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  • American Geophysical Union  (602)
  • American Physical Society  (347)
  • BioMed Central  (218)
  • 2015-2019  (694)
  • 2010-2014  (470)
  • 1940-1944  (3)
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  • 1
    Publication Date: 2012-10-11
    Description: Background: The bacterium Caulobacter crescentus is a popular model for the study of cell cycle regulation and senescence. The large prolate siphophage phiCbK has been an important tool in C. crescentus biology, and has been studied in its own right as a model for viral morphogenesis. Although a system of some interest, to date little genomic information is available on phiCbK or its relatives. Results: Five novel phiCbK-like C. crescentus bacteriophages, CcrMagneto, CcrSwift, CcrKarma, CcrRogue and CcrColossus, were isolated from the environment. The genomes of phage phiCbK and these five environmental phage isolates were obtained by 454 pyrosequencing. The phiCbK-like phage genomes range in size from 205 kb encoding 318 proteins (phiCbK) to 280 kb encoding 448 proteins (CcrColossus), and were found to contain nonpermuted terminal redundancies of 10 to 17 kb. A novel method of terminal ligation was developed to map genomic termini, which confirmed termini predicted by coverage analysis. This suggests that sequence coverage discontinuities may be useable as predictors of genomic termini in phage genomes. Genomic modules encoding virion morphogenesis, lysis and DNA replication proteins were identified. The phiCbK-like phages were also found to encode a number of intriguing proteins; all contain a clearly T7-like DNA polymerase, and five of the six encode a possible homolog of the C. crescentus cell cycle regulator GcrA, which may allow the phage to alter the host cell's replicative state. The structural proteome of phage phiCbK was determined, identifying the portal, major and minor capsid proteins, the tail tape measure and possible tail fiber proteins. All six phage genomes are clearly related; phiCbK, CcrMagneto, CcrSwift, CcrKarma and CcrRogue form a group related at the DNA level, while CcrColossus is more diverged but retains significant similarity at the protein level. Conclusions: Due to their lack of any apparent relationship to other described phages, this group is proposed as the founding cohort of a new phage type, the phiCbK-like phages. This work will serve as a foundation for future studies on morphogenesis, infection and phage-host interactions in C. crescentus.
    Electronic ISSN: 1471-2164
    Topics: Biology
    Published by BioMed Central
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  • 2
    Publication Date: 2012-10-10
    Description: Background The bacterium Caulobacter crescentus is a popular model for the study of cell cycle regulation and senescence. The large prolate siphophage phiCbK has been an important tool in C. crescentus biology, and has been studied in its own right as a model for viral morphogenesis. Although a system of some interest, to date little genomic information is available on phiCbK or its relatives. Results Five novel phiCbK-like C. crescentus bacteriophages, CcrMagneto, CcrSwift, CcrKarma, CcrRogue and CcrColossus, were isolated from the environment. The genomes of phage phiCbK and these five environmental phage isolates were obtained by 454 pyrosequencing. The phiCbK-like phage genomes range in size from 205 kb encoding 318 proteins (phiCbK) to 280 kb encoding 448 proteins (CcrColossus), and were found to contain nonpermuted terminal redundancies of 10 to 17 kb. A novel method of terminal ligation was developed to map genomic termini, which confirmed termini predicted by coverage analysis. This suggests that sequence coverage discontinuities may be useable as predictors of genomic termini in phage genomes. Genomic modules encoding virion morphogenesis, lysis and DNA replication proteins were identified. The phiCbK-like phages were also found to encode a number of intriguing proteins; all contain a clearly T7-like DNA polymerase, and five of the six encode a possible homolog of the C. crescentus cell cycle regulator GcrA, which may allow the phage to alter the host cell’s replicative state. The structural proteome of phage phiCbK was determined, identifying the portal, major and minor capsid proteins, the tail tape measure and possible tail fiber proteins. All six phage genomes are clearly related; phiCbK, CcrMagneto, CcrSwift, CcrKarma and CcrRogue form a group related at the DNA level, while CcrColossus is more diverged but retains significant similarity at the protein level. Conclusions Due to their lack of any apparent relationship to other described phages, this group is proposed as the founding cohort of a new phage type, the phiCbK-like phages. This work will serve as a foundation for future studies on morphogenesis, infection and phage-host interactions in C. crescentus.
    Electronic ISSN: 1471-2164
    Topics: Biology
    Published by BioMed Central
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  • 3
    Publication Date: 2022-05-25
    Description: Author Posting. © American Geophysical Union, 2011. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry Geophysics Geosystems 12 (2011): Q07025, doi:10.1029/2010GC003438.
