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Team:Groningen/Literature
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Literature
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Buoyancy related literature:
- Buoyant density: Poole 1977, Bylund 1991, Baldwin 1995
- Gas vesicles: Bowen 1965, Walsby 1979, Walsby 1994, Li 1998, Sivertsen 2008, Holland 2009
Our metal related literature by subject:
| Cu | Zn | As | Cd | Sb | Hg | ||
|---|---|---|---|---|---|---|---|
| Importers | GlpF | Meng 2004, Rosen 2009 | Meng 2004 | ||||
| [http://partsregistry.org/Part:BBa_K190018 HmtA] | Lewinson 2009 | Lewinson 2009 | |||||
| Exporters | ArsB | Tisa 1989, Carlin 1995, | Tisa 1989, Carlin 1995, Rosen 1996, Meng 2004, Summers 2009 | ||||
| Accumulators | ArsR | Carlin 1995, Rosen 1996, Chen 1997, Kostal 2004, Rensing 2005, Summers 2009 | Carlin 1995, Rosen 1996, Summers 2009 | ||||
| ArsD | Chen 1997, Lin 2007-1/2, Summers 2009 | Chen 1997, Lin 2007-1/2, Summers 2009 | |||||
| SmtA | Shi 1992 | Shi 1992, Turner 1995, Robinson 2001, Blindauer 2002 | Shi 1992 | Shi 1992 | |||
| MymT | |||||||
| MT | Morris 1999,Ngu 2006,Singh 2008, Merrifield 2004 | Deng 2007 | Chen1998 | ||||
| Unclassified | Brady 1994, Gold 2008 | Chang 1998, Blindauer 2001, Kao 2008 | Brady 1994, Chang 1998, | Deng 2008 | |||
| Promoters | Mills 1994 , Khunajakr 1999, Liu 2004, Moore 2005, Ettema2006 , Liu 2006, Liu 2008, Catini 2008, Nawapan 2009 | Thelwell 1998, Liu 2004, Moore2005, Hirose 2006, Kloosterman 2008 | Summers 2009 | Liu 2004, Moore 2005 |
- Alon 2007
Uri Alon (2007). Introduction to systems biology: design principles of biological circuits Chapman & Hall/CRC. ISBN 978-1-58488-642-6
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- Baldwin 1995
- W.W. Baldwin, Richard Myer, Nicole Powell, et al (August 1995). "[http://www.springerlink.com/content/nu1lkduf3w89fmd8 Buoyant density of Escherichia coli is determined solely by the osmolarity of the culture medium]". Archives of Microbiology 164(2): 155-157
- Beyer 2004
- Andreas Beyer, Jens Hollunder, Heinz-Peter Nasheuer and Thomas Wilhelm (August 2004). "[http://dx.doi.org/10.1074/mcp.M400099-MCP200 Post-transcriptional Expression Regulation in the Yeast Saccharomyces cerevisiae on a Genomic Scale]". Molecular & Cellular Proteomics 3: 1083-1092
- Blancato 2006
- Blancato VS, Magni C, Lolkema JS. (October 2006). "[http://dx.doi.org/doi:10.1016/j.jmb.2009.02.015 Functional characterization and Me ion specificity of a Ca-citrate transporter from Enterococcus faecalis]". FEBS journal 273(22): 5121-5130
- Bowen 1965
- C.C. Bowen and T.E. Jensen ( March 1965). "[http://dx.doi.org/10.1126/science.147.3664.1460 Blue-Green Algae: Fine Structure of the Gas Vacuoles]". Science 147(3664): 1460 - 1462
- Blindauer 2002
- Claudia A. Blindauer, Mark D. Harrison, Andrea K. Robinson, et al (2002). "[http://dx.doi.org/10.1046/j.1365-2958.2002.03109.x Multiple bacteria encode metallothioneins and SmtA-like zinc fingers]". Molecular Microbiology 45(5): 1421-1432
- Blindauer 2001
- Blindauer CA, Harrison MD, et al (2001). "[http://www.ncbi.nlm.nih.gov/pubmed/11493688 A metallothionein containing a zinc finger within a four-metal cluster protects a bacterium from zinc toxicity.]". Proc Natl Acad Sci USA. 98(17): ):9593-9598
- Busenlehner 2003
- Busenlehner L.S., Pennella M.A. & Giedroc D.P., (June 2003) "[http://dx.doi.org/10.1155/2006/837139 The SmtB/ArsR family of metalloregulatory transcriptional repressors: structural insights into prokaryotic metal resistance]". FEMS Microbiology Reviews, 2003, 27, 131-143.
