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De la Fuente IM, Cortes JM, Malaina I, Pérez-Yarza G, Martinez L, López JI, Fedetz M, Carrasco-Pujante J. The main sources of molecular organization in the cell. Atlas of self-organized and self-regulated dynamic biostructures. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2025; 195:167-191. [PMID: 39805422 DOI: 10.1016/j.pbiomolbio.2025.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2024] [Accepted: 01/10/2025] [Indexed: 01/16/2025]
Abstract
One of the most important goals of contemporary biology is to understand the principles of the molecular order underlying the complex dynamic architecture of cells. Here, we present an overview of the main driving forces involved in the cellular molecular complexity and in the emergent functional dynamic structures, spanning from the most basic molecular organization levels to the complex emergent integrative systemic behaviors. First, we address the molecular information processing which is essential in many complex fundamental mechanisms such as the epigenetic memory, alternative splicing, regulation of transcriptional system, and the adequate self-regulatory adaptation to the extracellular environment. Next, we approach the biochemical self-organization, which is central to understand the emergency of metabolic rhythms, circadian oscillations, and spatial traveling waves. Such a complex behavior is also fundamental to understand the temporal compartmentalization of the cellular metabolism and the dynamic regulation of many physiological activities. Numerous examples of biochemical self-organization are considered here, which show that practically all the main physiological processes in the cell exhibit this type of dynamic molecular organization. Finally, we focus on the biochemical self-assembly which, at a primary level of organization, is a basic but important mechanism for the order in the cell allowing biomolecules in a disorganized state to form complex aggregates necessary for a plethora of essential structures and physiological functions. In total, more than 500 references have been compiled in this review. Due to these main sources of order, systemic functional structures emerge in the cell, driving the metabolic functionality towards the biological complexity.
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Affiliation(s)
- Ildefonso M De la Fuente
- Department of Mathematics, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, Leioa, 48940, Spain.
| | - Jesus M Cortes
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of the Basque Country, UPV/EHU, Leioa, 48940, Spain; Biobizkaia Health Research Institute, Barakaldo, 48903, Spain; IKERBASQUE: The Basque Foundation for Science, Bilbao, Spain
| | - Iker Malaina
- Department of Mathematics, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, Leioa, 48940, Spain
| | - Gorka Pérez-Yarza
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of the Basque Country, UPV/EHU, Leioa, 48940, Spain
| | - Luis Martinez
- Department of Mathematics, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, Leioa, 48940, Spain
| | - José I López
- Biobizkaia Health Research Institute, Barakaldo, 48903, Spain
| | - Maria Fedetz
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine "López-Neyra", CSIC, Granada, 18016, Spain
| | - Jose Carrasco-Pujante
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of the Basque Country, UPV/EHU, Leioa, 48940, Spain
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Abstract
Bacteria commonly live in surface-associated communities where steep gradients of antibiotics and other chemical compounds can occur. While many bacterial species move on surfaces, we know surprisingly little about how such antibiotic gradients affect cell motility. Here, we study the behaviour of the opportunistic pathogen Pseudomonas aeruginosa in stable spatial gradients of several antibiotics by tracking thousands of cells in microfluidic devices as they form biofilms. Unexpectedly, these experiments reveal that bacteria use pili-based ('twitching') motility to navigate towards antibiotics. Our analyses suggest that this behaviour is driven by a general response to the effects of antibiotics on cells. Migrating bacteria reach antibiotic concentrations hundreds of times higher than their minimum inhibitory concentration within hours and remain highly motile. However, isolating cells - using fluid-walled microfluidic devices - reveals that these bacteria are terminal and unable to reproduce. Despite moving towards their death, migrating cells are capable of entering a suicidal program to release bacteriocins that kill other bacteria. This behaviour suggests that the cells are responding to antibiotics as if they come from a competing colony growing nearby, inducing them to invade and attack. As a result, clinical antibiotics have the potential to lure bacteria to their death.
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3
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van Krugten J, Danné N, Peterman EJG. A local interplay between diffusion and intraflagellar transport distributes TRPV-channel OCR-2 along C. elegans chemosensory cilia. Commun Biol 2022; 5:720. [PMID: 35858995 PMCID: PMC9300729 DOI: 10.1038/s42003-022-03683-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 07/06/2022] [Indexed: 02/07/2023] Open
Abstract
To survive, Caenorhabditis elegans depends on sensing soluble chemicals with transmembrane proteins (TPs) in the cilia of its chemosensory neurons. Cilia rely on intraflagellar transport (IFT) to facilitate the distribution of cargo, such as TPs, along the ciliary axoneme. Here, we use fluorescence imaging of living worms and perform single-molecule tracking experiments to elucidate the dynamics underlying the ciliary distribution of the sensory TP OCR-2. Quantitative analysis reveals that the ciliary distribution of OCR-2 depends on an intricate interplay between transport modes that depends on the specific location in the cilium: in dendrite and transition zone, directed transport is predominant. Along the cilium motion is mostly due to normal diffusion together with a small fraction of directed transport, while at the ciliary tip subdiffusion dominates. These insights in the role of IFT and diffusion in ciliary dynamics contribute to a deeper understanding of ciliary signal transduction and chemosensing.
