99751
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Sugiyama A, Ueda Y, Zushi T, Takase H, Yazaki K. Changes in the bacterial community of soybean rhizospheres during growth in the field. PLoS One 2014; 9:e100709. [PMID: 24955843 PMCID: PMC4067361 DOI: 10.1371/journal.pone.0100709] [Citation(s) in RCA: 109] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Accepted: 05/30/2014] [Indexed: 12/28/2022] Open
Abstract
Highly diverse communities of bacteria inhabiting soybean rhizospheres play pivotal roles in plant growth and crop production; however, little is known about the changes that occur in these communities during growth. We used both culture-dependent physiological profiling and culture independent DNA-based approaches to characterize the bacterial communities of the soybean rhizosphere during growth in the field. The physiological properties of the bacterial communities were analyzed by a community-level substrate utilization assay with BioLog Eco plates, and the composition of the communities was assessed by gene pyrosequencing. Higher metabolic capabilities were found in rhizosphere soil than in bulk soil during all stages of the BioLog assay. Pyrosequencing analysis revealed that differences between the bacterial communities of rhizosphere and bulk soils at the phylum level; i.e., Proteobacteria were increased, while Acidobacteria and Firmicutes were decreased in rhizosphere soil during growth. Analysis of operational taxonomic units showed that the bacterial communities of the rhizosphere changed significantly during growth, with a higher abundance of potential plant growth promoting rhizobacteria, including Bacillus, Bradyrhizobium, and Rhizobium, in a stage-specific manner. These findings demonstrated that rhizosphere bacterial communities were changed during soybean growth in the field.
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Affiliation(s)
- Akifumi Sugiyama
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto, Japan
| | - Yoshikatsu Ueda
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto, Japan
| | - Takahiro Zushi
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto, Japan
| | - Hisabumi Takase
- Faculty of Bioenvironmental Science, Kyoto Gakuen University, Kameoka, Kyoto, Japan
| | - Kazufumi Yazaki
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto, Japan
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99752
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Baumann R, Kaempfer S, Chegou NN, Oehlmann W, Loxton AG, Kaufmann SHE, van Helden PD, Black GF, Singh M, Walzl G. Serologic diagnosis of tuberculosis by combining Ig classes against selected mycobacterial targets. J Infect 2014; 69:581-9. [PMID: 24968240 DOI: 10.1016/j.jinf.2014.05.014] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Revised: 05/14/2014] [Accepted: 05/16/2014] [Indexed: 11/30/2022]
Abstract
INTRODUCTION Accurate, simple and cost-effective diagnostic tests are needed for diagnosis of active tuberculosis (TB). Serodiagnosis is attractive as it can be harnessed for point-of-care tests. METHODS We evaluated, in a blinded fashion, the sensitivity and specificity of serologic immunoglobulin (Ig)G, IgA and/or IgM responses to Apa, heat shock protein (HSP) 16.3, HSP20, PE35, probable thiol peroxidase Tpx and lipoarabinomannan (LAM) in 42 HIV-negative South African pulmonary TB patients and 67 control individuals. The status of latent Mycobacterium tuberculosis infection (LTBI) among controls was defined through the TST and IFN-γ release assays (IGRAs). We evaluated 47 definite LTBI (IGRA(+)/LTBI), 8 putative LTBI (IGRA(-)/TST(+)) and 12 TB-uninfected (non-LTBI) subjects. RESULTS In contrast to anti-PE35 IgA, anti-PE35 IgG and particularly anti-Apa IgA, performances of anti-LAM IgG and selected anti-protein antibodies were less affected by inclusion of LTBI participants into the analysis. Anti-LAM IgG showed with a sensitivity/specificity of 71.4%/86.6% (p < 0.001) the best discrimination between TB and non-TB subjects. Selected five-antibody-combinations (including anti-LAM IgG, anti-LAM IgA and anti-Tpx IgG) further improved this performance to an accuracy exceeding 86%. CONCLUSIONS Antibody responses to some Mycobacterium tuberculosis antigens often also reflect latent infection explaining the poor performance of antibody-based tests for active TB in TB-endemic settings. Our results suggest that rather a combination of serological responses against selected protein and non-protein antigens and different Ig classes should be investigated for TB serodiagnostics.
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Affiliation(s)
- Ralf Baumann
- DST/NRF Centre of Excellence for Biomedical TB Research and MRC Centre for TB Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, P.O. Box 19063, Tygerberg 7505, South Africa; Lionex Diagnostics and Therapeutics, 38126 Braunschweig, Germany
| | - Susanne Kaempfer
- Lionex Diagnostics and Therapeutics, 38126 Braunschweig, Germany
| | - Novel N Chegou
- DST/NRF Centre of Excellence for Biomedical TB Research and MRC Centre for TB Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, P.O. Box 19063, Tygerberg 7505, South Africa
| | - Wulf Oehlmann
- Lionex Diagnostics and Therapeutics, 38126 Braunschweig, Germany
| | - André G Loxton
- DST/NRF Centre of Excellence for Biomedical TB Research and MRC Centre for TB Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, P.O. Box 19063, Tygerberg 7505, South Africa
| | - Stefan H E Kaufmann
- Department of Immunology, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117 Berlin, Germany
| | - Paul D van Helden
- DST/NRF Centre of Excellence for Biomedical TB Research and MRC Centre for TB Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, P.O. Box 19063, Tygerberg 7505, South Africa
| | - Gillian F Black
- DST/NRF Centre of Excellence for Biomedical TB Research and MRC Centre for TB Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, P.O. Box 19063, Tygerberg 7505, South Africa
| | - Mahavir Singh
- Lionex Diagnostics and Therapeutics, 38126 Braunschweig, Germany.
| | - Gerhard Walzl
- DST/NRF Centre of Excellence for Biomedical TB Research and MRC Centre for TB Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, P.O. Box 19063, Tygerberg 7505, South Africa
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99753
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Pyochelin potentiates the inhibitory activity of gallium on Pseudomonas aeruginosa. Antimicrob Agents Chemother 2014; 58:5572-5. [PMID: 24957826 DOI: 10.1128/aac.03154-14] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Gallium (Ga) is an iron mimetic that has successfully been repurposed for antibacterial chemotherapy. To improve the antibacterial potency of Ga on Pseudomonas aeruginosa, the effect of complexation with a variety of siderophores and synthetic chelators was tested. Ga complexed with the pyochelin siderophore (at a 1:2 ratio) was more efficient than Ga(NO3)3 in inhibiting P. aeruginosa growth, and its activity was dependent on increased Ga entrance into the cell through the pyochelin translocon.
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99754
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Shigella reroutes host cell central metabolism to obtain high-flux nutrient supply for vigorous intracellular growth. Proc Natl Acad Sci U S A 2014; 111:9929-34. [PMID: 24958876 DOI: 10.1073/pnas.1406694111] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Shigella flexneri proliferate in infected human epithelial cells at exceptionally high rates. This vigorous growth has important consequences for rapid progression to life-threatening bloody diarrhea, but the underlying metabolic mechanisms remain poorly understood. Here, we used metabolomics, proteomics, and genetic experiments to determine host and Shigella metabolism during infection in a cell culture model. The data suggest that infected host cells maintain largely normal fluxes through glycolytic pathways, but the entire output of these pathways is captured by Shigella, most likely in the form of pyruvate. This striking strategy provides Shigella with an abundant favorable energy source, while preserving host cell ATP generation, energy charge maintenance, and survival, despite ongoing vigorous exploitation. Shigella uses a simple three-step pathway to metabolize pyruvate at high rates with acetate as an excreted waste product. The crucial role of this pathway for Shigella intracellular growth suggests targets for antimicrobial chemotherapy of this devastating disease.
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99755
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Gómez-Sagasti MT, Becerril JM, Martín I, Epelde L, Garbisu C. cDNA microarray assessment of early gene expression profiles in Escherichia coli cells exposed to a mixture of heavy metals. Cell Biol Toxicol 2014; 30:207-32. [DOI: 10.1007/s10565-014-9281-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 06/12/2014] [Indexed: 12/30/2022]
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99756
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Signaling mechanisms and disrupted cytoskeleton in the diphenyl ditelluride neurotoxicity. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2014; 2014:458601. [PMID: 25050142 PMCID: PMC4090446 DOI: 10.1155/2014/458601] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 02/26/2014] [Indexed: 01/14/2023]
Abstract
Evidence from our group supports that diphenyl ditelluride (PhTe)2 neurotoxicity depends on modulation of signaling pathways initiated at the plasma membrane. The (PhTe)2-evoked signal is transduced downstream of voltage-dependent Ca2+ channels (VDCC), N-methyl-D-aspartate receptors (NMDA), or metabotropic glutamate receptors activation via different kinase pathways (protein kinase A, phospholipase C/protein kinase C, mitogen-activated protein kinases (MAPKs), and Akt signaling pathway). Among the most relevant cues of misregulated signaling mechanisms evoked by (PhTe)2 is the cytoskeleton of neural cells. The in vivo and in vitro exposure to (PhTe)2 induce hyperphosphorylation/hypophosphorylation of neuronal and glial intermediate filament (IF) proteins (neurofilaments and glial fibrillary acidic protein, resp.) in different brain structures of young rats. Phosphorylation of IFs at specific sites modulates their association/disassociation and interferes with important physiological roles, such as axonal transport. Disrupted cytoskeleton is a crucial marker of neurodegeneration and is associated with reactive astrogliosis and apoptotic cell death. This review focuses the current knowledge and important results on the mechanisms of (PhTe)2 neurotoxicity with special emphasis on the cytoskeletal proteins and their differential regulation by kinases/phosphatases and Ca2+-mediated mechanisms in developmental rat brain. We propose that the disrupted cytoskeletal homeostasis could support brain damage provoked by this neurotoxicant.
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99757
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Visualizing the kinetic power stroke that drives proton-coupled zinc(II) transport. Nature 2014; 512:101-4. [PMID: 25043033 PMCID: PMC4144069 DOI: 10.1038/nature13382] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Accepted: 04/14/2014] [Indexed: 01/30/2023]
Abstract
The proton gradient is a principal energy source for respiration-dependent active transport, but the structural mechanisms of proton-coupled transport processes are poorly understood. YiiP is a proton-coupled zinc transporter found in the cytoplasmic membrane of Escherichia coli. Its transport site receives protons from water molecules that gain access to its hydrophobic environment and transduces the energy of an inward proton gradient to drive Zn(II) efflux. This membrane protein is a well-characterized member of the family of cation diffusion facilitators that occurs at all phylogenetic levels. Here we show, using X-ray-mediated hydroxyl radical labelling of YiiP and mass spectrometry, that Zn(II) binding triggers a highly localized, all-or-nothing change of water accessibility to the transport site and an adjacent hydrophobic gate. Millisecond time-resolved dynamics reveal a concerted and reciprocal pattern of accessibility changes along a transmembrane helix, suggesting a rigid-body helical re-orientation linked to Zn(II) binding that triggers the closing of the hydrophobic gate. The gated water access to the transport site enables a stationary proton gradient to facilitate the conversion of zinc-binding energy to the kinetic power stroke of a vectorial zinc transport. The kinetic details provide energetic insights into a proton-coupled active-transport reaction.
