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Author (up) Baylis, H.A.; Vazquez-Manrique, R.P. file  url
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  Title Genetic analysis of IP3 and calcium signalling pathways in C. elegans Type Journal Article
  Year 2012 Publication Biochimica et Biophysica Acta Abbreviated Journal Biochim Biophys Acta  
  Volume 1820 Issue 8 Pages 1253-1268  
  Keywords Animals; Caenorhabditis elegans--genetics, metabolism, physiology; Caenorhabditis elegans Proteins--genetics, metabolism; Calcium Signaling; Inositol 1,4,5-Trisphosphate Receptors--genetics, metabolism; Inositol Phosphates--physiology; Mutagenesis; Phenotype; Protein Interaction Maps; RNA Interference; Reverse Genetics  
  Abstract BACKGROUND: The nematode, Caenorhabditis elegans is an established model system that is particularly well suited to genetic analysis. C. elegans is easily manipulated and we have an in depth knowledge of many aspects of its biology. Thus, it is an attractive system in which to pursue integrated studies of signalling pathways. C. elegans has a complement of calcium signalling molecules similar to that of other animals. SCOPE OF REVIEW: We focus on IP3 signalling. We describe how forward and reverse genetic approaches, including RNAi, have resulted in a tool kit which enables the analysis of IP3/Ca2+ signalling pathways. The importance of cell and tissue specific manipulation of signalling pathways and the use of epistasis analysis are highlighted. We discuss how these tools have increased our understanding of IP3 signalling in specific developmental, physiological and behavioural roles. Approaches to imaging calcium signals in C. elegans are considered. MAJOR CONCLUSIONS: A wide selection of tools is available for the analysis of IP3/Ca2+ signalling in C. elegans. This has resulted in detailed descriptions of the function of IP3/Ca2+ signalling in the animal's biology. Nevertheless many questions about how IP3 signalling regulates specific processes remain. GENERAL SIGNIFICANCE: Many of the approaches described may be applied to other calcium signalling systems. C. elegans offers the opportunity to dissect pathways, perform integrated studies and to test the importance of the properties of calcium signalling molecules to whole animal function, thus illuminating the function of calcium signalling in animals. This article is part of a Special Issue entitled Biochemical, biophysical and genetic approaches to intracellular calcium signalling.  
  Call Number Serial 258  
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Author (up) Delcour, A.H. file  url
openurl 
  Title Outer membrane permeability and antibiotic resistance Type Journal Article
  Year 2009 Publication Biochimica et Biophysica Acta Abbreviated Journal Biochim Biophys Acta  
  Volume 1794 Issue 5 Pages 808-816  
  Keywords Anti-Bacterial Agents/metabolism; Bacterial Outer Membrane Proteins/*metabolism; Cell Membrane Permeability/genetics/*physiology; Drug Resistance, Microbial/*genetics; Gram-Negative Bacteria/*genetics/metabolism; Lipopolysaccharides/physiology; Porins/chemistry/metabolism  
  Abstract To date most antibiotics are targeted at intracellular processes, and must be able to penetrate the bacterial cell envelope. In particular, the outer membrane of gram-negative bacteria provides a formidable barrier that must be overcome. There are essentially two pathways that antibiotics can take through the outer membrane: a lipid-mediated pathway for hydrophobic antibiotics, and general diffusion porins for hydrophilic antibiotics. The lipid and protein compositions of the outer membrane have a strong impact on the sensitivity of bacteria to many types of antibiotics, and drug resistance involving modifications of these macromolecules is common. This review will describe the molecular mechanisms for permeation of antibiotics through the outer membrane, and the strategies that bacteria have deployed to resist antibiotics by modifications of these pathways.  