    Description: The volcanic origin of the Samoan archipelago can be explained by one of three models, specifically, by a hot spot forming over a mantle plume, by lithospheric extension resulting from complex subduction tectonics in the region, or by a combination of these two processes, either acting sequentially or synchronously. In this paper, we present results of 36 high-resolution 40Ar/39Ar incremental heating age analyses for the initial (submarine) phase of Samoan volcanoes, ranging from 13.2 Ma for the westernmost Samoan seamounts to 0.27 Ma in the eastern Samoan volcanic province. Taken as a whole, our new age data point to a hot spot origin for the shield-building volcanism in the Samoan lineament, whereby seamounts younger than 5 Ma are consistent with a model of constant 7.1 cm/yr plate motion, analogous to GPS measurements for the Pacific Plate in this region. This makes our new 40Ar/39Ar ages of the submarine basalts all older compared to recent absolute plate motion (APM) models by Wessel et al. (2008), which are based on the inversion of twelve independent seamount trails in the Pacific relative to a fixed reference frame of hot spots and which predict faster plate motions of around 9.3 cm/yr in the vicinity of Samoa. The Samoan ages are also older than APM models by Steinberger et al. (2004) taking into account the motion of hot spots in the Pacific alone or globally. The age systematics become more complicated toward the younger end of the Samoan seamount trail, where its morphology bifurcates into two en echelon subtracks, termed the VAI and MALU trends, as they emanate from two eruptive centers at Vailulu'u and Malumalu seamount, respectively. Spaced ∼50 km apart, the VAI and MALU trends have distinct geochemical characters and independent but overlapping linear 40Ar/39Ar age progressions since 1.5 Ma. These phenomena are not unique to Samoa, as they have been observed at the Hawaiian hot spot, and can be attributed to a geochemical zoning in its underlying mantle source or plume. Moreover, the processes allowing for the emergence of two distinct eruptive centers in the Samoan archipelago, the stepped offset of these subtracks, and their slight obliqueness with respect to the overall seamount trail orientation may very well be controlled by local tectonics, stresses, and extension, also causing the rejuvenated volcanism on the main islands of Savai'i, Upolu, and Tutuila since 0.4 Ma.
    Description: Financial support is provided by NSF‐OCE 0002875 and NSF‐OCE 0351437.
    Keywords: Ar-40/Ar-39 geochronology ; Seamounts ; Pacific plate ; Hot spots ; Intraplate volcanism ; Zoned mantle plume
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 4
    Publication Date: 2022-05-25
    Description: Author Posting. © American Geophysical Union, 2010. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Paleoceanography 25 (2010): PA1102, doi:10.1029/2009PA001871.
    Description: Instrumental data suggest that major shifts in tropical Pacific atmospheric dynamics and hydrology have occurred within the past century, potentially in response to anthropogenic warming. To better understand these trends, we use the hydrogen isotopic ratios of terrestrial higher plant leaf waxes (δDwax) in marine sediments from southwest Sulawesi, Indonesia, to compile a detailed reconstruction of central Indo-Pacific Warm Pool (IPWP) hydrologic variability spanning most of the last two millennia. Our paleodata are highly correlated with a monsoon reconstruction from Southeast Asia, indicating that intervals of strong East Asian summer monsoon (EASM) activity are associated with a weaker Indonesian monsoon (IM). Furthermore, the centennial-scale oscillations in our data follow known changes in Northern Hemisphere climate (e.g., the Little Ice Age and Medieval Warm Period) implying a dynamic link between Northern Hemisphere temperatures and IPWP hydrology. The inverse relationship between the EASM and IM suggests that migrations of the Intertropical Convergence Zone and associated changes in monsoon strength caused synoptic hydrologic shifts in the IPWP throughout most of the past two millennia.
    Description: This research was supported by the U.S. NSF, the Ocean and Climate Change Institute at WHOI, and a National Defense Science and Engineering Graduate Fellowship to J. Tierney.
    Keywords: Tropical Pacific climate ; Compound-specific hydrogen isotopes
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/postscript
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  • 5
    Publication Date: 2022-10-26
    Description: Author Posting. © American Geophysical Union, 2019. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research-Solid Earth 124(1), (2019): 631-657, doi:10.1029/2018JB016598.