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99758
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Szakal C, Tsytsikova L, Carlander D, Duncan TV. Measurement Methods for the Oral Uptake of Engineered Nanomaterials from Human Dietary Sources: Summary and Outlook. Compr Rev Food Sci Food Saf 2014; 13:669-678. [DOI: 10.1111/1541-4337.12080] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 03/13/2014] [Indexed: 11/30/2022]
Affiliation(s)
- Christopher Szakal
- Materials Measurement Science Div; Natl. Inst. of Standards and Technology; 100 Bureau Drive Gaithersburg MD 20899-8371 U.S.A
| | - Lyubov Tsytsikova
- Center for Risk Science Innovation and Application; ILSI Research Foundation; 1156 Fifteenth ST. NW, Suite 200 Washington, DC, 20005-1743 U.S.A
| | - David Carlander
- Nanotechnology Industries Assoc; 101 Ave. Louise 1050 Brussels Belgium
| | - Timothy V. Duncan
- Center for Food Safety and Applied Nutrition; United States Food and Drug Administration; 6502 South Archer Rd Bedford Park IL 60516-1957 U.S.A
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99759
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Simmons KJ, Jackson SM, Brueckner F, Patching SG, Beckstein O, Ivanova E, Geng T, Weyand S, Drew D, Lanigan J, Sharples DJ, Sansom MSP, Iwata S, Fishwick CWG, Johnson AP, Cameron AD, Henderson PJF. Molecular mechanism of ligand recognition by membrane transport protein, Mhp1. EMBO J 2014; 33:1831-44. [PMID: 24952894 PMCID: PMC4195764 DOI: 10.15252/embj.201387557] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The hydantoin transporter Mhp1 is a sodium-coupled secondary active transport protein of the nucleobase-cation-symport family and a member of the widespread 5-helix inverted repeat superfamily of transporters. The structure of Mhp1 was previously solved in three different conformations providing insight into the molecular basis of the alternating access mechanism. Here, we elucidate detailed events of substrate binding, through a combination of crystallography, molecular dynamics, site-directed mutagenesis, biochemical/biophysical assays, and the design and synthesis of novel ligands. We show precisely where 5-substituted hydantoin substrates bind in an extended configuration at the interface of the bundle and hash domains. They are recognised through hydrogen bonds to the hydantoin moiety and the complementarity of the 5-substituent for a hydrophobic pocket in the protein. Furthermore, we describe a novel structure of an intermediate state of the protein with the external thin gate locked open by an inhibitor, 5-(2-naphthylmethyl)-L-hydantoin, which becomes a substrate when leucine 363 is changed to an alanine. We deduce the molecular events that underlie acquisition and transport of a ligand by Mhp1.
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Affiliation(s)
- Katie J Simmons
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Scott M Jackson
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Florian Brueckner
- Membrane Protein Laboratory, Diamond Light Source Harwell Science and Innovation Campus, Chilton, Didcot, UK Division of Molecular Biosciences, Membrane Protein Crystallography Group Imperial College, London, UK Rutherford Appleton Laboratory, Research Complex at Harwell, Harwell, Oxford, Didcot, UK
| | - Simon G Patching
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Oliver Beckstein
- Department of Physics, Arizona State University, Tempe, AZ, USA Department of Biochemistry, University of Oxford, Oxford, UK
| | - Ekaterina Ivanova
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Tian Geng
- Membrane Protein Laboratory, Diamond Light Source Harwell Science and Innovation Campus, Chilton, Didcot, UK Division of Molecular Biosciences, Membrane Protein Crystallography Group Imperial College, London, UK Rutherford Appleton Laboratory, Research Complex at Harwell, Harwell, Oxford, Didcot, UK
| | - Simone Weyand
- Membrane Protein Laboratory, Diamond Light Source Harwell Science and Innovation Campus, Chilton, Didcot, UK Division of Molecular Biosciences, Membrane Protein Crystallography Group Imperial College, London, UK Rutherford Appleton Laboratory, Research Complex at Harwell, Harwell, Oxford, Didcot, UK
| | - David Drew
- Division of Molecular Biosciences, Membrane Protein Crystallography Group Imperial College, London, UK
| | - Joseph Lanigan
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - David J Sharples
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - So Iwata
- Membrane Protein Laboratory, Diamond Light Source Harwell Science and Innovation Campus, Chilton, Didcot, UK Division of Molecular Biosciences, Membrane Protein Crystallography Group Imperial College, London, UK Rutherford Appleton Laboratory, Research Complex at Harwell, Harwell, Oxford, Didcot, UK
| | - Colin W G Fishwick
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - A Peter Johnson
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Alexander D Cameron
- Membrane Protein Laboratory, Diamond Light Source Harwell Science and Innovation Campus, Chilton, Didcot, UK Division of Molecular Biosciences, Membrane Protein Crystallography Group Imperial College, London, UK School of Life Sciences, University of Warwick, Coventry, UK
| | - Peter J F Henderson
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
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99760
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Acanthamoeba DNA can be directly amplified from corneal scrapings. Parasitol Res 2014; 113:3267-72. [PMID: 24951167 DOI: 10.1007/s00436-014-3989-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 06/06/2014] [Indexed: 10/25/2022]
Abstract
This study evaluated the performance of direct amplification of Acanthamoeba-DNA bypassing DNA extraction in the diagnosis of Acanthamoeba keratitis in clinically suspected cases in comparison to direct microscopic examination and in vitro culture. Corneal scrapings were collected from 110 patients who were clinically suspected to have Acanthamoeba keratitis, 63 contact lens wearers (CLW), and 47 non-contact lens wearers (NCLW). Taken samples were subjected to direct microscopic examination, cultivation onto the non-nutrient agar plate surface seeded with Escherichia coli, and PCR amplification. The diagnostic performance of these methods was statistically compared. The results showed that Acanthamoeba infection was detected in 21 (19.1%) of clinically suspected cases (110); 17 (81%) of them were CLW and the remaining 4 (19%) positive cases were NCLW. Regarding the used diagnostic methods, it was found that direct amplification of Acanthamoeba DNA bypassing nucleic acid extraction was superior to microscopy and culture in which 21 cases (19.1%) were positive for Acanthamoeba by PCR compared to 19 positive cases by culture (17.3%) and one case (0.9%) by direct smear. The difference in detection rates between culture and direct smear was highly statistically significant (P = 0.001). On the other hand, there was no significant difference in detection rates between culture and PCR (P = 0.86). On using culture as the gold standard, PCR showed three false-positive samples that were negative by culture and one false-negative sample that was positive by culture. At the same time, direct smear showed 18 false-negative samples. The sensitivity, specificity, positive predictive value, negative predictive value, and diagnostic accuracy of PCR were 94.7, 96.7, 85.7, 98.9, and 96.4, respectively, while those of direct smear were 5.3, 100, 100, 83.5, and 83.6, respectively. In conclusion, direct amplification of Acanthamoeba-DNA bypassing DNA extraction is a reliable, specific, sensitive method in the diagnosis of Acanthamoeba keratitis in clinically suspected cases. It should set up in ophthalmological centers as an easy diagnostic tool.
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99761
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Soukoulis C, Fisk ID, Bohn T. Ice Cream as a Vehicle for Incorporating Health-Promoting Ingredients: Conceptualization and Overview of Quality and Storage Stability. Compr Rev Food Sci Food Saf 2014; 13:627-655. [DOI: 10.1111/1541-4337.12083] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 04/07/2014] [Indexed: 12/19/2022]
Affiliation(s)
- Christos Soukoulis
- Environment and Agro-biotechnologies Dept; Public Research Centre - Gabriel Lippmann; 41, rue du Brill L-4422 Belvaux Luxembourg
| | - Ian D. Fisk
- Div. of Food Sciences, School of Biosciences, Univ. of Nottingham; Sutton Bonington Campus; Leicestershire Loughborough LE12 5RD UK
| | - Torsten Bohn
- Environment and Agro-biotechnologies Dept; Public Research Centre - Gabriel Lippmann; 41, rue du Brill L-4422 Belvaux Luxembourg
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99762
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Fusco V, Quero GM. Culture-Dependent and Culture-Independent Nucleic-Acid-Based Methods Used in the Microbial Safety Assessment of Milk and Dairy Products. Compr Rev Food Sci Food Saf 2014; 13:493-537. [DOI: 10.1111/1541-4337.12074] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 03/08/2014] [Indexed: 12/12/2022]
Affiliation(s)
- Vincenzina Fusco
- Nal. Research Council of Italy; Inst. of Sciences of Food Production (CNR-ISPA); Bari Italy
| | - Grazia Marina Quero
- Nal. Research Council of Italy; Inst. of Sciences of Food Production (CNR-ISPA); Bari Italy
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99763
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Ceuppens S, Li D, Uyttendaele M, Renault P, Ross P, Ranst MV, Cocolin L, Donaghy J. Molecular Methods in Food Safety Microbiology: Interpretation and Implications of Nucleic Acid Detection. Compr Rev Food Sci Food Saf 2014; 13:551-577. [DOI: 10.1111/1541-4337.12072] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 03/09/2014] [Indexed: 11/27/2022]
Affiliation(s)
- Siele Ceuppens
- Faculty of Bioscience Engineering; Laboratory of Food Microbiology and Food Preservation (LFMFP); Dept. of Food Safety and Food Quality; Ghent Univ.; Ghent Belgium
| | - Dan Li
- Faculty of Bioscience Engineering; Laboratory of Food Microbiology and Food Preservation (LFMFP); Dept. of Food Safety and Food Quality; Ghent Univ.; Ghent Belgium
| | - Mieke Uyttendaele
- Faculty of Bioscience Engineering; Laboratory of Food Microbiology and Food Preservation (LFMFP); Dept. of Food Safety and Food Quality; Ghent Univ.; Ghent Belgium
| | - Pierre Renault
- Inst. Scientifique de Recherche Agronomique (INRA); France
| | - Paul Ross
- Moorepark Biotechnology Centre; Teagasc; Moorepark; Fermoy Co. Cork Ireland
| | | | - Luca Cocolin
- Dept. of Agricultural; Forest and Food Sciences; Univ. of Torino; Grugliasco Torino Italy
| | - John Donaghy
- Food Safety Microbiology Group; Nestle Research Center; Lausanne Switzerland
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99764
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Dyguda-Kazimierowicz E, Roszak S, Sokalski WA. Alkaline Hydrolysis of Organophosphorus Pesticides: The Dependence of the Reaction Mechanism on the Incoming Group Conformation. J Phys Chem B 2014; 118:7277-89. [DOI: 10.1021/jp503382j] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Szczepan Roszak
- Department of Chemistry, Wrocław University of Technology Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - W. Andrzej Sokalski
- Department of Chemistry, Wrocław University of Technology Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland
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99765
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Ainsaar K, Mumm K, Ilves H, Hõrak R. The ColRS signal transduction system responds to the excess of external zinc, iron, manganese, and cadmium. BMC Microbiol 2014; 14:162. [PMID: 24946800 PMCID: PMC4074579 DOI: 10.1186/1471-2180-14-162] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 06/17/2014] [Indexed: 11/26/2022] Open
Abstract
Background The ColRS two-component system has been shown to contribute to the membrane functionality and stress tolerance of Pseudomonas putida as well as to the virulence of Pseudomonas aeruginosa and plant pathogenic Xanthomonas species. However, the conditions activating the ColRS pathway and the signal(s) sensed by ColS have remained unknown. Here we aimed to analyze the role of the ColRS system in metal tolerance of P. putida and to test whether ColS can respond to metal excess. Results We show that the ColRS system is necessary for P. putida to tolerate the excess of iron and zinc, and that it also contributes to manganese and cadmium tolerance. Excess of iron, zinc, manganese or cadmium activates ColRS signaling and as a result modifies the expression of ColR-regulated genes. Our data suggest that the genes in the ColR regulon are functionally redundant, as several loci have to be deleted to observe a significant decrease in metal tolerance. Site-directed mutagenesis of ColS revealed that excess of iron and, surprisingly, also zinc are sensed by a conserved ExxE motif in ColS’s periplasmic domain. While ColS is able to sense different metals, it still discriminates between the two oxidation states of iron, specifically responding to ferric and not ferrous iron. We propose a signal perception model involving a dimeric ColS, where each monomer donates one ExxE motif for metal binding. Conclusions Several transition metals are essential for living organisms in certain amounts, but toxic in excess. We show that ColRS is a sensor system which detects and responds to the excess of physiologically important metals such as zinc, iron and manganese. Thus, the ColRS system is an important factor for metal homeostasis and tolerance in P. putida.