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Affiliation(s)
- Jaap van Krugten
- LaserLaB and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, De Boelelaan, 1081 HV, Amsterdam, The Netherlands
| | - Noémie Danné
- LaserLaB and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, De Boelelaan, 1081 HV, Amsterdam, The Netherlands
| | - Erwin J G Peterman
- LaserLaB and Department of Physics and Astronomy, Vrije Universiteit Amsterdam, De Boelelaan, 1081 HV, Amsterdam, The Netherlands.
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4
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Park J, Lee HH, Jung H, Seo YS. Transcriptome analysis to understand the effects of the toxoflavin and tropolone produced by phytopathogenic Burkholderia on Escherichia coli. J Microbiol 2019; 57:781-794. [DOI: 10.1007/s12275-019-9330-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 07/18/2019] [Accepted: 07/25/2019] [Indexed: 12/13/2022]
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5
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Virgile C, Hauk P, Wu HC, Shang W, Tsao CY, Payne GF, Bentley WE. Engineering bacterial motility towards hydrogen-peroxide. PLoS One 2018; 13:e0196999. [PMID: 29750783 PMCID: PMC5947916 DOI: 10.1371/journal.pone.0196999] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 04/24/2018] [Indexed: 11/19/2022] Open
Abstract
Synthetic biologists construct innovative genetic/biological systems to treat environmental, energy, and health problems. Many systems employ rewired cells for non-native product synthesis, while a few have employed the rewired cells as 'smart' devices with programmable function. Building on the latter, we developed a genetic construct to control and direct bacterial motility towards hydrogen peroxide, one of the body's immune response signaling molecules. A motivation for this work is the creation of cells that can target and autonomously treat disease, the latter signaled by hydrogen peroxide release. Bacteria naturally move towards a variety of molecular cues (e.g., nutrients) in the process of chemotaxis. In this work, we engineered bacteria to recognize and move towards hydrogen peroxide, a non-native chemoattractant and potential toxin. Our system exploits oxyRS, the native oxidative stress regulon of E. coli. We first demonstrated H2O2-mediated upregulation motility regulator, CheZ. Using transwell assays, we showed a two-fold increase in net motility towards H2O2. Then, using a 2D cell tracking system, we quantified bacterial motility descriptors including velocity, % running (of tumble/run motions), and a dynamic net directionality towards the molecular cue. In CheZ mutants, we found that increased H2O2 concentration (0-200 μM) and induction time resulted in increased running speeds, ultimately reaching the native E. coli wild-type speed of ~22 μm/s with a ~45-65% ratio of running to tumbling. Finally, using a microfluidic device with stable H2O2 gradients, we characterized responses and the potential for "programmed" directionality towards H2O2 in quiescent fluids. Overall, the synthetic biology framework and tracking analysis in this work will provide a framework for investigating controlled motility of E. coli and other 'smart' probiotics for signal-directed treatment.
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Affiliation(s)
- Chelsea Virgile
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, United States of America
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, United States of America
| | - Pricila Hauk
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, United States of America
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, United States of America
| | - Hsuan-Chen Wu
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Wu Shang
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, United States of America
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, United States of America
| | - Chen-Yu Tsao
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, United States of America
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, United States of America
| | - Gregory F. Payne
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, United States of America
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, United States of America
| | - William E. Bentley
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, United States of America
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland, United States of America
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Arora PK, Srivastava A, Garg SK, Singh VP. Recent advances in degradation of chloronitrophenols. BIORESOURCE TECHNOLOGY 2018; 250:902-909. [PMID: 29229201 DOI: 10.1016/j.biortech.2017.12.007] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 12/03/2017] [Accepted: 12/04/2017] [Indexed: 06/07/2023]
Abstract
Chloronitrophenols (CNPs) constitute a group of environmental pollutants that are widely distributed in our surrounding environment due to human based activities. This group of chemicals is highly toxic to living beings due to its mutagenic and carcinogenic nature. Examples include 2-chloro-4-nitrophenol, 4-chloro-2-nitrophenol, 2-chloro-5-nitrophenol, 4-chloro-3-nitrophenol and 2,6-dichloro-4-nitrophenol. Several methods including advanced oxidation processes, adsorption and bacterial degradation have been used for degradation of CNPs. Among, bacterial degradation is an eco-friendly and effective way to degrade CNPs. Several bacterial metabolic pathways have been proposed for degradation of CNPs and their genes and enzymes have been identified in bacteria. These bacteria were able to degrade CNPs in broth culture and soil. Therefore, CNPs-degrading bacteria are suitable candidates for bioremediation of CNPs-contaminated sites. Few CNP-degrading bacteria exhibited chemotaxis towards CNPs to enhance their biodegradation. The present review summarizes recent progress in degradation of CNPs.
