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  • 1
    Online Resource
    Online Resource
    Cham :Springer International Publishing :
    Keywords: Bacteria. ; Microbial genetics. ; Cytology. ; Evolution (Biology). ; Biomathematics. ; Bacteria. ; Microbial Genetics. ; Cell Biology. ; Evolutionary Biology. ; Mathematical and Computational Biology.
    Description / Table of Contents: Chapter 1. Introduction -- Chapter 2. Around the Circadian Clock: Review and Preview -- Chapter 3. A retrospective: on disproving the transcription-translation feedback loop model in cyanobacteria -- Chapter 4. Mechanistic Aspects of the Cyanobacterial Circadian Clock -- Chapter 5. Mechanism of the cyanobacterial circadian clock protein KaiC to measure 24 hours -- Chapter 6. Oscillation and Input Compensation in the Cyanobacterial Kai Proteins -- Chapter 7. Insights into the Evolution of Circadian Clocks Gleaned from Bacteria -- Chapter 8. Reasons for Seeking Information on the Molecular Structure and Dynamics of Circadian Clock Components in Cyanobacteria -- Chapter 9. Single-molecule methods applied to circadian proteins with special on atomic force microscopy -- Chapter 10. Diversity of timing systems in Cyanobacteria and beyond -- Chapter 11. An In Vitro Approach to Elucidating Clock-modulating Metabolites -- Chapter 12. Damped Oscillation in the Cyanobacterial Clock System -- Chapter 13. Roles of phosphorylation of KaiC in the cyanobacterial circadian clock -- Chapter 14. Reprogramming metabolic networks and manipulating circadian clocks for biotechnological applications -- Chapter 15. Insights from Mathematical Modeling/Simulations of the in vitro KaiABC clock -- Chapter 16. Basic Biology of Rhythms & the Microbiome -- Chapter 17. Disease Implications of the Circadian Clocks and Microbiota Interface -- Chapter 18. Circadian organization of the gut commensal bacterium Klebsiella aerogenes -- Chapter 19. Daily rhythmicity in coastal microbial mats -- Chapter 20. Daily and Seasonal Rhythms of Marine Phages of Cyanobacteria.
    Abstract: This book addresses multiple aspects of biological clocks in prokaryotes. The first part of the book deals with the circadian clock system in cyanobacteria, i.e. the pioneer of bacterial clocks. Starting with the history and background of cyanobacteria and circadian rhythms in microorganisms, the topics range from the molecular basis, structure and evolution of the circadian clock to modelling approaches, Kai systems in cyanobacteria and biotechnological applications. In the second part, emergent timekeeping properties of bacteria in microbiomes and bacteria other than cyanobacteria are discussed. Since the discovery of circadian rhythms in cyanobacteria in the late 1980s, the field has exploded with new information. The cyanobacterial model system for studying circadian rhythms (Synechococcus elongatus), has allowed a detailed genetic dissection of the bacterial clock due to state-of-the-art methods in molecular, structural, and evolutionary biology. Cutting-edge research spanning from cyanobacteria and circadian phenomena in other kinds of bacteria, to microbiomes has now given the field another major boost. This book is aimed at junior and senior researchers alike. Students or researchers new to the field of biological clocks in prokaryotes will get a comprehensive overview, while more experienced researchers will get an update on the latest developments.
    Type of Medium: Online Resource
    Pages: XXIV, 415 p. 89 illus., 83 illus. in color. , online resource.
    Edition: 1st ed. 2021.
    ISBN: 9783030721589
    DDC: 579.3
    Language: English
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  • 2
    Publication Date: 2022-05-25
    Description: Author Posting. © Elsevier B.V., 2007. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Organic Geochemistry 38 (2007): 884-896, doi:10.1016/j.orggeochem.2007.02.005.
