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  • 1
    Publication Date: 2015-01-22
    Description: Macro-scale species richness studies often use museum specimens as their main source of information. However, such datasets are often strongly biased due to variation in sampling effort in space and time. These biases may strongly affect diversity estimates and may, thereby, obstruct solid inference on the underlying diversity drivers, as well as mislead conservation prioritization. In recent years, this has resulted in an increased focus on developing methods to correct for sampling bias. In this study, we use sample-size-correcting methods to examine patterns of tropical plant diversity in Ecuador, one of the most species-rich and climatically heterogeneous biodiversity hotspots. Species richness estimates were calculated based on 205,735 georeferenced specimens of 15,788 species using the Margalef diversity index, the Chao estimator, the second-order Jackknife and Bootstrapping resampling methods, and Hill numbers and rarefaction. Species richness was heavily correlated with sampling effort, and only rarefaction was able to remove this effect, and we recommend this method for estimation of species richness with “big data” collections. We evaluate the effectiveness of different methods for correcting sampling bias when mapping species richness across a well-studied area with a comprehensive collection of museum records. We found that nearly all estimates of species richness remained heavily correlated with sampling effort, with only rarefaction being effective in removing this bias to provide reliable estimates of species richness. Therefore, we recommend using rarefaction when basing species richness estimates on such museum data.
    Electronic ISSN: 2045-7758
    Topics: Biology
    Published by Wiley
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  • 2
    Publication Date: 2011-01-04
    Description: Intracellular membrane fusion is mediated by the concerted action of N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) and Sec1/Munc18 (SM) proteins. During fusion, SM proteins bind the N-terminal peptide (N-peptide) motif of the SNARE subunit syntaxin, but the function of this interaction is unknown. Here, using FRET-based biochemical reconstitution and Caenorhabditis elegans genetics, we show that the N-peptide of syntaxin-1 recruits the SM protein Munc18-1/nSec1 to the SNARE bundle, facilitating their assembly into a fusion-competent complex. The recruitment is achieved through physical tethering rather than allosteric activation of Munc18-1. Consistent with the recruitment role, the N-peptide is not spatially constrained along syntaxin-1, and it is functional when translocated to another SNARE subunit SNAP-25 or even when simply anchored in the target membrane. The N-peptide function is restricted to an early initiation stage of the fusion reaction. After association, Munc18-1 and the SNARE bundle together drive membrane merging without further involving the N-peptide. Thus, the syntaxin N-peptide is an initiation factor for the assembly of the SNARE-SM membrane fusion complex.
    Keywords: Feature Articles
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 3
    Publication Date: 2019
    Description: Abstract The magnetosheath and near‐Earth solar wind emit X‐rays due to charge‐exchange between the extended atmosphere and highly ionized particles in the solar wind. These emissions can be used to remotely sense the dynamic processes in this region. The Solar Wind Magnetosphere Ionosphere Link Explorer mission will carry out these measurements. In a previous paper, we looked at the effect of photon counting statistics on determining the location of the magnetopause and bow shock. In this paper we explore, through simulations, the more challenging question of orbital viewing geometry bias when the model and the emissions do not match each other exactly. Our simulations conclude that while care must be taken to avoid false minima in the fitting, there is very little to no orbital bias in extracting the position and large‐scale shape of the magnetopause and bow shocks from 2‐D X‐ray images from the future Solar Wind Magnetosphere Ionosphere Link Explorer mission.
    Print ISSN: 2169-9380
    Electronic ISSN: 2169-9402
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 4
    Publication Date: 2019
    Description: Abstract Imaging magnetospheric satellite missions provide information, which is complementary to in situ observations. Imaging is often able to provide an instantaneous picture of large‐scale structures, whereas in situ measurements, even multipoint in situ measurements, can only provide an average view of large‐scale structure. But imaging also presents some challenges. When three‐dimensional structures need to be extracted from two‐dimensional images, it is necessary to either make suitable assumptions or record a large enough number of images from different viewing geometries to allow a reconstruction (e.g., tomography). Imaging data exist over a wide range of sources including visible light, ultraviolet light, extreme ultraviolet, energetic neutral atoms, and X‐rays, each informing different physical mechanisms. In this paper we consider the extraction of the geometry of the magnetopause and the bow shock from single X‐ray images expected from the Solar wind Magnetosphere Ionosphere Link Explorer (SMILE) mission. We examine the effect of photon‐counting noise in determining the boundary geometries. We also consider the effect of different viewing geometries in the form of orbital vantage point and target look direction. Finally, we consider the effect of background noise. We find that our approach is relatively robust to viewing geometry effects and works at low count rates.
