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  • 1
    Publikationsdatum: 2011-06-15
    Beschreibung: Glycosaminoglycan polysaccharides play critical roles in many cellular processes, ranging from viral invasion and angiogenesis to spinal cord injury. Their diverse biological activities are derived from an ability to regulate a remarkable number of proteins. However, few methods exist for the rapid identification of glycosaminoglycan–protein interactions and for studying the potential of glycosaminoglycans to assemble multimeric protein complexes. Here, we report a multidisciplinary approach that combines new carbohydrate microarray and computational modeling methodologies to elucidate glycosaminoglycan–protein interactions. The approach was validated through the study of known protein partners for heparan and chondroitin sulfate, including fibroblast growth factor 2 (FGF2) and its receptor FGFR1, the malarial protein VAR2CSA, and tumor necrosis factor-α (TNF-α). We also applied the approach to identify previously undescribed interactions between a specific sulfated epitope on chondroitin sulfate, CS-E, and the neurotrophins, a critical family of growth factors involved in the development, maintenance, and survival of the vertebrate nervous system. Our studies show for the first time that CS is capable of assembling multimeric signaling complexes and modulating neurotrophin signaling pathways. In addition, we identify a contiguous CS-E-binding site by computational modeling that suggests a potential mechanism to explain how CS may promote neurotrophin-tyrosine receptor kinase (Trk) complex formation and neurotrophin signaling. Together, our combined microarray and computational modeling methodologies provide a general, facile means to identify new glycosaminoglycan–protein–protein interactions, as well as a molecular-level understanding of those complexes.
    Print ISSN: 0027-8424
    Digitale ISSN: 1091-6490
    Thema: Biologie , Medizin , Allgemeine Naturwissenschaft
    Standort Signatur Erwartet Verfügbarkeit
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  • 2
    Publikationsdatum: 2012-04-19
    Beschreibung: Ecology, Volume 93, Issue 3, Page 554-564, March 2012.
    Print ISSN: 0012-9658
    Digitale ISSN: 1939-9170
    Thema: Biologie
    Publiziert von Wiley im Namen von The Ecological Society of America (ESA).
    Standort Signatur Erwartet Verfügbarkeit
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  • 3
    Publikationsdatum: 2014-04-25
    Beschreibung: : Individuals living in endemic areas generally harbour multiple parasite strains. Multiplicity of infection (MOI) can be an indicator of immune status and transmission intensity. It has a potentially confounding effect on a number of population genetic analyses, which often assume isolates are clonal. Polymerase chain reaction-based approaches to estimate MOI can lack sensitivity. For example, in the human malaria parasite Plasmodium falciparum , genotyping of the merozoite surface protein ( MSP1/2 ) genes is a standard method for assessing MOI, despite the apparent problem of underestimation. The availability of deep coverage data from massively parallizable sequencing technologies means that MOI can be detected genome wide by considering the abundance of heterozygous genotypes. Here, we present a method to estimate MOI, which considers unique combinations of polymorphisms from sequence reads. The method is implemented within the estMOI software. When applied to clinical P.falciparum isolates from three continents, we find that multiple infections are common, especially in regions with high transmission. Availability and implementation: estMOI is freely available from http://pathogenseq.lshtm.ac.uk . Contact: samuel.assefa@lshtm.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Digitale ISSN: 1460-2059
    Thema: Biologie , Informatik , Medizin
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 4
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    American Association for the Advancement of Science (AAAS)
    Publikationsdatum: 2011-09-10