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Affiliation(s)
| | | | | | - Rita Hõrak
- Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia.
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99766
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Saxon EB, Jackson RW, Bhumbra S, Smith T, Sockett RE. Bdellovibrio bacteriovorus HD100 guards against Pseudomonas tolaasii brown-blotch lesions on the surface of post-harvest Agaricus bisporus supermarket mushrooms. BMC Microbiol 2014; 14:163. [PMID: 24946855 PMCID: PMC4077555 DOI: 10.1186/1471-2180-14-163] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 06/12/2014] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Pseudomonas tolaasii is a problematic pathogen of cultured mushrooms, forming dark brown 'blotches' on mushroom surfaces and causing spoilage during crop growth and post-harvest . Treating P. tolaasii infection is difficult, as other, commensal bacterial species such as Pseudomonas putida are necessary for mushroom growth, so treatments must be relatively specific. RESULTS We have found that P. tolaasii is susceptible to predation in vitro by the δ-proteobacterium Bdellovibrio bacteriovorus. This effect also occurred in funga, where B. bacteriovorus was administered to post-harvest mushroom caps before and after administration of the P. tolaasii pathogen. A significant, visible improvement in blotch appearance, after incubation, was observed on administration of Bdellovibrio. A significant reduction in viable P. tolaasii cell numbers, recovered from the mushroom tissue, was detected. This was accompanied by a more marked reduction in blotch severity on Bdellovibrio administration. We found that there was in some cases an accompanying overgrowth of presumed-commensal, non-Pseudomonas bacteria on post-harvest mushroom caps after Bdellovibrio-treatment. These bacteria were identified (by 16SrRNA gene sequencing) as Enterobacter species, which were seemingly resistant to predation. We visualised predatory interactions occuring between B. bacteriovorus and P. tolaasii on the post-harvest mushroom cap surface by Scanning Electron Microscopy, seeing predatory invasion of P. tolaasii by B. bacteriovorus in funga. This anti-P. tolaasii effect worked well in post-harvest supermarket mushrooms, thus Bdellovibrio was not affected by any pre-treatment of mushrooms for commercial/consumer purposes. CONCLUSIONS The soil-dwelling B. bacteriovorus HD100 preys upon and kills P. tolaasii, on mushroom surfaces, and could therefore be applied to prevent spoilage in post-harvest situations where mushrooms are stored and packaged for sale.
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Affiliation(s)
- Emma B Saxon
- Genetics, School of Life Sciences, University of Nottingham, Medical School, Queen’s Medical Centre, Nottingham NG7 2UH, UK
| | - Robert W Jackson
- School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AJ, UK
| | - Shobita Bhumbra
- Genetics, School of Life Sciences, University of Nottingham, Medical School, Queen’s Medical Centre, Nottingham NG7 2UH, UK
| | - Tim Smith
- Genetics, School of Life Sciences, University of Nottingham, Medical School, Queen’s Medical Centre, Nottingham NG7 2UH, UK
| | - R Elizabeth Sockett
- Genetics, School of Life Sciences, University of Nottingham, Medical School, Queen’s Medical Centre, Nottingham NG7 2UH, UK
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99767
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Hoffmann J, Altenbuchner J. Hyaluronic acid production with Corynebacterium glutamicum: effect of media composition on yield and molecular weight. J Appl Microbiol 2014; 117:663-78. [PMID: 24863652 DOI: 10.1111/jam.12553] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 05/19/2014] [Accepted: 05/19/2014] [Indexed: 02/02/2023]
Abstract
AIMS Corynebacterium glutamicum was tested as an alternative host for heterologous production of hyaluronic acid (HA). METHODS AND RESULTS A set of expression vectors containing hasA, encoding HA synthase from Streptococcus equi subsp. zooepidemicus, alone or in combination with genes encoding enzymes for HA precursor production (hasB, hasC, glmU from Pseudomonas putida KT2440) or bacterial haemoglobin (vgb from Vitreoscilla sp.) was constructed. Recombinant Coryne. glutamicum strains were cultivated in two different minimal media, CGXII and MEK700. HA was isolated from the culture broth by ethanol precipitation or ultrafiltration. Analyses of the isolated HA revealed that overall production was higher in CGXII medium (1241 mg l(-1)) than in MEK700 medium (363 mg l(-1)), but molecular weight of the product was higher in MEK700 (>1·4 MDa) than in CGXII (<270 kDa). Coexpression of hasB, hasC or glmU had no effect on HA yield and did not improve molecular weight of the product. Coexpression of vgb lowered HA yield about 1·5-fold and did not affect molecular weight of the product. Microscopy of negative-stained cultures revealed that Coryne. glutamicum produces no distinct HA capsule. CONCLUSIONS Regulation of cell growth and gene expression level of hasA are reasonable starting points for controlling the molecular weight of HA produced by Coryne. glutamicum. SIGNIFICANCE AND IMPACT OF THE STUDY Corynebacterium glutamicum has a great potential as an alternative production host for HA. The fact that Coryne. glutamicum produces no distinct HA capsule facilitates HA isolation and improves overall yield.
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Affiliation(s)
- J Hoffmann
- Institute of Industrial Genetics, University of Stuttgart, Stuttgart, Germany
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99768
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Bazet Lyonnet B, Diacovich L, Cabruja M, Bardou F, Quémard A, Gago G, Gramajo H. Pleiotropic effect of AccD5 and AccE5 depletion in acyl-coenzyme A carboxylase activity and in lipid biosynthesis in mycobacteria. PLoS One 2014; 9:e99853. [PMID: 24950047 PMCID: PMC4064979 DOI: 10.1371/journal.pone.0099853] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 05/18/2014] [Indexed: 11/19/2022] Open
Abstract
Mycobacteria contain a large variety of fatty acids which are used for the biosynthesis of several complex cell wall lipids that have been implicated in the ability of the organism to resist host defenses. The building blocks for the biosynthesis of all these lipids are provided by a fairly complex set of acyl-CoA carboxylases (ACCases) whose subunit composition and roles within these organisms have not yet been clearly established. Previous biochemical and structural studies provided strong evidences that ACCase 5 from Mycobacterium tuberculosis is formed by the AccA3, AccD5 and AccE5 subunits and that this enzyme complex carboxylates acetyl-CoA and propionyl-CoA with a clear substrate preference for the latest. In this work we used a genetic approach to unambiguously demonstrate that the products of both accD5 and accE5 genes are essential for the viability of Mycobacterium smegmatis. By obtaining a conditional mutant on the accD5-accE5 operon, we also demonstrated that the main physiological role of this enzyme complex was to provide the substrates for fatty acid and mycolic acid biosynthesis. Furthermore, enzymatic and biochemical analysis of the conditional mutant provided strong evidences supporting the notion that AccD5 and/or AccE5 have an additional role in the carboxylation of long chain acyl-CoA prior to mycolic acid condensation. These studies represent a significant step towards a better understanding of the roles of ACCases in mycobacteria and confirm ACCase 5 as an interesting target for the development of new antimycobacterial drugs.
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Affiliation(s)
- Bernardo Bazet Lyonnet
- Laboratory of Physiology and Genetics of Actinomycetes, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Lautaro Diacovich
- Laboratory of Physiology and Genetics of Actinomycetes, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Matías Cabruja
- Laboratory of Physiology and Genetics of Actinomycetes, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Fabienne Bardou
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), Département Tuberculose et Biologie des Infections, Toulouse, France
- Université de Toulouse, UPS, IPBS, Toulouse, France
| | - Annaïk Quémard
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), Département Tuberculose et Biologie des Infections, Toulouse, France
- Université de Toulouse, UPS, IPBS, Toulouse, France
| | - Gabriela Gago
- Laboratory of Physiology and Genetics of Actinomycetes, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
- * E-mail: (GG); (HG)
| | - Hugo Gramajo
- Laboratory of Physiology and Genetics of Actinomycetes, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
- * E-mail: (GG); (HG)
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99769
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Soen Y. Environmental disruption of host-microbe co-adaptation as a potential driving force in evolution. Front Genet 2014; 5:168. [PMID: 24999350 PMCID: PMC4064665 DOI: 10.3389/fgene.2014.00168] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 05/20/2014] [Indexed: 01/08/2023] Open
Abstract
The microbiome is known to have a profound effect on the development, physiology and health of its host. Whether and how it also contributes to evolutionary diversification of the host is, however, unclear. Here we hypothesize that disruption of the microbiome by new stressful environments interferes with host-microbe co-adaptation, contributes to host destabilization, and can drive irreversible changes in the host prior to its genetic adaptation. This hypothesis is based on three presumptions: (1) the microbiome consists of heritable partners which contribute to the stability (canalization) of host development and physiology in frequently encountered environments, (2) upon encountering a stressful new environment, the microbiome adapts much faster than the host, and (3) this differential response disrupts cooperation, contributes to host destabilization and promotes reciprocal changes in the host and its microbiome. This dynamic imbalance relaxes as the host and its microbiome establish a new equilibrium state in which they are adapted to one another and to the altered environment. Over long time in this new environment, the changes in the microbiome contribute to the canalization of the altered state. This scenario supports stability of the adapted patterns, while promoting variability which may be beneficial in new stressful conditions, thus allowing the organism to balance stability and flexibility based on contextual demand. Additionally, interaction between heritable microbial and epigenetic/physiological changes can promote new outcomes which persist over a wide range of timescales. A sufficiently persistent stress can further induce irreversible changes in the microbiome which may permanently alter the organism prior to genetic changes in the host. Epigenetic and microbial changes therefore provide a potential infrastructure for causal links between immediate responses to new environments and longer-term establishment of evolutionary adaptations.
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Affiliation(s)
- Yoav Soen
- Department of Biological Chemistry, Weizmann Institute of ScienceRehovot, Israel
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99770
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Microbial community degradation of widely used quaternary ammonium disinfectants. Appl Environ Microbiol 2014; 80:5892-900. [PMID: 24951783 DOI: 10.1128/aem.01255-14] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Benzalkonium chlorides (BACs) are disinfectants widely used in a variety of clinical and environmental settings to prevent microbial infections, and they are frequently detected in nontarget environments, such as aquatic and engineered biological systems, even at toxic levels. Therefore, microbial degradation of BACs has important ramifications for alleviating disinfectant toxicity in nontarget environments as well as compromising disinfectant efficacy in target environments. However, how natural microbial communities respond to BAC exposure and what genes underlie BAC biodegradation remain elusive. Our previous metagenomic analysis of a river sediment microbial community revealed that BAC exposure selected for a low-diversity community, dominated by several members of the Pseudomonas genus that quickly degraded BACs. To elucidate the genetic determinants of BAC degradation, we conducted time-series metatranscriptomic analysis of this microbial community during a complete feeding cycle with BACs as the sole carbon and energy source under aerobic conditions. Metatranscriptomic profiles revealed a candidate gene for BAC dealkylation, the first step in BAC biodegradation that results in a product 500 times less toxic. Subsequent biochemical assays and isolate characterization verified that the putative amine oxidase gene product was functionally capable of initiating BAC degradation. Our analysis also revealed cooperative interactions among community members to alleviate BAC toxicity, such as the further degradation of BAC dealkylation by-products by organisms not encoding amine oxidase. Collectively, our results advance the understanding of BAC aerobic biodegradation and provide genetic biomarkers to assess the critical first step of this process in nontarget environments.