  Call Number Serial 1539  
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Author (up) Favelukes, G.; Stoppani, A.O. url  openurl
  Title Baker's-yeast fumarase, a thiol enzyme Type Journal Article
  Year 1958 Publication Biochimica et Biophysica Acta Abbreviated Journal Biochim Biophys Acta  
  Volume 28 Issue 3 Pages 654-655  
  Keywords *Hydro-Lyases; Saccharomyces cerevisiae/*metabolism; *Hydrases; *SACCHAROMYCES CEREVISIAE/metabolism  
  Abstract  
  Call Number Grinnell @ engelk @ Serial 483  
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Author (up) Heinisch, J.J. file  url
doi  openurl
  Title Baker's yeast as a tool for the development of antifungal kinase inhibitors--targeting protein kinase C and the cell integrity pathway Type Journal Article
  Year 2005 Publication Biochimica et Biophysica Acta Abbreviated Journal Biochim Biophys Acta  
  Volume 1754 Issue 1-2 Pages 171-182  
  Keywords Antifungal Agents/*chemistry/metabolism/pharmacology; Cell Cycle/*drug effects; Cell Wall/drug effects/metabolism; Enzyme Inhibitors/*chemistry/metabolism/pharmacology; Humans; MAP Kinase Signaling System/drug effects; Models, Biological; Protein Kinase C/*antagonists & inhibitors/chemistry/drug effects/metabolism; Protein Kinases/genetics/metabolism; Recombinant Fusion Proteins/chemistry/*metabolism; Saccharomyces cerevisiae/chemistry/enzymology/*metabolism; Saccharomyces cerevisiae Proteins/*antagonists & inhibitors/chemistry/drug effects/metabolism  
  Abstract Today, the yeast Saccharomyces cerevisiae is probably the best-studied eukaryotic organism. This review first focuses on the signaling process which is mediated by the unique yeast protein kinase C (Pkc1p) and a downstream mitogen-activated protein kinase (MAPK) cascade. This pathway ensures cellular integrity by sensing cell surface stress and controlling cell wall biosynthesis and progression through the cell cycle. The domain structure of Pkc1p is conserved from yeast to humans. A yeast system for heterologous expression of specific domains in a chimeric yeast/mammalian PKC enzyme (“domain shuffling”) is depicted. It is also proposed how this system could be employed for the study of protein kinase inhibitors in high-throughput screens. Moreover, a reporter assay that allows a quantitative readout of the activity of the cell integrity signaling pathway is introduced. Since a variety of protein kinases take part in the signal transduction, this broadens the range of targets for potential inhibitors.  
  Call Number Serial 554  
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Author (up) Jaswal, S.S. file  url
openurl 
  Title Biological insights from hydrogen exchange mass spectrometry Type Journal Article
  Year 2013 Publication Biochimica et Biophysica Acta Abbreviated Journal Biochim Biophys Acta  
  Volume 1834 Issue 6 Pages 1188-1201  
  Keywords Deuterium/chemistry; Deuterium Exchange Measurement/methods; Hydrogen/*chemistry; Kinetics; Mass Spectrometry/*methods; Protein Conformation; Protein Folding; Thermodynamics  
  Abstract Over the past two decades, hydrogen exchange mass spectrometry (HXMS) has achieved the status of a widespread and routine approach in the structural biology toolbox. The ability of hydrogen exchange to detect a range of protein dynamics coupled with the accessibility of mass spectrometry to mixtures and large complexes at low concentrations result in an unmatched tool for investigating proteins challenging to many other structural techniques. Recent advances in methodology and data analysis are helping HXMS deliver on its potential to uncover the connection between conformation, dynamics and the biological function of proteins and complexes. This review provides a brief overview of the HXMS method and focuses on four recent reports to highlight applications that monitor structure and dynamics of proteins and complexes, track protein folding, and map the thermodynamics and kinetics of protein unfolding at equilibrium. These case studies illustrate typical data, analysis and results for each application and demonstrate a range of biological systems for which the interpretation of HXMS in terms of structure and conformational parameters provides unique insights into function. This article is part of a Special Issue entitled: Mass spectrometry in structural biology.  