    Beschreibung: During courtship flights, males of some hummingbird species produce diverse sounds with tail feathers of varying shapes. We show that these sounds are produced by air flowing past a feather, causing it to aeroelastically flutter and generate flutter-induced sound. Scanning laser doppler vibrometery and high-speed video of individual feathers of different sizes and shapes in a wind tunnel revealed multiple vibratory modes that produce a range of acoustic frequencies and harmonic structures. Neighboring feathers can be aerodynamically coupled and flutter either at the same frequency, resulting in sympathetic vibrations that increase loudness, or at different frequencies, resulting in audible interaction frequencies. Aeroelastic flutter is intrinsic to stiff airfoils such as feathers and thus explains tonal sounds that are common in bird flight.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Clark, Christopher J -- Elias, Damian O -- Prum, Richard O -- New York, N.Y. -- Science. 2011 Sep 9;333(6048):1430-3. doi: 10.1126/science.1205222.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology and Evolutionary Biology, Post Office Box 208105, Yale University, New Haven, CT 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21903810" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): *Animal Communication ; Animals ; Biological Evolution ; Birds/anatomy & histology/*physiology ; Feathers/anatomy & histology/*physiology ; Female ; Flight, Animal ; Male ; Mating Preference, Animal ; Movement ; *Sound ; Tail/physiology ; Vibration ; Wind
    Print ISSN: 0036-8075
    Digitale ISSN: 1095-9203
    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 5
    Publikationsdatum: 2012-07-27
    Beschreibung: The rapid disruption of tropical forests probably imperils global biodiversity more than any other contemporary phenomenon. With deforestation advancing quickly, protected areas are increasingly becoming final refuges for threatened species and natural ecosystem processes. However, many protected areas in the tropics are themselves vulnerable to human encroachment and other environmental stresses. As pressures mount, it is vital to know whether existing reserves can sustain their biodiversity. A critical constraint in addressing this question has been that data describing a broad array of biodiversity groups have been unavailable for a sufficiently large and representative sample of reserves. Here we present a uniquely comprehensive data set on changes over the past 20 to 30 years in 31 functional groups of species and 21 potential drivers of environmental change, for 60 protected areas stratified across the world's major tropical regions. Our analysis reveals great variation in reserve 'health': about half of all reserves have been effective or performed passably, but the rest are experiencing an erosion of biodiversity that is often alarmingly widespread taxonomically and functionally. Habitat disruption, hunting and forest-product exploitation were the strongest predictors of declining reserve health. Crucially, environmental changes immediately outside reserves seemed nearly as important as those inside in determining their ecological fate, with changes inside reserves strongly mirroring those occurring around them. These findings suggest that tropical protected areas are often intimately linked ecologically to their surrounding habitats, and that a failure to stem broad-scale loss and degradation of such habitats could sharply increase the likelihood of serious biodiversity declines.