    Print ISSN: 2169-9380
    Electronic ISSN: 2169-9402
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 5
    Publication Date: 2011-09-14
    Description: The enzymatic degradation of recalcitrant plant biomass is one of the key industrial challenges of the 21st century. Accordingly, there is a continuing drive to discover new routes to promote polysaccharide degradation. Perhaps the most promising approach involves the application of “cellulase-enhancing factors,” such as those from the glycoside hydrolase (CAZy) GH61 family. Here we show that GH61 enzymes are a unique family of copper-dependent oxidases. We demonstrate that copper is needed for GH61 maximal activity and that the formation of cellodextrin and oxidized cellodextrin products by GH61 is enhanced in the presence of small molecule redox-active cofactors such as ascorbate and gallate. By using electron paramagnetic resonance spectroscopy and single-crystal X-ray diffraction, the active site of GH61 is revealed to contain a type II copper and, uniquely, a methylated histidine in the copper's coordination sphere, thus providing an innovative paradigm in bioinorganic enzymatic catalysis.
    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: 2014-08-22
    Description: We present time series photometric observations of 13 transits in the planetary systems WASP-24, WASP-25 and WASP-26. All three systems have orbital obliquity measurements, WASP-24 and WASP-26 have been observed with Spitzer , and WASP-25 was previously comparatively neglected. Our light curves were obtained using the telescope-defocussing method and have scatters of 0.5–1.2 mmag relative to their best-fitting geometric models. We use these data to measure the physical properties and orbital ephemerides of the systems to high precision, finding that our improved measurements are in good agreement with previous studies. High-resolution Lucky Imaging observations of all three targets show no evidence for faint stars close enough to contaminate our photometry. We confirm the eclipsing nature of the star closest to WASP-24 and present the detection of a detached eclipsing binary within 4.25 arcmin of WASP-26.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 7
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2002-11-02
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pitman, Nigel C A -- Jorgensen, Peter M -- New York, N.Y. -- Science. 2002 Nov 1;298(5595):989.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Tropical Conservation, Box 90381, Duke University, Durham, NC 27708-0381, USA. ncp@duke.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12411696" target="_blank"〉PubMed〈/a〉
    Keywords: Budgets ; *Conservation of Natural Resources/economics ; Costs and Cost Analysis ; *Ecosystem ; *Plants ; *Tropical Climate
    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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  • 8
    Publication Date: 2009-01-24
    Description: Regeneration of injured neurons can restore function, but most neurons regenerate poorly or not at all. The failure to regenerate in some cases is due to a lack of activation of cell-intrinsic regeneration pathways. These pathways might be targeted for the development of therapies that can restore neuron function after injury or disease. Here, we show that the DLK-1 mitogen-activated protein (MAP) kinase pathway is essential for regeneration in Caenorhabditis elegans motor neurons. Loss of this pathway eliminates regeneration, whereas activating it improves regeneration. Further, these proteins also regulate the later step of growth cone migration. We conclude that after axon injury, activation of this MAP kinase cascade is required to switch the mature neuron from an aplastic state to a state capable of growth.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2729122/" 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/PMC2729122/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hammarlund, Marc -- Nix, Paola -- Hauth, Linda -- Jorgensen, Erik M -- Bastiani, Michael -- 1R21NS060275/NS/NINDS NIH HHS/ -- NS034307/NS/NINDS NIH HHS/ -- R21 NS060275-02/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2009 Feb 6;323(5915):802-6. doi: 10.1126/science.1165527. Epub 2009 Jan 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112-0840, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19164707" target="_blank"〉PubMed〈/a〉
    Keywords: Aging ; Animals ; Axons/*physiology/ultrastructure ; Axotomy ; Caenorhabditis elegans/genetics/*physiology ; Caenorhabditis elegans Proteins/genetics/*metabolism ; Growth Cones/physiology ; MAP Kinase Kinase 4/genetics/metabolism ; MAP Kinase Kinase Kinases/genetics/*metabolism ; *MAP Kinase Signaling System ; Mitogen-Activated Protein Kinases/genetics/metabolism ; Models, Biological ; Motor Neurons/*physiology ; Mutation ; Nerve Regeneration/physiology ; RNA Interference ; gamma-Aminobutyric Acid/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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  • 9
