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  • Articles  (17)
  • Animals  (9)
  • Biological physics  (5)
  • Artifacts  (2)
  • Dynamics, dynamical systems, lattice effects
  • 2010-2014  (17)
  • 2012  (17)
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  • Articles  (17)
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  • 2010-2014  (17)
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  • 1
    Publication Date: 2012-08-24
    Description: Author(s): Christian A. Yates, Ruth E. Baker, Radek Erban, and Philip K. Maini Throughout development, chemical cues are employed to guide the functional specification of underlying tissues while the spatiotemporal distributions of such chemicals can be influenced by the growth of the tissue itself. These chemicals, termed morphogens, are often modeled using partial differenti... [Phys. Rev. E 86, 021921] Published Thu Aug 23, 2012
    Keywords: Biological physics
    Print ISSN: 1539-3755
    Electronic ISSN: 1550-2376
    Topics: Physics
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  • 2
    Publication Date: 2012-06-21
    Description: Author(s): Charles Baker, Tao Jia, and Rahul V. Kulkarni A wealth of new research has highlighted the critical roles of small noncoding RNAs (sRNAs) in diverse processes, such as quorum sensing and cellular responses to stress. The pathways controlling these processes often have a central motif composed of a master regulator protein whose expression is co... [Phys. Rev. E 85, 061915] Published Wed Jun 20, 2012
    Keywords: Biological physics
    Print ISSN: 1539-3755
    Electronic ISSN: 1550-2376
    Topics: Physics
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  • 3
    Publication Date: 2012-05-30
    Description: Author(s): Stuart T. Johnston, Matthew J. Simpson, and Ruth E. Baker Random walk models based on an exclusion process with contact effects are often used to represent collective migration where individual agents are affected by agent-to-agent adhesion. Traditional mean-field representations of these processes take the form of a nonlinear diffusion equation which, for... [Phys. Rev. E 85, 051922] Published Tue May 29, 2012
    Keywords: Biological physics
    Print ISSN: 1539-3755
    Electronic ISSN: 1550-2376
    Topics: Physics
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  • 4
    Publication Date: 2012-09-21
    Description: Author(s): Christopher H. Baker, Donald A. Jordan, and Pamela M. Norris The continuous wavelet transform is employed to analyze the dynamics and time-dependent energy distribution of phonon wave-packet propagation and scattering in molecular dynamics simulations. The equations of the one-dimensional continuous wavelet transform are presented and then discretized for imp... [Phys. Rev. B 86, 104306] Published Thu Sep 20, 2012
    Keywords: Dynamics, dynamical systems, lattice effects
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
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  • 5
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    Nature Publishing Group (NPG)
    Publication Date: 2012-08-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baker, Monya -- England -- Nature. 2012 Aug 23;488(7412):443. doi: 10.1038/488443a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22914147" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; California ; Crops, Agricultural/economics/genetics/metabolism ; Food Labeling/economics/*legislation & jurisprudence ; *Food, Genetically Modified/economics ; Herbicides ; Humans ; Pest Control, Biological/economics/legislation & jurisprudence ; Public Opinion
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 6
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    Nature Publishing Group (NPG)
    Publication Date: 2012-07-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baker, Monya -- England -- Nature. 2012 Jul 18;487(7407):282-3. doi: 10.1038/487282a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22810669" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Databases, Genetic/trends ; Gene Expression Profiling ; *Genetic Research/economics ; Humans ; Research/economics/*trends
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 2012-07-18
    Description: Protein stability, assembly, localization and regulation often depend on the formation of disulphide crosslinks between cysteine side chains. Enzymes known as sulphydryl oxidases catalyse de novo disulphide formation and initiate intra- and intermolecular dithiol/disulphide relays to deliver the disulphides to substrate proteins. Quiescin sulphydryl oxidase (QSOX) is a unique, multi-domain disulphide catalyst that is localized primarily to the Golgi apparatus and secreted fluids and has attracted attention owing to its overproduction in tumours. In addition to its physiological importance, QSOX is a mechanistically intriguing enzyme, encompassing functions typically carried out by a series of proteins in other disulphide-formation pathways. How disulphides are relayed through the multiple redox-active sites of QSOX and whether there is a functional benefit to concatenating these sites on a single polypeptide are open questions. Here we present the first crystal structure of an intact QSOX enzyme, derived from a trypanosome parasite. Notably, sequential sites in the disulphide relay were found more than 40 A apart in this structure, too far for direct disulphide transfer. To resolve this puzzle, we trapped and crystallized an intermediate in the disulphide hand-off, which showed a 165 degrees domain rotation relative to the original structure, bringing the two active sites within disulphide-bonding distance. The comparable structure of a mammalian QSOX enzyme, also presented here, shows further biochemical features that facilitate disulphide transfer in metazoan orthologues. Finally, we quantified the contribution of concatenation to QSOX activity, providing general lessons for the understanding of multi-domain enzymes and the design of new catalytic relays.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3521037/" 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/PMC3521037/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Alon, Assaf -- Grossman, Iris -- Gat, Yair -- Kodali, Vamsi K -- DiMaio, Frank -- Mehlman, Tevie -- Haran, Gilad -- Baker, David -- Thorpe, Colin -- Fass, Deborah -- GM26643/GM/NIGMS NIH HHS/ -- P41 RR001081/RR/NCRR NIH HHS/ -- R01 GM026643/GM/NIGMS NIH HHS/ -- England -- Nature. 2012 Aug 16;488(7411):414-8. doi: 10.1038/nature11267.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22801504" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Animals ; Biocatalysis ; Catalytic Domain ; Crystallography, X-Ray ; Disulfides/*metabolism ; Humans ; Mice ; Models, Molecular ; Oxidation-Reduction ; Oxidoreductases/*chemistry/*metabolism ; Protein Conformation ; Rotation ; Trypanosoma brucei brucei/*enzymology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 8
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    Nature Publishing Group (NPG)
    Publication Date: 2012-08-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baker, Monya -- England -- Nature. 2012 Aug 2;488(7409):13-4. doi: 10.1038/488013a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22859177" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Brain Neoplasms/drug therapy/pathology ; Cell Tracking/*methods ; Glioblastoma/drug therapy/pathology ; Intestinal Neoplasms/drug therapy/pathology ; Mice ; Neoplastic Stem Cells/*cytology/drug effects/*pathology ; Reproducibility of Results ; Skin Neoplasms/drug therapy/pathology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 9
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    Nature Publishing Group (NPG)
    Publication Date: 2012-06-09
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baker, Monya -- England -- Nature. 2012 Jun 6;486(7401):141-6. doi: 10.1038/486141a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22678297" target="_blank"〉PubMed〈/a〉
    Keywords: Artifacts ; *Biological Specimen Banks/economics/standards/statistics & numerical data/supply ; & distribution ; Guidelines as Topic ; Humans ; Paraffin Embedding ; Preservation, Biological/economics/instrumentation/*methods/*standards ; Specimen Handling/methods/*standards ; Tissue Fixation
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 10
    Publication Date: 2012-12-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baker, David -- Lidster, Katie -- Sottomayor, Ana -- Amor, Sandra -- G1000094/1/National Centre for the Replacement, Refinement and Reduction of Animals in Research/United Kingdom -- England -- Nature. 2012 Dec 6;492(7427):41. doi: 10.1038/492041a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23222599" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Publishing/*standards ; Research Design/*standards
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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