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  • 1
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    Genome analysis of the platypus reveals unique signatures of evolution (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-05-10
    Description: We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic innovations. We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology. Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified. Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2803040/" 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/PMC2803040/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Warren, Wesley C -- Hillier, LaDeana W -- Marshall Graves, Jennifer A -- Birney, Ewan -- Ponting, Chris P -- Grutzner, Frank -- Belov, Katherine -- Miller, Webb -- Clarke, Laura -- Chinwalla, Asif T -- Yang, Shiaw-Pyng -- Heger, Andreas -- Locke, Devin P -- Miethke, Pat -- Waters, Paul D -- Veyrunes, Frederic -- Fulton, Lucinda -- Fulton, Bob -- Graves, Tina -- Wallis, John -- Puente, Xose S -- Lopez-Otin, Carlos -- Ordonez, Gonzalo R -- Eichler, Evan E -- Chen, Lin -- Cheng, Ze -- Deakin, Janine E -- Alsop, Amber -- Thompson, Katherine -- Kirby, Patrick -- Papenfuss, Anthony T -- Wakefield, Matthew J -- Olender, Tsviya -- Lancet, Doron -- Huttley, Gavin A -- Smit, Arian F A -- Pask, Andrew -- Temple-Smith, Peter -- Batzer, Mark A -- Walker, Jerilyn A -- Konkel, Miriam K -- Harris, Robert S -- Whittington, Camilla M -- Wong, Emily S W -- Gemmell, Neil J -- Buschiazzo, Emmanuel -- Vargas Jentzsch, Iris M -- Merkel, Angelika -- Schmitz, Juergen -- Zemann, Anja -- Churakov, Gennady -- Kriegs, Jan Ole -- Brosius, Juergen -- Murchison, Elizabeth P -- Sachidanandam, Ravi -- Smith, Carly -- Hannon, Gregory J -- Tsend-Ayush, Enkhjargal -- McMillan, Daniel -- Attenborough, Rosalind -- Rens, Willem -- Ferguson-Smith, Malcolm -- Lefevre, Christophe M -- Sharp, Julie A -- Nicholas, Kevin R -- Ray, David A -- Kube, Michael -- Reinhardt, Richard -- Pringle, Thomas H -- Taylor, James -- Jones, Russell C -- Nixon, Brett -- Dacheux, Jean-Louis -- Niwa, Hitoshi -- Sekita, Yoko -- Huang, Xiaoqiu -- Stark, Alexander -- Kheradpour, Pouya -- Kellis, Manolis -- Flicek, Paul -- Chen, Yuan -- Webber, Caleb -- Hardison, Ross -- Nelson, Joanne -- Hallsworth-Pepin, Kym -- Delehaunty, Kim -- Markovic, Chris -- Minx, Pat -- Feng, Yucheng -- Kremitzki, Colin -- Mitreva, Makedonka -- Glasscock, Jarret -- Wylie, Todd -- Wohldmann, Patricia -- Thiru, Prathapan -- Nhan, Michael N -- Pohl, Craig S -- Smith, Scott M -- Hou, Shunfeng -- Nefedov, Mikhail -- de Jong, Pieter J -- Renfree, Marilyn B -- Mardis, Elaine R -- Wilson, Richard K -- 062023/Wellcome Trust/United Kingdom -- HG002238/HG/NHGRI NIH HHS/ -- MC_U137761446/Medical Research Council/United Kingdom -- P01 CA013106/CA/NCI NIH HHS/ -- P01 CA013106-37/CA/NCI NIH HHS/ -- R01 GM59290/GM/NIGMS NIH HHS/ -- R01 HG002939/HG/NHGRI NIH HHS/ -- R01 HG004037/HG/NHGRI NIH HHS/ -- R01 HG004037-02/HG/NHGRI NIH HHS/ -- R01HG02385/HG/NHGRI NIH HHS/ -- Medical Research Council/United Kingdom -- England -- Nature. 2008 May 8;453(7192):175-83. doi: 10.1038/nature06936.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA. wwarren@wustl.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18464734" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Composition ; Dentition ; *Evolution, Molecular ; Female ; Genome/*genetics ; Genomic Imprinting/genetics ; Humans ; Immunity/genetics ; Male ; Mammals/genetics ; MicroRNAs/genetics ; Milk Proteins/genetics ; Phylogeny ; Platypus/*genetics/immunology/physiology ; Receptors, Odorant/genetics ; Repetitive Sequences, Nucleic Acid/genetics ; Reptiles/genetics ; Sequence Analysis, DNA ; Spermatozoa/metabolism ; Venoms/genetics ; Zona Pellucida/metabolism
    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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  • 2
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    Crystal structure of (Z)-N-benzylidene-1-phenylmethanamine oxide hydrogen peroxide monosolvate (2017)
    International Union of Crystallography (IUC)
    Details
    Publication Date: 2017-10-21
    Description: The title adduct, C14H13NO·H2O2, consists of (Z)-N-benzylidene-1-phenylmethanamine oxide and hydrogen peroxide molecules in a 1:1 ratio. The organic coformer adopts a skew geometry with an inter-aryl-ring dihedral angle of 81.9 (2)°. In the crystal, the organic and peroxide molecules are linked through both peroxide O—H donor groups to oxide O-atom acceptors, giving one-dimensional chains extending along the b axis. Present also are weak intermolecular C—H...O hydrogen-bonding interactions.
