Team:Paris/Papers
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- | == | + | ==Bibliography== |
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+ | In order to class our reading, you can see here a part of it. Some sith the [X] symbol doe not figure in the wiki as support for the main parts. Every paper can be numeroted several time in different parts. Some reading does not figure here, but are link with all the information in its respective part. | ||
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+ | For the references of the Ethical part fo to the [https://2009.igem.org/Team:Paris/Ethics_Materials#top Material] or [https://2009.igem.org/Team:Paris/EthicalReportReferences#bottom References]. | ||
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+ | ==OMV Overview== | ||
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- | == | + | ==OMV Production== |
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- | == | + | ==OMV Adressing== |
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- | == | + | ==OMV Reception== |
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- | == | + | ==OMV Signal transduction== |
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Revision as of 03:34, 22 October 2009
Contents |
Bibliography
In order to class our reading, you can see here a part of it. Some sith the [X] symbol doe not figure in the wiki as support for the main parts. Every paper can be numeroted several time in different parts. Some reading does not figure here, but are link with all the information in its respective part.
For the references of the Ethical part fo to the Material or References.
OMV Overview
N° | Date | Authors | Article | Pubmed |
[X] | 1999 | Terry J. Beveridge | Structures of gram-negative cell walls and their derived membrane vesicles. | 10438737 |
[X] | 2003 | Miller SI & Guina T. | Bacterial vesicle formation as a mechanism of protein transfer to animals. | 14531993 |
[X] | 2005 | Kuehn MJ & Kesty NC. | Bacterial outer membrane vesicles and the host-pathogen interaction. | 16291643 |
[X] | 2006 | McBroom AJ & Kuehn MJ. | Outer membrane vesicle production by Escherichia coli is independent of membrane instability. | 16855227 |
[1] | 2007 | McBroom AJ & Kuehn MJ. | Release of outer membrane vesicles by Gram-negative bacteria is a novel envelope stress response. | 17163978 |
[2] | 2009 | Deatherage BL & Cookson BT. | Biogenesis of bacterial membrane vesicles | 19432795 |
[X] | 2009 | Purnick PE & Weiss R. | The second wave of synthetic biology: from modules to systems. | 19461664 |
OMV Production
N° | Date | Authors | Article | Pubmed |
[X] | 2008 | Mashburn-Warren L & Whiteley M. | Interaction of quorum signals with outer membrane lipids: insights into prokaryotic membrane vesicle formation. | 18630345 |
OmpA | ||||
---|---|---|---|---|
[2] | 2001 | Arora A. & Tamm LK. | Structure of outer membrane protein A transmembrane domain by NMR spectroscopy. | 11276254 |
[X] | 2007 | Brown EA & Hardwidge PR. | Biochemical characterization of the enterotoxigenic Escherichia coli LeoA protein. | 17975086 |
[X] | 2008 | Burgess NK & Fleming KG. | Beta-barrel proteins that reside in the Escherichia coli outer membrane in vivo demonstrate varied folding behavior in vitro. | 18641391 |
Tol/Pal | ||||
[X] | 1986 | Robert CHEN & Ulf HENNING. | Nucleotide sequence of the gene for the peptidoglycan-associated lipoprotein of Escherichia coli K12 | 210680 |
[3] | 1995 | Lazzaroni & Geli - | Transmembrane alpha-helix interactions are required for the functional assembly of the Escherichia coli Tol complex. | 179564 |
