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  • 1
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    P-V-T equation of state and high-pressure behavior of CaCO3 aragonite (2015)
    Mineralogical Society of America
    Details
    Publication Date: 2015-10-02
    Description: The equation of state of aragonite was determined by in situ synchrotron X-ray diffraction experiments on a hot-pressed polycrystalline specimen of aragonite within its stability field up to 5.8 GPa and 1173 K. As a complement to this experimental study, first-principle density functional theory calculations were performed up to 20 GPa at 0 K. Thermoelastic parameters for aragonite (CaCO 3 ) were derived by a least-squares fit of the experimental P-V-T data to the third-order Birch-Murnaghan equation of state (EOS), yielding the bulk modulus and its pressure and temperature derivatives K 0 = 65.24 ± 0.24 GPa, K ' 0 = 4.95 ± 0.12, ( K T / T ) P = –0.024 ± 0.002 GPa/K and volume thermal expansion α 300 = (6.1 ± 0.7) x 10 –5 K –1 . The analyses of the axial compressibility at ambient temperature show that the c -axis is much more compressible than the a - and b- axes. Based on first-principle calculations, the anisotropic compression behavior of aragonite structure is explained by the heterogeneous shortening of 〈Ca-O〉 and 〈C-O〉 bond lengths and the rotation of 〈O-C-O〉 angles along the a -, b -, and c -axes, whereas the unit-cell volume change of aragonite under compression is accommodated by comparable compression rate of the CaO 9 polyhedra and the voids in the crystal lattice. The results attained from this study provide important thermoelastic parameters for understanding the thermodynamic behavior and chemical reactions involving aragonite at subduction zone conditions.
    Print ISSN: 0003-004X
    Electronic ISSN: 1945-3027
    Topics: Geosciences
    Published by Mineralogical Society of America
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  • 2
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    Elasticity and phase transformation at high pressure in coesite from experiments and first-principles calculations (2016)
    Mineralogical Society of America
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    Publication Date: 2016-05-03
    Description: The crystal structure and equation of state of coesite (space group C 2 /c ) and its high-pressure polymorph coesite-II (space group P 2 1 /n ) under pressure have been studied using X-ray powder diffraction in a diamond-anvil cell (DAC) up to 31 GPa at room-temperature and first-principles calculations at 0 K up to 45 GPa. New diffraction peaks appear above 20 GPa, indicating the formation of coesite-II structure. The calculated enthalpies provide theoretical support for the pressure-induced phase transformation from coesite to coesite-II at ~21.4 GPa. Compared with coesite, the coesite-II structure is characterized by a "doubled" b -axis and the breakdown of the linear Si1-O1-Si1 angle in coesite into two distinct angles—one is ~176°, close to linear, whereas the other decreases by 22 to 158°. Coesite is very anisotropic with the a -axis the shortest and twice more compressible than the b- and c -axis. By comparison, coesite-II is not so anisotropic with similar compressibilities in its a -, b -, and c -axis. As analyzed by a third-order Eulerian finite strain equation of state, the bulk modulus of coesite at 21.4 GPa is 182.3 GPa, and that of coesite-II is 140.8 GPa, indicating that coesite-II is much more compressible than coesite. The existence of coesite-II in the coldest subduction zone will change the elasticity and anisotropic properties of the subducting materials dramatically.
    Print ISSN: 0003-004X
    Electronic ISSN: 1945-3027
    Topics: Geosciences
    Published by Mineralogical Society of America
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  • 3
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    A highly effective and adjustable dual plasmid system for O-GlcNAcylated recombinant protein production in E. coli (2015)
    Oxford University Press
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    Publication Date: 2015-05-28
    Description: O -GlcNAcylation is a ubiquitous, dynamic and reversible post-translational protein modification in metazoans, and it is catalysed and removed by O -GlcNAc transferase (OGT) and O -GlcNAcase, respectively. Prokaryotes lack endogenous OGT activity. It has been reported that coexpression of mammalian OGT with its target substrates in Escherichia coli produce O -GlcNAcylated recombinant proteins, but the plasmids used were not compatible, and the expression of both OGT and its target protein were induced by the same inducer. Here, we describe a compatible dual plasmid system for coexpression of OGT and its target substrate for O -GlcNAcylated protein production in E. coli . The approach was validated using the CKII and p53 protein as control. This compatible dual plasmid system contains an arabinose-inducible OGT expression vector with a pUC origin and an isopropyl β - d -thiogalactopyranoside-inducible OGT target substrate expression vector bearing a p15A origin. The dual plasmid system produces recombinant proteins with varying O -GlcNAcylation levels by altering the inducer concentration. More importantly, the O -GlcNAcylation efficiency was much higher than the previously reported system. Altogether, we established an adjustable compatible dual plasmid system that can effectively yield O -GlcNAcylated proteins in E. coli .
    Print ISSN: 0021-924X
    Electronic ISSN: 1756-2651
    Topics: Biology , Chemistry and Pharmacology
    Published by Oxford University Press on behalf of The Japanese Biochemical Society (JBS).
