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  • 1
    Publication Date: 2015-06-04
    Description: The main goal of this study was to develop a method for the extraction and indirect estimation of the quantity of calcium oxalate (CaOx) in the foliage of trees. Foliar tissue was collected from a single tree of each species (five conifers and five hardwoods) for comparison of extractions in different solvents using 10 replicates per species from the same pool of tissue. For each species, calcium (Ca) and oxalate were extracted sequentially in double deionized water and 2N acetic acid, and finally, five replicate samples were extracted in 5% (0.83N) perchloric acid (PCA) and the other five in 2N hydrochloric acid (HCl); three cycles of freezing and thawing were used for each solvent. Total ions were extracted by microwave digestion. Calcium was quantified with an inductively coupled plasma emission spectrophotometer method and oxalate was eluted and quantified using a high performance liquid chromatography method. This experiment was repeated again with two conifer and two hardwood species using four trees per species, and two analytical replicates for each tree. We report here that, regardless of age of individual trees within a species, time of collection or species type, the third extraction in PCA or HCl resulted in near equimolar quantities of Ca and oxalate ( r 2  ≥ 0.99). This method provides an easy estimate of the quantity of CaOx crystals using a small sample of foliar tissue. An additional benefit of PCA is that it precipitates the nucleic acids and proteins, allowing the quantification of several free/soluble metabolites such as amino acids, polyamines, organic acids and inorganic elements all from a single sample extract.
    Print ISSN: 0829-318X
    Electronic ISSN: 1758-4469
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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  • 2
    Publication Date: 2011-05-26
    Description: For thousands of years, humans have inhabited locations that are highly vulnerable to the impacts of climate change, earthquakes, and floods. In order to investigate the extent to which Holocene environmental changes may have impacted on cultural evolution, we present new geologic, geomorphic, and chronologic data from the Qazvin Plain in northwest Iran that provides a backdrop of natural environmental changes for the simultaneous cultural dynamics observed on the Central Iranian Plateau. Well-resolved archaeological data from the neighbouring settlements of Zagheh (7170—6300 yr BP), Ghabristan (6215—4950 yr BP) and Sagzabad (4050—2350 yr BP) indicate that Holocene occupation of the Hajiarab alluvial fan was interrupted by a 900 year settlement hiatus. Multiproxy climate data from nearby lakes in northwest Iran suggest a transition from arid early-Holocene conditions to more humid middle-Holocene conditions from c . 7550 to 6750 yr BP, coinciding with the settlement of Zagheh, and a peak in aridity at c . 4550 yr BP during the settlement hiatus. Palaeoseismic investigations indicate that large active fault systems in close proximity to the tell sites incurred a series of large (M W ~7.1) earthquakes with return periods of ~500—1000 years during human occupation of the tells. Mapping and optically stimulated luminescence (OSL) chronology of the alluvial sequences reveals changes in depositional style from coarse-grained unconfined sheet flow deposits to proximal channel flow and distally prograding alluvial deposits sometime after c . 8830 yr BP, possibly reflecting an increase in moisture following the early-Holocene arid phase. The coincidence of major climate changes, earthquake activity, and varying sedimentation styles with changing patterns of human occupation on the Hajiarab fan indicate links between environmental and anthropogenic systems. However, temporal coincidence does not necessitate a fundamental causative dependency.