    Description: Nuclear magnetic resonance spectroscopy of marine high molecular weight dissolved organic matter (HMWDOM) in surface waters show that 〉50% of the carbon is a compositionally well-defined family of acylated-polysaccharides that are conserved across ocean basins. However, acid hydrolysis of HMWDOM followed by chromatographic analyses recover only 10-20% of the carbon as neutral, amino, and acidic sugars. Most carbohydrate in HMWDOM therefore remains uncharacterized. Here we use acid hydrolysis followed by Ag+ and Pb2+ cation exchange chromatography to separate HMWDOM hydrolysis products for characterization by 1-D and 2-D NMR spectroscopy. In addition to neutral sugars identified in past studies, we find 3-Omethylglucose, 3-O-methylrhamnose, 2-O-methylrhamnose and 2-O-methylfucose. We also find 3-deoxysugars to be present, although their complete structures could not be determined. Methyl sugars are widely distributed in plant and bacterial structural carbohydrates, such as cell wall polysaccharides, and their presence in HMWDOM suggests that structural carbohydrates may contribute to DOM in surface seawater. We find most HMWDOM carbohydrate is not depolymerized by acid hydrolysis, and that the nonhydrolyzable component includes 6-deoxysugars.
    Description: Funding was provided by the Ocean Carbon Sequestration Research Program, Biological and Environmental Research (BER), U.S. Department of Energy grant DEFG0200ER62999 and the National Sciences Foundation Chemical Oceanography Program grant OCE 9818654. Christos Panagiotopoulos received support through the Postdoctoral Fellowship Program of the Woods Hole Oceanographic Institution, and DJR received support through the Stanley Watson Chair in Oceanography.
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
    Format: application/pdf
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  • 3
    Publication Date: 2022-05-25
    Description: © The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 7 (2017): 6040, doi:10.1038/s41598-017-05590-9.
    Description: Selection of microorganisms in marine sediment is shaped by energy-yielding electron acceptors for respiration that are depleted in vertical succession. However, some taxa have been reported to reflect past depositional conditions suggesting they have experienced weak selection after burial. In sediments underlying the Arabian Sea oxygen minimum zone (OMZ), we performed the first metagenomic profiling of sedimentary DNA at centennial-scale resolution in the context of a multi-proxy paleoclimate reconstruction. While vertical distributions of sulfate reducing bacteria and methanogens indicate energy-based selection typical of anoxic marine sediments, 5–15% of taxa per sample exhibit depth-independent stratigraphies indicative of paleoenvironmental selection over relatively short geological timescales. Despite being vertically separated, indicator taxa deposited under OMZ conditions were more similar to one another than those deposited in bioturbated intervals under intervening higher oxygen. The genomic potential for denitrification also correlated with palaeo-OMZ proxies, independent of sediment depth and available nitrate and nitrite. However, metagenomes revealed mixed acid and Entner-Dourdoroff fermentation pathways encoded by many of the same denitrifier groups. Fermentation thus may explain the subsistence of these facultatively anaerobic microbes whose stratigraphy follows changing paleoceanographic conditions. At least for certain taxa, our analysis provides evidence of their paleoenvironmental selection over the last glacial-interglacial cycle.
    Description: his work was primarily supported by NSF MGG Grant #1357017 to MJLC, VG, and LG, and the KAUST-WHOI Special Academic Partnership Program OCRF-SP-WHOI-2013 (grants 7000000463 to XI and 7000000464 to MJLC). Additional financial support was provided via a C-DEBI grant #OCE-0939564 to WDO.
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 4
    Publication Date: 2022-05-25
    Description: Author Posting. © The Author(s), 2018. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Limnology and Oceanography Methods 16 (2018): 286-298, doi:10.1002/lom3.10245.