[X] | 1999 | Derouiche & Loret | Circular dichroism and molecular modeling of the E. coli TolA periplasmic domains. | 10380085 |
[4] | 2001 | Lloubès & RJournet L. | The Tol-Pal proteins of the Escherichia coli cell envelope: an energized system required for outer membrane integrity? | 11501670 |
[X] | 2002 | Dubuisson JF & Lazzaroni JC. | Mutational analysis of the TolA C-terminal domain of Escherichia coli and genetic evidence for an interaction between TolA and TolB. | 12142433 |
[X] | 2003 | Llamas M & ARamos JL. | Role of Pseudomonas putida tol-oprL gene products in uptake of solutes through the cytoplasmic membrane. | 12896989 |
[5] | 2004 | Henry T & Lloubès R. | Improved methods for producing outer membrane vesicles in Gram-negative bacteria. | 15249060 |
OMV Adressing
N° | Date | Authors | Article | Pubmed |
[X] | 1997 | Kadurugamuwa JL & Beveridge TJ. | Natural release of virulence factors in membrane vesicles by Pseudomonas aeruginosa and the effect of aminoglycoside antibiotics on their release. | 9421308 |
[X] | 1998 | Santini CL & Wu LF. | A novel sec-independent periplasmic protein translocation pathway in Escherichia coli. | 9427745 |
[X] | 2000 | Berks BC & Palmer T. | The Tat protein export pathway. | 10652088 |
[X] | 2001 | Mishima Y & Murata K. | Super-channel in bacteria: function and structure of the macromolecule import system mediated by a pit-dependent ABC transporter. | 11731126 |
[X] | 2001 | Sargent F & Berks BC. | Purified components of the Escherichia coli Tat protein transport system form a double-layered ring structure. | 11422364 |
[X] | 2001 | Yahr TL & Wickner WT. | Functional reconstitution of bacterial Tat translocation in vitro. | 11350936 |
[X] | 2004 | Robinson C & Bolhuis A. | Tat-dependent protein targeting in prokaryotes and chloroplasts. | 15546663 |
[X] | 2006 | Sargent F & Palmer T. | Pathfinders and trailblazers: a prokaryotic targeting system for transport of folded proteins. | 16445746 |
[X] | 2006 | Lee PA & Georgiou G. | The bacterial twin-arginine translocation pathway. | 16756481 |
[X] | 2007 | Maillard J & Sargent F. | Structural diversity in twin-arginine signal peptide-binding proteins. | 17901208 |
[X] | 2007 | Sargent F. | The twin-arginine transport system: moving folded proteins across membranes. | 17956229 |
[X] | 2008 | Ferrandez Y & Condemine G. | Novel mechanism of outer membrane targeting of proteins in Gram-negative bacteria. | 18643934 |
[X] | 2008 | Thie H & Hust M. | SRP and Sec pathway leader peptides for antibody phage display and antibody fragment production in E. coli. | 18504019 |
[X] | 2009 | Pradel N & Bonnet R | Sec- and Tat-dependent translocation of beta-lactamases across the Escherichia coli inner membrane. | 18643934 |
[X] | 2009 | de Marco A. | Strategies for successful recombinant expression of disulfide bond-dependent proteins in Escherichia coli. | 19442264 |
ClyA | ||||
---|---|---|---|---|
[5] [1] | 2008 | Kim JY & DeLisa MP. | Engineered bacterial outer membrane vesicles with enhanced functionality. | 18511069 |
[1] [2] | 2009 | Mueller M & Ban N. | The structure of a cytolytic alpha-helical toxin pore reveals its assembly mechanism. | 19421192 |
OmpA | ||||
[1] | 2002 | Wang Y. | The function of OmpA in Escherichia coli. | 11906175 |
[X] | 2008 | Dramsi S & Arthur M. | Covalent attachment of proteins to peptidoglycan. | 18266854 |
OMV Reception
N° | Date | Authors | Article | Pubmed |
Adhesin | ||||
---|---|---|---|---|
[X] | 1989 | Smeal T & Karin M. | Different requirements for formation of Jun:Jun and Jun:Fos complexes. | 2516828 |