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Laurance, William F -- Useche, D Carolina -- Rendeiro, Julio -- Kalka, Margareta -- Bradshaw, Corey J A -- Sloan, Sean P -- Laurance, Susan G -- Campbell, Mason -- Abernethy, Kate -- Alvarez, Patricia -- Arroyo-Rodriguez, Victor -- Ashton, Peter -- Benitez-Malvido, Julieta -- Blom, Allard -- Bobo, Kadiri S -- Cannon, Charles H -- Cao, Min -- Carroll, Richard -- Chapman, Colin -- Coates, Rosamond -- Cords, Marina -- Danielsen, Finn -- De Dijn, Bart -- Dinerstein, Eric -- Donnelly, Maureen A -- Edwards, David -- Edwards, Felicity -- Farwig, Nina -- Fashing, Peter -- Forget, Pierre-Michel -- Foster, Mercedes -- Gale, George -- Harris, David -- Harrison, Rhett -- Hart, John -- Karpanty, Sarah -- Kress, W John -- Krishnaswamy, Jagdish -- Logsdon, Willis -- Lovett, Jon -- Magnusson, William -- Maisels, Fiona -- Marshall, Andrew R -- McClearn, Deedra -- Mudappa, Divya -- Nielsen, Martin R -- Pearson, Richard -- Pitman, Nigel -- van der Ploeg, Jan -- Plumptre, Andrew -- Poulsen, John -- Quesada, Mauricio -- Rainey, Hugo -- Robinson, Douglas -- Roetgers, Christiane -- Rovero, Francesco -- Scatena, Frederick -- Schulze, Christian -- Sheil, Douglas -- Struhsaker, Thomas -- Terborgh, John -- Thomas, Duncan -- Timm, Robert -- Urbina-Cardona, J Nicolas -- Vasudevan, Karthikeyan -- Wright, S Joseph -- Arias-G, Juan Carlos -- Arroyo, Luzmila -- Ashton, Mark -- Auzel, Philippe -- Babaasa, Dennis -- Babweteera, Fred -- Baker, Patrick -- Banki, Olaf -- Bass, Margot -- Bila-Isia, Inogwabini -- Blake, Stephen -- Brockelman, Warren -- Brokaw, Nicholas -- Bruhl, Carsten A -- Bunyavejchewin, Sarayudh -- Chao, Jung-Tai -- Chave, Jerome -- Chellam, Ravi -- Clark, Connie J -- Clavijo, Jose -- Congdon, Robert -- Corlett, Richard -- Dattaraja, H S -- Dave, Chittaranjan -- Davies, Glyn -- Beisiegel, Beatriz de Mello -- da Silva, Rosa de Nazare Paes -- Di Fiore, Anthony -- Diesmos, Arvin -- Dirzo, Rodolfo -- Doran-Sheehy, Diane -- Eaton, Mitchell -- Emmons, Louise -- Estrada, Alejandro -- Ewango, Corneille -- Fedigan, Linda -- Feer, Francois -- Fruth, Barbara -- Willis, Jacalyn Giacalone -- Goodale, Uromi -- Goodman, Steven -- Guix, Juan C -- Guthiga, Paul -- Haber, William -- Hamer, Keith -- Herbinger, Ilka -- Hill, Jane -- Huang, Zhongliang -- Sun, I Fang -- Ickes, Kalan -- Itoh, Akira -- Ivanauskas, Natalia -- Jackes, Betsy -- Janovec, John -- Janzen, Daniel -- Jiangming, Mo -- Jin, Chen -- Jones, Trevor -- Justiniano, Hermes -- Kalko, Elisabeth -- Kasangaki, Aventino -- Killeen, Timothy -- King, Hen-biau -- Klop, Erik -- Knott, Cheryl -- Kone, Inza -- Kudavidanage, Enoka -- Ribeiro, Jose Lahoz da Silva -- Lattke, John -- Laval, Richard -- Lawton, Robert -- Leal, Miguel -- Leighton, Mark -- Lentino, Miguel -- Leonel, Cristiane -- Lindsell, Jeremy -- Ling-Ling, Lee -- Linsenmair, K Eduard -- Losos, Elizabeth -- Lugo, Ariel -- Lwanga, Jeremiah -- Mack, Andrew L -- Martins, Marlucia -- McGraw, W Scott -- McNab, Roan -- Montag, Luciano -- Thompson, Jo Myers -- Nabe-Nielsen, Jacob -- Nakagawa, Michiko -- Nepal, Sanjay -- Norconk, Marilyn -- Novotny, Vojtech -- O'Donnell, Sean -- Opiang, Muse -- Ouboter, Paul -- Parker, Kenneth -- Parthasarathy, N -- Pisciotta, Katia -- Prawiradilaga, Dewi -- Pringle, Catherine -- Rajathurai, Subaraj -- Reichard, Ulrich -- Reinartz, Gay -- Renton, Katherine -- Reynolds, Glen -- Reynolds, Vernon -- Riley, Erin -- Rodel, Mark-Oliver -- Rothman, Jessica -- Round, Philip -- Sakai, Shoko -- Sanaiotti, Tania -- Savini, Tommaso -- Schaab, Gertrud -- Seidensticker, John -- Siaka, Alhaji -- Silman, Miles R -- Smith, Thomas B -- de Almeida, Samuel Soares -- Sodhi, Navjot -- Stanford, Craig -- Stewart, Kristine -- Stokes, Emma -- Stoner, Kathryn E -- Sukumar, Raman -- Surbeck, Martin -- Tobler, Mathias -- Tscharntke, Teja -- Turkalo, Andrea -- Umapathy, Govindaswamy -- van Weerd, Merlijn -- Rivera, Jorge Vega -- Venkataraman, Meena -- Venn, Linda -- Verea, Carlos -- de Castilho, Carolina Volkmer -- Waltert, Matthias -- Wang, Benjamin -- Watts, David -- Weber, William -- West, Paige -- Whitacre, David -- Whitney, Ken -- Wilkie, David -- Williams, Stephen -- Wright, Debra D -- Wright, Patricia -- Xiankai, Lu -- Yonzon, Pralad -- Zamzani, Franky -- England -- Nature. 2012 Sep 13;489(7415):290-4. doi: 10.1038/nature11318.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Tropical Environmental and Sustainability Science and School of Marine and Tropical Biology, James Cook University, Cairns, Queensland 4878, Australia. bill.laurance@jcu.edu.au〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22832582" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Agriculture/statistics & numerical data ; Animals ; *Biodiversity ; Conservation of Natural Resources/*statistics & numerical data ; Data Collection ; Ecology/statistics & numerical data ; Endangered Species/*statistics & numerical data ; Environmental Pollution/adverse effects/statistics & numerical data ; Fires/statistics & numerical data ; Forestry/statistics & numerical data ; Interviews as Topic ; Mining/statistics & numerical data ; Population Growth ; Rain ; Reproducibility of Results ; Research Personnel ; Surveys and Questionnaires ; Temperature ; Trees/*physiology ; *Tropical Climate