    Publication Date: 2013-10-19
    Description: The vast extent of the Amazon Basin has historically restricted the study of its tree communities to the local and regional scales. Here, we provide empirical data on the commonness, rarity, and richness of lowland tree species across the entire Amazon Basin and Guiana Shield (Amazonia), collected in 1170 tree plots in all major forest types. Extrapolations suggest that Amazonia harbors roughly 16,000 tree species, of which just 227 (1.4%) account for half of all trees. Most of these are habitat specialists and only dominant in one or two regions of the basin. We discuss some implications of the finding that a small group of species--less diverse than the North American tree flora--accounts for half of the world's most diverse tree community.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉ter Steege, Hans -- Pitman, Nigel C A -- Sabatier, Daniel -- Baraloto, Christopher -- Salomao, Rafael P -- Guevara, Juan Ernesto -- Phillips, Oliver L -- Castilho, Carolina V -- Magnusson, William E -- Molino, Jean-Francois -- Monteagudo, Abel -- Nunez Vargas, Percy -- Montero, Juan Carlos -- Feldpausch, Ted R -- Coronado, Euridice N Honorio -- Killeen, Tim J -- Mostacedo, Bonifacio -- Vasquez, Rodolfo -- Assis, Rafael L -- Terborgh, John -- Wittmann, Florian -- Andrade, Ana -- Laurance, William F -- Laurance, Susan G W -- Marimon, Beatriz S -- Marimon, Ben-Hur Jr -- Guimaraes Vieira, Ima Celia -- Amaral, Ieda Leao -- Brienen, Roel -- Castellanos, Hernan -- Cardenas Lopez, Dairon -- Duivenvoorden, Joost F -- Mogollon, Hugo F -- Matos, Francisca Dionizia de Almeida -- Davila, Nallarett -- Garcia-Villacorta, Roosevelt -- Stevenson Diaz, Pablo Roberto -- Costa, Flavia -- Emilio, Thaise -- Levis, Carolina -- Schietti, Juliana -- Souza, Priscila -- Alonso, Alfonso -- Dallmeier, Francisco -- Montoya, Alvaro Javier Duque -- Fernandez Piedade, Maria Teresa -- Araujo-Murakami, Alejandro -- Arroyo, Luzmila -- Gribel, Rogerio -- Fine, Paul V A -- Peres, Carlos A -- Toledo, Marisol -- Aymard C, Gerardo A -- Baker, Tim R -- Ceron, Carlos -- Engel, Julien -- Henkel, Terry W -- Maas, Paul -- Petronelli, Pascal -- Stropp, Juliana -- Zartman, Charles Eugene -- Daly, Doug -- Neill, David -- Silveira, Marcos -- Paredes, Marcos Rios -- Chave, Jerome -- Lima Filho, Diogenes de Andrade -- Jorgensen, Peter Moller -- Fuentes, Alfredo -- Schongart, Jochen -- Cornejo Valverde, Fernando -- Di Fiore, Anthony -- Jimenez, Eliana M -- Penuela Mora, Maria Cristina -- Phillips, Juan Fernando -- Rivas, Gonzalo -- van Andel, Tinde R -- von Hildebrand, Patricio -- Hoffman, Bruce -- Zent, Eglee L -- Malhi, Yadvinder -- Prieto, Adriana -- Rudas, Agustin -- Ruschell, Ademir R -- Silva, Natalino -- Vos, Vincent -- Zent, Stanford -- Oliveira, Alexandre A -- Schutz, Angela Cano -- Gonzales, Therany -- Trindade Nascimento, Marcelo -- Ramirez-Angulo, Hirma -- Sierra, Rodrigo -- Tirado, Milton -- Umana Medina, Maria Natalia -- van der Heijden, Geertje -- Vela, Cesar I A -- Vilanova Torre, Emilio -- Vriesendorp, Corine -- Wang, Ophelia -- Young, Kenneth R -- Baider, Claudia -- Balslev, Henrik -- Ferreira, Cid -- Mesones, Italo -- Torres-Lezama, Armando -- Urrego Giraldo, Ligia Estela -- Zagt, Roderick -- Alexiades, Miguel N -- Hernandez, Lionel -- Huamantupa-Chuquimaco, Isau -- Milliken, William -- Palacios Cuenca, Walter -- Pauletto, Daniela -- Valderrama Sandoval, Elvis -- Valenzuela Gamarra, Luis -- Dexter, Kyle G -- Feeley, Ken -- Lopez-Gonzalez, Gabriela -- Silman, Miles R -- New York, N.Y. -- Science. 2013 Oct 18;342(6156):1243092. doi: 10.1126/science.1243092.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Naturalis Biodiversity Center, Leiden, Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24136971" target="_blank"〉PubMed〈/a〉
    Keywords: *Biodiversity ; Models, Biological ; Population ; *Rivers ; South America ; Trees/*classification/*physiology
    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: 2004-06-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schuske, Kim -- Jorgensen, Erik M -- New York, N.Y. -- Science. 2004 Jun 18;304(5678):1750-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112-0840, USA. jorgensen@biology.utah.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15205517" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Newborn ; Brain/metabolism ; Carrier Proteins/genetics/*metabolism ; Cell Membrane/physiology ; Cells, Cultured ; Excitatory Postsynaptic Potentials ; Glutamic Acid/metabolism ; Hippocampus/cytology/metabolism ; Membrane Fusion ; *Membrane Transport Proteins ; Mice ; Mice, Knockout ; Models, Neurological ; Mutation ; Neurons/*metabolism ; *Synaptic Transmission ; Synaptic Vesicles/*metabolism/physiology ; Vesicular Glutamate Transport Protein 1 ; Vesicular Glutamate Transport Protein 2 ; *Vesicular Transport Proteins
    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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