[X] | 1994 | Heffernan EJ & Guiney DG. | Specificity of the complement resistance and cell association phenotypes encoded by the outer membrane protein genes rck from Salmonella typhimurium and ail from Yersinia enterocolitica. | 7927803 |
[X] | 2003 | Veiga E & Fernández LA. | Autotransporters as scaffolds for novel bacterial adhesins: surface properties of Escherichia coli cells displaying Jun/Fos dimerization domains. | 12949111 |
[6] | 2004 | Kesty NC & Kuehn MJ. | Incorporation of heterologous outer membrane and periplasmic proteins into Escherichia coli outer membrane vesicles. | 14578354 |
G3P | ||||
[X] | 1982 | JEF D. BOEKE & PETER MODEL | A prokaryotic membrane anchor sequence: carboxyl terminus of bacteriophage f1 gene III protein retains it in the membrane. | 6291030 |
[8] | 1999 | Chatellier J & Riechmann L. | Interdomain interactions within the gene 3 protein of filamentous phage. | 10606756 |
[9] | 1999 | Lubkowski J & Wlodawer A. | Filamentous phage infection: crystal structure of g3p in complex with its coreceptor, the C-terminal domain of TolA. | 10404600 |
[10] | 2002 | Baek H & Cha S. | An improved helper phage system for efficient isolation of specific antibody molecules in phage display. | 11861923 |
[11] | 2003 | Karlsson F & Malmborg-Hager AC. | The mechanism of bacterial infection by filamentous phages involves molecular interactions between TolA and phage protein 3 domains. | 12670988 |
Snare | ||||
[17] | 2000 | Waters MG & Hughson FM. | Membrane tethering and fusion in the secretory and endocytic pathways. | 11208146 |
[X] | 2000 | Woodbury DJ & Rognlien K. | The t-SNARE syntaxin is sufficient for spontaneous fusion of synaptic vesicles to planar membranes. | 11067766 |
[X] | 2002 | Bowen ME,Brunger AT. | Mutational analysis of synaptobrevin transmembrane domain oligomerization. | 12501216 |
[X] | 2003 | Hu C & Rothman JE. | Fusion of cells by flipped SNAREs. | 12805548 |
[X] | 2003 | Weninger K & Brunger AT. | Single-molecule studies of SNARE complex assembly reveal parallel and antiparallel configurations. | 14657376 |
[X] | 2006 | Giraudo CG & Rothman JE. | A clamping mechanism involved in SNARE-dependent exocytosis. | 16794037 |
[X] | 2006 | Low HH & Löwe J. | A bacterial dynamin-like protein. | 17122778 |
[X] | 2007 | Weninger K & Brunger AT. | Accessory proteins stabilize the acceptor complex for synaptobrevin, the 1:1 syntaxin/SNAP-25 complex. | 18275821 |
[X] | 2008 | Delevoye C & Subtil A. | SNARE protein mimicry by an intracellular bacterium. | 18369472 |
[18] | 2009 | Giraudo CG & Rothman JE. | Alternative zippering as an on-off switch for SNARE-mediated fusion. | 19164750 |
OMV Signal transduction
N° | Date | Authors | Article | Pubmed |
[X] | 1984 | Lopilato JE & Beckwith JR. | D-ribose metabolism in Escherichia coli K-12: genetics, regulation, and transport. | 6327616 |
[X] | 1995 | Härle C & Braun V. | Signal transfer through three compartments: transcription initiation of the Escherichia coli ferric citrate transport system from the cell surface. | 7729419 |
[1] | 1998 | Tomii K & Kanehisa M. | A comparative analysis of ABC transporters in complete microbial genomes. | 9799792 |
[X] | 1999 | De Wulf P & Lin EC. | The CpxRA signal transduction system of Escherichia coli: growth-related autoactivation and control of unanticipated target operons. | 10542180 |
[6] | 2000 | Stock AM & Goudreau PN. | Two-component signal transduction. | 10966457 |
[X] | 2000 | Yaron S & Matthews KR. | Vesicle-mediated transfer of virulence genes from Escherichia coli O157:H7 to other enteric bacteria. | 11010892 |
