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  • 1
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    Water, Vol. 11, Pages 520: Remediation of Stormwater Pollutants by Porous Asphalt Pavement (2019)
    MDPI
    In: Water
    Details
    Publication Date: 2019
    Description: Porous Asphalt (PA) pavements are an increasingly adopted tool in the green stormwater infrastructure toolbox to manage stormwater in urbanized watersheds across the United States. This technology has seen particular interest in western Washington State, where permeable pavements are recognized as an approved best management practice per the National Pollutant Discharge Elimination System (NPDES) municipal stormwater permit. Stormwater effluent concentrations from six PA cells were compared with runoff concentrations from three standard impervious asphalt cells to quantify pollutant removal efficiencies by porous asphalt systems. Additionally, the effects of maintenance and pavement age on pollutant removal efficiencies were examined. Twelve natural and artificial storms were examined over a five-year period. Street dirt and pollutant spikes were added to the pavements prior to some storm events to simulate high loading conditions. Results from this work show that porous asphalt pavements are highly efficient at removing particulate pollutants, specifically coarse sediments (98.7%), total Pb ( 98.4%), total Zn (97.8%), and total suspended solids (93.4%). Dissolved metals and Polycyclic Aromatic Hydrocarbons (PAH) were not significantly removed. Removal efficiencies for total Pb, total Zn, motor oil, and diesel H. improved with the age of the system. Annual maintenance of the pavements with a regenerative air street sweeper did not yield significant pollutant removal efficiency differences between maintained and unmaintained PA cells.
    Electronic ISSN: 2073-4441
    Topics: Energy, Environment Protection, Nuclear Power Engineering
    Published by MDPI
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  • 2
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    Depsipeptide Intermediates Interrogate Proposed Biosynthesis of Cereulide, the Emetic Toxin of Bacillus cereus (2015)
    Springer Nature
    Details
    Publication Date: 2015-05-28
    Description: Cereulide and isocereulides A-G are biosynthesized as emetic toxins by Bacillus cereus via a non-ribosomal peptide synthetase (NRPS) called Ces. Although a thiotemplate mechanisms involving cyclo-trimerization of ready-made D-O-Leu-D-Ala-L-O-Val-L-Val via a thioesterase (TE) domain is proposed for cereulide biosynthesis, the exact mechanism is far from being understood. UPLC-TOF MS analysis of B. cereus strains in combination with 13C-labeling experiments now revealed tetra-, octa-, and dodecapeptides of a different sequence, namely (L-O-Val-L-Val-D-O-Leu-D-Ala)1-3, as intermediates of cereulide biosynthesis. Surprisingly, also di-, hexa-, and decadepsipeptides were identified which, together with the structures of the previously reported isocereulides E, F, and G, do not correlate to the currently proposed mechanism for cereulide biosynthesis and violate the canonical NRPS biosynthetic logic. UPLC-TOF MS metabolite analysis and bioinformatic gene cluster analysis highlighted dipeptides rather than single amino or hydroxy acids as the basic modules in tetradepsipeptide assembly and proposed the CesA C-terminal C* domain and the CesB C-terminal TE domain to function as a cooperative esterification and depsipeptide elongation center repeatedly recruiting the action of the C* domain to oligomerize tetradepsipeptides prior to the release of cereulide from the TE domain by macrocyclization. Scientific Reports 5 doi: 10.1038/srep10637
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
    Published by Springer Nature
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  • 3
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    The BioGRID interaction database: 2015 update (2015)
    Oxford University Press
    Details
    Publication Date: 2015-01-16