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Affiliation(s)
- Pankaj Kumar Arora
- Department of Plant Science, MJP Rohilkhand University, Bareilly 243006, India; Department of Environmental Microbiology, Babasaheb Bhimrao Ambedkar University, Lucknow 226025, India.
| | - Alok Srivastava
- Department of Plant Science, MJP Rohilkhand University, Bareilly 243006, India
| | - Sanjay Kumar Garg
- Department of Plant Science, MJP Rohilkhand University, Bareilly 243006, India
| | - Vijai Pal Singh
- Department of Plant Science, MJP Rohilkhand University, Bareilly 243006, India
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7
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Bhuyan T, Singh AK, Dutta D, Unal A, Ghosh SS, Bandyopadhyay D. Magnetic Field Guided Chemotaxis of iMushbots for Targeted Anticancer Therapeutics. ACS Biomater Sci Eng 2017; 3:1627-1640. [DOI: 10.1021/acsbiomaterials.7b00086] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tamanna Bhuyan
- Centre
for Nanotechnology, ‡Department of Mechanical Engineering, §Department of Biosciences
and Bioengineering, and ∥Department of Chemical Engineering, Indian Institute of Technology Guwahati, Assam 781039, India
| | - Amit Kumar Singh
- Centre
for Nanotechnology, ‡Department of Mechanical Engineering, §Department of Biosciences
and Bioengineering, and ∥Department of Chemical Engineering, Indian Institute of Technology Guwahati, Assam 781039, India
| | - Deepanjalee Dutta
- Centre
for Nanotechnology, ‡Department of Mechanical Engineering, §Department of Biosciences
and Bioengineering, and ∥Department of Chemical Engineering, Indian Institute of Technology Guwahati, Assam 781039, India
| | - Aynur Unal
- Centre
for Nanotechnology, ‡Department of Mechanical Engineering, §Department of Biosciences
and Bioengineering, and ∥Department of Chemical Engineering, Indian Institute of Technology Guwahati, Assam 781039, India
| | - Siddhartha Sankar Ghosh
- Centre
for Nanotechnology, ‡Department of Mechanical Engineering, §Department of Biosciences
and Bioengineering, and ∥Department of Chemical Engineering, Indian Institute of Technology Guwahati, Assam 781039, India
| | - Dipankar Bandyopadhyay
- Centre
for Nanotechnology, ‡Department of Mechanical Engineering, §Department of Biosciences
and Bioengineering, and ∥Department of Chemical Engineering, Indian Institute of Technology Guwahati, Assam 781039, India
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8
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Ortega-Calvo JJ, Jimenez-Sanchez C, Pratarolo P, Pullin H, Scott TB, Thompson IP. Tactic response of bacteria to zero-valent iron nanoparticles. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2016; 213:438-445. [PMID: 26967351 DOI: 10.1016/j.envpol.2016.01.093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 01/29/2016] [Accepted: 01/29/2016] [Indexed: 06/05/2023]
Abstract
The microbial assessment of pollutant toxicity rarely includes behavioral responses. In this study, we investigated the tactic response of Pseudomonas putida G7, a representative of soil bacterium, towards engineered zero-valent iron nanoparticles (nZVIs), as a new end-point assessment of toxicity. The study integrated the characterization of size distribution and charge of nZVIs and tactic reaction response by means of inverted capillary assay and computer-assisted motion analysis of motility behavior. Iron nanoparticles (diameter ≤ 100 nm) were prepared in the absence of oxygen to prevent aggregation, and then exposed in aerobic conditions. We first demonstrate that iron nanoparticles can elicit a negative tactic response in bacteria at low but environmentally-relevant, sub-lethal concentrations (1-10 μg/L). Cells were repelled by nZVIs in the concentration gradients created inside the capillaries, and a significant increase in turning events, characteristic of negative taxis, was detected under exposure to nZVIs. These tactic responses were not detectable after sustained exposure of the nanoparticles to oxygen. This new behavioral assessment may be prospected for the design of sensitive bioassays for nanomaterial toxicity.
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Affiliation(s)
- José-Julio Ortega-Calvo
- Department of Engineering Science, University of Oxford, Parks Road OX1 3PJ, United Kingdom; Instituto de Recursos Naturales y Agrobiología, C.S.I.C., Apartado 1052, E-41080-Seville, Spain
| | - Celia Jimenez-Sanchez
- Instituto de Recursos Naturales y Agrobiología, C.S.I.C., Apartado 1052, E-41080-Seville, Spain
| | - Paolo Pratarolo
- Instituto de Recursos Naturales y Agrobiología, C.S.I.C., Apartado 1052, E-41080-Seville, Spain
| | - Huw Pullin
- Interface Analysis Centre, University of Bristol, United Kingdom
| | - Thomas B Scott
- Interface Analysis Centre, University of Bristol, United Kingdom
| | - Ian P Thompson
- Department of Engineering Science, University of Oxford, Parks Road OX1 3PJ, United Kingdom.
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9
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Armoza-Zvuloni R, Schneider A, Sher D, Shaked Y. Rapid Hydrogen Peroxide release from the coral Stylophora pistillata during feeding and in response to chemical and physical stimuli. Sci Rep 2016; 6:21000. [PMID: 26875833 PMCID: PMC4753443 DOI: 10.1038/srep21000] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 01/15/2016] [Indexed: 11/23/2022] Open
Abstract
Corals make use of different chemical compounds during interactions with prey, predators and aggressors. Hydrogen Peroxide (H2O2) is produced and released by a wide range of organisms as part of their defense against grazers or pathogens. In coral reefs, the large fluxes and relatively long half-life of H2O2, make it a potentially important info-chemical or defense molecule. Here we describe a previously unstudied phenomenon of rapid H2O2 release from the reef-building coral Stylophora pistillata during feeding on zooplankton and in response to chemical and physical stimuli. Following stimuli, both symbiotic and bleached corals were found to rapidly release H2O2 to the surrounding water for a short period of time (few minutes). The H2O2 release was restricted to the site of stimulus, and an increase in physical stress and chemical stimuli concentration resulted in elevated H2O2 release. Omission of calcium (a key regulator of exocytotic processes) from the experimental medium inhibited H2O2 release. Hence we suggest that H2O2 is actively released in response to stimuli, rather than leaking passively from the coral tissue. We estimate that at the site of stimulus H2O2 can reach concentrations potentially high enough to deter predators or motile, potentially pathogenic, bacteria.