    Print ISSN: 0028-0836
    Digitale ISSN: 1476-4687
    Thema: Biologie , Chemie und Pharmazie , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 6
    Publikationsdatum: 2011-11-11
    Beschreibung: Author(s): S. Al-Assam, S. R. Clark, C. J. Foot, and D. Jaksch [Phys. Rev. B 84, 205108] Published Thu Nov 10, 2011
    Schlagwort(e): Electronic structure and strongly correlated systems
    Print ISSN: 1098-0121
    Digitale ISSN: 1095-3795
    Thema: Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 7
    Publikationsdatum: 2013-10-12
    Beschreibung: Upon its completion, the Herschel Astrophysics Terahertz Large Area Survey (H-ATLAS) will be the largest sub-millimetre survey to date, detecting close to half-a-million sources. It will only be possible to measure spectroscopic redshifts for a small fraction of these sources. However, if the rest-frame spectral energy distribution (SED) of a typical H-ATLAS source is known, this SED and the observed Herschel fluxes can be used to estimate the redshifts of the H-ATLAS sources without spectroscopic redshifts. In this paper, we use a sub-set of 40 H-ATLAS sources with previously measured redshifts in the range 0.5 〈  z  〈 4.2 to derive a suitable average template for high-redshift H-ATLAS sources. We find that a template with two dust components ( T c = 23.9 K, T h = 46.9 K and ratio of mass of cold dust to mass of warm dust of 30.1) provides a good fit to the rest-frame fluxes of the sources in our calibration sample. We use a jackknife technique to estimate the accuracy of the redshifts estimated with this template, finding a root mean square of z /(1 +  z ) = 0.26. For sources for which there is prior information that they lie at z  〉 1, we estimate that the rms of z /(1 +  z ) = 0.12. We have used this template to estimate the redshift distribution for the sources detected in the H-ATLAS equatorial fields, finding a bimodal distribution with a mean redshift of 1.2, 1.9 and 2.5 for 250, 350 and 500 μm selected sources, respectively.
    Print ISSN: 0035-8711
    Digitale ISSN: 1365-2966
    Thema: Physik
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 8
    Publikationsdatum: 2014-05-06
    Beschreibung: We present a comparison of the physical properties of a rest-frame 250-μm-selected sample of massive, dusty galaxies from 0 〈 z  〈 5.3. Our sample comprises 29 high-redshift submillimetre galaxies (SMGs) from the literature and 843 dusty galaxies at z  〈 0.5 from the Herschel -Astrophysical TeraHertz Large Area Survey (H-ATLAS), selected to have a similar stellar mass to the SMGs. The z  〉 1 SMGs have an average star formation rate (SFR) of $390^{+80}_{-70}\,$  M  yr –1 , which is 120 times that of the low-redshift sample matched in stellar mass to the SMGs (SFR = 3.3 ± 0.2 M  yr –1 ). The SMGs harbour a substantial mass of dust ( $1.2^{+0.3}_{-0.2}\times {10}^9\,$  M ), compared to (1.6 ± 0.1) 10 8  M for low-redshift dusty galaxies. At low redshifts, the dust luminosity is dominated by the diffuse interstellar medium, whereas a large fraction of the dust luminosity in SMGs originates from star-forming regions. At the same dust mass, SMGs are offset towards a higher SFR compared to the low-redshift H-ATLAS galaxies. This is not only due to the higher gas fraction in SMGs but also because they are undergoing a more efficient mode of star formation, which is consistent with their bursty star formation histories. The offset in SFR between SMGs and low-redshift galaxies is similar to that found in CO studies, suggesting that dust mass is as good a tracer of molecular gas as CO.
