- Shendure, Jay -- Kitzman, Jacob O -- Malik, Harmit S -- 5T32 HD0741/HD/NICHD NIH HHS/ -- HG006283/HG/NHGRI NIH HHS/ -- R01 GM074108/GM/NIGMS NIH HHS/ -- R01 GM115914/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2015 Dec 18;350(6267):1552-5. doi: 10.1126/science.aac7504.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of Utah, Salt Lake City, UT 84112, USA. nitin.phadnis@utah.edu hsmalik@fhcrc.org. ; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA. ; Department of Biology, University of Utah, Salt Lake City, UT 84112, USA. ; Genome Sciences, University of Washington, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA. ; Genome Sciences, University of Washington, Seattle, WA 98195, USA. Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA. ; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA. Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA. nitin.phadnis@utah.edu hsmalik@fhcrc.org.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26680200" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; Carrier Proteins/genetics/*physiology ; Cell Cycle/*genetics ; Chimera/genetics ; Crosses, Genetic ; Drosophila melanogaster/*genetics/growth & development ; Drosophila simulans/*genetics/growth & development ; Gene Expression Regulation, Developmental ; Genes, Essential/genetics/physiology ; Genes, Insect ; Genes, Lethal/genetics/*physiology ; *Genetic Speciation ; Male ; Molecular Sequence Data ; *Reproductive Isolation
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  • 8
    Publication Date: 2015-06-20
    Description: We describe a general approach to designing two-dimensional (2D) protein arrays mediated by noncovalent protein-protein interfaces. Protein homo-oligomers are placed into one of the seventeen 2D layer groups, the degrees of freedom of the lattice are sampled to identify configurations with shape-complementary interacting surfaces, and the interaction energy is minimized using sequence design calculations. We used the method to design proteins that self-assemble into layer groups P 3 2 1, P 4 2(1) 2, and P 6. Projection maps of micrometer-scale arrays, assembled both in vitro and in vivo, are consistent with the design models and display the target layer group symmetry. Such programmable 2D protein lattices should enable new approaches to structure determination, sensing, and nanomaterial engineering.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gonen, Shane -- DiMaio, Frank -- Gonen, Tamir -- Baker, David -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2015 Jun 19;348(6241):1365-8. doi: 10.1126/science.aaa9897.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA. Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA. ; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA. ; Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA. gonent@janelia.hhmi.org dabaker@uw.edu. ; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA. gonent@janelia.hhmi.org dabaker@uw.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26089516" target="_blank"〉PubMed〈/a〉
    Keywords: *Computer-Aided Design ; Cryoelectron Microscopy ; *Protein Array Analysis ; Protein Engineering/*methods ; Proteins/*chemistry
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  • 9
    Publication Date: 2015-09-05
    Description: Fusion of intracellular transport vesicles requires soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) and Sec1/Munc18-family (SM) proteins. Membrane-bridging SNARE complexes are critical for fusion, but their spontaneous assembly is inefficient and may require SM proteins in vivo. We report x-ray structures of Vps33, the SM subunit of the yeast homotypic fusion and vacuole protein-sorting (HOPS) complex, bound to two individual SNAREs. The two SNAREs, one from each membrane, are held in the correct orientation and register for subsequent complex assembly. Vps33 and potentially other SM proteins could thus act as templates for generating partially zipped SNARE assembly intermediates. HOPS was essential to mediate SNARE complex assembly at physiological SNARE concentrations. Thus, Vps33 appears to catalyze SNARE complex assembly through specific SNARE motif recognition.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4727825/" 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/PMC4727825/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baker, Richard W -- Jeffrey, Philip D -- Zick, Michael -- Phillips, Ben P -- Wickner, William T -- Hughson, Frederick M -- GM071574/GM/NIGMS NIH HHS/ -- GM23377/GM/NIGMS NIH HHS/ -- R01 GM071574/GM/NIGMS NIH HHS/ -- T32 GM007388/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2015 Sep 4;349(6252):1111-4. doi: 10.1126/science.aac7906.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA. ; Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA. ; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA. hughson@princeton.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26339030" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallography, X-Ray ; Membrane Proteins/chemistry/metabolism ; Munc18 Proteins/*metabolism ; Protein Binding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Qa-SNARE Proteins/*metabolism ; R-SNARE Proteins/*metabolism ; Saccharomyces cerevisiae ; Saccharomyces cerevisiae Proteins/chemistry/*metabolism/ultrastructure ; Synaptosomal-Associated Protein 25/chemistry/metabolism ; Vesicular Transport Proteins/chemistry/*metabolism/ultrastructure
    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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  • 10
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2015-03-07
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baker, Stephen -- 089276/Wellcome Trust/United Kingdom -- 100087/Wellcome Trust/United Kingdom -- 100087/Z/12/Z/Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2015 Mar 6;347(6226):1064-6. doi: 10.1126/science.aaa2868.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam. Centre for Tropical Medicine, Oxford University, Oxford, UK. Centre for Tropical Medicine, Oxford University, Oxford, UK. sbaker@oucru.org.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25745145" target="_blank"〉PubMed〈/a〉
    Keywords: Cholera/epidemiology ; Communicable Diseases/*epidemiology ; *Developed Countries ; *Drug Resistance, Bacterial/genetics ; Humans ; Pandemics ; Poverty ; Salmonella typhi/ultrastructure ; Typhoid Fever/epidemiology/microbiology ; Vibrio cholerae/drug effects/genetics
    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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