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99771
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Membrane fluidity and temperature sensing are coupled via circuitry comprised of Ole1, Rsp5, and Hsf1 in Candida albicans. EUKARYOTIC CELL 2014; 13:1077-84. [PMID: 24951438 PMCID: PMC4135801 DOI: 10.1128/ec.00138-14] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Temperature is a ubiquitous environmental variable which can profoundly influence the physiology of living cells as it changes over time and space. When yeast cells are exposed to a sublethal heat shock, normal metabolic functions become repressed and the heat shock transcription factor Hsf1 is activated, inducing heat shock proteins (HSPs). Candida albicans, the most prevalent human fungal pathogen, is an opportunistic pathogen that has evolved as a relatively harmless commensal of healthy individuals. Even though C. albicans occupies thermally buffered niches, it has retained the classic heat shock response, activating Hsf1 during slow thermal transitions such as the increases in temperature suffered by febrile patients. However, the mechanism of temperature sensing in fungal pathogens remains enigmatic. A few studies with Saccharomyces cerevisiae suggest that thermal stress is transduced into a cellular signal at the level of the membrane. In this study, we manipulated the fluidity of C. albicans membrane to dissect mechanisms of temperature sensing. We determined that in response to elevated temperature, levels of OLE1, encoding a fatty acid desaturase, decrease. Subsequently, loss of OLE1 triggers expression of FAS2, encoding a fatty acid synthase. Furthermore, depletion of OLE1 prevents full activation of Hsf1, thereby reducing HSP expression in response to heat shock. This reduction in Hsf1 activation is attributable to the E3 ubiquitin ligase Rsp5, which regulates OLE1 expression. To our knowledge, this is the first study to define a molecular link between fatty acid synthesis and the heat shock response in the fungal kingdom.
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99772
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Martinez RJ, Wu CH, Beazley MJ, Andersen GL, Conrad ME, Hazen TC, Taillefert M, Sobecky PA. Microbial community responses to organophosphate substrate additions in contaminated subsurface sediments. PLoS One 2014; 9:e100383. [PMID: 24950228 PMCID: PMC4065101 DOI: 10.1371/journal.pone.0100383] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 05/27/2014] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Radionuclide- and heavy metal-contaminated subsurface sediments remain a legacy of Cold War nuclear weapons research and recent nuclear power plant failures. Within such contaminated sediments, remediation activities are necessary to mitigate groundwater contamination. A promising approach makes use of extant microbial communities capable of hydrolyzing organophosphate substrates to promote mineralization of soluble contaminants within deep subsurface environments. METHODOLOGY/PRINCIPAL FINDINGS Uranium-contaminated sediments from the U.S. Department of Energy Oak Ridge Field Research Center (ORFRC) Area 2 site were used in slurry experiments to identify microbial communities involved in hydrolysis of 10 mM organophosphate amendments [i.e., glycerol-2-phosphate (G2P) or glycerol-3-phosphate (G3P)] in synthetic groundwater at pH 5.5 and pH 6.8. Following 36 day (G2P) and 20 day (G3P) amended treatments, maximum phosphate (PO4(3-)) concentrations of 4.8 mM and 8.9 mM were measured, respectively. Use of the PhyloChip 16S rRNA microarray identified 2,120 archaeal and bacterial taxa representing 46 phyla, 66 classes, 110 orders, and 186 families among all treatments. Measures of archaeal and bacterial richness were lowest under G2P (pH 5.5) treatments and greatest with G3P (pH 6.8) treatments. Members of the phyla Crenarchaeota, Euryarchaeota, Bacteroidetes, and Proteobacteria demonstrated the greatest enrichment in response to organophosphate amendments and the OTUs that increased in relative abundance by 2-fold or greater accounted for 9%-50% and 3%-17% of total detected Archaea and Bacteria, respectively. CONCLUSIONS/SIGNIFICANCE This work provided a characterization of the distinct ORFRC subsurface microbial communities that contributed to increased concentrations of extracellular phosphate via hydrolysis of organophosphate substrate amendments. Within subsurface environments that are not ideal for reductive precipitation of uranium, strategies that harness microbial phosphate metabolism to promote uranium phosphate precipitation could offer an alternative approach for in situ sequestration.
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Affiliation(s)
- Robert J. Martinez
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama, United States of America
| | - Cindy H. Wu
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Melanie J. Beazley
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama, United States of America
| | - Gary L. Andersen
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Mark E. Conrad
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Terry C. Hazen
- Department of Civil and Environmental Engineering, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Martial Taillefert
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Patricia A. Sobecky
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama, United States of America
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99773
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Stucken K, John U, Cembella A, Soto-Liebe K, Vásquez M. Impact of nitrogen sources on gene expression and toxin production in the diazotroph Cylindrospermopsis raciborskii CS-505 and non-diazotroph Raphidiopsis brookii D9. Toxins (Basel) 2014; 6:1896-915. [PMID: 24956074 PMCID: PMC4073136 DOI: 10.3390/toxins6061896] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 05/31/2014] [Accepted: 06/09/2014] [Indexed: 11/16/2022] Open
Abstract
Different environmental nitrogen sources play selective roles in the development of cyanobacterial blooms and noxious effects are often exacerbated when toxic cyanobacteria are dominant. Cylindrospermopsis raciborskii CS-505 (heterocystous, nitrogen fixing) and Raphidiopsis brookii D9 (non-N2 fixing) produce the nitrogenous toxins cylindrospermopsin (CYN) and paralytic shellfish toxins (PSTs), respectively. These toxin groups are biosynthesized constitutively by two independent putative gene clusters, whose flanking genes are target for nitrogen (N) regulation. It is not yet known how or if toxin biosynthetic genes are regulated, particularly by N-source dependency. Here we show that binding boxes for NtcA, the master regulator of N metabolism, are located within both gene clusters as potential regulators of toxin biosynthesis. Quantification of intra- and extracellular toxin content in cultures at early stages of growth under nitrate, ammonium, urea and N-free media showed that N-sources influence neither CYN nor PST production. However, CYN and PST profiles were altered under N-free medium resulting in a decrease in the predicted precursor toxins (doCYN and STX, respectively). Reduced STX amounts were also observed under growth in ammonium. Quantification of toxin biosynthesis and transport gene transcripts revealed a constitutive transcription under all tested N-sources. Our data support the hypothesis that PSTs and CYN are constitutive metabolites whose biosynthesis is correlated to cyanobacterial growth rather than directly to specific environmental conditions. Overall, the constant biosynthesis of toxins and expression of the putative toxin-biosynthesis genes supports the usage of qPCR probes in water quality monitoring of toxic cyanobacteria.
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Affiliation(s)
- Karina Stucken
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany.
| | - Uwe John
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany.
| | - Allan Cembella
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany.
| | - Katia Soto-Liebe
- Department of Molecular Genetics and Microbiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile.
| | - Mónica Vásquez
- Department of Molecular Genetics and Microbiology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile.
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99774
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Jacobsen ID, Lüttich A, Kurzai O, Hube B, Brock M. In vivo imaging of disseminated murine Candida albicans infection reveals unexpected host sites of fungal persistence during antifungal therapy. J Antimicrob Chemother 2014; 69:2785-96. [PMID: 24951534 DOI: 10.1093/jac/dku198] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES Candida albicans is an important fungal pathogen that can cause life-threatening disseminated infections. To determine the efficacy of therapy in murine models, a determination of renal fungal burden as cfu is commonly used. However, this approach provides only a snapshot of the current situation in an individual animal and cryptic sites of infection may easily be missed. Thus, we aimed to develop real-time non-invasive imaging to monitor infection in vivo. METHODS Bioluminescent C. albicans reporter strains were developed based on a bioinformatical approach for codon optimization. The reporter strains were analysed in vitro and in vivo in the murine model of systemic candidiasis. RESULTS Reporter strains allowed the in vivo monitoring of infection and a determination of fungal burden, with a high correlation between bioluminescence and cfu count. We confirmed the kidney as the main target organ but additionally observed the translocation of C. albicans to the urinary bladder. The treatment of infected mice with caspofungin and fluconazole significantly improved the clinical outcome and clearance of C. albicans from the kidneys; however, unexpectedly, viable fungal cells persisted in the gall bladder. Fungi were secreted with bile and detected in the faeces, implicating the gall bladder as a reservoir for colonization by C. albicans after antifungal therapy. Bile extracts significantly decreased the susceptibility of C. albicans to various antifungals in vitro, thereby probably contributing to its persistence. CONCLUSIONS Using in vivo imaging, we identified cryptic sites of infection and persistence of C. albicans in the gall bladder during otherwise effective antifungal treatment. Bile appears to directly interfere with antifungal activity.
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Affiliation(s)
- Ilse D Jacobsen
- Microbial Immunology, Hans Knoell Institute, Leibniz Institute for Natural Product Research and Infection Biology, Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Anja Lüttich
- Microbial Pathogenicity Mechanisms, Hans Knoell Institute, Leibniz Institute for Natural Product Research and Infection Biology, Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Oliver Kurzai
- Septomics Research Center, Friedrich-Schiller University Jena and Leibniz Institute for Natural Product Research and Infection Biology, Albert-Einstein Strasse 10, 07745 Jena, Germany
| | - Bernhard Hube
- Microbial Pathogenicity Mechanisms, Hans Knoell Institute, Leibniz Institute for Natural Product Research and Infection Biology, Beutenbergstrasse 11a, 07745 Jena, Germany Friedrich Schiller University, Jena, Germany Center for Sepsis Control and Care, Universitätsklinikum Jena, Jena, Germany
| | - Matthias Brock
- Friedrich Schiller University, Jena, Germany Microbial Biochemistry and Physiology, Hans Knoell Institute, Leibniz Institute for Natural Product Research and Infection Biology, Beutenbergstrasse 11a, 07745 Jena, Germany
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99775
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Ghamrawi S, Rénier G, Saulnier P, Cuenot S, Zykwinska A, Dutilh BE, Thornton C, Faure S, Bouchara JP. Cell wall modifications during conidial maturation of the human pathogenic fungus Pseudallescheria boydii. PLoS One 2014; 9:e100290. [PMID: 24950099 PMCID: PMC4065047 DOI: 10.1371/journal.pone.0100290] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 05/22/2014] [Indexed: 01/27/2023] Open
Abstract
Progress in extending the life expectancy of cystic fibrosis (CF) patients remains jeopardized by the increasing incidence of fungal respiratory infections. Pseudallescheria boydii (P. boydii), an emerging pathogen of humans, is a filamentous fungus frequently isolated from the respiratory secretions of CF patients. It is commonly believed that infection by this fungus occurs through inhalation of airborne conidia, but the mechanisms allowing the adherence of Pseudallescheria to the host epithelial cells and its escape from the host immune defenses remain largely unknown. Given that the cell wall orchestrates all these processes, we were interested in studying its dynamic changes in conidia as function of the age of cultures. We found that the surface hydrophobicity and electronegative charge of conidia increased with the age of culture. Melanin that can influence the cell surface properties, was extracted from conidia and estimated using UV-visible spectrophotometry. Cells were also directly examined and compared using electron paramagnetic resonance (EPR) that determines the production of free radicals. Consistent with the increased amount of melanin, the EPR signal intensity decreased suggesting polymerization of melanin. These results were confirmed by flow cytometry after studying the effect of melanin polymerization on the surface accessibility of mannose-containing glycoconjugates to fluorescent concanavalin A. In the absence of melanin, conidia showed a marked increase in fluorescence intensity as the age of culture increased. Using atomic force microscopy, we were unable to find rodlet-forming hydrophobins, molecules that can also affect conidial surface properties. In conclusion, the changes in surface properties and biochemical composition of the conidial wall with the age of culture highlight the process of conidial maturation. Mannose-containing glycoconjugates that are involved in immune recognition, are progressively masked by polymerization of melanin, an antioxidant that is commonly thought to allow fungal escape from the host immune defenses.