- Brady 1994
- Brady D, Rose PD, Duncan JR. (1994). "[http://www.ncbi.nlm.nih.gov/pubmed/18618649 The use of hollow fiber cross-flow microfiltration in bioaccumulation and continuous removal of heavy metals from solution by Saccharomyces cerevisiae.]". Biotechnol Bioeng. 44(11):1362-1366
- Bylund 1991
- J.E. Bylund, M.A. Haines, K. Walsh, et al (September 1991). "[http://jb.asm.org/cgi/content/abstract/173/17/5396 Buoyant density studies of several mecillinam-resistant and division mutants of Escherichia coli]". Journal of Bacteriology 173(17): 5396-5402
- Cadosch 2008
- Cadosch D, Meagher J, Gautschi OP, Filgueira L. (December 2008). "[http://www.ncbi.nlm.nih.gov/pubmed/19133293 Uptake and intracellular distribution of various metal ions in human monocyte-derived dendritic cells detected by Newport Green DCF diacetate ester]". Journal Neurosci Methods. 178(1):182-187
- Catini 2008
- Cantini F., Banci L. & Solioz M., (October 2008) "[http://dx.doi.org/10.1042/BJ20081713 The copper-responsive repressor CopR of Lactococcus lactis is a ‘winged helix’ protein]". Biochem. J., 2009, 417, 493–499.
- Carlin 1995
- Arthur Carlin, Weiping Shi, Saibal Dey and Barry P. Rosen (February 1995). "[http://www.ncbi.nlm.nih.gov/pubmed/7860609 The ars Operon of Escherichia coli Confers Arsenical and Antimonial Resistance]". Journal of Bacteriology 177(4): 981-986
- Chen 1997
- Yanxiang Chen and Barry P. Rosen (May 1997). "[http://www.ncbi.nlm.nih.gov/pubmed/9162059 Metalloregulatory Properties of the ArsD Repressor]". The Journal of Biological Chemistry 272(22): 14257-14262
- Chen 1997-2
- Chen S, Wilson DB. (1997). "[http://www.ncbi.nlm.nih.gov/pubmed/9342882 Genetic engineering of bacteria and their potential for Hg2+ bioremediation] ". Biodegradation 8(2): 97-103
- Chen 1998
- Chen S, Kim E, Shuler ML, Wilson DB. (1998). "[http://www.ncbi.nlm.nih.gov/pubmed/9758654 Hg2+ removal by genetically engineered Escherichia coli in a hollow fiber bioreactor]". Biotechnol Prog. 14(5):667-671
- Chen 2008
- Chen P.R. & He C., (March 2008) "[http://dx.doi.org/10.1016/j.cbpa.2007.12.010 Selective recognition of metal ions by metalloregulatory proteins, Current Opinion in Chemical Biology]". 2008, 12, 214–221.