    Keywords: crystal structureperoxosolvateN-oxidenitronehydrogen-bond motif
    Electronic ISSN: 1600-5368
    Topics: Chemistry and Pharmacology , Geosciences
    Published by International Union of Crystallography (IUC)
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  • 3
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    Di-μ-pyridyl-1:2κ2N:C2;2:1κ2N:C2-μ-tetrahydrofuran-κ2O:O-bis[bromo(tetrahydrofuran)magnesium(II)] tetrahydrofuran hemisolvate (2016)
    International Union of Crystallography (IUC)
    Details
    Publication Date: 2016-12-01
    Description: The title compound, [Mg2Br2(C5H4N)2(C4H8O)3]·0.5C4H8O, contains dimeric associations of Mg atoms bridged by tetrahydrofuran (THF) molecules. The coordination polyhedron of the Mg atom is a slightly distorted MgCNO2Br trigonal bipyramid with two THF molecules in the axial positions. One O atom occupies a site with symmetry 2.
    Electronic ISSN: 1600-5368
    Topics: Chemistry and Pharmacology , Geosciences
    Published by International Union of Crystallography (IUC)
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  • 4
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    Supramolecular Organogels Based on N-Benzyl, N′-Acylbispidinols (2019)
    Molecular Diversity Preservation International
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    Publication Date: 2019-01-11
    Description: The acylation of unsymmetrical N-benzylbispidinols in aromatic solvents without an external base led to the formation of supramolecular gels, which possess different thicknesses and degrees of stability depending on the substituents in para-positions of the benzylic group as well as on the nature of the acylating agent and of the solvent used. Structural features of the native gels as well as of their dried forms were studied by complementary techniques including Fourier-transform infrared (FTIR) and attenuated total reflection (ATR) spectroscopy, atomic force microscopy (AFM), transmission electron microscopy (TEM), scanning electron microscopy (SEM), and small-angle X-ray scattering and diffraction (SAXS). Structures of the key crystalline compounds were established by X-ray diffraction. An analysis of the obtained data allowed speculation on the crucial structural and condition factors that governed the gel formation. The most important factors were as follows: (i) absence of base, either external or internal; (ii) presence of HCl; (iii) presence of carbonyl and hydroxyl groups to allow hydrogen bonding; and (iv) presence of two (hetero)aromatic rings at both sides of the molecule. The hydrogen bonding involving amide carbonyl, hydroxyl at position 9, and, very probably, ammonium N-H+ and Cl− anion appears to be responsible for the formation of infinite molecular chains required for the first step of gel formation. Subsequent lateral cooperation of molecular chains into fibers occurred, presumably, due to the aromatic π−π-stacking interactions. Supercritical carbon dioxide drying of the organogels gave rise to aerogels with morphologies different from that of air-dried samples.