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Affiliation(s)
- Rachel Armoza-Zvuloni
- Interuniversity Institute for Marine Sciences, Eilat, 88103, Israel
- The Fredy & Nadine Herrmann Institute of Earth Sciences, The Hebrew University, Jerusalem, 91904, Israel
| | - Avi Schneider
- Interuniversity Institute for Marine Sciences, Eilat, 88103, Israel
| | - Daniel Sher
- Department of Marine Biology, Charney School of Marine Sciences, Haifa University, Haifa, Israel
| | - Yeala Shaked
- Interuniversity Institute for Marine Sciences, Eilat, 88103, Israel
- The Fredy & Nadine Herrmann Institute of Earth Sciences, The Hebrew University, Jerusalem, 91904, Israel
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Ronen A, Duan W, Wheeldon I, Walker S, Jassby D. Microbial Attachment Inhibition through Low-Voltage Electrochemical Reactions on Electrically Conducting Membranes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:12741-12750. [PMID: 26377588 DOI: 10.1021/acs.est.5b01281] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Bacterial biofilm formation on membrane surfaces remains a serious challenge in water treatment systems. The impact of low voltages on microbial attachment to electrically conducting ultrafiltration membranes was investigated using a direct observation cross-flow membrane system mounted on a fluorescence microscope. Escherichia coli and microparticle deposition and detachment rates were measured as a function of the applied electrical potential to the membrane surface. Selecting bacteria and particles with low surface charge minimized electrostatic interactions between the bacteria and charged membrane surface. Application of an electrical potential had a significant impact on the detachment of live bacteria in comparison to dead bacteria and particles. Image analysis indicated that when a potential of 1.5 V was applied to the membrane/counter electrode pair, the percent of dead bacteria was 32±2.1 and 67±3.6% when the membrane was used as a cathode or anode, respectively, while at a potential of 1 V, 92±2.4% were alive. The application of low electrical potentials resulted in the production of low (μM) concentrations of hydrogen peroxide (HP) through the electroreduction of oxygen. The electrochemically produced HP reduced microbial cell viability and increased cellular permeability. Exposure to low concentrations of electrochemically produced HP on the membrane surface prevents bacterial attachment, thus ensuring biofilm-free conditions during membrane filtration operations.
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Affiliation(s)
- Avner Ronen
- Department of Chemical and Environmental Engineering, University of California , Riverside, California 92521, United States
| | - Wenyan Duan
- Department of Chemical and Environmental Engineering, University of California , Riverside, California 92521, United States
| | - Ian Wheeldon
- Department of Chemical and Environmental Engineering, University of California , Riverside, California 92521, United States
| | - Sharon Walker
- Department of Chemical and Environmental Engineering, University of California , Riverside, California 92521, United States
| | - David Jassby
- Department of Chemical and Environmental Engineering, University of California , Riverside, California 92521, United States
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Guard BC, Barr JW, Reddivari L, Klemashevich C, Jayaraman A, Steiner JM, Vanamala J, Suchodolski JS. Characterization of microbial dysbiosis and metabolomic changes in dogs with acute diarrhea. PLoS One 2015; 10:e0127259. [PMID: 26000959 PMCID: PMC4441376 DOI: 10.1371/journal.pone.0127259] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Accepted: 04/14/2015] [Indexed: 12/19/2022] Open
Abstract
Limited information is available regarding the metabolic consequences of intestinal dysbiosis in dogs with acute onset of diarrhea. The aim of this study was to evaluate the fecal microbiome, fecal concentrations of short-chain fatty acids (SCFAs), as well as serum and urine metabolites in healthy dogs (n=13) and dogs with acute diarrhea (n=13). The fecal microbiome, SCFAs, and serum/urine metabolite profiles were characterized by 454-pyrosequencing of the 16S rRNA genes, GC/MS, and untargeted and targeted metabolomics approach using UPLC/MS and HPLC/MS, respectively. Significantly lower bacterial diversity was observed in dogs with acute diarrhea in regards to species richness, chao1, and Shannon index (p=0.0218, 0.0176, and 0.0033; respectively). Dogs with acute diarrhea had significantly different microbial communities compared to healthy dogs (unweighted Unifrac distances, ANOSIM p=0.0040). While Bacteroidetes, Faecalibacterium, and an unclassified genus within Ruminococcaceae were underrepresented, the genus Clostridium was overrepresented in dogs with acute diarrhea. Concentrations of fecal propionic acid were significantly decreased in acute diarrhea (p=0.0033), and were correlated to a decrease in Faecalibacterium (ρ=0.6725, p=0.0332). The predicted functional gene content of the microbiome (PICRUSt) revealed overrepresentations of genes for transposase enzymes as well as methyl accepting chemotaxis proteins in acute diarrhea. Serum concentrations of kynurenic acid and urine concentrations of 2-methyl-1H-indole and 5-Methoxy-1H-indole-3-carbaldehyde were significantly decreased in acute diarrhea (p=0.0048, 0.0185, and 0.0330, respectively). These results demonstrate that the fecal dysbiosis present in acute diarrhea is associated with altered systemic metabolic states.