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  • 4
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    Alterations in Ovarian Cancer Cell Adhesion Drive Taxol Resistance by Increasing Microtubule Dynamics in a FAK-dependent Manner (2015)
    Springer Nature
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    Publication Date: 2015-04-18
    Description: Chemorefractory ovarian cancer patients show extremely poor prognosis. Microtubule-stabilizing Taxol (paclitaxel) is a first-line treatment against ovarian cancer. Despite the close interplay between microtubules and cell adhesion, it remains unknown if chemoresistance alters the way cells adhere to their extracellular environment, a process critical for cancer metastasis. To investigate this, we isolated Taxol-resistant populations of OVCAR3 and SKOV3 ovarian cancer cell lines. Though Taxol-resistant cells neither effluxed more drug nor gained resistance to other chemotherapeutics, they did display increased microtubule dynamics. These changes in microtubule dynamics coincided with faster attachment rates and decreased adhesion strength, which correlated with increased surface β1-integrin expression and decreased focal adhesion formation, respectively. Adhesion strength correlated best with Taxol-sensitivity, and was found to be independent of microtubule polymerization but dependent on focal adhesion kinase (FAK), which was up-regulated in Taxol-resistant cells. FAK inhibition also decreased microtubule dynamics to equal levels in both populations, indicating alterations in adhesive signaling are up-stream of microtubule dynamics. Taken together, this work demonstrates that Taxol-resistance dramatically alters how ovarian cancer cells adhere to their extracellular environment causing down-stream increases in microtubule dynamics, providing a therapeutic target that may improve prognosis by not only recovering drug sensitivity, but also decreasing metastasis. Scientific Reports 5 doi: 10.1038/srep09529
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
    Published by Springer Nature
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  • 5
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    Thermodynamically stabilized {beta}-CsPbI3-based perovskite solar cells with efficiencies 〉18% (2019)
    American Association for the Advancement of Science (AAAS)
    In: Science
    Details
    Publication Date: 2019
    Description: 〈p〉Although β-CsPbI〈sub〉3〈/sub〉 has a bandgap favorable for application in tandem solar cells, depositing and stabilizing β-CsPbI〈sub〉3〈/sub〉 experimentally has remained a challenge. We obtained highly crystalline β-CsPbI〈sub〉3〈/sub〉 films with an extended spectral response and enhanced phase stability. Synchrotron-based x-ray scattering revealed the presence of highly oriented β-CsPbI〈sub〉3〈/sub〉 grains, and sensitive elemental analyses—including inductively coupled plasma mass spectrometry and time-of-flight secondary ion mass spectrometry—confirmed their all-inorganic composition. We further mitigated the effects of cracks and pinholes in the perovskite layer by surface treating with choline iodide, which increased the charge-carrier lifetime and improved the energy-level alignment between the β-CsPbI〈sub〉3〈/sub〉 absorber layer and carrier-selective contacts. The perovskite solar cells made from the treated material have highly reproducible and stable efficiencies reaching 18.4% under 45 ± 5°C ambient conditions.〈/p〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 6
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    CRISPR-ERA: a comprehensive design tool for CRISPR-mediated gene editing, repression and activation (2015)
    Oxford University Press
    Details
    Publication Date: 2015-11-05
    Description: : The CRISPR/Cas9 system was recently developed as a powerful and flexible technology for targeted genome engineering, including genome editing (altering the genetic sequence) and gene regulation (without altering the genetic sequence). These applications require the design of single guide RNAs (sgRNAs) that are efficient and specific. However, this remains challenging, as it requires the consideration of many criteria. Several sgRNA design tools have been developed for gene editing, but currently there is no tool for the design of sgRNAs for gene regulation. With accumulating experimental data on the use of CRISPR/Cas9 for gene editing and regulation, we implement a comprehensive computational tool based on a set of sgRNA design rules summarized from these published reports. We report a genome-wide sgRNA design tool and provide an online website for predicting sgRNAs that are efficient and specific. We name the tool CRISPR-ERA, for clustered regularly interspaced short palindromic repeat-mediated e diting, r epression, and a ctivation (ERA). Availability and implementation : http://CRISPR-ERA.stanford.edu . Contact : stanley.qi@stanford.edu or xwwang@tsinghua.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 7
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    Cements, sulfate, and Burgess Shale preservation [Letters (Online Only)] (2012)
    National Academy of Sciences
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    Publication Date: 2012-07-11
    Description: In his work, Butterfield (1) makes several claims about carbonate cements in the Walcott Quarry Member of the Burgess Shale, including the contention that they are not regularly associated with fossil-bearing beds. This claim is inaccurate. Each millimeter- to centimeter-scale bed within the interval is cemented by calcite (figures 2–5 in ref. 2), including the exceptionally fossiliferous Great Marella Layer referred to in the work (1), which contains cements dispersed throughout its thickness and a prominently-cemented top (Fig. 1). The work by Butterfield (1) also suggests that the carbonate cements in the Burgess Shale were derived from recrystallization of coarse-grained...
