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  • 1
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2007-04-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sauer, Uwe -- Heinemann, Matthias -- Zamboni, Nicola -- New York, N.Y. -- Science. 2007 Apr 27;316(5824):550-1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Systems Biology, ETH Zurich, Switzerland. sauer@ethz.ch〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17463274" target="_blank"〉PubMed〈/a〉
    Keywords: Computational Biology ; Escherichia coli/*genetics/growth & development/*metabolism ; Escherichia coli Proteins/genetics/metabolism ; Genes, Bacterial ; *Metabolic Networks and Pathways/genetics ; Mutation ; *Proteome ; RNA, Bacterial/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Systems Biology/*methods ; *Transcription, Genetic
    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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  • 2
    Publication Date: 2012-05-26
    Description: The transport of pyruvate, the end product of glycolysis, into mitochondria is an essential process that provides the organelle with a major oxidative fuel. Although the existence of a specific mitochondrial pyruvate carrier (MPC) has been anticipated, its molecular identity remained unknown. We report that MPC is a heterocomplex formed by two members of a family of previously uncharacterized membrane proteins that are conserved from yeast to mammals. Members of the MPC family were found in the inner mitochondrial membrane, and yeast mutants lacking MPC proteins showed severe defects in mitochondrial pyruvate uptake. Coexpression of mouse MPC1 and MPC2 in Lactococcus lactis promoted transport of pyruvate across the membrane. These observations firmly establish these proteins as essential components of the MPC.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Herzig, Sebastien -- Raemy, Etienne -- Montessuit, Sylvie -- Veuthey, Jean-Luc -- Zamboni, Nicola -- Westermann, Benedikt -- Kunji, Edmund R S -- Martinou, Jean-Claude -- MC_U105663139/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2012 Jul 6;337(6090):93-6. doi: 10.1126/science.1218530. Epub 2012 May 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Biology, University of Geneva, Geneva, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22628554" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Anion Transport Proteins/chemistry/genetics/*metabolism ; Biological Transport ; Biosynthetic Pathways ; Culture Media ; Lactococcus lactis/genetics/metabolism ; Leucine/metabolism ; Mice ; Mitochondria/*metabolism ; Mitochondrial Membrane Transport Proteins/chemistry/genetics/*metabolism ; Mitochondrial Membranes/*metabolism ; Molecular Sequence Data ; Proprotein Convertase 1/chemistry/genetics/*metabolism ; Proprotein Convertase 2 ; Pyruvic Acid/*metabolism ; Recombinant Proteins/metabolism ; Saccharomyces cerevisiae/genetics/growth & development/metabolism ; Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism ; Thioctic Acid/biosynthesis/metabolism ; Valine/metabolism
    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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  • 3
    Publication Date: 2012-05-05
    Description: Although the network topology of metabolism is well known, understanding the principles that govern the distribution of fluxes through metabolism lags behind. Experimentally, these fluxes can be measured by (13)C-flux analysis, and there has been a long-standing interest in understanding this functional network operation from an evolutionary perspective. On the basis of (13)C-determined fluxes from nine bacteria and multi-objective optimization theory, we show that metabolism operates close to the Pareto-optimal surface of a three-dimensional space defined by competing objectives. Consistent with flux data from evolved Escherichia coli, we propose that flux states evolve under the trade-off between two principles: optimality under one given condition and minimal adjustment between conditions. These principles form the forces by which evolution shapes metabolic fluxes in microorganisms' environmental context.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schuetz, Robert -- Zamboni, Nicola -- Zampieri, Mattia -- Heinemann, Matthias -- Sauer, Uwe -- New York, N.Y. -- Science. 2012 May 4;336(6081):601-4. doi: 10.1126/science.1216882.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Systems Biology, Eidgenossische Technische Hochschule Zurich, Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22556256" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Adenosine Triphosphate/metabolism ; Aerobiosis ; Algorithms ; Bacteria/growth & development/*metabolism ; *Biological Evolution ; Biomass ; Computer Simulation ; Escherichia coli/genetics/growth & development/*metabolism ; Glucose/metabolism ; *Metabolic Networks and Pathways ; Models, Biological
    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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  • 4
    Publication Date: 2012-12-04