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Affiliation(s)
- Blake C. Guard
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - James W. Barr
- Emergency and Critical Care, Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Lavanya Reddivari
- Department of Plant Science, Penn State University, University Park, Pennsylvania, United States of America
| | - Cory Klemashevich
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Arul Jayaraman
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas, United States of America
- Department of Microbial Pathogenesis and Immunology, Texas A&M Health Science Center, College Station, Texas, United States of America
| | - Jörg M. Steiner
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Jairam Vanamala
- Department of Food Science, Penn State University, University Park, Pennsylvania, United States of America
- The Penn State Hershey Cancer Institute, Hershey, Pennsylvania, United States of America
| | - Jan S. Suchodolski
- Gastrointestinal Laboratory, Department of Small Animal Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
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12
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Chemotaxis Away from 4-Chloro-2-nitrophenol, 4-Nitrophenol, and 2,6-Dichloro-4-nitrophenol byBacillus subtilisPA-2. J CHEM-NY 2015. [DOI: 10.1155/2015/296231] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial strain PA-2 exhibits chemotaxis away from 4-chloro-2-nitrophenol, 4-nitrophenol, and 2,6-dichloro-4-nitrophenol. This strain was identified asBacillus subtilison the basis of the 16S rRNA gene sequencing. The drop plate assay and the chemical-in-plug method were used to demonstrate negative chemotactic behavior of strain PA-2. The growth studies showed that strain PA-2 did not utilize 4-chloro-2-nitrophenol, 4-nitrophenol, and 2,6-dichloro-4-nitrophenol as its sole sources of carbon and energy. This is the first report of negative chemotaxis of 4-chloro-2-nitrophenol, 4-nitrophenol, and 2,6-dichloro-4-nitrophenol by any bacterium.
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Najem S, Grant M. The chaser and the chased: a phase-field model of an immune response. SOFT MATTER 2014; 10:9715-9720. [PMID: 25365918 DOI: 10.1039/c4sm01842g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In this paper we present a model for an immune response to an invading pathogen. Particularly, we follow the motion of a neutrophil as it migrates to the site of infection guided by chemical cues, a mechanism termed chemotaxis, with the ability to reorient itself as the pathogen changes its position. In the process, the cell undergoes morphological alterations, in addition to the structural changes observed at its leading edge. Also, we derive a condition for a successful immune reaction by relating the speed of the neutrophil to that of the pathogen and to the diffusion coefficient of the chemical attractant.
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Affiliation(s)
- Sara Najem
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.
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14
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Chlorine stress mediates microbial surface attachment in drinking water systems. Appl Microbiol Biotechnol 2014; 99:2861-9. [DOI: 10.1007/s00253-014-6166-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 10/10/2014] [Accepted: 10/14/2014] [Indexed: 10/24/2022]
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15
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Reuter M, Hayward NJ, Black SS, Miller S, Dryden DTF, Booth IR. Mechanosensitive channels and bacterial cell wall integrity: does life end with a bang or a whimper? J R Soc Interface 2013; 11:20130850. [PMID: 24258154 PMCID: PMC3869158 DOI: 10.1098/rsif.2013.0850] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Mechanogated channels are fundamental components of bacterial cells that enable retention of physical integrity during extreme increases in cell turgor. Optical tweezers combined with microfluidics have been used to study the fate of individual Escherichia coli cells lacking such channels when subjected to a bursting stress caused by increased turgor. Fluorescence-activated cell sorting and electron microscopy complement these studies. These analyses show that lysis occurs with a high probability, but the precise path differs between individual cells. By monitoring the loss of cytoplasmic green fluorescent protein, we have determined that some cells release this protein but remain phase dark (granular) consistent with the retention of the majority of large proteins. By contrast, most cells suffer cataclysmic wall failure leading to loss of granularity but with the retention of DNA and overall cell shape (protein-depleted ghosts). The time span of these events induced by hypo-osmotic shock varies but is of the order of milliseconds. The data are interpreted in terms of the timing of mechanosensitive channel gating relative to osmotically induced water influx.