    Electronic ISSN: 2079-4991
    Topics: Physics
    Published by Molecular Diversity Preservation International
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  • 5
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    Combined X-ray Crystallographic, IR/Raman Spectroscopic, and Periodic DFT Investigations of New Multicomponent Crystalline Forms of Anthelmintic Drugs: A Case Study of Carbendazim Maleate (2020)
    Molecular Diversity Preservation International
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    Publication Date: 2020-05-21
    Description: Synthesis of multicomponent solid forms is an important method of modifying and fine-tuning the most critical physicochemical properties of drug compounds. The design of new multicomponent pharmaceutical materials requires reliable information about the supramolecular arrangement of molecules and detailed description of the intermolecular interactions in the crystal structure. It implies the use of a combination of different experimental and theoretical investigation methods. Organic salts present new challenges for those who develop theoretical approaches describing the structure, spectral properties, and lattice energy Elatt. These crystals consist of closed-shell organic ions interacting through relatively strong hydrogen bonds, which leads to Elatt 〉 200 kJ/mol. Some technical problems that a user of periodic (solid-state) density functional theory (DFT) programs encounters when calculating the properties of these crystals still remain unsolved, for example, the influence of cell parameter optimization on the Elatt value, wave numbers, relative intensity of Raman-active vibrations in the low-frequency region, etc. In this work, various properties of a new two-component carbendazim maleate crystal were experimentally investigated, and the applicability of different DFT functionals and empirical Grimme corrections to the description of the obtained structural and spectroscopic properties was tested. Based on this, practical recommendations were developed for further theoretical studies of multicomponent organic pharmaceutical crystals.
    Electronic ISSN: 1420-3049
    Topics: Chemistry and Pharmacology
    Published by Molecular Diversity Preservation International
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  • 6
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    Crystal Structures, Thermal Analysis, and Dissolution Behavior of New Solid Forms of the Antiviral Drug Arbidol with Dicarboxylic Acids (2015)
    Molecular Diversity Preservation International
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    Publication Date: 2015-12-04
    Electronic ISSN: 2073-4352
    Topics: Physics
    Published by Molecular Diversity Preservation International
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  • 7
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    Real-Time Observation of Fibrous Zeolites Reactivity in Contact with Simulated Lung Fluids (SLFs) Obtained by Atomic Force Microscope (AFM) (2019)
    Molecular Diversity Preservation International
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    Publication Date: 2019-01-29
    Description: Inhalation of fibrous erionite particles has been linked to malignant mesothelioma. Accordingly, erionite is considered the most carcinogenic mineral. The reactivity and the nature of erionite biotoxicity has been the subject of intensive research. Despite very close chemical and structural relationships between erionite and offretite, the reactivity of offretite in lung fluids remains unknown. In this paper, the interaction of erionite and offretite surfaces with simulated lung fluids was investigated by means of in situ atomic force microscope (AFM). To simulate different environments in the lungs, artificial lysosomal fluid (ALF) and Gamble’s solution were used. In ALF (4.15 〈 pH 〈 4.31) the dissolution of erionite and offretite surfaces was detected, as well as an evident removal of particles (mainly attributed to impurities) from the crystal faces. Instead, the growth of a layer of a yet unknown phase on the surface of both zeolites was observed during the interaction with Gamble’s solution (7.4 〈 pH 〈 8.48). The thickness of this layer reached a few tens of nanometers and covered all the observed areas. The understanding of the observed processes is of paramount importance, since they could be potentially involved in the mechanisms triggering the toxicological effects of erionite fibres.
    Electronic ISSN: 2075-163X
    Topics: Geosciences
    Published by Molecular Diversity Preservation International
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  • 8
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    Immobilization of (Aqueous) Cations in Low pH M-S-H Cement (2021)
    Molecular Diversity Preservation International
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    Publication Date: 2021-03-26
    Description: Incorporation of heavy metal ions in cement hydrates is of great interest for the storage and immobilization of toxic, hazardous, and radioactive wastes using cementitious matrix. Magnesium silicate hydrate (M-S-H) is a low pH alternative cementitious binder to commonly used Portland cement. Low pH cements have been considered as promising matrix for municipal and nuclear waste immobilization in the last decades. It is however crucial to assure that the incorporation of secondary ions is not detrimental for the formation of the hydration products. Herein, we investigate the early stages of formation of M-S-H from electrolyte solutions in presence of a wide range of metal cations (LiI, BaII, CsI, CrIII, FeIII, CoII, NiII, CuI, ZnII, PbII, AlIII). The final solid products obtained after 24 h have been characterized via powder X-ray diffraction (PXRD), attenuated total reflectance-Fourier transformed infrared spectroscopy (FTIR-ATR), elemental analysis via energy-dispersive X-ray spectroscopy (EDX), scanning electron microscopy (SEM), and high-resolution transmission electron microscopy (HR-TEM). In all the experiments, the main precipitated phase after 24 h was confirmed to be M-S-H with a ratio (total metal/Si) close to one. The obtained M-S-H products showed strong immobilization capacity for the secondary metal cations and can incorporate up to 30% of the total metal content at the early stages of M-S-H formation without significantly delaying the nucleation of the M-S-H. It has been observed that presence of Cr, Co, and Fe in the solution is prolonging the growth period of M-S-H. This is related to a higher average secondary metal/total metal ratio in the precipitated material. Secondary phases that co-precipitate in some of the experiments (Fe, Pb, Ni, and Zn) were also effectively trapped within in the M-S-H matrix. Barium was the only element in which the formation of a secondary carbonate phase isolated from the M-S-H precipitates was detected.