    Description: Lithospheric seismic anisotropy illuminates mid‐ocean ridge dynamics and the thermal evolution of oceanic plates. We utilize short‐period (5–7.5 s) ambient‐noise surface waves and 15‐ to 150‐s Rayleigh waves measured across the NoMelt ocean‐bottom array to invert for the complete radial and azimuthal anisotropy in the upper ∼35 km of ∼70‐Ma Pacific lithospheric mantle, and azimuthal anisotropy through the underlying asthenosphere. Strong azimuthal variations in Rayleigh‐ and Love‐wave velocity are observed, including the first clearly measured Love‐wave 2θ and 4θ variations. Inversion of averaged dispersion requires radial anisotropy in the shallow mantle (2‐3%) and the lower crust (4‐5%), with horizontal velocities (VSH) faster than vertical velocities (VSV). Azimuthal anisotropy is strong in the mantle, with 4.5–6% 2θ variation in VSV with fast propagation parallel to the fossil‐spreading direction (FSD), and 2–2.5% 4θ variation in VSH with a fast direction 45° from FSD. The relative behavior of 2θ, 4θ, and radial anisotropy in the mantle are consistent with ophiolite petrofabrics, linking outcrop and surface‐wave length scales. VSV remains fast parallel to FSD to ∼80 km depth where the direction changes, suggesting spreading‐dominated deformation at the ridge. The transition at ∼80 km perhaps marks the dehydration boundary and base of the lithosphere. Azimuthal anisotropy strength increases from the Moho to ∼30 km depth, consistent with flow models of passive upwelling at the ridge. Strong azimuthal anisotropy suggests extremely coherent olivine fabric. Weaker radial anisotropy implies slightly nonhorizontal fabric or the presence of alternative (so‐called E‐type) peridotite fabric. Presence of radial anisotropy in the crust suggests subhorizontal layering and/or shearing during crustal accretion.
    Description: We thank the captain, crew, and engineers of the R/V Marcus G. Langseth for making the data collection possible. OBS were provided by Scripps Institution of Oceanography via the Ocean Bottom Seismograph Instrument Pool (http://www.obsip.org), which is funded by the National Science Foundation. All waveform data used in this study are archived at the IRIS Data Management Center (http://www.iris.edu) with network code ZA for 2011–2013, and all OBS orientations are included in Table S1. The 1‐D transversely isotropic and azimuthally anisotropic models and their uncertainties from this study can be found in the supporting information. This work was supported by NSF grants OCE‐0928270 and OCE‐1538229 (J. B. Gaherty), EAR‐1361487 (G. Hirth), and OCE‐0938663 (D. Lizarralde, J. A. Collins, and R. L. Evans), and an NSF Graduate Research Fellowship DGE‐16‐44869 to J. B. Russell. The authors thank the editor as well as reviewers Donald Forsyth, Hitoshi Kawakatsu, and Thorsten Becker for their constructive comments, which significantly improved this manuscript. J. B. Russell thanks Natalie J. Accardo for kindly sharing codes and expertise that contributed greatly to the analysis.
    Description: 2019-06-26
    Keywords: Seismic anisotropy ; Ambient‐noise tomography ; Oceanic lithosphere ; Love‐wave anisotropy ; Surface waves
    Repository Name: Woods Hole Open Access Server
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  • 6
    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in GigaScience 5 (2016): 14, doi:10.1186/s13742-016-0118-5.
    Description: Systems biology promises to revolutionize medicine, yet human wellbeing is also inherently linked to healthy societies and environments (sustainability). The IDEA Consortium is a systems ecology open science initiative to conduct the basic scientific research needed to build use-oriented simulations (avatars) of entire social-ecological systems. Islands are the most scientifically tractable places for these studies and we begin with one of the best known: Moorea, French Polynesia. The Moorea IDEA will be a sustainability simulator modeling links and feedbacks between climate, environment, biodiversity, and human activities across a coupled marine–terrestrial landscape. As a model system, the resulting knowledge and tools will improve our ability to predict human and natural change on Moorea and elsewhere at scales relevant to management/conservation actions.
    Description: Work was supported in part by: the Institute of Theoretical Physics and the Pauli Center at ETH Zurich; the US National Science Foundation (NSF Moorea Coral Reef Long Term Ecological Research Site, OCE-1236905; Socio-Ecosystem Dynamics of Natural-Human Networks on Model Islands, CNH-1313830; Coastal SEES: Adaptive Capacity, Resilience, and Coral Reef State Shifts in Social-ecological Systems, OCE-1325652, OCE-1325554); the Gordon and Betty Moore Foundation (Berkeley Initiative in Global Change Biology; Genomic Standards Consortium); Courtney Ross and the Ross Institute; UC Berkeley Vice Chancellor for Research; CRIOBE; and the France Berkeley Fund (FBF 2014-0015).
    Keywords: Computational ecology ; Biodiversity ; Genomics ; Biocode ; Earth observations ; Social-ecological system ; Ecosystem dynamics ; Climate change scenarios ; Predictive modeling
    Repository Name: Woods Hole Open Access Server
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  • 7
    Publication Date: 2015-11-06
    Print ISSN: 1550-7998
    Electronic ISSN: 1550-2368
    Topics: Physics
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  • 8
    Publication Date: 1941-11-01
    Print ISSN: 0031-899X
    Electronic ISSN: 1536-6065
    Topics: Physics
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  • 9
  • 10
    Publication Date: 2013-10-16
    Print ISSN: 1550-7998
    Electronic ISSN: 1550-2368
    Topics: Physics
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