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Affiliation(s)
- Marcel Reuter
- School of Chemistry and COSMIC, University of Edinburgh, , The King's Buildings, Edinburgh EH9 3JJ, UK
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16
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Krell T, Lacal J, Reyes-Darias JA, Jimenez-Sanchez C, Sungthong R, Ortega-Calvo JJ. Bioavailability of pollutants and chemotaxis. Curr Opin Biotechnol 2013; 24:451-6. [DOI: 10.1016/j.copbio.2012.08.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Revised: 08/27/2012] [Accepted: 08/29/2012] [Indexed: 10/27/2022]
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17
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Lacal J, Reyes-Darias JA, García-Fontana C, Ramos JL, Krell T. Tactic responses to pollutants and their potential to increase biodegradation efficiency. J Appl Microbiol 2012; 114:923-33. [PMID: 23163356 DOI: 10.1111/jam.12076] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 11/07/2012] [Accepted: 11/11/2012] [Indexed: 11/26/2022]
Abstract
A significant number of bacterial strains are able to use toxic aromatic hydrocarbons as carbon and energy sources. In a number of cases, the evolution of the corresponding degradation pathway was accompanied by the evolution of tactic behaviours either towards or away from these toxic carbon sources. Reports are reviewed which show that a chemoattraction to heterogeneously distributed aromatic pollutants increases the bioavailability of these compounds and their biodegradation efficiency. An extreme form of chemoattraction towards aromatic pollutants, termed 'hyperchemotaxis', was described for Pseudomonas putida DOT-T1E, which is based on the action of the plasmid-encoded McpT chemoreceptor. Cells with this phenotype were found of being able to approach and of establishing contact with undiluted crude oil samples. Although close McpT homologues are found on other degradation plasmids, the sequence of their ligand-binding domains does not share significant similarity with that of NahY, the other characterized chemoreceptor for aromatic hydrocarbons. This may suggest the existence of at least two families of chemoreceptors for aromatic pollutants. The use of receptor chimers comprising the ligand-binding region of McpT for biosensing purposes is discussed.
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Affiliation(s)
- J Lacal
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
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18
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d'Onofrio A. Spatiotemporal effects of a possible chemorepulsion of tumor cells by immune system effectors. J Theor Biol 2011; 296:41-8. [PMID: 22119911 DOI: 10.1016/j.jtbi.2011.11.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Revised: 10/18/2011] [Accepted: 11/11/2011] [Indexed: 11/27/2022]
Abstract
Tumor-immune system interplay is a landmark of tumor development, and chemotactic attraction of immune system cells towards a tumor is a landmark of immune control. Since tumor cells are capable of chemotactic and chemorepulsive motion, based on a number of analogies between the behavior of tumor cells and that of bacteria, and on the production of potentially chemorepulsive semaphorins by immune systems effectors, we propose here the possibility of chemorepulsion of tumor cells, elicited by chemicals produced by immune system effectors such as macrophages and cytotoxic T lymphocytes. To study the effects of this hypothesized phenomenon within the framework of the interplay of neoplasias with the innate and adaptive immune system, we appropriately extend two well-known models: the tumor-macrophage models by Owen and Sherratt [Owen and Sherratt, J. Theor. Biol., 1998] and the Matzavinos-Chaplain model of tumor-CTL interaction [Matzavinos, Chaplain and Kuznetsov, Math. Med. Biol., 2004]. Our simulations suggest that this mechanism might allow a faster expansion of tumors, and in the concluding remarks we envisage a new possible route of immunoevasion.
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Affiliation(s)
- Alberto d'Onofrio
- Department of Experimental Oncology, European Institute of Oncology, Via Ripamonti 435, Milano I-20141, Italy.
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19
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Ortega-Calvo JJ, Molina R, Jimenez-Sanchez C, Dobson PJ, Thompson IP. Bacterial tactic response to silver nanoparticles. ENVIRONMENTAL MICROBIOLOGY REPORTS 2011; 3:526-34. [PMID: 23761331 DOI: 10.1111/j.1758-2229.2011.00252.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
In this study, we investigated the tactic response of Pseudomonas putida G7, a representative soil bacterium, towards silver nanoparticles (AgNPs). The study integrated the characterization of surface area and size distribution of AgNPs, toxicity determinations, based on ATP production, and assessment of the repellent reaction by means of an inverted capillary assay ('chemical-in-pond' method), and changes in the motility behaviour determined by computer-assisted motion analysis. Our data demonstrate, for the first time, that nanoparticles can elicit a negative tactic response in bacteria at low but environmentally relevant, sublethal concentrations. Data obtained by the chemical-in-pond method indicated that cells exposed to 0.1 mg l(-1) of two AgNPs preparations, differing in particle size (maximum diameter ≤ 100 nm and ≤ 150 nm respectively), were repelled in the gradients created inside the capillaries. However, cells exposed to similar low concentration of AgNO3 did not demonstrate any detectable repellent response, although it reduced cell viability by 20%, a decrease comparable to that caused by AgNPs. Computer analysis of swimming behaviour of cells exposed to AgNPs (0.2 mg l(-1) ) revealed a significant increase in turning events, as compared with unexposed controls, which is characteristic of bacterial repellent response. Greater AgNPs concentrations (up to 100 mg l(-1) ) also induced changes in the swimming behaviour, although they did not induce any detectable repellent response as determined by the chemical-in-pond assays. In contrast, AgNO3 failed to induce the repellent swimming behaviour within the wide range of concentrations tested (0.001-100 mg l(-1) ), and caused a significant inhibition of cell motility at a concentration above 0.1 mg l(-1) . The evidence presented here suggests there are likely to be alternative mechanisms by which nano-scale silver induces a repellent response, which is more direct than the toxic response of macro-forms of silver, attributed to ion formation and exposure.