    Print ISSN: 0959-6836
    Electronic ISSN: 1477-0911
    Topics: Geography , Geosciences
    Published by Sage
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  • 3
    Publication Date: 2009-01-13
    Description: Germline polymorphisms in model organisms and humans influence susceptibility to complex trait diseases such as inflammation and cancer. Mice of the Mus spretus species are resistant to tumour development, and crosses between M. spretus and susceptible Mus musculus strains have been used to map locations of genetic variants that contribute to skin cancer susceptibility. We have integrated germline polymorphisms with gene expression in normal skin from a M. musculus x M. spretus backcross to generate a network view of the gene expression architecture of mouse skin. Here we demonstrate how this approach identifies expression motifs that contribute to tissue organization and biological functions related to inflammation, haematopoiesis, cell cycle control and tumour susceptibility. Motifs associated with inflammation, epidermal barrier function and proliferation are differentially regulated in backcross mice susceptible or resistant to tumour development. The intestinal stem cell marker Lgr5 is identified as a candidate master regulator of the hair follicle, and the vitamin D receptor (Vdr) is linked to coordinated control of epidermal barrier function, inflammation and tumour susceptibility.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4460995/" 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/PMC4460995/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Quigley, David A -- To, Minh D -- Perez-Losada, Jesus -- Pelorosso, Facundo G -- Mao, Jian-Hua -- Nagase, Hiroki -- Ginzinger, David G -- Balmain, Allan -- P01 AR050440/AR/NIAMS NIH HHS/ -- U01 CA084244/CA/NCI NIH HHS/ -- U01 CA141455/CA/NCI NIH HHS/ -- England -- Nature. 2009 Mar 26;458(7237):505-8. doi: 10.1038/nature07683. Epub 2009 Jan 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19136944" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Cycle/genetics ; Crosses, Genetic ; Female ; Gene Expression Regulation/genetics ; Genetic Predisposition to Disease/*genetics ; Hair Follicle/metabolism ; Hematopoiesis/genetics ; Inflammation/*genetics/pathology ; Male ; Mice ; Quantitative Trait Loci ; Receptors, Calcitriol/genetics/metabolism ; Receptors, G-Protein-Coupled/genetics/metabolism ; Skin/*metabolism/*pathology ; Skin Neoplasms/*genetics/*pathology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2013-03-30
    Description: Mutations in the nuclear membrane zinc metalloprotease ZMPSTE24 lead to diseases of lamin processing (laminopathies), such as the premature aging disease progeria and metabolic disorders. ZMPSTE24 processes prelamin A, a component of the nuclear lamina intermediate filaments, by cleaving it at two sites. Failure of this processing results in accumulation of farnesylated, membrane-associated prelamin A. The 3.4 angstrom crystal structure of human ZMPSTE24 has a seven transmembrane alpha-helical barrel structure, surrounding a large, water-filled, intramembrane chamber, capped by a zinc metalloprotease domain with the catalytic site facing into the chamber. The 3.8 angstrom structure of a complex with a CSIM tetrapeptide showed that the mode of binding of the substrate resembles that of an insect metalloprotease inhibitor in thermolysin. Laminopathy-associated mutations predicted to reduce ZMPSTE24 activity map to the zinc metalloprotease peptide-binding site and to the bottom of the chamber.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Quigley, Andrew -- Dong, Yin Yao -- Pike, Ashley C W -- Dong, Liang -- Shrestha, Leela -- Berridge, Georgina -- Stansfeld, Phillip J -- Sansom, Mark S P -- Edwards, Aled M -- Bountra, Chas -- von Delft, Frank -- Bullock, Alex N -- Burgess-Brown, Nicola A -- Carpenter, Elisabeth P -- 092809/Wellcome Trust/United Kingdom -- Canadian Institutes of Health Research/Canada -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2013 Mar 29;339(6127):1604-7. doi: 10.1126/science.1231513.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Genomics Consortium, University of Oxford, Oxford, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23539603" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Catalytic Domain ; Crystallography, X-Ray ; Humans ; Lamin Type A ; Membrane Proteins/*chemistry/genetics ; Metabolism, Inborn Errors/genetics/*metabolism ; Metalloendopeptidases/*chemistry/genetics ; Molecular Sequence Data ; Nuclear Proteins/chemistry/genetics/*metabolism ; Progeria/genetics/metabolism ; Protein Conformation ; Protein Precursors/chemistry/genetics/*metabolism ; Substrate Specificity ; Thermolysin/chemistry
    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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  • 5
    Publication Date: 2014-11-05