    Description: The Biological General Repository for Interaction Datasets (BioGRID: http://thebiogrid.org ) is an open access database that houses genetic and protein interactions curated from the primary biomedical literature for all major model organism species and humans. As of September 2014, the BioGRID contains 749 912 interactions as drawn from 43 149 publications that represent 30 model organisms. This interaction count represents a 50% increase compared to our previous 2013 BioGRID update. BioGRID data are freely distributed through partner model organism databases and meta-databases and are directly downloadable in a variety of formats. In addition to general curation of the published literature for the major model species, BioGRID undertakes themed curation projects in areas of particular relevance for biomedical sciences, such as the ubiquitin-proteasome system and various human disease-associated interaction networks. BioGRID curation is coordinated through an Interaction Management System (IMS) that facilitates the compilation interaction records through structured evidence codes, phenotype ontologies, and gene annotation. The BioGRID architecture has been improved in order to support a broader range of interaction and post-translational modification types, to allow the representation of more complex multi-gene/protein interactions, to account for cellular phenotypes through structured ontologies, to expedite curation through semi-automated text-mining approaches, and to enhance curation quality control.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    Comparison of Population Level and Individual Level Endpoints To Evaluate Ecological Risk of Chemicals (2012)
    American Chemical Society (ACS)
    Details
    Publication Date: 2012-05-03
    Description: Environmental Science & Technology DOI: 10.1021/es3008968
    Print ISSN: 0013-936X
    Electronic ISSN: 1520-5851
    Topics: Chemistry and Pharmacology , Energy, Environment Protection, Nuclear Power Engineering
    Published by American Chemical Society (ACS)
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  • 5
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    Neural-specific elongation of 3' UTRs during Drosophila development [Developmental Biology] (2011)
    National Academy of Sciences
    Details
    Publication Date: 2011-09-21
    Description: The 3′ termini of eukaryotic mRNAs influence transcript stability, translation efficiency, and subcellular localization. Here we report that a subset of developmental regulatory genes, enriched in critical RNA-processing factors, exhibits synchronous lengthening of their 3′ UTRs during embryogenesis. The resulting UTRs are up to 20-fold longer than those found on typical Drosophila mRNAs. The large mRNAs emerge shortly after the onset of zygotic transcription, with several of these genes acquiring additional, phased UTR extensions later in embryogenesis. We show that these extended 3′ UTR sequences are selectively expressed in neural tissues and contain putative recognition motifs for the translational repressor, Pumilio, which also exhibits the 3′ lengthening phenomenon documented in this study. These findings suggest a previously unknown mode of posttranscriptional regulation that may contribute to the complexity of neurogenesis or neural function.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 6
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    Detection of functional haematopoietic stem cell niche using real-time imaging (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-12-05
    Description: Haematopoietic stem cell (HSC) niches, although proposed decades ago, have only recently been identified as separate osteoblastic and vascular microenvironments. Their interrelationships and interactions with HSCs in vivo remain largely unknown. Here we report the use of a newly developed ex vivo real-time imaging technology and immunoassaying to trace the homing of purified green-fluorescent-protein-expressing (GFP(+)) HSCs. We found that transplanted HSCs tended to home to the endosteum (an inner bone surface) in irradiated mice, but were randomly distributed and unstable in non-irradiated mice. Moreover, GFP(+) HSCs were more frequently detected in the trabecular bone area compared with compact bone area, and this was validated by live imaging bioluminescence driven by the stem-cell-leukaemia (Scl) promoter-enhancer. HSCs home to bone marrow through the vascular system. We found that the endosteum is well vascularized and that vasculature is frequently localized near N-cadherin(+) pre-osteoblastic cells, a known niche component. By monitoring individual HSC behaviour using real-time imaging, we found that a portion of the homed HSCs underwent active division in the irradiated mice, coinciding with their expansion as measured by flow assay. Thus, in contrast to central marrow, the endosteum formed a special zone, which normally maintains HSCs but promotes their expansion in response to bone marrow damage.