  Call Number Serial 975  
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Author (up) Liu, P.F.; Wang, Y.K.; Chang, W.C.; Chang, H.Y.; Pan, R.L. file  url
openurl 
  Title Regulation of Arabidopsis thaliana Ku genes at different developmental stages under heat stress Type Journal Article
  Year 2008 Publication Biochimica et Biophysica Acta Abbreviated Journal Biochim Biophys Acta  
  Volume 1779 Issue 6-7 Pages 402-407  
  Keywords Arabidopsis/*genetics/*growth & development/metabolism; Arabidopsis Proteins/*genetics; Base Sequence; DNA Helicases/*genetics; DNA Primers/genetics; DNA, Plant/genetics; DNA-Binding Proteins/*genetics; Down-Regulation; Gene Expression Regulation, Developmental; Gene Expression Regulation, Plant; *Genes, Plant; Hot Temperature; Mutation; Plants, Genetically Modified; Reverse Transcriptase Polymerase Chain Reaction; Signal Transduction; Sulfurtransferases/genetics; Tissue Distribution  
  Abstract Ku, a heterodimeric protein consisting of 70- and 80-kDa subunits, is involved in many cellular processes, such as DNA replication, cell cycle regulation and heat shock response. Moreover, the expression of Arabidopsis thaliana Ku genes (AtKu) is modulated by certain plant hormones through several signal transduction pathways. This study investigated how AtKu are regulated by heat stress. AtKu expression in 3-week-old young seedlings was down-regulated by heat stress in a time-dependent manner, as examined using real-time quantitative PCR, GUS reporter systems, and western blotting analysis. Additionally, the heat-induced repression of AtKu was mediated through the abscisic acid (ABA) biosynthetic pathway, as shown by the reversal of AtKu suppression in the ABA biosynthesis mutant, aba3, and by an increase in the ABA level as analyzed by reverse-phase high performance liquid chromatography. Heat stress-induced regulation of AtKu repression also involved ethylene signaling, DNA repair pathways, and fatty acid synthesis. Furthermore, AtKu expression was repressed in stems, rosette leaves, and cauline leaves in 4-5-week-old plants under heat stress, whereas it remained unchanged in roots and primary inflorescence, indicating that heat differentially modulated AtKu expression in distinct tissues of Arabidopsis.  
  Call Number Serial 485  
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Author (up) Mazzoni, C.; Falcone, C. file  url
openurl 
  Title Caspase-dependent apoptosis in yeast Type Journal Article
  Year 2008 Publication Biochimica et Biophysica Acta Abbreviated Journal Biochim Biophys Acta  
  Volume 1783 Issue 7 Pages 1320-1327  
  Keywords Apoptosis--genetics, physiology; Apoptosis Regulatory Proteins--metabolism; Caspases--metabolism; Mitochondria--metabolism; Saccharomyces cerevisiae--genetics, physiology; Saccharomyces cerevisiae Proteins--metabolism; Signal Transduction  
  Abstract Damaging environment, certain intracellular defects or heterologous expression of pro-apoptotic genes induce death in yeast cells exhibiting typical markers of apoptosis. In mammals, apoptosis can be directed by the activation of groups of proteases, called caspases, that cleave specific substrates and trigger cell death. In addition, in plants, fungi, Dictyostelium and metazoa, paracaspases and metacaspases have been identified that share some homologies with caspases but showing different substrate specificity. In the yeast Saccharomyces cerevisiae, a gene (MCA1/YCA1) has been identified coding for a metacaspase involved in the induction of cell death. Metacaspases are not biochemical, but sequence and functional homologes of caspases, as deletion of them rescues entirely different death scenarios. In this review we will summarize the current knowledge in S. cerevisiae on apoptotic processes, induced by internal and external triggers, which are dependent on the metacaspase gene YCA1.  