- Chang 1998
- Chang CC, Liao WF, Huang PC. (1998). "[http://www.ncbi.nlm.nih.gov/pubmed/9579658 Cysteine contributions to metal binding preference for Zn/Cd in the beta-domain of metallothionein]". Protein Eng. 11(1):42-46
- Deng 2003
- Deng X, Li QB, Lu YH, Sun DH, Huang YL, Chen XR. (2003). "[http://www.ncbi.nlm.nih.gov/pubmed/12727263 Bioaccumulation of nickel from aqueous solutions by genetically engineered Escherichia coli.]". Water Res. 37(10):2505-2511
- Deng 2007
- Deng X, Yi XE, Liu G. (2007). "[http://www.ncbi.nlm.nih.gov/pubmed/16890348 Cadmium removal from aqueous solution by gene-modified Escherichia coli JM109]". Journal Hazard Mater. 139(2):340-344
- Deng 2008
- Deng X, Hu ZL, Yi XE. (May 2008). "[http://www.ncbi.nlm.nih.gov/pubmed/17920767 Continuous treatment process of mercury removal from aqueous solution by growing recombinant E. coli cells and modeling study]". Journal Hazard Mater. 153(1-2):487-492
- Dey 1995
- Saibal Dey, Barry P. Rosen (1995). "[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=176602 Dual Mode of Energy Coupling by the Oxyanion Translocating ArsB Protein]". JOURNAL OF BACTERIOLOGY 177(2): 385–389
- Ettema 2006
- Thijs J. G. Ettema, Arie B. Brinkman et al (2006). "[http://dx.doi.org/10.1099/mic.0.28724-0 Molecular characterization of a conserved archaeal copper resistance (cop) gene cluster and its copper-responsive regulator in Sulfolobus solfataricus P2]". Microbiology 152: 1969-1979
- Fowler 1987
- Fowler BA. (1987). "[http://www.ncbi.nlm.nih.gov/pubmed/3297654 Intracellular compartmentation of metals in aquatic organisms: roles in mechanisms of cell injury]". Environ Health Perspect. 7(1): 121-128
- Gilchrist 2007
- Michael A. Gilchrist (2007). "[http://dx.doi.org/10.1093/molbev/msm169 Combining Models of Protein Translation and Population Genetics to Predict Protein Production Rates from Codon Usage Patterns]". Molecular Biology and Evolution 24(11): 2362-2372
- Gold 2008
- Gold B, Deng H, et al(2008). "[http://www.ncbi.nlm.nih.gov/pubmed/18724363 Identification of a copper-binding metallothionein in pathogenic mycobacteria]". Nat Chem Biol. 4(10): 609-616
- Goudar 1999
- Chetan T. Goudara, Jagadeesh R. Sonnadb and Ronald G. Duggleby (January 1999). "[http://dx.doi.org/10.1016/S0167-4838(98)00247-7 Parameter estimation using a direct solution of the integrated Michaelis-Menten equation]". Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology 1429(2): 377-383
- Guven 2007
- Basak Guven and Alan Howarda (September 2007). "[http://dx.doi.org/doi:10.1016/j.ecolmodel.2007.03.024 Identifying the critical parameters of a cyanobacterial growth and movement model by using generalised sensitivity analysis]". Ecological Modelling 207(1): 11-21
- Hirose 2006
- Hirose K, Ezaki B, Tong L Nakashima S, et al (August 2005) "[http://dx.doi.org/10.1016/j.toxlet.2005.11.008 Diamide stress induces a metallothionein BmtA through a repressor BxmR and is modulated by Zn-inducible BmtA in the cyanobacterium Oscillatoria brevis]". Toxicology Letters, 2006, 163, 250–256.