[X] | 2004 | Dwyer MA & Hellinga HW. | Periplasmic binding proteins: a versatile superfamily for protein engineering. | 15313245 |
[X] | 2006 | Braun V & Sauter A. | Gene regulation by transmembrane signaling. | 16718597 |
[X] | 2007 | Baker MD & Stock JB | Signal transduction: networks and integrated circuits in bacterial cognition. | 18054766 |
[X] | 2007 | Baker MD & Stock JB. | Systems biology of bacterial chemotaxis. | 16529985 |
[X] | 2007 | Ibrahim M & Monnet V. | Control of the transcription of a short gene encoding a cyclic peptide in Streptococcus thermophilus: a new quorum-sensing system? | 17921293 |
[X] | 2008 | Thie H & Hust M. | SRP and Sec pathway leader peptides for antibody phage display and antibody fragment production in E. coli. | 18504019 |
[9] | 2009 | Kyriakidis DA & Tiligada E. | Signal transduction and adaptive regulation through bacterial two-component systems: the Escherichia coli AtoSC paradigm. | 19198978 |
[X] | 2009 | Tomii & Kanehisa | comparative analysis of ABC transporter | pdf-link |
Modelling
N° | Date | Authors | Article | Pubmed |
Genetic Regulatory Network | ||||
---|---|---|---|---|
[1] | 1977 | Gillespie Daniel T. | Exact Stochastic Simlation of Coupled Chemical Equations | Gillespie1 |
[3] | 1997 | J.B. Andersen & S.Molin | New Stable Variants of Green Fluorescent Protein for Studies of Transient Gene Expression in Bacteria | LVA tag |
[6] | 1999 | M.Ellowitz & S.Leibler | A Synthetic oscillatory network of transcriptionnal regulators | 10659856 |
[2] | 1997 | D.T.Gillespie | The Chemical Langevin Equation | Gillespie2 |
[5] | 2002 | N.Rosenfold & U.Alon | Negative Autoregulation Speeds The Response TImes of Transcription Network | 2417193 |
[X] | 2002 | M.B.Ellowitz & P.S.Swain | Stochastic Gene Expression In A Single Cell | 12183631 |
[7] | 2003 | S.Mangan & U.Alon | Structure and function ot the feed-forward Loop Network Motif | 14530388 |
[4] | 2003 | S.Basu & R.Weiss | Spatiotemporal control of gene expression with pulse-generating networks | 15096621 |
[1] | 2005 | S.Hooshangi & R.Weiss | Ultrasensitivity and noise propagation in a synthetic transcriptional cascade | 15738412 |
[3] | 2006 | H.Li & L.Petzold | Logarithmic Direct Method for Discrete Stochastic Simulation of Chemically Reacting Systems | Sto.Sim |
[2] | 2007 | U.Alon | Network motifs : theory and experimental approaches | 117510665 |
[X] | 2006 | J.Stricker & J.Hasty | A Fast Robust and Tunable synthetic gene oscillator | 18971928 |
Vesicle biophysics model | ||||
[6] | 1977 | Harbich et al | Optical observation of rotationally symmetric lecithin vesicle shapes | J. Physique, 38:727–729 |
[4] | 1987 | Ou-Yang & Helfrich | Instability and deformation of a spherical vesicle by pressure | Phys. Rev. Lett., 59:2486-2488 |
[1] | 1991 | Lipowsky | The conformation of membranes | Nature, 349(6309):475-481 |
[5] | 1995 | Fattal et al | The vesicle-micelle transition in mixed lipid-surfactant | Langmuir, 11:1154-1161 |
[3] | 1998 | Zhou et al | On the origin of membrane vesicles in gram-negative bacteria | FEMS microbiology letters, 163(2):223-228 |
[8] | 2005 | Kuehn & Kesty | Bacterial outer membrane vesicles and the host pathogen interaction | Genes & Dev, 19:2645-2655 |
[2] | 2008 | Park & Uehara | How bacteria consume their own exoskeletons | Microbiol Mol Biol Rev, 72(2):211-227 |
[7] | 2009 | Deatherage et al | Biogenesis of bacterial membrane vesicles, | Mol Microbiol, 72(6):1395-1407 |
[9] | 2009 | Kumaran & Losick | Negative membrane curvature as a cue for subcellular localization of a bacterial protein. | PNAS USA, 106(32):13541-13545 |