    Description: Mechanisms controlling the proliferative activity of neural stem and progenitor cells (NSPCs) have a pivotal role to ensure life-long neurogenesis in the mammalian brain. How metabolic programs are coupled with NSPC activity remains unknown. Here we show that fatty acid synthase (Fasn), the key enzyme of de novo lipogenesis, is highly active in adult NSPCs and that conditional deletion of Fasn in mouse NSPCs impairs adult neurogenesis. The rate of de novo lipid synthesis and subsequent proliferation of NSPCs is regulated by Spot14, a gene previously implicated in lipid metabolism, that we found to be selectively expressed in low proliferating adult NSPCs. Spot14 reduces the availability of malonyl-CoA, which is an essential substrate for Fasn to fuel lipogenesis. Thus, we identify here a functional coupling between the regulation of lipid metabolism and adult NSPC proliferation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3587167/" 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/PMC3587167/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Knobloch, Marlen -- Braun, Simon M G -- Zurkirchen, Luis -- von Schoultz, Carolin -- Zamboni, Nicola -- Arauzo-Bravo, Marcos J -- Kovacs, Werner J -- Karalay, Ozlem -- Suter, Ueli -- Machado, Raquel A C -- Roccio, Marta -- Lutolf, Matthias P -- Semenkovich, Clay F -- Jessberger, Sebastian -- P30 DK020579/DK/NIDDK NIH HHS/ -- R01 DK076729/DK/NIDDK NIH HHS/ -- R01 DK088083/DK/NIDDK NIH HHS/ -- England -- Nature. 2013 Jan 10;493(7431):226-30. doi: 10.1038/nature11689. Epub 2012 Dec 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Brain Research Institute, Faculty of Medicine, University of Zurich, 8057 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23201681" target="_blank"〉PubMed〈/a〉
    Keywords: Adult Stem Cells/cytology/*metabolism ; Animals ; Cell Proliferation ; Dentate Gyrus/metabolism ; Fatty Acid Synthases/deficiency/genetics/*metabolism ; Gene Expression Profiling ; Hippocampus/cytology/metabolism ; *Lipogenesis ; Malonyl Coenzyme A/metabolism ; Mice ; Mice, Transgenic ; Neural Stem Cells/cytology/*metabolism ; Neurogenesis ; Nuclear Proteins/genetics/metabolism ; Transcription Factors/genetics/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2015-06-18
    Description: Fructose is a major component of dietary sugar and its overconsumption exacerbates key pathological features of metabolic syndrome. The central fructose-metabolising enzyme is ketohexokinase (KHK), which exists in two isoforms: KHK-A and KHK-C, generated through mutually exclusive alternative splicing of KHK pre-mRNAs. KHK-C displays superior affinity for fructose compared with KHK-A and is produced primarily in the liver, thus restricting fructose metabolism almost exclusively to this organ. Here we show that myocardial hypoxia actuates fructose metabolism in human and mouse models of pathological cardiac hypertrophy through hypoxia-inducible factor 1alpha (HIF1alpha) activation of SF3B1 and SF3B1-mediated splice switching of KHK-A to KHK-C. Heart-specific depletion of SF3B1 or genetic ablation of Khk, but not Khk-A alone, in mice, suppresses pathological stress-induced fructose metabolism, growth and contractile dysfunction, thus defining signalling components and molecular underpinnings of a fructose metabolism regulatory system crucial for pathological growth.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mirtschink, Peter -- Krishnan, Jaya -- Grimm, Fiona -- Sarre, Alexandre -- Horl, Manuel -- Kayikci, Melis -- Fankhauser, Niklaus -- Christinat, Yann -- Cortijo, Cedric -- Feehan, Owen -- Vukolic, Ana -- Sossalla, Samuel -- Stehr, Sebastian N -- Ule, Jernej -- Zamboni, Nicola -- Pedrazzini, Thierry -- Krek, Wilhelm -- England -- Nature. 2015 Jun 25;522(7557):444-9. doi: 10.1038/nature14508. Epub 2015 Jun 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Health Sciences, ETH Zurich, 8093 Zurich, Switzerland. ; Department of Medicine, University of Lausanne, 1011 Lausanne, Switzerland. ; Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland. ; MRC-Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK. ; Universitatsmedizin Gottingen, Klinik fur Kardiologie und Pneumologie, D-37075 Gottingen, and DZHK (German Centre for Cardiovascular Research), Partner Site Gottingen, Germany. ; Department of Anesthesiology and Critical Care Medicine, University Hospital Jena, 07747 Jena, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26083752" target="_blank"〉PubMed〈/a〉
    Keywords: Alternative Splicing ; Animals ; Cardiomyopathy, Hypertrophic/genetics/*metabolism/pathology/physiopathology ; Disease Models, Animal ; Fructokinases/deficiency/genetics/*metabolism ; Fructose/*metabolism ; Humans ; Hypoxia-Inducible Factor 1, alpha Subunit/genetics/*metabolism ; Isoenzymes/deficiency/genetics/metabolism ; Male ; Metabolic Syndrome X/metabolism ; Mice ; Phosphoproteins/deficiency/genetics/*metabolism ; Ribonucleoprotein, U2 Small Nuclear/deficiency/genetics/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 6
    Electronic Resource
    Electronic Resource
    Springer
    Applied microbiology and biotechnology 54 (2000), S. 243-247 
    ISSN: 1432-0614