- Hoefnagel 2002
- M.H.N. Hoefnagel, A. van der Burgt, D.E. Martens, et al (March 2002). "[http://dx.doi.org/10.1023/A:1020313409954 Time Dependent Responses of Glycolytic Intermediates in a Detailed Glycolytic Model of Lactococcus Lactis During Glucose Run-Out Experiments]". Molecular Biology Reports 29: 157-161
- Holland 2009
- Daryl P. Holland, Anthony E. Walsby (January 2009). "[http://dx.doi.org/10.1016/j.mimet.2009.02.005 Digital recordings of gas-vesicle collapse used to measure turgor pressure and cell–water relations of cyanobacterial cells ]". Journal of Microbiological Methods 77: 214-224
- Kao 2008
- Kao WC, Huang CC, Chang JS (October 2008). "[http://www.ncbi.nlm.nih.gov/pubmed/18313216 Biosorption of nickel, chromium and zinc by MerP-expressing recombinant Escherichia coli.]". J Hazard Mater. 158(1): 100-106
- Kelly 2009
- Jason R. Kelly, Adam J. Rubin, Joseph H. Davis, et al (March 2009). "[http://dx.doi.org/10.1186/1754-1611-3-4 Measuring the activity of BioBrick promoters using an in vivo reference standard]". Journal of Biological Engineering 3: 4
- Khunajakr 1999
- Nongpanga Khunajakr, Chun-Qiang Liu et al (March 1999). "[http://dx.doi.org/10.1016/S0378-1119(98)00395-3 A plasmid-encoded two-component regulatory system involved in copper-inducible transcription in Lactococcus lactis]". Gene229(1-1): 229-235
- Kloosterman 2008
- Tomas G. Kloosterman, Robert M. Witwicki et al (2008). "[http://dx.doi.org/10.1128/JB.00307-08 Opposite Effects of Mn2+ and Zn2+ on PsaR-Mediated Expression of the Virulence Genes pcpA, prtA, and psaBCA of Streptococcus pneumonia]". J Bacterio190(15): 5382–5393
- Kostal 2004
- Jan Kostal, Rosanna Yang, Cindy H. Wu, et al (August 2004). "[http://dx.doi.org/10.1128/AEM.70.8.4582-4587.2004 Enhanced Arsenic Accumulation in Engineered Bacterial Cells Expressing ArsR]". Applied and Environmental Microbiology 70(8): 4582–4587
- Lewinson 2009
- Lewinson O, Lee AT, Rees DC. (2009). "[http://www.ncbi.nlm.nih.gov/pubmed/19264958 A P-type ATPase importer that discriminates between essential and toxic transition metals]". PNAS 106(12): 4677-4682
- Li 1998
- Ning Li and Maura C. Cannon (May 1998). "Gas Vesicle Genes Identified in Bacillus megaterium and Functional Expression in Escherichia coli". Journal of Bacteriology 180(9): 2450–2458
- Lin 2007-1
- Yung-Feng Lin, Jianbo Yang and Barry P. Rosen (April 2007). "[http://dx.doi.org/10.1074/jbc.M700886200 ArsD Residues Cys12, Cys13, and Cys18 Form an As(III)-binding Site Required for Arsenic Metallochaperone Activity]". The Journal of Biological Chemistry 282(23): 16783–16791
- Lin 2007-2
- Yung-Feng Lin, Jianbo Yang and Barry P. Rosen (December 2007). "[http://dx.doi.org/10.1007/s10863-007-9113-y ArsD: an As(III) metallochaperone for the ArsAB As(III)-translocating ATPase]". Journal of Bioenergetics and Biomembranes 39: 453-458
- Liu 2004
- Tong Liu, Susumu Nakashima et al (April 2004) "[http://dx.doi.org/10.1074/jbc.M310560200 A Novel Cyanobacterial SmtB/ArsR Family Repressor Regulates the Expression of a CPx-ATPase and a Metallothionein in Response to Both Cu(I)/Ag(I) and Zn(II)/Cd(II)]". The Journal of Biological Chemistry, 2004, Vol. 279, No. 17, 17810–17818.
- Liu 2006
- Tong Liu Arati Ramesh et al(December 2006). "[http://dx.doi.org/10.1038/nchembio844 CsoR is a novel Mycobacterium tuberculosis copper-sensing transcriptional regulator]". Nature Chemical Biology 3: 60-68
- Liu 2008
- Tong Liu, Xiaohua Chen, Zhen Ma, et al (September 2008) "[http://dx.doi.org/10.1021/bi801313y A CuI-sensing ArsR family Metal Sensor Protein with a Relaxed Metal Selectivity Profile]". Biochemistry, 2008, 47(40), 10564–10575.