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Affiliation(s)
- Sarah Ghamrawi
- L’UNAM Université, Université d’Angers, Groupe d’Etude des Interactions Hôte-Pathogène EA 3142, Angers, France
- * E-mail:
| | - Gilles Rénier
- L’UNAM Université, Université d’Angers, Groupe d’Etude des Interactions Hôte-Pathogène EA 3142, Angers, France
- Laboratoire de Parasitologie-Mycologie, Centre Hospitalier Universitaire, Angers, France
| | - Patrick Saulnier
- L’UNAM Université, University d’Angers, INSERM U646, Angers, France
| | - Stéphane Cuenot
- L’UNAM Université, Université de Nantes, Institut des Matériaux Jean Rouxel, Nantes, France
| | - Agata Zykwinska
- L’UNAM Université, Université de Nantes, Institut des Matériaux Jean Rouxel, Nantes, France
| | - Bas E. Dutilh
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
- Department of Marine Biology, Institute of Biology, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Christopher Thornton
- Department of Biosciences, University of Exeter, Biosciences, Exeter, United Kingdom
| | | | - Jean-Philippe Bouchara
- L’UNAM Université, Université d’Angers, Groupe d’Etude des Interactions Hôte-Pathogène EA 3142, Angers, France
- Laboratoire de Parasitologie-Mycologie, Centre Hospitalier Universitaire, Angers, France
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99776
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Moradigaravand D, Engelstädter J. The impact of natural transformation on adaptation in spatially structured bacterial populations. BMC Evol Biol 2014; 14:141. [PMID: 24951188 PMCID: PMC4080760 DOI: 10.1186/1471-2148-14-141] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 06/08/2014] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Recent studies have demonstrated that natural transformation and the formation of highly structured populations in bacteria are interconnected. In spite of growing evidence about this connection, little is known about the dynamics of natural transformation in spatially structured bacterial populations. RESULTS In this work, we model the interdependency between the dynamics of the bacterial gene pool and those of environmental DNA in space to dissect the effect of transformation on adaptation. Our model reveals that even with only a single locus under consideration, transformation with a free DNA fragment pool results in complex adaptation dynamics that do not emerge in previous models focusing only on the gene shuffling effect of transformation at multiple loci. We demonstrate how spatial restriction on population growth and DNA diffusion in the environment affect the impact of transformation on adaptation. We found that in structured bacterial populations intermediate DNA diffusion rates predominantly cause transformation to impede adaptation by spreading deleterious alleles in the population. CONCLUSION Overall, our model highlights distinctive evolutionary consequences of bacterial transformation in spatially restricted compared to planktonic bacterial populations.
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Affiliation(s)
- Danesh Moradigaravand
- Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, 8092 Zürich, Switzerland.
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99777
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Gyöngyösi N, Káldi K. Interconnections of reactive oxygen species homeostasis and circadian rhythm in Neurospora crassa. Antioxid Redox Signal 2014; 20:3007-23. [PMID: 23964982 DOI: 10.1089/ars.2013.5558] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
SIGNIFICANCE Both circadian rhythm and the production of reactive oxygen species (ROS) are fundamental features of aerobic eukaryotic cells. The circadian clock enhances the fitness of organisms by enabling them to anticipate cycling changes in the surroundings. ROS generation in the cell is often altered in response to environmental changes, but oscillations in ROS levels may also reflect endogenous metabolic fluctuations governed by the circadian clock. On the other hand, an effective regulation and timing of antioxidant mechanisms may be crucial in the defense of cellular integrity. Thus, an interaction between the circadian timekeeping machinery and ROS homeostasis or signaling in both directions may be of advantage at all phylogenetic levels. RECENT ADVANCES The Frequency-White Collar-1 and White Collar-2 oscillator (FWO) of the filamentous fungus Neurospora crassa is well characterized at the molecular level. Several members of the ROS homeostasis were found to be controlled by the circadian clock, and ROS levels display circadian rhythm in Neurospora. On the other hand, multiple data indicate that ROS affect the molecular oscillator. CRITICAL ISSUES Increasing evidence suggests the interplay between ROS homeostasis and oscillators that may be partially or fully independent of the FWO. In addition, ROS may be part of a complex cellular network synchronizing non-transcriptional oscillators with timekeeping machineries based on the classical transcription-translation feedback mechanism. FUTURE DIRECTIONS Further investigations are needed to clarify how the different layers of the bidirectional interactions between ROS homeostasis and circadian regulation are interconnected.
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99778
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Monteiro DR, Takamiya AS, Feresin LP, Gorup LF, de Camargo ER, Delbem ACB, Henriques M, Barbosa DB. Silver colloidal nanoparticle stability: influence on Candida biofilms formed on denture acrylic. Med Mycol 2014; 52:627-35. [DOI: 10.1093/mmy/myu021] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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99779
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Allen HK, Trachsel J, Looft T, Casey TA. Finding alternatives to antibiotics. Ann N Y Acad Sci 2014; 1323:91-100. [DOI: 10.1111/nyas.12468] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Heather K. Allen
- United States Department of Agriculture Food Safety and Enteric Pathogens Research Unit National Animal Disease Center Agricultural Research Service Ames Iowa
| | - Julian Trachsel
- United States Department of Agriculture Food Safety and Enteric Pathogens Research Unit National Animal Disease Center Agricultural Research Service Ames Iowa
| | - Torey Looft
- United States Department of Agriculture Food Safety and Enteric Pathogens Research Unit National Animal Disease Center Agricultural Research Service Ames Iowa
| | - Thomas A. Casey
- United States Department of Agriculture Food Safety and Enteric Pathogens Research Unit National Animal Disease Center Agricultural Research Service Ames Iowa
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99780
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LacR is a repressor of lacABCD and LacT is an activator of lacTFEG, constituting the lac gene cluster in Streptococcus pneumoniae. Appl Environ Microbiol 2014; 80:5349-58. [PMID: 24951784 DOI: 10.1128/aem.01370-14] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Comparison of the transcriptome of Streptococcus pneumoniae strain D39 grown in the presence of either lactose or galactose with that of the strain grown in the presence of glucose revealed the elevated expression of various genes and operons, including the lac gene cluster, which is organized into two operons, i.e., lac operon I (lacABCD) and lac operon II (lacTFEG). Deletion of the DeoR family transcriptional regulator lacR that is present downstream of the lac gene cluster revealed elevated expression of lac operon I even in the absence of lactose. This suggests a function of LacR as a transcriptional repressor of lac operon I, which encodes enzymes involved in the phosphorylated tagatose pathway in the absence of lactose or galactose. Deletion of lacR did not affect the expression of lac operon II, which encodes a lactose-specific phosphotransferase. This finding was further confirmed by β-galactosidase assays with PlacA-lacZ and PlacT-lacZ in the presence of either lactose or glucose as the sole carbon source in the medium. This suggests the involvement of another transcriptional regulator in the regulation of lac operon II, which is the BglG-family transcriptional antiterminator LacT. We demonstrate the role of LacT as a transcriptional activator of lac operon II in the presence of lactose and CcpA-independent regulation of the lac gene cluster in S. pneumoniae.
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99781
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Inhibition of biofilm formation by T7 bacteriophages producing quorum-quenching enzymes. Appl Environ Microbiol 2014; 80:5340-8. [PMID: 24951790 DOI: 10.1128/aem.01434-14] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Bacterial growth in biofilms is the major cause of recalcitrant biofouling in industrial processes and of persistent infections in clinical settings. The use of bacteriophage treatment to lyse bacteria in biofilms has attracted growing interest. In particular, many natural or engineered phages produce depolymerases to degrade polysaccharides in the biofilm matrix and allow access to host bacteria. However, the phage-produced depolymerases are highly specific for only the host-derived polysaccharides and may have limited effects on natural multispecies biofilms. In this study, an engineered T7 bacteriophage was constructed to encode a lactonase enzyme with broad-range activity for quenching of quorum sensing, a form of bacterial cell-cell communication via small chemical molecules (acyl homoserine lactones [AHLs]) that is necessary for biofilm formation. Our results demonstrated that the engineered T7 phage expressed the AiiA lactonase to effectively degrade AHLs from many bacteria. Addition of the engineered T7 phage to mixed-species biofilms containing Pseudomonas aeruginosa and Escherichia coli resulted in inhibition of biofilm formation. Such quorum-quenching phages that can lyse host bacteria and express quorum-quenching enzymes to affect diverse bacteria in biofilm communities may become novel antifouling and antibiofilm agents in industrial and clinical settings.
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99782
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Jean NL, Bougault CM, Lodge A, Derouaux A, Callens G, Egan AJF, Ayala I, Lewis RJ, Vollmer W, Simorre JP. Elongated structure of the outer-membrane activator of peptidoglycan synthesis LpoA: implications for PBP1A stimulation. Structure 2014; 22:1047-54. [PMID: 24954617 PMCID: PMC4111904 DOI: 10.1016/j.str.2014.04.017] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 04/25/2014] [Accepted: 04/28/2014] [Indexed: 01/27/2023]
Abstract
The bacterial cell envelope contains the stress-bearing peptidoglycan layer, which is enlarged during cell growth and division by membrane-anchored synthases guided by cytoskeletal elements. In Escherichia coli, the major peptidoglycan synthase PBP1A requires stimulation by the outer-membrane-anchored lipoprotein LpoA. Whereas the C-terminal domain of LpoA interacts with PBP1A to stimulate its peptide crosslinking activity, little is known about the role of the N-terminal domain. Herein we report its NMR structure, which adopts an all-α-helical fold comprising a series of helix-turn-helix tetratricopeptide-repeat (TPR)-like motifs. NMR spectroscopy of full-length LpoA revealed two extended flexible regions in the C-terminal domain and limited, if any, flexibility between the N- and C-terminal domains. Analytical ultracentrifugation and small-angle X-ray scattering results are consistent with LpoA adopting an elongated shape, with dimensions sufficient to span from the outer membrane through the periplasm to interact with the peptidoglycan synthase PBP1A. LpoA’s N-terminal domain features an all-α-helical fold similar to TPR domains The C-terminal domain of E. coli LpoA contains two extensive flexible regions Full-length LpoA adopts an elongated structure with low interdomain flexibility LpoA can span the periplasm to stimulate the peptidoglycan synthase PBP1A
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Affiliation(s)
- Nicolas L Jean
- University Grenoble Alpes, Institut de Biologie Structurale, F-38027 Grenoble, France; CEA, DSV, Institut de Biologie Structurale, F-38027 Grenoble, France; CNRS, Institut de Biologie Structurale, F-38027 Grenoble, France
| | - Catherine M Bougault
- University Grenoble Alpes, Institut de Biologie Structurale, F-38027 Grenoble, France; CEA, DSV, Institut de Biologie Structurale, F-38027 Grenoble, France; CNRS, Institut de Biologie Structurale, F-38027 Grenoble, France
| | - Adam Lodge
- The Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, UK
| | - Adeline Derouaux
- The Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, UK
| | - Gilles Callens
- The Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, UK
| | - Alexander J F Egan
- The Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, UK
| | - Isabel Ayala
- University Grenoble Alpes, Institut de Biologie Structurale, F-38027 Grenoble, France; CEA, DSV, Institut de Biologie Structurale, F-38027 Grenoble, France; CNRS, Institut de Biologie Structurale, F-38027 Grenoble, France
| | - Richard J Lewis
- Institute for Cell and Molecular Biosciences, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Waldemar Vollmer
- The Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, UK.
| | - Jean-Pierre Simorre
- University Grenoble Alpes, Institut de Biologie Structurale, F-38027 Grenoble, France; CEA, DSV, Institut de Biologie Structurale, F-38027 Grenoble, France; CNRS, Institut de Biologie Structurale, F-38027 Grenoble, France.