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xie, Yucai -- Yin, Tong -- Wiegraebe, Winfried -- He, Xi C -- Miller, Diana -- Stark, Danny -- Perko, Katherine -- Alexander, Richard -- Schwartz, Joel -- Grindley, Justin C -- Park, Jungeun -- Haug, Jeff S -- Wunderlich, Joshua P -- Li, Hua -- Zhang, Simon -- Johnson, Teri -- Feldman, Ricardo A -- Li, Linheng -- England -- Nature. 2009 Jan 1;457(7225):97-101. doi: 10.1038/nature07639. Epub 2008 Dec 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Stowers Institute for Medical Research, 1000 E. 50th Street, Kansas City, Missouri 64110, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19052548" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigens, CD31/analysis ; Blood Vessels/cytology ; Bone Marrow/pathology ; Cadherins/analysis ; Cell Division ; *Cell Movement ; Cell Separation ; Femur/cytology ; Hematopoietic Stem Cells/*cytology ; Immunoassay/*methods ; Immunohistochemistry ; Mice ; Models, Animal ; Osteoblasts/cytology ; Stem Cell Niche/*cytology ; Tibia/cytology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 7
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    Astronomy: Searching for the cosmic dawn (2012)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2012-09-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stark, Daniel -- England -- Nature. 2012 Sep 20;489(7416):370-1. doi: 10.1038/489370a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22996545" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 8
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    DNA unwinding by MRN [Biochemistry] (2013)
    National Academy of Sciences
    Details
    Publication Date: 2013-11-20
    Description: The Mre11/Rad50/Nbs1 (MRN) complex initiates and coordinates DNA repair and signaling events at double-strand breaks. The interaction between MRN and DNA ends is critical for the recruitment of DNA-processing enzymes, end tethering, and activation of the ATM protein kinase. Here we visualized MRN binding to duplex DNA molecules using single-molecule...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 9
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    A Functional Link Between Bir1 and the Saccharomyces cerevisiae Ctf19 Kinetochore Complex Revealed Through Quantitative Fitness Analysis (2017)
    Genetics Society of America (GSA)
    Details
    Publication Date: 2017-09-08
    Description: The chromosomal passenger complex (CPC) is a key regulator of eukaryotic cell division, consisting of the protein kinase Aurora B/ Ipl1 in association with its activator (INCENP/ Sli15 ) and two additional proteins (Survivin/ Bir1 and Borealin/ Nbl1 ). Here, we report a genome-wide genetic interaction screen in Saccharomyces cerevisiae using the bir1 -17 mutant, identifying through quantitative fitness analysis deletion mutations that act as enhancers and suppressors. Gene knockouts affecting the Ctf19 kinetochore complex were identified as the strongest enhancers of bir1 -17 , while mutations affecting the large ribosomal subunit or the mRNA nonsense-mediated decay pathway caused strong phenotypic suppression. Thus, cells lacking a functional Ctf19 complex become highly dependent on Bir1 function and vice versa. The negative genetic interaction profiles of bir1 -17 and the cohesin mutant mcd1 -1 showed considerable overlap, underlining the strong functional connection between sister chromatid cohesion and chromosome biorientation. Loss of some Ctf19 components, such as Iml3 or Chl4 , impacted differentially on bir1 -17 compared with mutations affecting other CPC components: despite the synthetic lethality shown by either iml3 or chl4 in combination with bir1 -17 , neither gene knockout showed any genetic interaction with either ipl1 -321 or sli15 -3 . Our data therefore imply a specific functional connection between the Ctf19 complex and Bir1 that is not shared with Ipl1 .
    Electronic ISSN: 2160-1836
    Topics: Biology
    Published by Genetics Society of America (GSA)
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  • 10
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    Tailored Extraction Procedure Is Required To Ensure Recovery of the Main Lipid Classes in Whole Blood When Profiling the Lipidome of Dried Blood Spots (2016)
    American Chemical Society (ACS)
    Details
    Publication Date: 2016-09-15
    Description: Analytical Chemistry DOI: 10.1021/acs.analchem.6b03030
    Print ISSN: 0003-2700
    Electronic ISSN: 1520-6882
    Topics: Chemistry and Pharmacology
    Published by American Chemical Society (ACS)
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