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  • 1
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    Slx5/Slx8-dependent ubiquitin hotspots on chromatin contribute to stress tolerance (2019)
    Springer Nature
    Details
    Publication Date: 2019
    Description: 〈sec〉〈st〉Synopsis〈/st〉〈p〉〈textbox textbox-type="graphic"〉〈p〉〈inline-fig〉〈/inline-fig〉〈/p〉〈/textbox〉〈/p〉 〈p〉SUMO-targeted ubiquitin ligases (STUbLs), involved in nuclear quality control, genome maintenance and transcription, co-localize with ubiquitin to seven distinct genomic loci on yeast chromatin, which are determined by the transcription factor-like protein Euc1 and contribute to stress tolerance.〈/p〉 〈p〉 〈l type="unord"〉〈li〉〈p〉Seven "ubiquitin hotspots" are sites of Cdc48-dependent protein turnover within the yeast genome.〈/p〉〈/li〉 〈li〉〈p〉The previously uncharacterized protein Ymr111c/Euc1 binds a ubiquitin-hotspot DNA motif and recruits the STUbL Slx5/Slx8.〈/p〉〈/li〉 〈li〉〈p〉SUMO-dependent and -independent interactions between Euc1 and Slx5 cooperate for a novel bipartite Slx5/Slx8 recruitment mechanism.〈/p〉〈/li〉 〈li〉〈p〉Euc1 and ubiquitin hotspots are required for cellular stress tolerance when gene expression control and chromatin maintenance by Rpd3-HDACs or SWR1-C are impaired.〈/p〉〈/li〉〈/l〉 〈/p〉〈/sec〉
    Print ISSN: 0261-4189
    Electronic ISSN: 1460-2075
    Topics: Biology , Medicine
    Published by Springer Nature on behalf of The European Molecular Biology Organization (EMBO).
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  • 2
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    Slx5/Slx8-dependent ubiquitin hotspots on chromatin contribute to stress tolerance (2019)
    Springer Nature
    Details
    Publication Date: 2019
    Description: 〈p〉Chromatin is a highly regulated environment, and protein association with chromatin is often controlled by post-translational modifications and the corresponding enzymatic machinery. Specifically, SUMO-targeted ubiquitin ligases (STUbLs) have emerged as key players in nuclear quality control, genome maintenance, and transcription. However, how STUbLs select specific substrates among myriads of SUMOylated proteins on chromatin remains unclear. Here, we reveal a remarkable co-localization of the budding yeast STUbL Slx5/Slx8 and ubiquitin at seven genomic loci that we term "ubiquitin hotspots". Ubiquitylation at these sites depends on Slx5/Slx8 and protein turnover on the Cdc48 segregase. We identify the transcription factor-like Ymr111c/Euc1 to associate with these sites and to be a critical determinant of ubiquitylation. Euc1 specifically targets Slx5/Slx8 to ubiquitin hotspots via bipartite binding of Slx5 that involves the Slx5 SUMO-interacting motifs and an additional, novel substrate recognition domain. Interestingly, the Euc1-ubiquitin hotspot pathway acts redundantly with chromatin modifiers of the H2A.Z and Rpd3L pathways in specific stress responses. Thus, our data suggest that STUbL-dependent ubiquitin hotspots shape chromatin during stress adaptation.〈/p〉
    Print ISSN: 0261-4189
    Electronic ISSN: 1460-2075
    Topics: Biology , Medicine
    Published by Springer Nature on behalf of The European Molecular Biology Organization (EMBO).
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  • 3
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    On probabilistic inference in relational conditional logics (2012)
    Oxford University Press
    Details
    Publication Date: 2012-09-25
    Description: The principle of maximum entropy has proven to be a powerful approach for commonsense reasoning in probabilistic conditional logics on propositional languages. Due to this principle, reasoning is performed based on the unique model of a knowledge base that has maximum entropy. This kind of model-based inference fulfils many desirable properties for inductive inference mechanisms and is usually the best choice for reasoning from an information theoretical point of view. However, the expressive power of propositional formalisms for probabilistic reasoning is limited and in the past few years many proposals have been given for probabilistic reasoning in relational settings. It seems to be a common view that in order to interpret probabilistic first-order sentences, either a statistical approach that counts (tuples of) individuals has to be used, or the knowledge base has to be grounded to make a possible worlds semantics applicable, for a subjective interpretation of probabilities. Most of these proposals of the second type rely on extensions of traditional probabilistic models like Bayes nets or Markov networks whereas there are only few works on first-order extensions of probabilistic conditional logic. Here, we take an approach of lifting maximum entropy methods to the relational case by employing a relational version of probabilistic conditional logic. First, we propose two different semantics and model theories for interpreting first-order probabilistic conditional logic. We address the problems of ambiguity that are raised by the difference between subjective and statistical views, and develop a comprehensive list of desirable properties for inductive model-based probabilistic inference in relational frameworks. Finally, by applying the principle of maximum entropy in the two different semantical frameworks, we obtain inference operators that fulfill these properties and turn out to be reasonable choices for reasoning in first-order probabilistic conditional logic.