    Description: Compositional changes in marine particulate organic carbon (POC) throughout the water column trace important processes that underlie the biological pump’s efficiency. While labor-intensive, particle sampling efforts offer potential to expand the empirical POC archive at different stages in the water column, provided that organic composition is sufficiently preserved between sampling and analysis. The standard procedure for preserving organic matter composition in marine samples is to immediately store particles at -80°C to -20°C until they can be freeze-dried for analysis. This report investigates the effect of warmer drying and storage temperatures on POC composition, which applies to the majority of POC samples collected in the field without intention for organic analysis. Particle samples collected off Woods Hole, MA were immediately dried at 56°C, at room temperature, or stored at -80°C until being freeze-dried. Results show that oven- and air-drying did not shift the bulk composition (i.e., carbon and nitrogen content and stable isotope composition) of POC in the samples relative to freeze-drying. Similarly, warmer drying temperatures did not affect POC thermal stability, as inferred by ramped pyrolysis/oxidation (RPO), a growing technique that uses a continuous temperature ramp to differentiate components of organic carbon by their decomposition temperature. Oven- and air-drying did depress lipid abundances relative to freeze-drying, the extent of which depended on compound size and structure. The data suggest that field samples dried at room temperatures and 56°C are appropriate for assessing bulk POC composition and thermal stability, but physical mechanisms such as molecular volatilization bias their lipid composition.
    Description: This research was funded by the National Science Foundation (NSF) Graduate Research Fellowship program and the NSF Cooperative Agreement for the Operation of a National Ocean Sciences Accelerator Mass Spectrometry Facility (OCE-0753487).
    Keywords: Particulate organic carbon composition ; Sample drying treatment ; Ramped oxidation
    Repository Name: Woods Hole Open Access Server
    Type: Preprint
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  • 5
    Publication Date: 2022-05-25
    Description: Author Posting. © American Geophysical Union, 2017. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geophysical Research Letters 44 (2017): 2407–2415, doi:10.1002/2016GL071348.
    Description: We present concentration and isotopic profiles of total, size, and polarity fractionated dissolved organic carbon (DOC) from Station ALOHA (A Long-term Oligotrophic Habitat Assessment), an oligotrophic site in the North Pacific Ocean. The data show that, between the surface and 3500 m, low molecular weight (LMW) hydrophilic DOC, LMW hydrophobic DOC, and high molecular weight (HMW) DOC constitute 22–33%, 45–52%, and 23–35% of DOC, respectively. LMW hydrophilic DOC is more isotopically depleted (δ13C of −23.9‰ to −31.5‰ and Δ14C of −304‰ to −795‰; mean age of 2850 to 15000 years) than the LMW hydrophobic DOC (δ13C of −22‰ to −23‰ and Δ14C of −270‰ to −568‰; 2470 to 6680 years) and HMW DOC (δ13C of ~−21‰ and Δ14C of −24‰ to −294‰; 135–2700 years). Our analyses suggest that a large fraction of DOC may be derived from allochthonous sources such as terrestrial and hydrothermal DOC and cycle on much longer time scales of 〉10000 years or enter the ocean as preaged carbon.
    Description: NSF Cooperative Agreement for the Operation of a National Ocean Sciences Accelerator Mass Spectrometry Facility Grant Number: OCE-0753487; Gordon and Betty Moore Foundation Grant Numbers: GBMF3298, GBMF3794; Simons Foundation Grant Number: 329108
    Description: 2017-09-07
    Keywords: Carbon cycling ; Carbon isotopes ; Radiocarbon ; Biogeochemical cycles
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 6
    Publication Date: 2022-05-25
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Biogeosciences 9 (2012): 2485-2495, doi:10.5194/bg-9-2485-2012.