    Print ISSN: 0035-8711
    Digitale ISSN: 1365-2966
    Thema: Physik
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 9
    Publikationsdatum: 2013-03-16
    Beschreibung: The Herschel -Astrophysical Terahertz Large Area Survey (H-ATLAS) provides an unprecedented opportunity to search for blazars at sub-mm wavelengths. We cross-matched the Faint Images of the Radio Sky at Twenty-cm (FIRST) radio source catalogue with the 11 655 sources brighter than 35 mJy at 500 μm in the ~135 deg 2 of the sky covered by the H-ATLAS equatorial fields at 9 h and 15 h , plus half of the field at 12 h . We found that 379 of the H-ATLAS sources have a FIRST counterpart within 10 arcsec, including eight catalogued blazars (plus one known blazar that was found at the edge of one of the H-ATLAS maps). To search for additional blazar candidates we have devised new diagnostic diagrams and found that known blazars occupy a region of the log ( S 500 μm / S 350 μm ) versus log ( S 500 μm / S 1.4 GHz ) plane separated from that of sub-mm sources with radio emission powered by star formation, but shared with radio galaxies and steep-spectrum radio quasars. Using this diagnostic we have selected 12 further possible candidates that turn out to be scattered in the ( r  – z ) versus ( u  – r ) plane or in the Wide-Field Infrared Survey Explorer colour–colour diagram, where known blazars are concentrated in well defined strips. This suggests that the majority of them are not blazars. Based on an inspection of all the available photometric data, including unpublished VISTA Kilo-degree Infrared Galaxy survey photometry and new radio observations, we found that the spectral energy distributions (SEDs) of only one out of the 12 newly selected sources are compatible with being synchrotron dominated at least up to 500 μm, i.e. with being a blazar. Another object may consist of a faint blazar nucleus inside a bright star-forming galaxy. The possibility that some blazar hosts are endowed with active star formation is supported by our analysis of the SEDs of Planck Early Release Compact Source Catalogue blazars detected at both 545 and 857 GHz. The estimated rest-frame synchrotron peak frequencies of H-ATLAS blazars are in the range 11.5 ≤ log ( peak, Hz ) ≤ 13.7, implying that these objects are low synchrotron peak. Six of them also show evidence of an ultraviolet excess that can be attributed to emission from the accretion disc. Allowing for the possibility of misidentifications and of contamination of the 500 μm flux density by the dusty torus or by the host galaxy, we estimate that there are seven or eight pure synchrotron sources brighter than S 500 μm = 35 mJy over the studied area, a result that sets important constraints on blazar evolutionary models.
    Print ISSN: 0035-8711
    Digitale ISSN: 1365-2966
    Thema: Physik
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 10
    Publikationsdatum: 2013-10-29
    Beschreibung: We present an analysis of CO molecular gas tracers in a sample of 500 μm-selected Herschel Astrophysical Terahertz Large Area Survey (H-ATLAS) galaxies at z 〈 0.05 ( cz 〈 14990 km s –1 ). Using 22-500 μm photometry from Wide-Field Infrared Survey Explorer , Infrared Astronomical Satellite and Herschel , with H i data from the literature, we investigate correlations between warm and cold dust, and tracers of the gas in different phases. The correlation between global CO(3–2) line fluxes and far-infrared (FIR)-submillimetre (submm) fluxes weakens with increasing infrared wavelength ( 60 μm), as a result of colder dust being less strongly associated with dense gas. Conversely, CO(2–1) and H i line fluxes both appear to be better correlated with longer wavelengths, suggesting that cold dust is more strongly associated with diffuse atomic and molecular gas phases, consistent with it being at least partially heated by radiation from old stellar populations. The increased scatter at long wavelengths implies that submm fluxes are a poorer tracer of star formation rate (SFR). Fluxes at 22 and 60 μm are also better correlated with diffuse gas tracers than dense CO(3–2), probably due to very small grain emission in the diffuse interstellar medium, which is not correlated with SFR. The FIR/CO luminosity ratio and the dust mass/CO luminosity ratio both decrease with increasing luminosity, as a result of either correlations between mass and metallicity (changing CO/H 2 ) or between CO luminosity and excitation [changing CO(3–2)/CO(1–0)].
    Print ISSN: 0035-8711
    Digitale ISSN: 1365-2966
    Thema: Physik
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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