    Description: Next-generation sequencing of human tumours has refined our understanding of the mutational processes operative in cancer initiation and progression, yet major questions remain regarding the factors that induce driver mutations and the processes that shape mutation selection during tumorigenesis. Here we performed whole-exome sequencing on adenomas from three mouse models of non-small-cell lung cancer, which were induced either by exposure to carcinogens (methyl-nitrosourea (MNU) and urethane) or by genetic activation of Kras (Kras(LA2)). Although the MNU-induced tumours carried exactly the same initiating mutation in Kras as seen in the Kras(LA2) model (G12D), MNU tumours had an average of 192 non-synonymous, somatic single-nucleotide variants, compared with only six in tumours from the Kras(LA2) model. By contrast, the Kras(LA2) tumours exhibited a significantly higher level of aneuploidy and copy number alterations compared with the carcinogen-induced tumours, suggesting that carcinogen-induced and genetically engineered models lead to tumour development through different routes. The wild-type allele of Kras has been shown to act as a tumour suppressor in mouse models of non-small-cell lung cancer. We demonstrate that urethane-induced tumours from wild-type mice carry mostly (94%) Kras Q61R mutations, whereas those from Kras heterozygous animals carry mostly (92%) Kras Q61L mutations, indicating a major role for germline Kras status in mutation selection during initiation. The exome-wide mutation spectra in carcinogen-induced tumours overwhelmingly display signatures of the initiating carcinogen, while adenocarcinomas acquire additional C 〉 T mutations at CpG sites. These data provide a basis for understanding results from human tumour genome sequencing, which has identified two broad categories of tumours based on the relative frequency of single-nucleotide variations and copy number alterations, and underline the importance of carcinogen models for understanding the complex mutation spectra seen in human cancers.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4304785/" 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/PMC4304785/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Westcott, Peter M K -- Halliwill, Kyle D -- To, Minh D -- Rashid, Mamunur -- Rust, Alistair G -- Keane, Thomas M -- Delrosario, Reyno -- Jen, Kuang-Yu -- Gurley, Kay E -- Kemp, Christopher J -- Fredlund, Erik -- Quigley, David A -- Adams, David J -- Balmain, Allan -- 082356/Wellcome Trust/United Kingdom -- 13031/Cancer Research UK/United Kingdom -- A12401/Cancer Research UK/United Kingdom -- A13031/Cancer Research UK/United Kingdom -- A14356/Cancer Research UK/United Kingdom -- F31 CA180669/CA/NCI NIH HHS/ -- F31 CA180715/CA/NCI NIH HHS/ -- R01 CA111834/CA/NCI NIH HHS/ -- R01 CA184510/CA/NCI NIH HHS/ -- T32 GM007175/GM/NIGMS NIH HHS/ -- T32GM007175/GM/NIGMS NIH HHS/ -- U01 CA084244/CA/NCI NIH HHS/ -- U01 CA141455/CA/NCI NIH HHS/ -- U01 CA176287/CA/NCI NIH HHS/ -- U01 CA84244/CA/NCI NIH HHS/ -- UO1 CA176287/CA/NCI NIH HHS/ -- Cancer Research UK/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2015 Jan 22;517(7535):489-92. doi: 10.1038/nature13898. Epub 2014 Nov 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA [2] Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, USA. ; Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA. ; Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK. ; Department of Pathology, University of California San Francisco, San Francisco, California 94143, USA. ; Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA. ; Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institute, Stockholm 171 21, Sweden. ; 1] Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California 94158, USA [2] Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California 94158, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25363767" target="_blank"〉PubMed〈/a〉
    Keywords: Adenocarcinoma/chemically induced/genetics ; Animals ; Carcinogens/toxicity ; Carcinoma, Non-Small-Cell Lung/chemically induced/genetics ; Cell Transformation, Neoplastic/*chemically induced/*genetics ; DNA Copy Number Variations/genetics ; Disease Progression ; Female ; Genes, ras/*genetics ; Genomic Instability/genetics ; Germ-Line Mutation/genetics ; Humans ; Lung Neoplasms/*chemically induced/*genetics ; Male ; Methylnitrosourea/toxicity ; Mice ; Models, Genetic ; Mutation/*genetics ; Oncogene Protein p21(ras)/*genetics ; Point Mutation/genetics ; Proto-Oncogene Proteins p21(ras)/*genetics ; Urethane/toxicity
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 6
    Publication Date: 2015-03-15
    Description: TREK-2 (KCNK10/K2P10), a two-pore domain potassium (K2P) channel, is gated by multiple stimuli such as stretch, fatty acids, and pH and by several drugs. However, the mechanisms that control channel gating are unclear. Here we present crystal structures of the human TREK-2 channel (up to 3.4 angstrom resolution) in two conformations and in complex with norfluoxetine, the active metabolite of fluoxetine (Prozac) and a state-dependent blocker of TREK channels. Norfluoxetine binds within intramembrane fenestrations found in only one of these two conformations. Channel activation by arachidonic acid and mechanical stretch involves conversion between these states through movement of the pore-lining helices. These results provide an explanation for TREK channel mechanosensitivity, regulation by diverse stimuli, and possible off-target effects of the serotonin reuptake inhibitor Prozac.