    Electronic ISSN: 2076-3417
    Topics: Natural Sciences in General
    Published by Molecular Diversity Preservation International
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  • 9
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    Two Faces of Water in the Formation and Stabilization of Multicomponent Crystals of Zwitterionic Drug-Like Compounds (2021)
    Molecular Diversity Preservation International
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    Publication Date: 2021-03-06
    Description: Two new hydrated multicomponent crystals of zwitterionic 2-aminonicotinic acid with maleic and fumaric acids have been obtained and thoroughly characterized by a variety of experimental (X-ray analysis and terahertz Raman spectroscopy) and theoretical periodic density functional theory calculations, followed by Bader analysis of the crystalline electron density) techniques. It has been found that the Raman-active band in the region of 300 cm−1 is due to the vibrations of the intramolecular O-H...O bond in the maleate anion. The energy/enthalpy of the intermolecular hydrogen bonds was estimated by several empirical approaches. An analysis of the interaction networks reflects the structure-directing role of the water molecule in the examined multicomponent crystals. A general scheme has been proposed to explain the proton transfer between the components during the formation of multicomponent crystals in water. Water molecules were found to play the key role in this process, forming a “water wire” between the COOH group of the dicarboxylic acid and the COO– group of the zwitterion and the rendering crystal lattice of the considered multicomponent crystals.
    Electronic ISSN: 2073-8994
    Topics: Mathematics
    Published by Molecular Diversity Preservation International
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  • 10
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    Pb2+ Uptake by Magnesite: The Competition between Thermodynamic Driving Force and Reaction Kinetics (2021)
    Molecular Diversity Preservation International
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    Publication Date: 2021-04-14
    Description: The thermodynamic properties of carbonate minerals suggest a possibility for the use of the abundant materials (e.g., magnesite) for removing harmful divalent heavy metals (e.g., Pb2+). Despite the favourable thermodynamic condition for such transformation, batch experiments performed in this work indicate that the kinetic of the magnesite dissolution at room temperature is very slow. Another set of co-precipitation experiments from homogenous solution in the Mg-PbII-CO2-H2O system reveal that the solids formed can be grouped into two categories depending on the Pb/Mg ratio. The atomic ratio Pb/Mg is about 1 and 10 in the Mg-rich and Pb-rich phases, respectively. Both phases show a significant enrichment in Pb if compared with the initial stoichiometry of the aqueous solutions (Pb/Mg initial = 1 × 10 − 2–1 × 10−4). Finally, the growth of {10.4} magnesite surfaces in the absence and in the presence of Pb2+ was studied by in situ atomic force microscopy (AFM) measurements. In the presence of the foreign ion, a ten-fold increase in the spreading rate of the obtuse steps was observed. Further, the effect of solution ageing was also tested. We observed the nucleation of a secondary phase that quickly grows on the {10.4} surfaces of magnesite. The preferential incorporation of Pb2+ into the solid phase observed during precipitation and the catalytic effect of Pb2+ on magnesite growth are promising results for the development of environmental remediation processes. These processes, different from the transformation of magnesite into cerussite, are not limited by the slow dissolution rate of magnesite. Precipitation and growth require an external carbon source, thus they could be combined with carbon sequestration techniques.
    Electronic ISSN: 2075-163X
    Topics: Geosciences
    Published by Molecular Diversity Preservation International
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