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: Abstract Although acetate formation and tolerance are important criteria for various aspects of biotechnological process development, available studies on acetate tolerance in different species are disparate. We evaluate the response of eight bacterial strains, including two variants of Escherichia coli, two variants of Staphylococcus capitis, and one each of Acetobacter aceti, Gluconobacter suboxydans, Lactobacillus acetotolerans, and L. bulgaricus, to acetate challenges under identical conditions. Our findings were: (1) wild-type organisms of species that are considered tolerant of acetate perform only slightly better than E. coli in unadapted shaker cultures; (2) the ability to tolerate acetate is strongly dependent on the carbon source, and is, especially for E. coli, much greater on glycerol than on glucose; (3) respiration is not as important to acetate tolerance in E. coli and S. capitis as has been reported for the acetic acid bacteria; (4) S. capitis was the least affected by acetate under all conditions and grew at up to 44 g/l acetate without any preconditioning; and (5) qualitative high-throughput screening of growth characteristics can be achieved with relatively inexpensive multiwell plate readers.
    Type of Medium: Electronic Resource
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  • 7
    Publication Date: 2012-09-08
    Description: Motivation: Metabolite identification from tandem mass spectra is an important problem in metabolomics, underpinning subsequent metabolic modelling and network analysis. Yet, currently this task requires matching the observed spectrum against a database of reference spectra originating from similar equipment and closely matching operating parameters, a condition that is rarely satisfied in public repositories. Furthermore, the computational support for identification of molecules not present in reference databases is lacking. Recent efforts in assembling large public mass spectral databases such as MassBank have opened the door for the development of a new genre of metabolite identification methods. Results: We introduce a novel framework for prediction of molecular characteristics and identification of metabolites from tandem mass spectra using machine learning with the support vector machine. Our approach is to first predict a large set of molecular properties of the unknown metabolite from salient tandem mass spectral signals, and in the second step to use the predicted properties for matching against large molecule databases, such as PubChem. We demonstrate that several molecular properties can be predicted to high accuracy and that they are useful in de novo metabolite identification, where the reference database does not contain any spectra of the same molecule. Availability: An Matlab/Python package of the FingerID tool is freely available on the web at http://www.sourceforge.net/p/fingerid . Contact: markus.heinonen@cs.helsinki.fi
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 8
    Publication Date: 2000-08-15
    Print ISSN: 0175-7598
    Electronic ISSN: 1432-0614
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Published by Springer
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  • 9
    Publication Date: 2015-11-15
    Description: The Antarctic Peninsula (AP) is one of the three places on Earth that registered the most intense warming in the last 50 years, almost five times the global mean. This warming has strongly affected the cryosphere, causing the largest ice-shelf collapses ever observed and the retreat of 87% of glaciers. Ecosystem responses, although increasingly predicted, have been mainly reported for pelagic systems. However, and despite most Antarctic species being benthic, responses in the Antarctic benthos have been detected in only a few species, and major effects at assemblage level are unknown. This is probably due to the scarcity of baselines against which to assess change. We performed repeat surveys of coastal benthos in 1994, 1998, and 2010, analyzing community structure and environmental variables at King George Island, Antarctica. We report a marked shift in an Antarctic benthic community that can be linked to ongoing climate change. However, rather than temperature as the primary factor, we highlight the resulting increased sediment runoff, triggered by glacier retreat, as the potential causal factor. The sudden shift from a "filter feeders–ascidian domination" to a "mixed assemblage" suggests that thresholds (for example, of tolerable sedimentation) and alternative equilibrium states, depending on the reversibility of the changes, could be possible traits of this ecosystem. Sedimentation processes will be increasing under the current scenario of glacier retreat, and attention needs to be paid to its effects along the AP.
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
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  • 10
    Publication Date: 2012-07-18
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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