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Affiliation(s)
- José-Julio Ortega-Calvo
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, UK Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), C.S.I.C., Apartado 1052, E-41080-Seville, Spain
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20
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Donkó A, Ruisanchez E, Orient A, Enyedi B, Kapui R, Péterfi Z, de Deken X, Benyó Z, Geiszt M. Urothelial cells produce hydrogen peroxide through the activation of Duox1. Free Radic Biol Med 2010; 49:2040-8. [PMID: 21146788 DOI: 10.1016/j.freeradbiomed.2010.09.027] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2010] [Revised: 09/08/2010] [Accepted: 09/27/2010] [Indexed: 02/07/2023]
Abstract
Hydrogen peroxide (H(2)O(2)) has important messenger and effector functions in the plant and animal kingdom. Phagocytes produce H(2)O(2) to kill pathogens, and epithelial cells of large airways have also been reported to produce H(2)O(2) for signaling and host defense purposes. In this report, we show for the first time that urothelial cells produce H(2)O(2) in response to a calcium signal. Using a gene-deficient mouse model we also demonstrate that H(2)O(2) is produced by the NADPH oxidase Duox1, which is expressed in the mouse urothelium. In contrast, we found no evidence for the expression of lactoperoxidase, an enzyme that has been shown to cooperate with Duox enzymes. We also found that specific activation of TRPV4 calcium channels elicits a calcium signal and stimulates H(2)O(2) production in urothelial cells. Furthermore, we detected altered pressure responses in the urinary bladders of Duox1 knockout animals. Our results raise the possibility that mechanosensing in epithelial cells involves calcium-dependent H(2)O(2) production similar to that observed in plants.
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Affiliation(s)
- Agnes Donkó
- Department of Physiology, Semmelweis University, Budapest, Hungary
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21
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Allaoui A, Botteaux A, Dumont JE, Hoste C, De Deken X. Dual oxidases and hydrogen peroxide in a complex dialogue between host mucosae and bacteria. Trends Mol Med 2009; 15:571-9. [PMID: 19913458 DOI: 10.1016/j.molmed.2009.10.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Revised: 09/28/2009] [Accepted: 10/06/2009] [Indexed: 02/06/2023]
Abstract
Among the host defense mechanisms against bacteria, leukocyte phagocytosis leads to their hydrogen peroxide (H(2)O(2))-mediated destruction. The recent discovery of dual oxidase (DUOX)-dependent H(2)O(2) generation associated with peroxidase and thiocyanate secretion at the apex of mucosal cells has been similarly interpreted as a killing mechanism. However, the rapid degradation of H(2)O(2) would be expected to reduce the efficiency of this system. It has been demonstrated that H(2)O(2) acts as a chemorepellent for bacteria, and such an effect might be sufficient to block cellular infection. Therefore, H(2)O(2) generation might represent one of the mechanisms that allows the coexistence of mucosae with potentially harmful bacteria. Here, we discuss the possible role of DUOXes and H(2)O(2) in interactions between host mucosae and bacteria to maintain mucosal homeostasis.
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Affiliation(s)
- Abdelmounaaïm Allaoui
- Laboratoire de Bactériologie Moléculaire, Université Libre de Bruxelles (ULB), Campus Erasme, Route de Lennik 808, B-1070 Brussels, Belgium
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22
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Abstract
Production of superoxide anion O2*- by the membrane-bound enzyme NADPH oxidase of phagocytes is a long-known phenomenon; it is generally assumed that O2*-helps phagocytes kill bacterial intruders. The details and the chemistry of the killing process have, however, remained a mystery. Isoforms of NADPH oxidase exist in membranes of nearly every cell, suggesting that reactive oxygen species (ROS) participate in intra- and intercellular signaling processes. What the nature of the signal is exactly, how it is transmitted, and what structural characteristics a receptor of a "radical message" must have, have not been addressed convincingly. This review discusses how the action of messengers is in agreement with radical-specific behavior. In search for the smallest common denominator of cellular free radical activity we hypothesize that O2*- and its conjugate acid, HO2*, may have evolved under primordial conditions as regulators of membrane mechanics and that isoprostanes, widely used markers of "oxidative stress", may be an adventitious correlate of this biologic activity of O2*-/HO2*. An overall picture is presented that suggests that O2*-/HO2* radicals, by modifying cell membranes, help other agents gain access to the hydrophobic region of phospholipid bilayers and hence contribute to lipid-dependent signaling cascades. With this, O2*-/HO2* are proposed as indispensable adjuvants for the generation of cellular signals, for membrane transport, channel gating and hence, in a global sense, for cell viability and growth. We also suggest that many of the allegedly O2*- dependent bacterial pathologies and carcinogenic derailments are due to membrane-modifying activity rather than other chemical reactions of O2*-/HO2*. A consequence of this picture is the potential evolution of the "radical theory of ageing" to a "lipid theory of aging".
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Affiliation(s)
- Manfred Saran
- Institut für Strahlenbiologie, GSF-Forschungszentrum für Umwelt und Gesundheit, 85764, Neuherberg, Germany.