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99783
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Moreira APB, Duytschaever G, Chimetto Tonon LA, Fróes AM, de Oliveira LS, Amado-Filho GM, Francini-Filho RB, De Vos P, Swings J, Thompson CC, Thompson FL. Photobacterium sanctipauli sp. nov. isolated from bleached Madracis decactis (Scleractinia) in the St Peter & St Paul Archipelago, Mid-Atlantic Ridge, Brazil. PeerJ 2014; 2:e427. [PMID: 25024905 PMCID: PMC4081156 DOI: 10.7717/peerj.427] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 05/22/2014] [Indexed: 11/20/2022] Open
Abstract
Five novel strains of Photobacterium (A-394T, A-373, A-379, A-397 and A-398) were isolated from bleached coral Madracis decactis (scleractinian) in the remote St Peter & St Archipelago (SPSPA), Mid-Atlantic Ridge, Brazil. Healthy M. decactis specimens were also surveyed, but no strains were related to them. The novel isolates formed a distinct lineage based on the 16S rRNA, recA, and rpoA gene sequences analysis. Their closest phylogenetic neighbours were Photobacterium rosenbergii, P. gaetbulicola, and P. lutimaris, sharing 96.6 to 95.8% 16S rRNA gene sequence similarity. The novel species can be differentiated from the closest neighbours by several phenotypic and chemotaxonomic markers. It grows at pH 11, produces tryptophane deaminase, presents the fatty acid C18:0, but lacks C16:0 iso. The whole cell protein profile, based in MALDI-TOF MS, distinguished the strains of the novel species among each other and from the closest neighbors. In addition, we are releasing the whole genome sequence of the type strain. The name Photobacterium sanctipauli sp. nov. is proposed for this taxon. The G + C content of the type strain A-394(T) (= LMG27910(T) = CAIM1892(T)) is 48.2 mol%.
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Affiliation(s)
- Ana Paula B Moreira
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ) , Rio de Janeiro , Brazil
| | - Gwen Duytschaever
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ) , Rio de Janeiro , Brazil
| | | | - Adriana M Fróes
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ) , Rio de Janeiro , Brazil
| | - Louisi S de Oliveira
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ) , Rio de Janeiro , Brazil
| | | | | | - Paul De Vos
- BCCM/LMG Bacteria Collection, Ghent University , Ghent , Belgium ; Laboratory of Microbiology, Faculty of Sciences, Ghent University , Ghent , Belgium
| | - Jean Swings
- BCCM/LMG Bacteria Collection, Ghent University , Ghent , Belgium ; Laboratory of Microbiology, Faculty of Sciences, Ghent University , Ghent , Belgium
| | - Cristiane C Thompson
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ) , Rio de Janeiro , Brazil
| | - Fabiano L Thompson
- Institute of Biology, Federal University of Rio de Janeiro (UFRJ) , Rio de Janeiro , Brazil ; Laboratório de Sistemas Avançados de Gestão de Produção - SAGE - COPPE, Federal University of Rio de Janeiro , Rio de Janeiro , Brazil
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99784
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Spinler JK, Sontakke A, Hollister EB, Venable SF, Oh PL, Balderas MA, Saulnier DMA, Mistretta TA, Devaraj S, Walter J, Versalovic J, Highlander SK. From prediction to function using evolutionary genomics: human-specific ecotypes of Lactobacillus reuteri have diverse probiotic functions. Genome Biol Evol 2014; 6:1772-89. [PMID: 24951561 PMCID: PMC4122935 DOI: 10.1093/gbe/evu137] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The vertebrate gut symbiont Lactobacillus reuteri has diversified into separate clades reflecting host origin. Strains show evidence of host adaptation, but how host–microbe coevolution influences microbial-derived effects on hosts is poorly understood. Emphasizing human-derived strains of L. reuteri, we combined comparative genomic analyses with functional assays to examine variations in host interaction among genetically distinct ecotypes. Within clade II or VI, the genomes of human-derived L. reuteri strains are highly conserved in gene content and at the nucleotide level. Nevertheless, they share only 70–90% of total gene content, indicating differences in functional capacity. Human-associated lineages are distinguished by genes related to bacteriophages, vitamin biosynthesis, antimicrobial production, and immunomodulation. Differential production of reuterin, histamine, and folate by 23 clade II and VI strains was demonstrated. These strains also differed with respect to their ability to modulate human cytokine production (tumor necrosis factor, monocyte chemoattractant protein-1, interleukin [IL]-1β, IL-5, IL-7, IL-12, and IL-13) by myeloid cells. Microarray analysis of representative clade II and clade VI strains revealed global regulation of genes within the reuterin, vitamin B12, folate, and arginine catabolism gene clusters by the AraC family transcriptional regulator, PocR. Thus, human-derived L. reuteri clade II and VI strains are genetically distinct and their differences affect their functional repertoires and probiotic features. These findings highlight the biological impact of microbe:host coevolution and illustrate the functional significance of subspecies differences in the human microbiome. Consideration of host origin and functional differences at the subspecies level may have major impacts on probiotic strain selection and considerations of microbial ecology in mammalian species.
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Affiliation(s)
- Jennifer K Spinler
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TXDepartment of Pathology & Immunology, Baylor College of Medicine, Houston, TX
| | - Amrita Sontakke
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TXDepartment of Pathology & Immunology, Baylor College of Medicine, Houston, TX
| | - Emily B Hollister
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TXDepartment of Pathology & Immunology, Baylor College of Medicine, Houston, TX
| | - Susan F Venable
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TXDepartment of Pathology & Immunology, Baylor College of Medicine, Houston, TX
| | - Phaik Lyn Oh
- Department of Food Science and Technology, University of Nebraska, Lincoln
| | - Miriam A Balderas
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX
| | - Delphine M A Saulnier
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TXDepartment of Pathology & Immunology, Baylor College of Medicine, Houston, TXPresent address: Department of Gastrointestinal Microbiology, German Institute of Human Nutrition, Nuthetal, Germany
| | - Toni-Ann Mistretta
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TXDepartment of Pathology & Immunology, Baylor College of Medicine, Houston, TX
| | - Sridevi Devaraj
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TXDepartment of Pathology & Immunology, Baylor College of Medicine, Houston, TX
| | - Jens Walter
- Department of Food Science and Technology, University of Nebraska, LincolnPresent address: Departments of Agricultural, Food, & Nutritional Science and Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - James Versalovic
- Texas Children's Microbiome Center, Department of Pathology, Texas Children's Hospital, Houston, TXDepartment of Pathology & Immunology, Baylor College of Medicine, Houston, TXDepartment of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TX
| | - Sarah K Highlander
- Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, TXHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TXPresent address: Genomic Medicine, J. Craig Venter Institute, La Jolla, CA
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99785
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Sonnleitner E, Bläsi U. Regulation of Hfq by the RNA CrcZ in Pseudomonas aeruginosa carbon catabolite repression. PLoS Genet 2014; 10:e1004440. [PMID: 24945892 PMCID: PMC4063720 DOI: 10.1371/journal.pgen.1004440] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 04/30/2014] [Indexed: 01/10/2023] Open
Abstract
Carbon Catabolite repression (CCR) allows a fast adaptation of Bacteria to changing nutrient supplies. The Pseudomonas aeruginosa (PAO1) catabolite repression control protein (Crc) was deemed to act as a translational regulator, repressing functions involved in uptake and utilization of carbon sources. However, Crc of PAO1 was recently shown to be devoid of RNA binding activity. In this study the RNA chaperone Hfq was identified as the principle post-transcriptional regulator of CCR in PAO1. Hfq is shown to bind to A-rich sequences within the ribosome binding site of the model mRNA amiE, and to repress translation in vitro and in vivo. We further report that Crc plays an unknown ancillary role, as full-fledged repression of amiE and other CCR-regulated mRNAs in vivo required its presence. Moreover, we show that the regulatory RNA CrcZ, transcription of which is augmented when CCR is alleviated, binds to Hfq with high affinity. This study on CCR in PAO1 revealed a novel concept for Hfq function, wherein the regulatory RNA CrcZ acts as a decoy to abrogate Hfq-mediated translational repression of catabolic genes and thus highlights the central role of RNA based regulation in CCR of PAO1. Carbon assimilation in Bacteria is governed by a mechanism known as carbon catabolite repression (CCR). In contrast to several other bacterial clades CCR in Pseudomonas species appears to be primarily regulated at the post-transcriptional level. In this study, we have identified the RNA chaperone Hfq as the principle post-transcriptional regulator of CCR in P. aeruginosa (PAO1). Hfq is shown to act as a translational regulator and to prevent ribosome loading through binding to A-rich sequences within the ribosome binding site of mRNAs, which encode enzymes involved in carbon utilization. It has been previously shown that the synthesis of the RNA CrcZ is augmented in the presence of non-preferred carbon sources. Here, we show that the CrcZ RNA binds to and sequesters Hfq, which in turn abrogates Hfq-mediated translational repression of mRNAs, the encoded functions of which are required for the breakdown of non-preferred carbon sources. This novel mechanistic twist on Hfq function not only highlights the central role of RNA based regulation in CCR of PAO1 but also broadens the view of Hfq-mediated post-transcriptional mechanisms.
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Affiliation(s)
- Elisabeth Sonnleitner
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Vienna, Austria
- * E-mail: (ES); (UB)
| | - Udo Bläsi
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Vienna, Austria
- * E-mail: (ES); (UB)
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99786
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Quorum sensing signalling and biofilm formation of brewery-derived bacteria, and inhibition of signalling by natural compounds. Curr Microbiol 2014; 69:617-27. [PMID: 24944110 DOI: 10.1007/s00284-014-0627-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 04/28/2014] [Indexed: 01/13/2023]
Abstract
Bacteria use quorum sensing signalling in various functions, e.g. while forming biofilms, and inhibition of this signalling could be one way to control biofilm formation. The aim of this study was to evaluate the production of signalling molecules and its correlation with the biofilm formation capability of bacteria isolated from brewery filling process. A further aim was to study berry extracts and wood-derived terpenes for their possible quorum sensing inhibitory effects. Out of the twenty bacteria studied, five produced short-chain and five long-chain AHL (acyl homoserine lactone) signalling molecules when tested with the Chromobacterium violaceum CV026 reporter bacterium. Production of AI-2 (autoinducer-2) signalling molecules was detected from nine strains with the Vibrio harveyi BB170 bioassay. Over half of the strains produced biofilm in the microtitre plate assay, but the production of AHL and AI-2 signalling molecules and biofilm formation capability did not directly correlate with each other. Out of the 13 berry extracts and wood-derived terpenes screened, four compounds decreased AHL signalling without effect on growth. These were betulin, raspberry extract and two cloudberry extracts. The effect of these compounds on biofilm formation of the selected six bacterial strains varied. The phenolic extract of freeze-dried cloudberry fruit caused a statistically significant reduction of biofilm formation of Obesumbacterium proteus strain. Further experiments should aim at identifying the active compounds and revealing whether quorum sensing inhibition causes structural changes in the biofilms formed.