    Print ISSN: 1367-0751
    Electronic ISSN: 1368-9894
    Topics: Mathematics
    Published by Oxford University Press
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  • 4
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    Strong enhancement of forbidden atomic transitions using plasmonic nanostructures (2012)
    American Physical Society (APS)
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    Publication Date: 2012-02-02
    Description: Author(s): A. M. Kern and O. J. F. Martin We investigate the mediation of symmetry-forbidden atomic transitions using plasmonic nanostructures. We show that the excitation of the electric dipole-forbidden, quadrupole-allowed 6  2 S 1/2 −5  2 D 5/2 transition in cesium may be enhanced by more than 6 orders of magnitude in the intense, inhomogeneous... [Phys. Rev. A 85, 022501] Published Wed Feb 01, 2012
    Keywords: Atomic and molecular structure and dynamics
    Print ISSN: 1050-2947
    Electronic ISSN: 1094-1622
    Topics: Physics
    Published by American Physical Society (APS)
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  • 5
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    Experimental evidence for delayed contingent cooperation among wild dwarf mongooses [Evolution] (2018)
    National Academy of Sciences
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    Publication Date: 2018-06-13
    Description: Many animals participate in biological markets, with strong evidence existing for immediate cooperative trades. In particular, grooming is often exchanged for itself or other commodities, such as coalitionary support or access to food and mates. More contentious is the possibility that nonhuman animals can rely on memories of recent events,...
    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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    A Papaver somniferum 10-gene cluster for synthesis of the anticancer alkaloid noscapine (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-06-02
    Description: Noscapine is an antitumor alkaloid from opium poppy that binds tubulin, arrests metaphase, and induces apoptosis in dividing human cells. Elucidation of the biosynthetic pathway will enable improvement in the commercial production of noscapine and related bioactive molecules. Transcriptomic analysis revealed the exclusive expression of 10 genes encoding five distinct enzyme classes in a high noscapine-producing poppy variety, HN1. Analysis of an F(2) mapping population indicated that these genes are tightly linked in HN1, and bacterial artificial chromosome sequencing confirmed that they exist as a complex gene cluster for plant alkaloids. Virus-induced gene silencing resulted in accumulation of pathway intermediates, allowing gene function to be linked to noscapine synthesis and a novel biosynthetic pathway to be proposed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Winzer, Thilo -- Gazda, Valeria -- He, Zhesi -- Kaminski, Filip -- Kern, Marcelo -- Larson, Tony R -- Li, Yi -- Meade, Fergus -- Teodor, Roxana -- Vaistij, Fabian E -- Walker, Carol -- Bowser, Tim A -- Graham, Ian A -- New York, N.Y. -- Science. 2012 Jun 29;336(6089):1704-8. doi: 10.1126/science.1220757. Epub 2012 May 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22653730" target="_blank"〉PubMed〈/a〉
    Keywords: Antineoplastic Agents, Phytogenic/*biosynthesis ; *Genes, Plant ; Molecular Sequence Data ; *Multigene Family ; Noscapine/*metabolism ; Papaver/enzymology/*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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  • 7
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    Thermal and electrical conductivity of amorphous and graphitized carbide-derived carbon monoliths (2016)
    Wiley
    Details
    Publication Date: 2016-02-11
    Description: In this study, the influence of graphitization and composition of carbide-derived carbon (CDC) monoliths on the electrical and thermal conductivity was investigated. Carbon monoliths with porosities of 69 to 87 % were synthesized employing biomorphous macroporous TiC and SiC as precursors. Graphitization was carried out in situ during high temperature chlorination at 800 to 1300 °C with and without addition of nickel, iron and cobalt chloride to the carbide. The graphitized monoliths showed improved properties. Moreover, the study showed that despite graphitic carbon also glass-like carbon, stemming from the carbide synthesis, increases the thermal and electrical conductivity significantly. Effective electrical conductivities of 2000 and 3500 S m -1 were determined for graphitized TiC-CDC and SiC-CDC respectively. Effective thermal conductivities of up to 1.8 W m -1 K -1 were obtained.