- Meng 2004
- Yu-Ling Meng, Zijuan Liu and Barry P. Rosen (February 2004). "[http://dx.doi.org/10.1074/jbc.M400037200 As(III) and Sb(III) Uptake by GlpF and Efflux by ArsB in Escherichia coli]". Journal of Biological Chemistry 279: 18334-18341
- Merrifield 2004
- M. E. Merrifield, T. Ngu, M. J. Stillman et al (September 2004). "[http://www.ncbi.nlm.nih.gov/pubmed/15464992 Arsenic binding to Fucus vesiculosus metallothionein.]". Biochemical and Biophysical Research Communications 324 : 127–132
- Mills 1994
- Scott D. Mills Chun-Keun Lim and Donald A. Cooksey (1994). "[http://dx.doi.org/10.1007/BF00286685 Purification and characterization of CopR, a transcriptional activator protein that binds to a conserved domain (cop box) in copper- inducible promoters of Pseudomonas syringae]". Molecular and General Genetics MGG 244(4): 1432-1874
- Moore 2005
- Charles M. Moore, Ahmed Gaballa et al (May 2005). "[http://dx.doi.org/10.1111/j.1365-2958.2005.04642.x Genetic and physiological responses of Bacillus subtilis to metal ion stress]". Molecular Microbiology57(1): 27-40
- Morris 1999
- C.A. Morris, B. Nicolaus, V. Sampson et al (March 1999). "[http://www.ncbi.nlm.nih.gov/pubmed/10024535 Identification and characterization of a recombinant metallothionein protein from a marine alga, Fucus vesiculosus]". The Biochemical journal 338(2): 553-560
- Nawapan 2009
- Sirikan Nawapan, Nisanart Charoenlap et al (August 2009). "[http://dx.doi.org/10.1046/10.1128/JB.00384-09 Functional and Expression Analyses of the cop Operon, Required for Copper Resistance in Agrobacterium tumefaciens]". American Society for Microbiology 191(16): 5159-5168
- Neves 1999
- Ana Rute Neves, Ana Ramos, Marta C. Nunes, et al (1999). "[http://dx.doi.org/10.1002/(SICI)1097-0290(19990720)64%3A2%3C200%3A%3AAID-BIT9%3E3.0.CO%3B2-K In vivo nuclear magnetic resonance studies of glycolytic kinetics in Lactococcus lactis]". Biotechnology and Bioengineering 64: 200-212
- Ngu 2006
- Thanh T. Ngu, M. Stillman (April 2006). "[http://dx.doi.org/10.1021/ja062914c Arsenic Binding to Human Metallothionein]". J. Am. Chem. Soc 128 (38): 12473–12483
- Pennella 2005
- Pennella M.A. & Giedroc D.P., (August 2005) "[http://dx.doi.org/10.1007/s10534-005-3716-8 Structural determinants of metal selectivity in prokaryotic metal-responsive transcriptional regulator]". BioMetals, 2005, 18, 413–428.
