Team:Groningen/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:

Alon 2007

Uri Alon (2007). Introduction to systems biology: design principles of biological circuits Chapman & Hall/CRC. ISBN 978-1-58488-642-6

Baldwin 1995

W.W. Baldwin, Richard Myer, Nicole Powell, et al (August 1995). "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). "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). "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). "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). "Multiple bacteria encode metallothioneins and SmtA-like zinc fingers". Molecular Microbiology 45(5): 1421-1432

Blindauer 2001

Blindauer CA, Harrison MD, et al (2001). "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) "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). "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). "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). "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) "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). "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). "Metalloregulatory Properties of the ArsD Repressor". The Journal of Biological Chemistry 272(22): 14257-14262

Chen 1997-2

Chen S, Wilson DB. (1997). "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). "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) "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). "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). "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). "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). "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). "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). "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). "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). "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). "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). "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). "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) "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). "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). "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). "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). "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). "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). "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). "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). "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). "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). "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) "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). "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) "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). "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). "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). "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). "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). "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). "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). "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). "Arsenic Binding to Human Metallothionein". J. Am. Chem. Soc 128 (38): 12473–12483

Pennella 2005

Pennella M.A. & Giedroc D.P., (August 2005) "Structural determinants of metal selectivity in prokaryotic metal-responsive transcriptional regulator". BioMetals, 2005, 18, 413–428.

Poole 1977

R.K. Poole (1977). "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). "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). "Microbial Metallothioneins". Advances in Microbial Physiology 44: 183-213

Rosen 1996

Barry P. Rosen (August 1996). "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). "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). "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). "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). "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). "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., "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). "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). "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). "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). "Gas Vesicles". Microbiological reviews 58(1): 94-144

Miscellaneous:

• Primer design Bioworks
• Promotor measurement
• OpenWetWare
• E. coli DH10B genome (with BLAST)