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99787
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Steiner I, Livneh V, Hoffmann C, Nass D, Mor O, Chapman J. Steroid-responsive, progressive, focal measles virus brain infection. Ann Neurol 2014; 75:967-70. [PMID: 24817010 DOI: 10.1002/ana.24183] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Revised: 05/09/2014] [Accepted: 05/09/2014] [Indexed: 11/06/2022]
Abstract
Chronic measles virus infection of the brain causes subacute sclerosing panencephalitis (SSPE), a progressive, relentless fatal disorder. We report a 52-year-old male who developed focal, chronic persistent measles virus infection of the brain following interferon and ribavirin therapy for hepatitis C, and who responded to steroid therapy. This case, diametrically different from SSPE, has 2 unique features, its focal nature and its permissive response to steroids, that may add to the understanding of the pathogenesis of SSPE and the mechanism enabling viruses to evade the immune response and establish persistent brain infection.
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Affiliation(s)
- Israel Steiner
- Department of Neurology, Rabin Medical Center, Petach Tikva, Israel
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99788
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A novel peptidoglycan binding protein crucial for PBP1A-mediated cell wall biogenesis in Vibrio cholerae. PLoS Genet 2014; 10:e1004433. [PMID: 24945690 PMCID: PMC4063736 DOI: 10.1371/journal.pgen.1004433] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 04/25/2014] [Indexed: 02/02/2023] Open
Abstract
The bacterial cell wall, which is comprised of a mesh of polysaccharide strands crosslinked via peptide bridges (peptidoglycan, PG), is critical for maintenance of cell shape and survival. PG assembly is mediated by a variety of Penicillin Binding Proteins (PBP) whose fundamental activities have been characterized in great detail; however, there is limited knowledge of the factors that modulate their activities in different environments or growth phases. In Vibrio cholerae, the cause of cholera, PG synthesis during the transition into stationary phase is primarily mediated by the bifunctional enzyme PBP1A. Here, we screened an ordered V. cholerae transposon library for mutants that are sensitive to growth inhibition by non-canonical D-amino acids (DAA), which prevent growth and maintenance of cell shape in PBP1A-deficient V. cholerae. In addition to PBP1A and its lipoprotein activator LpoA, we found that CsiV, a small periplasmic protein with no previously described function, is essential for growth in the presence of DAA. Deletion of csiV, like deletion of lpoA or the PBP1A-encoding gene mrcA, causes cells to lose their rod shape in the presence of DAA or the beta-lactam antibiotic cefsulodin, and all three mutations are synthetically lethal with deletion of mrcB, which encodes PBP1B, V. cholerae's second key bifunctional PBP. CsiV interacts with LpoA and PG but apparently not with PBP1A, supporting the hypothesis that CsiV promotes LpoA's role as an activator of PBP1A, and thereby modulates V. cholerae PG biogenesis. Finally, the requirement for CsiV in PBP1A-mediated growth of V. cholerae can be overcome either by augmenting PG synthesis or by reducing PG degradation, thereby highlighting the importance of balancing these two processes for bacterial survival.
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99789
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Sazanov LA. The mechanism of coupling between electron transfer and proton translocation in respiratory complex I. J Bioenerg Biomembr 2014; 46:247-53. [PMID: 24943718 DOI: 10.1007/s10863-014-9554-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 06/03/2014] [Indexed: 10/25/2022]
Abstract
NADH-ubiquinone oxidoreductase (complex I) is the first and largest enzyme in the respiratory chain of mitochondria and many bacteria. It couples the transfer of two electrons between NADH and ubiquinone to the translocation of four protons across the membrane. Complex I is an L-shaped assembly formed by the hydrophilic (peripheral) arm, containing all the redox centres performing electron transfer and the membrane arm, containing proton-translocating machinery. Mitochondrial complex I consists of 44 subunits of about 1 MDa in total, whilst the prokaryotic enzyme is simpler and generally consists of 14 conserved "core" subunits. Recently we have determined the first atomic structure of the entire complex I, using the enzyme from Thermus thermophilus (536 kDa, 16 subunits, 9 Fe-S clusters, 64 TM helices). Structure suggests a unique coupling mechanism, with redox energy of electron transfer driving proton translocation via long-range (up to ~200 Å) conformational changes. It resembles a steam engine, with coupling elements (akin to coupling rods) linking parts of this molecular machine.
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Affiliation(s)
- Leonid A Sazanov
- Medical Research Council Mitochondrial Biology Unit, Hills road, Cambridge, CB2 0XY, United Kingdom,
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99790
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Kidzeru EB, Hesseling AC, Passmore JAS, Myer L, Gamieldien H, Tchakoute CT, Gray CM, Sodora DL, Jaspan HB. In-utero exposure to maternal HIV infection alters T-cell immune responses to vaccination in HIV-uninfected infants. AIDS 2014; 28:1421-30. [PMID: 24785950 PMCID: PMC4333196 DOI: 10.1097/qad.0000000000000292] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE In sub-Saharan Africa, HIV-exposed uninfected (HEU) infants have higher morbidity and mortality than HIV-unexposed infants. To evaluate whether immune dysfunction contributes to this vulnerability of HEU infants, we conducted a longitudinal, observational cohort study to assess T-cell immune responses to infant vaccines (Mycobacterium bovis BCG and acellular pertussis) and staphylococcal enterotoxin B (SEB). In total, 46 HEU and 46 HIV-unexposed infants were recruited from Khayelitsha, Cape Town. METHODS Vaccine-specific T-cell proliferation (Ki67 expression) and intracellular expression of four cytokines [interferon-γ, interleukin (IL)-2, IL-13 and IL-17] were measured after whole blood stimulation with antigens at 6 and 14 weeks of age. RESULTS HEU infants demonstrated elevated BCG-specific CD4 and CD8 T-cell proliferative responses at 14 weeks (P = 0.041 and 0.002, respectively). These responses were significantly increased even after adjusting for birth weight, feeding mode and gestational age. Similar to BCG, increased CD4 and CD8 T-cell proliferation was evident in response to SEB stimulation (P = 0.004 and 0.002, respectively), although pertussis-specific T cells proliferated comparably between the two groups. Within HEU infants, maternal CD4 cell count and length of antenatal antiretroviral exposure had no effect on T-cell proliferation to BCG or SEB. HIV exposure significantly diminished measurable cytokine polyfunctionality in response to BCG, Bordetella pertussis and SEB stimulation. CONCLUSION These data show for the first time, when adjusting for confounders, that exposure to HIV in utero is associated with significant alterations to CD4 and CD8T-cell immune responses in infants to vaccines and nonspecific antigens.
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Affiliation(s)
- Elvis B. Kidzeru
- Division of Immunology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town
| | - Anneke C. Hesseling
- Desmond Tutu TB Centre, Faculty of Medicine and Health Sciences, Stellenbosch University, Parow
| | - Jo-Ann S. Passmore
- Division of Virology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town
- National Health Laboratory Services, South Africa
| | - Landon Myer
- Division of Epidemiology & Biostatistics, School of Public Health & Family Medicine, University of Cape Town, Cape Town, South Africa
| | - Hoyam Gamieldien
- Division of Immunology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town
- Division of Virology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town
| | | | - Clive M. Gray
- Division of Immunology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town
- National Health Laboratory Services, South Africa
| | | | - Heather B. Jaspan
- Division of Immunology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town
- Seattle Biomedical Research Institute, Seattle, Washington, USA
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99791
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Borrero-de Acuña JM, Bielecka A, Häussler S, Schobert M, Jahn M, Wittmann C, Jahn D, Poblete-Castro I. Production of medium chain length polyhydroxyalkanoate in metabolic flux optimized Pseudomonas putida. Microb Cell Fact 2014; 13:88. [PMID: 24948031 PMCID: PMC4077159 DOI: 10.1186/1475-2859-13-88] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 06/06/2014] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Pseudomnas putida is a natural producer of medium chain length polyhydroxyalkanoates (mcl-PHA), a polymeric precursor of bioplastics. A two-fold increase of mcl-PHA production via inactivation of the glucose dehydrogenase gene gcd, limiting the metabolic flux towards side products like gluconate was achieved before. Here, we investigated the overproduction of enzymes catalyzing limiting steps of mcl-PHA precursor formation. RESULTS A genome-based in silico model for P. putida KT2440 metabolism was employed to identify potential genetic targets to be engineered for the improvement of mcl-PHA production using glucose as sole carbon source. Here, overproduction of pyruvate dehydrogenase subunit AcoA in the P. putida KT2440 wild type and the Δgcd mutant strains led to an increase of PHA production. In controlled bioreactor batch fermentations PHA production was increased by 33% in the acoA overexpressing wild type and 121% in the acoA overexpressing Δgcd strain in comparison to P. putida KT2440. Overexpression of pgl-encoding 6-phosphoglucolactonase did not influence PHA production. Transcriptome analyses of engineered PHA producing P. putida in comparison to its parental strains revealed the induction of genes encoding glucose 6-phosphate dehydrogenase and pyruvate dehydrogenase. In addition, NADPH seems to be quantitatively consumed for efficient PHA synthesis, since a direct relationship between low levels of NADPH and high concentrations of the biopolymer were observed. In contrast, intracellular levels of NADH were found increased in PHA producing organisms. CONCLUSION Production of mcl-PHAs was enhanced in P. putida when grown on glucose via overproduction of a pyruvate dehydrogenase subunit (AcoA) in combination with a deletion of the glucose dehydrogenase (gcd) gene as predicted by in silico elementary flux mode analysis.