    Description: Phytoplankton and bacterial pigment compositions were determined by high performance liquid chromatography (HPLC) and liquid chromatography-mass spectrometry (LC-MS) in two freshwater reservoirs (Tillari Dam and Selaulim Dam), which are located at the foothills of the Western Ghats in India. These reservoirs experience anoxia in the hypolimnion during summer. Water samples were collected from both reservoirs during anoxic periods while one of them (Tillari Reservoir) was also sampled in winter, when convective mixing results in well-oxygenated conditions throughout the water column. During the period of anoxia (summer), bacteriochlorophyll (BChl) e isomers and isorenieratene, characteristic of brown sulfur bacteria, were dominant in the anoxic (sulfidic) layer of the Tillari Reservoir under low light intensities. The winter observations showed the dominance of small cells of Chlorophyll b-containing green algae and cyanobacteria, with minor presence of fucoxanthin-containing diatoms and peridinin-containing dinoflagellates. Using total BChl e concentration observed in June, the standing stock of brown sulfur bacteria carbon in the anoxic compartment of Tillari Reservoir was estimated to be 2.27 gC m−2, which is much higher than the similar estimate for carbon derived from oxygenic photosynthesis (0.82 gC m−2. The Selaulim Reservoir also displayed similar characteristics with the presence of BChl e isomers and isorenieratene in the anoxic hypolimnion during summer. Although sulfidic conditions prevailed in the water column below the thermocline, the occurrence of photo-autotrophic bacteria was restricted only to mid-depths (maximal concentration of BChl e isomers was detected at 0.2% of the surface incident light). This shows that the vertical distribution of photo-autotrophic sulfur bacteria is primarily controlled by light penetration in the water column where the presence of H2S provides a suitable biogeochemical environment for them to flourish.
    Description: Financial support for this work was provided by the Council of Scientific & Industrial Research (CSIR) and Ministry of Earth Sciences (MoES). S. Kurian acknowledges POGO-SCOR for financial support to visit WHOI. R. Roy, G. Narvenkar and A. Sarkar received fellowship support from CSIR. D. Repeta acknowledges support from US National Science Foundation Center Award EF0424599 to the Center for Microbial Oceanography: Research and Education (C-MORE).
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 7
    Publication Date: 2022-05-26
    Description: Retention and release of No. 2 fuel oil compounds by Mytilus edulis contaminated by a small oil spill in the Cape Cod Canal in 1983 has been studied for the population "in situ" and for a subsample transplanted to a clean laboratory seawater system. Compounds analyzed include C13 to C24 n-alkanes; pristane; phytane; C2-, C3-naphthalenes; fluorene; phenanthrene; C1-, C2-, C3-phenanthrenes; fluoranthene; pyrene and dibenzothiophene. Biological half-lives were determined for the compounds from Day-3 to Day-29 following the spill and ranged from 1.5 days for C2-naphthalenes to 9.9 days for C2-phenanthrenes. Biological half-lives for the unresolved complex mixture determined by gas chromatographic analyses were 17 days for the alkane-cycloalkane fraction and 35 days for the aromatic fraction. Results compared favorably with data from a small oil spill contaminating the same mussel population at the same time of the year in 1978, although marked differences were noted for certain parameters. Gas chromatographic-mass spectrometer analyses of C2- and C3-phenanthrenes revealed changes in relative abundance of compounds within isomer groups from samples at Day-29 to the time when no further detection of fuel oil was noted. These results suggest a release or metabolism of these compounds which is molecular structure specific. This study also demonstrated the feasibility of training an analyst unfamiliar with analyses of hydrocarbons in tissues to conduct high resolution glass capillary GC analyses and some aspects of GCMS data systems output within a period of four to five months.
    Description: Financial support from the Ministry of Education and the Ministry of Agriculture, Animal Husbandry, and Fisheries, Beijing, China; and from the Andrew W. Mellon Foundation and the Richard King Mellon Foundation to the Coastal Research Center, Woods Hole Oceanographic Institution
    Keywords: Mytilus edulis ; Oil spills ; Oil pollution of the sea
    Repository Name: Woods Hole Open Access Server
    Type: Technical Report
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  • 8
    ISSN: 1520-510X
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Accounts of chemical research 6 (1973), S. 341-347 
    ISSN: 1520-4898
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Inorganic chemistry 3 (1964), S. 1487-1491 
    ISSN: 1520-510X
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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