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dong, Yin Yao -- Pike, Ashley C W -- Mackenzie, Alexandra -- McClenaghan, Conor -- Aryal, Prafulla -- Dong, Liang -- Quigley, Andrew -- Grieben, Mariana -- Goubin, Solenne -- Mukhopadhyay, Shubhashish -- Ruda, Gian Filippo -- Clausen, Michael V -- Cao, Lishuang -- Brennan, Paul E -- Burgess-Brown, Nicola A -- Sansom, Mark S P -- Tucker, Stephen J -- Carpenter, Elisabeth P -- 084655/Wellcome Trust/United Kingdom -- 092809/Z/10/Z/Wellcome Trust/United Kingdom -- Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2015 Mar 13;347(6227):1256-9. doi: 10.1126/science.1261512.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK. ; Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK. Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK. ; Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK. OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 3PN, UK. ; Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK. OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 3PN, UK. Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK. ; Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK. Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK. ; Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK. ; Pfizer Neusentis, Granta Park, Cambridge CB21 6GS, UK. ; OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 3PN, UK. Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK. ; Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK. OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 3PN, UK. liz.carpenter@sgc.ox.ac.uk stephen.tucker@physics.ox.ac.uk. ; Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK. OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 3PN, UK. liz.carpenter@sgc.ox.ac.uk stephen.tucker@physics.ox.ac.uk.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25766236" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arachidonic Acid/pharmacology ; Binding Sites ; Crystallography, X-Ray ; Fluoxetine/analogs & derivatives/chemistry/metabolism/pharmacology ; Humans ; *Ion Channel Gating ; Models, Molecular ; Molecular Dynamics Simulation ; Molecular Sequence Data ; Potassium/metabolism ; Potassium Channels, Tandem Pore Domain/antagonists & ; inhibitors/*chemistry/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary
    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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  • 7
    Electronic Resource
    Electronic Resource
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 75 (1994), S. 58-62 
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The pressure dependencies of the zero-dispersion wavelength λ0 for dispersion-shifted fiber on the spool and in a submarine lightwave (SL) cabled sample were measured using pressures P up to 10 kpsi. The spool results showed a mean zero-dispersion shift dλ0/dP of close to +0.04 nm/kpsi. The corresponding shift for the SL cabled fiber was much smaller (less than 0.01 nm/kpsi) and the results were much less reproducible. This was believed to be due to the pressure-shielding effect of the cable structure. A theoretical calculation of dλ0/dP has been carried out for the unshielded fiber using a two-term (electronic and lattice) Sellmeier formalism. Assuming the dominant effect to be of fiber material (rather than waveguide design) origin, we find that the electronic and lattice contributions are of opposite sign with a resultant that agrees with experiment to within the combined accuracy of the experiment and theory.
    Type of Medium: Electronic Resource
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  • 8
    Publication Date: 2019
    Description: Abstract We use Coulomb stress change (CSC) analyses and seismicity data to model the physical and statistical behavior of the multifault source of the 4 September 2010 Mw 7.1 Darfield earthquake in New Zealand. Geodetic and seismologic data indicate this earthquake initiated on a severely misoriented reverse fault and propagated across a structurally complex fault network including optimally oriented faults. The observed rupture sequence is most successfully modeled if maximum CSC imposed by rupture of the hypocentral fault on to receiver faults exceeds theoretical threshold values of 1 to 5 MPa that are assigned based on fault slip tendency and stress drop analyses. CSC modeling using the same criteria but initiating the earthquake on other faults in the network results in a multifault rupture cascade for five of seven scenarios. Analysis of earthquake frequency‐magnitude distributions indicates that a Gutenberg‐Richter frequency‐magnitude distribution for the near‐source region cannot be rejected in favor of a characteristic earthquake distribution. However, characteristic behavior is more favored probabilistically because ruptures initiating on individual source faults in the system are statistically more likely to cascade into multifault ruptures with larger amalgamated Mw (Mwmax = 7.1) than to remain confined to the hypocentral source fault (Mw = 6.3 to 6.8). Our favored hypothesis is that system rupture behavior is regulated by misoriented faults that occupy critical geometric positions within the network, as previously proposed for the 2010 El Mayor‐Cucapah earthquake in Baja California. Other fault networks globally may exhibit similar physical and statistical behaviors.
    Print ISSN: 2169-9313
    Electronic ISSN: 2169-9356
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 9
  • 10
    Publication Date: 1994-01-01
    Print ISSN: 0021-8979
    Electronic ISSN: 1089-7550
    Topics: Physics
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