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Affiliation(s)
| | - Agata Bielecka
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, D-38124 Braunschweig, Germany
| | - Susanne Häussler
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, D-38124 Braunschweig, Germany
| | - Max Schobert
- Institute of Microbiology, Technische Universität Braunschweig D-38106, Braunschweig, Germany
| | - Martina Jahn
- Institute of Microbiology, Technische Universität Braunschweig D-38106, Braunschweig, Germany
| | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, D-66123 Saarbrücken, Germany
| | - Dieter Jahn
- Institute of Microbiology, Technische Universität Braunschweig D-38106, Braunschweig, Germany
| | - Ignacio Poblete-Castro
- Universidad Andrés Bello, Facultad de Ciencias Biológicas, Biosystems Engineering group, 8340176 Santiago, Chile
- Microbial Drugs group, Helmholtz Centre for Infection Research, D-38124 Braunschweig, Germany
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99792
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Koskella B. Research highlights for issue 5: the role of the microbiome in shaping evolution. Evol Appl 2014; 7:519-20. [PMID: 24944565 PMCID: PMC4055173 DOI: 10.1111/eva.12167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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99793
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Sarraf NS, Shi R, McDonald L, Baardsnes J, Zhang L, Cygler M, Ekiel I. Structure of CbpA J-domain bound to the regulatory protein Cbpm explains its specificity and suggests evolutionary link between Cbpm and transcriptional regulators. PLoS One 2014; 9:e100441. [PMID: 24945826 PMCID: PMC4063869 DOI: 10.1371/journal.pone.0100441] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 05/23/2014] [Indexed: 11/24/2022] Open
Abstract
CbpA is one of the six E. coli DnaJ/Hsp40 homologues of DnaK co-chaperones and the only one that is additionally regulated by a small protein CbpM, conserved in γ-proteobacteria. CbpM inhibits the co-chaperone and DNA binding activities of CbpA. This regulatory function of CbpM is accomplished through reversible interaction with the N-terminal J-domain of CbpA, which is essential for the interaction with DnaK. CbpM is highly specific for CbpA and does not bind DnaJ despite the high degree of structural and functional similarity between the J-domains of CbpA and DnaJ. Here we report the crystal structure of the complex of CbpM with the J-domain of CbpA. CbpM forms dimers and the J-domain of CbpA interacts with both CbpM subunits. The CbpM-binding surface of CbpA is highly overlapping with the CbpA interface for DnaK, providing a competitive model for regulation through forming mutually exclusive complexes. The structure also provides the explanation for the strict specificity of CbpM for CbpA, which we confirmed by making mutants of DnaJ that became regulated by CbpM. Interestingly, the structure of CbpM reveals a striking similarity to members of the MerR family of transcriptional regulators, suggesting an evolutionary connection between the functionally distinct bacterial co-chaperone regulator CbpM and the transcription regulator HspR.
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Affiliation(s)
- Naghmeh S. Sarraf
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, Canada
- Life Sciences, National Research Council of Canada, Montréal, Québec, Canada
| | - Rong Shi
- Département de biochimie, de microbiologie et de bio-informatique, et L'Institut de biologie intégrative et des systèmes, et PROTEO, Université Laval, Québec City, Québec, Canada
| | - Laura McDonald
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, Canada
- Life Sciences, National Research Council of Canada, Montréal, Québec, Canada
| | - Jason Baardsnes
- Life Sciences, National Research Council of Canada, Montréal, Québec, Canada
| | - Linhua Zhang
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
| | - Miroslaw Cygler
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- * E-mail: (IE); (MC)
| | - Irena Ekiel
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, Canada
- Life Sciences, National Research Council of Canada, Montréal, Québec, Canada
- * E-mail: (IE); (MC)
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99794
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Pan Z, Xu L, Zhu Y, Shi H, Chen Z, Chen M, Chen Q, Liu B. Characterization of a new cry2Ab gene of Bacillus thuringiensis with high insecticidal activity against Plutella xylostella L. World J Microbiol Biotechnol 2014; 30:2655-62. [PMID: 24943249 DOI: 10.1007/s11274-014-1689-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 06/11/2014] [Indexed: 10/25/2022]
Abstract
Bacillus thuringiensis (Bt) strain FJAT-12 was a novel Bt strain isolated by Agricultural Bio-Resources Institute, Fujian Academy of Agricultural Science. In this study, a new cry2Ab gene was cloned from Bt strain FJAT-12 and named as cry2Ab30 by Bt delta-endotoxin Nomenclature Committee. The sequencing results showed there were two mutations in conservative sites which led to two amino acids modification. Homology modeling indicated that the two changes were located in β-sheet of Domain II. A prokaryotic expression vector pET30a-cry2Ab30 was constructed and the expressed protein was analyzed by western blot using Cry2Ab antibody. The expression conditions including IPTG concentration, revolution and temperature were optimized to get the highest expression level by SDS-PAGE and BandScan. The bioassay results also showed that the Cry2Ab30 toxin had high insecticidal activity against Plutella xylostella and the LC50 value was 0.0103 μg.mL(-1). The two mutations in β-sheet of Domain II might contribute to insecticidal activity of Cry2Ab30 toxin against Plutella xylostella.
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Affiliation(s)
- Zhizhen Pan
- Agricultural Bio-Resources Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
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99795
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Abstract
Although the analysis of linkage disequilibrium (LD) plays a central role in many areas of population genetics, the sampling variance of LD is known to be very large with high sensitivity to numbers of nucleotide sites and individuals sampled. Here we show that a genome-wide analysis of the distribution of heterozygous sites within a single diploid genome can yield highly informative patterns of LD as a function of physical distance. The proposed statistic, the correlation of zygosity, is closely related to the conventional population-level measure of LD, but is agnostic with respect to allele frequencies and hence likely less prone to outlier artifacts. Application of the method to several vertebrate species leads to the conclusion that >80% of recombination events are typically resolved by gene-conversion-like processes unaccompanied by crossovers, with the average lengths of conversion patches being on the order of one to several kilobases in length. Thus, contrary to common assumptions, the recombination rate between sites does not scale linearly with distance, often even up to distances of 100 kb. In addition, the amount of LD between sites separated by <200 bp is uniformly much greater than can be explained by the conventional neutral model, possibly because of the nonindependent origin of mutations within this spatial scale. These results raise questions about the application of conventional population-genetic interpretations to LD on short spatial scales and also about the use of spatial patterns of LD to infer demographic histories.
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99796
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Bautista-Santos A, Zinker S. The P1/P2 protein heterodimers assemble to the ribosomal stalk at the moment when the ribosome is committed to translation but not to the native 60S ribosomal subunit in Saccharomyces cerevisiae. Biochemistry 2014; 53:4105-12. [PMID: 24922111 DOI: 10.1021/bi500341w] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The four structural acidic ribosomal proteins that dissociate from P1A/P2B and P1B/P2A heterodimers of Saccharomyces cerevisiae were searched in the 60S ribosomal subunit, the 80S monosome, and the polysomal fractions after ribosome profile centrifugation in sucrose gradients in TMN buffer, and after dissociation of monosomes and polysomes to small and large ribosomal subunits in LMS buffer. Analysis by isoelectric focusing, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and Western blotting of these fractions or the purified acidic protein samples showed eight bands that correspond to the acidic ribosomal proteins in the 60S dissociated subunits of the 80S monosome and polysomes. After samples had been radiolabeled with (32)P, four bands were shown to correspond to the phosphorylated form of the acidic ribosomal proteins located in the 80S monosome and the polysomes. Surprisingly, native 60S subunits have no acidic ribosomal proteins. Altogether, these findings indicate that P1/P2 heterodimers bind to P0 when both ribosomal subunits are joined and committed to translation, and they detached from the stalk, just after the small and large ribosomal subunits were separated from the mRNA. Evidence that the phosphorylated and unphosphorylated P1 and P2 acidic ribosomal proteins are part of the functional stalk is also presented.
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Affiliation(s)
- A Bautista-Santos
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional , México D.F. 07360, México
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99797
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Modeling bacterial quorum sensing in open and closed environments: potential discrepancies between agar plate and culture flask experiments. J Mol Model 2014; 20:2248. [DOI: 10.1007/s00894-014-2248-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Accepted: 04/10/2014] [Indexed: 01/12/2023]
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99798
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Dröge J, Buczek D, Suzuki Y, Makałowski W. Amoebozoa possess lineage-specific globin gene repertoires gained by individual horizontal gene transfers. Int J Biol Sci 2014; 10:689-701. [PMID: 25013378 PMCID: PMC4081604 DOI: 10.7150/ijbs.8327] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 03/24/2014] [Indexed: 12/13/2022] Open
Abstract
The Amoebozoa represent a clade of unicellular amoeboid organisms that display a wide variety of lifestyles, including free-living and parasitic species. For example, the social amoeba Dictyostelium discoideum has the ability to aggregate into a multicellular fruiting body upon starvation, while the pathogenic amoeba Entamoeba histolytica is a parasite of humans. Globins are small heme proteins that are present in almost all extant organisms. Although several genomes of amoebozoan species have been sequenced, little is known about the phyletic distribution of globin genes within this phylum. Only two flavohemoglobins (FHbs) of D. discoideum have been reported and characterized previously while the genomes of Entamoeba species are apparently devoid of globin genes. We investigated eleven amoebozoan species for the presence of globin genes by genomic and phylogenetic in silico analyses. Additional FHb genes were identified in the genomes of four social amoebas and the true slime mold Physarum polycephalum. Moreover, a single-domain globin (SDFgb) of Hartmannella vermiformis, as well as two truncated hemoglobins (trHbs) of Acanthamoeba castellanii were identified. Phylogenetic evidence suggests that these globin genes were independently acquired via horizontal gene transfer from some ancestral bacteria. Furthermore, the phylogenetic tree of amoebozoan FHbs indicates that they do not share a common ancestry and that a transfer of FHbs from bacteria to amoeba occurred multiple times.
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Affiliation(s)
- Jasmin Dröge
- 1. Institute of Bioinformatics, Faculty of Medicine, University of Muenster, Niels Stensen Str. 14, 48149 Muenster, Germany
| | - Dorota Buczek
- 1. Institute of Bioinformatics, Faculty of Medicine, University of Muenster, Niels Stensen Str. 14, 48149 Muenster, Germany ; 2. Institute of Molecular Biology and Biotechnology, A. Mickiewicz University, Poznan, Poland
| | - Yutaka Suzuki
- 3. Department of Medical Genomic Sciences, University of Tokyo, Tokyo, Japan
| | - Wojciech Makałowski
- 1. Institute of Bioinformatics, Faculty of Medicine, University of Muenster, Niels Stensen Str. 14, 48149 Muenster, Germany ; 3. Department of Medical Genomic Sciences, University of Tokyo, Tokyo, Japan
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99799
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Yang A, Zhang X, Agogué H, Dupuy C, Gong J. Contrasting spatiotemporal patterns and environmental drivers of diversity and community structure of ammonia oxidizers, denitrifiers, and anammox bacteria in sediments of estuarine tidal flats. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-014-0929-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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99800
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Jovanovic M, Lawton E, Schumacher J, Buck M. Interplay among Pseudomonas syringae HrpR, HrpS and HrpV proteins for regulation of the type III secretion system. FEMS Microbiol Lett 2014; 356:201-11. [PMID: 24863420 PMCID: PMC4145663 DOI: 10.1111/1574-6968.12476] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 05/15/2014] [Accepted: 05/16/2014] [Indexed: 11/28/2022] Open
Abstract
Pseudomonas syringae pv. tomato DC3000, a plant pathogenic gram-negative bacterium, employs the type III secretion system (T3SS) to cause disease in tomato and Arabidopsis and to induce the hypersensitive response in nonhost plants. The expression of T3SS is regulated by the HrpL extracytoplasmic sigma factor. Expression of HrpL is controlled by transcriptional activators HrpR and HrpS and negative regulator HrpV. In this study, we analysed the organization of HrpRS and HrpV regulatory proteins and interplay between them. We identified one key residue I26 in HrpS required for repression by HrpV. Substitution of I26 in HrpS abolishes its interaction with HrpV and impairs interactions between HrpS and HrpR and the self-association of HrpS. We show that HrpS self-associates and can associate simultaneously with HrpR and HrpV. We now propose that HrpS has a central role in the assembly of the regulatory HrpRSV complex. Deletion analysis of HrpR and HrpS proteins showed that C-terminal parts of HrpR and HrpS confer determinants indispensable for their self-assembly.
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Affiliation(s)
- Milija Jovanovic
- Department of Life Sciences, Imperial College London, London, UK
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