    Keywords: Letters
    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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  • 8
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    Phononic Frequency Combs through Nonlinear Resonances (2014)
    American Physical Society (APS)
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    Publication Date: 2014-02-22
    Description: Author(s): L. S. Cao, D. X. Qi, R. W. Peng, Mu Wang, and P. Schmelcher We explore an analogue of optical frequency combs in driven nonlinear phononic systems, and present a mechanism for generating phononic frequency combs through nonlinear resonances. In the underlying process, a set of phonon modes is simultaneously excited by the external driving which yields freque... [Phys. Rev. Lett. 112, 075505] Published Fri Feb 21, 2014
    Keywords: Condensed Matter: Structure, etc.
    Print ISSN: 0031-9007
    Electronic ISSN: 1079-7114
    Topics: Physics
    Published by American Physical Society (APS)
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  • 9
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    Retromer is required for apoptotic cell clearance by phagocytic receptor recycling (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-02-06
    Description: The cell surface receptor CED-1 mediates apoptotic cell recognition by phagocytic cells, enabling cell corpse clearance in Caenorhabditis elegans. Here, we found that the C. elegans intracellular protein sorting complex, retromer, was required for cell corpse clearance by mediating the recycling of CED-1. Retromer was recruited to the surfaces of phagosomes containing cell corpses, and its loss of function caused defective cell corpse removal. The retromer probably acted through direct interaction with CED-1 in the cell corpse recognition pathway. In the absence of retromer function, CED-1 associated with lysosomes and failed to recycle from phagosomes and cytosol to the plasma membrane. Thus, retromer is an essential mediator of apoptotic cell clearance by regulating phagocytic receptor(s) during cell corpse engulfment.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Didi -- Xiao, Hui -- Zhang, Kai -- Wang, Bin -- Gao, Zhiyang -- Jian, Youli -- Qi, Xiaying -- Sun, Jianwei -- Miao, Long -- Yang, Chonglin -- New York, N.Y. -- Science. 2010 Mar 5;327(5970):1261-4. doi: 10.1126/science.1184840. Epub 2010 Feb 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Key Laboratory of Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Datun Road, Chaoyang District, Beijing 100101, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20133524" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; *Apoptosis ; Caenorhabditis elegans/cytology/genetics/*physiology ; Caenorhabditis elegans Proteins/genetics/*metabolism ; Cell Membrane/metabolism ; Lysosomes/metabolism ; Membrane Proteins/*metabolism ; Microscopy, Electron, Transmission ; Molecular Sequence Data ; *Phagocytosis ; Phagosomes/*metabolism ; *Protein Transport ; RNA Interference ; Recombinant Fusion Proteins/metabolism ; Sorting Nexins ; Vesicular Transport Proteins/genetics/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 10
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    Editing of CD1d-bound lipid antigens by endosomal lipid transfer proteins (2003)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2003-12-20
    Description: It is now established that CD1 molecules present lipid antigens to T cells, although it is not clear how the exchange of lipids between membrane compartments and the CD1 binding groove is assisted. We report that mice deficient in prosaposin, the precursor to a family of endosomal lipid transfer proteins (LTP), exhibit specific defects in CD1d-mediated antigen presentation and lack Valpha14 NKT cells. In vitro, saposins extracted monomeric lipids from membranes and from CD1, thereby promoting the loading as well as the editing of lipids on CD1. Transient complexes between CD1, lipid, and LTP suggested a "tug-of-war" model in which lipid exchange between CD1 and LTP is on the basis of their respective affinities for lipids. LTPs constitute a previously unknown link between lipid metabolism and immunity and are likely to exert a profound influence on the repertoire of self, tumor, and microbial lipid antigens.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918537/" 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/PMC2918537/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhou, Dapeng -- Cantu, Carlos 3rd -- Sagiv, Yuval -- Schrantz, Nicolas -- Kulkarni, Ashok B -- Qi, Xiaoyang -- Mahuran, Don J -- Morales, Carlos R -- Grabowski, Gregory A -- Benlagha, Kamel -- Savage, Paul -- Bendelac, Albert -- Teyton, Luc -- 10435/Canadian Institutes of Health Research/Canada -- AI38339/AI/NIAID NIH HHS/ -- AI50867/AI/NIAID NIH HHS/ -- P01 AI53725/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2004 Jan 23;303(5657):523-7. Epub 2003 Dec 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology, University of Chicago, Chicago, IL 60637, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14684827" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Antigen Presentation ; Antigen-Presenting Cells/immunology/metabolism ; Antigens, CD1/*immunology/metabolism ; Antigens, CD1d ; Carrier Proteins/*metabolism ; Endosomes/*metabolism ; G(M2) Activator Protein ; Glycolipids/immunology ; Glycoproteins/deficiency/genetics/metabolism/*physiology ; Killer Cells, Natural/immunology ; Lipid Metabolism ; Lipids/*immunology ; Mice ; Proteins/metabolism ; Receptors, Antigen, T-Cell/immunology ; Saposins ; Sphingolipid Activator Proteins ; T-Lymphocytes/*immunology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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