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Botteaux A, Hoste C, Dumont JE, Van Sande J, Allaoui A. Potential role of Noxes in the protection of mucosae: H(2)O(2) as a bacterial repellent. Microbes Infect 2009; 11:537-44. [PMID: 19298864 DOI: 10.1016/j.micinf.2009.02.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2008] [Revised: 02/26/2009] [Accepted: 02/27/2009] [Indexed: 01/09/2023]
Abstract
Duox proteins are members of the NADPH oxidase (Nox) family and are responsible for hydrogen peroxide (H(2)O(2)) production by various tissue types including bronchial and intestinal mucosae. The antimicrobial killing role of H(2)O(2) in leukocytes and macrophages is generally considered as the paradigm of its function. We investigated here the positive role of H(2)O(2) in the prevention of cellular invasion by Salmonella. We show that H(2)O(2), under conditions that preserved bacterial growth, has a repellent effect on Salmonella motility on agar plates. In addition, H(2)O(2) produced by PCCl3, a rat thyroid cell line, reduces bacterial invasion of the cells by around 40%. To test whether the observed phenotype is attributable to H(2)O(2) production, we constructed a CHO stable cell line expressing Duox2 protein at the cell surface (CHO-D2). The transfected cells produce a high amount of H(2)O(2). Upon infection with Salmonella, the invasion of CHO-D2 cells was reduced by up to 60%. In both PCCl3 and CHO expressing Duox2 cells, normal invasion was restored upon incubation with catalase. Our data suggest that H(2)O(2) at reduced concentrations acts as a repellent for bacteria, keeping them away from cells, a situation that could naturally prevent mucosal cells infection in vivo.
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Affiliation(s)
- A Botteaux
- Laboratoire de Bactériologie Moléculaire, Université Libre de Bruxelles, Campus Erasme, Brussels, Belgium
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24
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Abstract
The dynamic process of thymocyte migration can now be visualized in real-time and in the context of the native thymic environment. With improved computational resources, key information can be extracted from real-time imaging data and the migratory behaviors of developing thymocytes can be quantitated. The extraction and exploitation of three dimensional data through time is providing new insight into the nature and regulation of intrathymic migration. In this review we discuss this interdisciplinary approach and the promise it holds for the study of thymocyte migration in situ.
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Affiliation(s)
- Colleen M Witt
- Division of Immunology, Department of Molecular and Cell Biology, 479 Life Sciences Addition, University of California, Berkeley, CA 94720, USA.
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25
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Pandey G, Jain RK. Bacterial chemotaxis toward environmental pollutants: role in bioremediation. Appl Environ Microbiol 2002; 68:5789-95. [PMID: 12450797 PMCID: PMC134409 DOI: 10.1128/aem.68.12.5789-5795.2002] [Citation(s) in RCA: 223] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Gunjan Pandey
- Institute of Microbial Technology, Chandigarh-160036, India
| | - Rakesh K. Jain
- Institute of Microbial Technology, Chandigarh-160036, India
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26
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Abstract
Many, if not most, bacterial species swim. The synthesis and operation of the flagellum, the most complex organelle of a bacterium, takes a significant percentage of cellular energy, particularly in the nutrient limited environments in which many motile species are found. It is obvious that motility accords cells a survival advantage over non-motile mutants under normal, poorly mixed conditions and is an important determinant in the development of many associations between bacteria and other organisms, whether as pathogens or symbionts and in colonization of niches and the development of biofilms. This survival advantage is the result of sensory control of swimming behaviour. Although too small to sense a gradient along the length of the cell, and unable to swim great distances because of buffetting by Brownian motion and the curvature resulting from a rotating flagellum, bacteria can bias their random swimming direction towards a more favourable environment. The favourable environment will vary from species to species and there is now evidence that in many species this can change depending on the current physiological growth state of the cell. In general, bacteria sense changes in a range of nutrients and toxins, compounds altering electron transport, acceptors or donors into the electron transport chain, pH, temperature and even the magnetic field of the Earth. The sensory signals are balanced, and may be balanced with other sensory pathways such as quorum sensing, to identify the optimum current environment. The central sensory pathway in this process is common to most bacteria and most effectors. The environmental change is sensed by a sensory protein. In most species examined this is a transmembrane protein, sensing the external environment, but there is increasing evidence for additional cytoplasmic receptors in many species. All receptors, whether sensing sugars, amino acids or oxygen, share a cytoplasmic signalling domain that controls the activity of a histidine protein kinase, CheA, via a linker protein, CheW. A reduction in an attractant generally leads to the increased autophosphorylation of CheA. CheA passes its phosphate to a small, single domain response regulator, CheY. CheY-P can interact with the flagellar motor to cause it to change rotational direction or stop. Signal termination either via a protein, CheZ, which increases the dephosphorylation rate of CheY-P or via a second CheY which acts as a phosphate sink, allows the cell to swim off again, usually in a new direction. In addition to signal termination the receptor must be reset, and this occurs via methylation of the receptor to return it to a non-signalling conformation. The way in which bacteria use these systems to move to optimum environments and the interaction of the different sensory pathways to produce species-specific behavioural response will be the subject of this review.
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Affiliation(s)
- J P Armitage
- Department of Biochemistry, University of Oxford, UK
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27
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L. Armesto X, Canle L. M, V. García M, A. Santaballa J. Aqueous chemistry of N-halo-compounds. Chem Soc Rev 1998. [DOI: 10.1039/a827453z] [Citation(s) in RCA: 112] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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