  Call Number Serial 850  
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Author (up) Perez, V.I.; Bokov, A.; Van Remmen, H.; Mele, J.; Ran, Q.; Ikeno, Y.; Richardson, A. file  url
openurl 
  Title Is the oxidative stress theory of aging dead? Type Journal Article
  Year 2009 Publication Biochimica et Biophysica Acta Abbreviated Journal Biochim Biophys Acta  
  Volume 1790 Issue 10 Pages 1005-1014  
  Keywords Aging/genetics/*physiology; Animals; Catalase/genetics/metabolism; Humans; Mice; Mice, Knockout; Mice, Transgenic; Oxidative Stress/*physiology; Superoxide Dismutase/genetics/metabolism; Survival Analysis  
  Abstract Currently, the oxidative stress (or free radical) theory of aging is the most popular explanation of how aging occurs at the molecular level. While data from studies in invertebrates (e.g., C. elegans and Drosophila) and rodents show a correlation between increased lifespan and resistance to oxidative stress (and in some cases reduced oxidative damage to macromolecules), direct evidence showing that alterations in oxidative damage/stress play a role in aging are limited to a few studies with transgenic Drosophila that overexpress antioxidant enzymes. Over the past eight years, our laboratory has conducted an exhaustive study on the effect of under- or overexpressing a large number and wide variety of genes coding for antioxidant enzymes. In this review, we present the survival data from these studies together. Because only one (the deletion of the Sod1 gene) of the 18 genetic manipulations we studied had an effect on lifespan, our data calls into serious question the hypothesis that alterations in oxidative damage/stress play a role in the longevity of mice.  
  Call Number Serial 1929  
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Author (up) Richards, G.R.; Vanderpool, C.K. file  url
doi  openurl
  Title Molecular call and response: the physiology of bacterial small RNAs Type Journal Article
  Year 2011 Publication Biochimica et Biophysica Acta Abbreviated Journal Biochim Biophys Acta  
  Volume 1809 Issue 10 Pages 525-531  
  Keywords Carbon/chemistry; Cyclic AMP/metabolism; Escherichia coli/genetics; Gene Expression Regulation, Bacterial; Genes, Bacterial; Homeostasis; Iron/metabolism; Models, Biological; Models, Genetic; RNA, Bacterial/*genetics/*physiology; RNA, Untranslated/genetics  
  Abstract The vital role of bacterial small RNAs (sRNAs) in cellular regulation is now well-established. Although many diverse mechanisms by which sRNAs bring about changes in gene expression have been thoroughly described, comparatively less is known about their biological roles and effects on cell physiology. Nevertheless, for some sRNAs, insight has been gained into the intricate regulatory interplay that is required to sense external environmental and internal metabolic cues and turn them into physiological outcomes. Here, we review examples of regulation by selected sRNAs, emphasizing signals and regulators required for sRNA expression, sRNA regulatory targets, and the resulting consequences for the cell. We highlight sRNAs involved in regulation of the processes of iron homeostasis (RyhB, PrrF, and FsrA) and carbon metabolism (Spot 42, CyaR, and SgrS).  
  Call Number Serial 411  
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Author (up) Tischer, W.; Strotmann, H. file  url
openurl 
  Title Relationship between inhibitor binding by chloroplasts and inhibition of photosynthetic electron transport Type Journal Article
  Year 1977 Publication Biochimica et Biophysica Acta Abbreviated Journal Biochim Biophys Acta  
  Volume 460 Issue 1 Pages 113-125  
  Keywords Atrazine/metabolism/*pharmacology; Binding Sites; *Carbamates; Chloroplasts/drug effects/*metabolism; Diuron/pharmacology; Electron Transport; Herbicides/metabolism/*pharmacology; Kinetics; Mathematics; Photophosphorylation/*drug effects; Plants; Triazines/metabolism/*pharmacology  
  Abstract The binding of radioactively labelled atrazin, metribuzin and phenmedipham by broken chloroplasts was studied. From the double-reciprocal plots (bound vs. free inhibitors) a high affinity binding reaction is graphically isolated which is related to the inhibition of photosynthetic electron transport. It is concluded that the specific binding sites correspond to the electron carrier molecules which are attacked by the inhibitors. The relative concentration of specific binding sites is 1 per 300-500 chlorophyll molecules. The binding of the labelled substances is competitively inhibited by each of the indicated unlabelled substances, by DCMU and by several pyridazinone derivatives. These results suggest that triazines, triazinones, pyridazinones, biscarbamates and phenylureas interfere with the same electron carrier of the photosynthetic electron transport chain, according to the same molecular mechanism.  
  Call Number Serial 544  
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