    Print ISSN: 0930-7516
    Electronic ISSN: 1521-4125
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Published by Wiley
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  • 8
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    The octahaem MccA is a haem c-copper sulfite reductase (2015)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2015-02-03
    Description: The six-electron reduction of sulfite to sulfide is the pivot point of the biogeochemical cycle of the element sulfur. The octahaem cytochrome c MccA (also known as SirA) catalyses this reaction for dissimilatory sulfite utilization by various bacteria. It is distinct from known sulfite reductases because it has a substantially higher catalytic activity and a relatively low reactivity towards nitrite. The mechanistic reasons for the increased efficiency of MccA remain to be elucidated. Here we show that anoxically purified MccA exhibited a 2- to 5.5-fold higher specific sulfite reductase activity than the enzyme isolated under oxic conditions. We determined the three-dimensional structure of MccA to 2.2 A resolution by single-wavelength anomalous dispersion. We find a homotrimer with an unprecedented fold and haem arrangement, as well as a haem bound to a CX15CH motif. The heterobimetallic active-site haem 2 has a Cu(I) ion juxtaposed to a haem c at a Fe-Cu distance of 4.4 A. While the combination of metals is reminiscent of respiratory haem-copper oxidases, the oxidation-labile Cu(I) centre of MccA did not seem to undergo a redox transition during catalysis. Intact MccA tightly bound SO2 at haem 2, a dehydration product of the substrate sulfite that was partially turned over due to photoreduction by X-ray irradiation, yielding the reaction intermediate SO. Our data show the biometal copper in a new context and function and provide a chemical rationale for the comparatively high catalytic activity of MccA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hermann, Bianca -- Kern, Melanie -- La Pietra, Luigi -- Simon, Jorg -- Einsle, Oliver -- England -- Nature. 2015 Apr 30;520(7549):706-9. doi: 10.1038/nature14109. Epub 2015 Feb 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Lehrstuhl Biochemie, Institut fur Biochemie, Albert-Ludwigs-Universitat Freiburg, Albertstrasse 21, 79104 Freiburg, Germany. ; Microbial Energy Conversion &Biotechnology, Department of Biology, Technische Universitat Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany. ; 1] Lehrstuhl Biochemie, Institut fur Biochemie, Albert-Ludwigs-Universitat Freiburg, Albertstrasse 21, 79104 Freiburg, Germany [2] BIOSS Centre for Biological Signalling Studies, Schanzlestrasse 1, 79104 Freiburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25642962" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/isolation & purification/metabolism ; Biocatalysis ; Catalytic Domain ; Copper/*metabolism ; Crystallography, X-Ray ; Cysteine/analogs & derivatives/metabolism ; Heme/*analogs & derivatives/metabolism ; Models, Molecular ; Oxidation-Reduction ; Oxidoreductases Acting on Sulfur Group Donors/*chemistry/isolation & ; purification/metabolism ; Sulfites/metabolism ; Sulfur Dioxide/metabolism ; Wolinella/*enzymology
    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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  • 9
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    Plant science. Morphinan biosynthesis in opium poppy requires a P450-oxidoreductase fusion protein (2015)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2015-06-27
    Description: Morphinan alkaloids from the opium poppy are used for pain relief. The direction of metabolites to morphinan biosynthesis requires isomerization of (S)- to (R)-reticuline. Characterization of high-reticuline poppy mutants revealed a genetic locus, designated STORR [(S)- to (R)-reticuline] that encodes both cytochrome P450 and oxidoreductase modules, the latter belonging to the aldo-keto reductase family. Metabolite analysis of mutant alleles and heterologous expression demonstrate that the P450 module is responsible for the conversion of (S)-reticuline to 1,2-dehydroreticuline, whereas the oxidoreductase module converts 1,2-dehydroreticuline to (R)-reticuline rather than functioning as a P450 redox partner. Proteomic analysis confirmed that these two modules are contained on a single polypeptide in vivo. This modular assembly implies a selection pressure favoring substrate channeling. The fusion protein STORR may enable microbial-based morphinan production.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Winzer, Thilo -- Kern, Marcelo -- King, Andrew J -- Larson, Tony R -- Teodor, Roxana I -- Donninger, Samantha L -- Li, Yi -- Dowle, Adam A -- Cartwright, Jared -- Bates, Rachel -- Ashford, David -- Thomas, Jerry -- Walker, Carol -- Bowser, Tim A -- Graham, Ian A -- BB/K018809/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2015 Jul 17;349(6245):309-12. doi: 10.1126/science.aab1852. Epub 2015 Jun 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK. ; Bioscience Technology Facility, Department of Biology, University of York, York YO10 5DD, UK. ; GlaxoSmithKline, 1061 Mountain Highway, Post Office Box 168, Boronia, Victoria 3155, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26113639" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Benzylisoquinolines/chemistry/*metabolism ; Cytochrome P-450 Enzyme System/genetics/*metabolism ; Genetic Loci ; Isoquinolines/chemistry/*metabolism ; Molecular Sequence Data ; Morphinans/chemistry/*metabolism ; Mutation ; Oxidation-Reduction ; Papaver/*enzymology/genetics ; Plant Proteins/genetics/*metabolism ; Quaternary Ammonium Compounds/chemistry/*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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    Mendicodinium mataschenensis: a new endemic dinoflagellate cyst from the Late Miocene (Tortonian) of Lake Pannon (Austria) (2013)
    American Association of Stratigraphic Palynologists (AASP)
    Details
    Publication Date: 2013-07-10
    Description: The organic-walled dinoflagellate cyst Mendicodinium mataschenensis is introduced here as a new species. The taxon derives from lower Tortonian clays from the Mataschen clay pit in Styria, Austria. These deposits formed in Lake Pannon, which was characterized throughout the Late Miocene by its highly endemic and rapidly evolving biota. As most species of Mendicodinium are known from restricted marine and brackish paleoenvironments, its occurrence in Lake Pannon may be considered further evidence for the brackish water conditions prevailing in this lake.
    Print ISSN: 0191-6122
    Electronic ISSN: 1558-9188
    Topics: Geosciences
    Published by American Association of Stratigraphic Palynologists (AASP)
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