- Poole 1977
- R.K. Poole (1977). "[http://mic.sgmjournals.org/cgi/content/abstract/98/1/177 Fluctuations in Buoyant Density during the Cell Cycle of Escherichia coli K12]". Journal of General Microbiology 98: 177-186
- Rensing 2005
- Christopher Rensing (June 2005). "[http://dx.doi.org/10.1128/JB.187.12.3909-3912.2005 Form and Function in Metal-Dependent Transcriptional Regulation: Dawn of the Enlightenment]". Journal of Bacteriology 187(12): 3909–3912
- Robinson 2001
- Nigel J. Robinson, Simon K. Whitehall and Jennifer S. Cavet (2001). "[http://www.ncbi.nlm.nih.gov/pubmed/11407113 Microbial Metallothioneins]". Advances in Microbial Physiology 44: 183-213
- Rosen 1996
- Barry P. Rosen (August 1996). "[http://dx.doi.org/10.1007/s007750050053 Bacterial resistance to heavy metals and metalloids]". Journal of Biological Inorganic Chemistry 1(4): 273-277
- Rosen 2009
- Barry P. Rosen and Zijuan Liu (April 2009). "[http://dx.doi.org/10.1016/j.envint.2008.07.023 Transport pathways for arsenic and selenium: A minireview]". Environment International 35(3): 512-515
- Schwartz 2008
- Russel Schwartz (2008). Biological modeling and simulation: a survey of practical models, algorithms, and numerical methods MIT Press. ISBN 978-0-262-19584-3
- Shi 1992
- Jianguo Shi, William P. Lindsay, James W. Huckle (June 1992). "[http://dx.doi.org/10.1016/0014-5793(92)80509-F Cyanobacterial metallothionein gene expressed in Escherichia coli: Metal-binding properties of the expressed protein]". FEBS Letters 303(2-3): 159-163
- Singh 2008
- Shailendra Singh, Ashok Mulchandani, Wilfred Chen (February 2008). "[http://dx.doi.org/10.1128/AEM.02871-07 Highly Selective and Rapid Arsenic Removal by Metabolically Engineered Escherichia coli Cells Expressing Fucus vesiculosus Metallothionein]". MICROBIOLOGY 74(9): 2924–2927
- Sivertsen 2008
- Astrid C. Sivertsen, Marvin J. Bayro, et al ( april 2008). "[http://dx.doi.org/doi:10.1016/j.jmb.2009.02.015 Solid-State NMR Evidence for Inequivalent GvpA Subunits in Gas Vesicles]". Journal of Molecular Biology 387(4): 1032-1039
- Summers 2009
- Anne O. Summers (April 2009). "[http://dx.doi.org/10.1016/j.mib.2009.02.003 Damage control: regulating defenses against toxic metals and metalloids]". Current Opinion in Microbiology 12(2): 138-144
- Thelwell 1998
- Thelwell C., Robinson N.J. & Turner-Cavet J.S., "[http://dx.doi.org/10.1073/pnas.95.18.10728 An SmtB-like repressor from Synechocystis PCC 6803 regulates a zinc exporter]". Proc. Natl. Acad. Sci. USA, 1998, Vol. 95, 10728–10733.
- Tisa 1989
- Louis S. Tisa and Barry P. Rosen (January 1990). "[http://www.ncbi.nlm.nih.gov/pubmed/1688427 Molecular characterization of an anion pump. The ArsB protein is the membrane anchor for the ArsA protein]". The journal of biological chemistry 265(1): 190-194
- Turner 1995
- Jennifer S. Turner, Nigel J. Robinson and Amit Gupta (March 1995). "[http://dx.doi.org/10.1007/BF01569937 Construction of Zn2+/Cd2+-tolerant cyanobacteria with a modified metallothionein divergon: Further analysis of the function and regulation of smt]". Journal of Industrial Microbiology and Biotechnology 14(3-4): 259-264
- Walsby 1979
- A.E. Walsby (April 1979). "[http://dx.doi.org/10.1016/0022-2836(79)90281-X Average thickness of the gas vesicle wall in Anabaena flos-aquae]". Journal of Molecular Biology 129(2): 279-285
- Walsby 1994
- A.E. Walsby (March 1994). "[http://www.ncbi.nlm.nih.gov/pubmed/8177173 Gas Vesicles]". Microbiological reviews 58(1): 94-144
Miscellaneous:
- [http://ginkgobioworks.com/cgi/primer.cgi Primer design Bioworks]
- [http://openwetware.org/wiki/The_BioBricks_Foundation:Standards/Technical/Measurement Promotor measurement]
- [http://openwetware.org/wiki/Main_Page OpenWetWare]
- [http://www.hgsc.bcm.tmc.edu/projects/microbial/microbial-detail.xsp?project_id=105 E. coli DH10B genome] (with BLAST)
