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Team:ESBS-Strasbourg/Essential publications
From 2008.igem.org
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== Project essentials == | == Project essentials == | ||
* ''Caroline M. Ajo-Franklin et al. Rational design of memory in eukaryotic cells. (2007)'' PMID 17875664 | * ''Caroline M. Ajo-Franklin et al. Rational design of memory in eukaryotic cells. (2007)'' PMID 17875664 | ||
| + | * '' | ||
| + | * ''Christina B. Tyson et al. Dependency of size of Saccharomyces cerevisiae cells on growth rate. (1978)'' PMID 374379 | ||
<br> | <br> | ||
| - | == | + | == Transcriptional/translational control == |
* ''Gudrun Bjornsdottir and Lawrence C. Myers. Minimal components of the RNA polymerase II transcription apparatus determine the consensus TATA box. (2008)'' PMID 18385157 | * ''Gudrun Bjornsdottir and Lawrence C. Myers. Minimal components of the RNA polymerase II transcription apparatus determine the consensus TATA box. (2008)'' PMID 18385157 | ||
| - | |||
* ''Wei Zhouet al. Isolation and identification of short nucleotide sequences that affect translation initiation in Saccharomyces cerevisiae. (2002)'' PMID 12679518 | * ''Wei Zhouet al. Isolation and identification of short nucleotide sequences that affect translation initiation in Saccharomyces cerevisiae. (2002)'' PMID 12679518 | ||
* ''Thomas Masek et al. Hepatitis C virus internal ribosome entry site initiates protein synthesis at the authentic initiation codon in yeast. (2007)'' PMID 17554033 | * ''Thomas Masek et al. Hepatitis C virus internal ribosome entry site initiates protein synthesis at the authentic initiation codon in yeast. (2007)'' PMID 17554033 | ||
| Line 21: | Line 22: | ||
== Eukaryotic activation/repression domains == | == Eukaryotic activation/repression domains == | ||
| + | * ''Gerald Thiel et al. How mammalian transcriptional repressors work. (2004)'' PMID: 15233782 | ||
* ''Gemma Bellí et al. An activator/repressor dual system allows tight tetracycline-regulated gene expression in budding yeast. (1998)'' PMID 9461451 | * ''Gemma Bellí et al. An activator/repressor dual system allows tight tetracycline-regulated gene expression in budding yeast. (1998)'' PMID 9461451 | ||
* ''Jae-Ryeon Ryu et al. Cell-type specificity of short-range transcriptional repressors. (2001)'' PMID 11687630 | * ''Jae-Ryeon Ryu et al. Cell-type specificity of short-range transcriptional repressors. (2001)'' PMID 11687630 | ||
| Line 27: | Line 29: | ||
== Prokaryotic DNA binding domains (+ affinity mutations) == | == Prokaryotic DNA binding domains (+ affinity mutations) == | ||
| + | * ''M. Madan Babu and Sarah A. Teichmann. Functional determinants of transcription factors in Escherichia coli: protein families and binding sites. (2003)'' PMID 12547514 | ||
* ''Christian Berens and Wolfgang Hillen. Gene regulation by tetracyclines. Constraints of resistance regulation in bacteria shape TetR for application in eukaryotes. (2003)'' PMID 12869186 | * ''Christian Berens and Wolfgang Hillen. Gene regulation by tetracyclines. Constraints of resistance regulation in bacteria shape TetR for application in eukaryotes. (2003)'' PMID 12869186 | ||
* ''A. Wissmann et al. Amino acids determining operator binding specificity in the helix-turn-helix motif of Tn10 Tet repressor. (1991)'' PMID 1756721 | * ''A. Wissmann et al. Amino acids determining operator binding specificity in the helix-turn-helix motif of Tn10 Tet repressor. (1991)'' PMID 1756721 | ||
| Line 36: | Line 39: | ||
* ''Sofie R. Salama. G1 cyclin degradation: the PEST motif of yeast Cln2 is necessary, but not sufficient, for rapid protein turnover. (1994)'' PMID 7969135 | * ''Sofie R. Salama. G1 cyclin degradation: the PEST motif of yeast Cln2 is necessary, but not sufficient, for rapid protein turnover. (1994)'' PMID 7969135 | ||
* ''Carolina Mateus and Simon V. Avery. Destabilized green fluorescent protein for monitoring dynamic changes in yeast gene expression with flow cytometry. (2000)'' PMID 11015728 | * ''Carolina Mateus and Simon V. Avery. Destabilized green fluorescent protein for monitoring dynamic changes in yeast gene expression with flow cytometry. (2000)'' PMID 11015728 | ||
| - | * '' Catherine Berset et al. Transferable domain in the G(1) cyclin Cln2 sufficient to switch degradation of Sic1 from the E3 ubiquitin ligase SCF(Cdc4) to SCF(Grr1). (2002)'' PMID 12052857 | + | * ''Catherine Berset et al. Transferable domain in the G(1) cyclin Cln2 sufficient to switch degradation of Sic1 from the E3 ubiquitin ligase SCF(Cdc4) to SCF(Grr1). (2002)'' PMID 12052857 |
| + | * ''Matthew D. Petroski and Raymond J. Deshaies. Redundant degrons ensure the rapid destruction of Sic1 at the G1/S transition of the budding yeast cell cycle. (2003)'' PMID 12963827 | ||
<br> | <br> | ||
== Nuclear localistation == | == Nuclear localistation == | ||
| + | * ''Gabriel Schlenstedt et al. Reconstitution of nuclear protein transport with semi-intact yeast cells. (1993)'' PMID: 8227140 | ||
* ''Julia M. Sidorova et al. Cell cycle-regulated phosphorylation of Swi6 controls its nuclear localization. (1995)'' PMID 8590795 | * ''Julia M. Sidorova et al. Cell cycle-regulated phosphorylation of Swi6 controls its nuclear localization. (1995)'' PMID 8590795 | ||
* ''Michelle T. Harreman. Regulation of nuclear import by phosphorylation adjacent to nuclear localization signals. (2004)'' PMID 14998990 | * ''Michelle T. Harreman. Regulation of nuclear import by phosphorylation adjacent to nuclear localization signals. (2004)'' PMID 14998990 | ||
| Line 59: | Line 64: | ||
== Toggle switches == | == Toggle switches == | ||
| - | * '' Timothy S. Gardner et al. Construction of a genetic toggle switch in Escherichia coli. (2000)'' PMID 10659857 | + | * ''Timothy S. Gardner et al. Construction of a genetic toggle switch in Escherichia coli. (2000)'' PMID 10659857 |
| + | * ''Beat P. Kramer and Martin Fussenegger. Hysteresis in a synthetic mammalian gene network. (2005)'' PMID 15972812 | ||
<br> | <br> | ||
Revision as of 12:29, 7 August 2008
|
Essential publications
Project essentials
- Caroline M. Ajo-Franklin et al. Rational design of memory in eukaryotic cells. (2007) PMID 17875664
- Christina B. Tyson et al. Dependency of size of Saccharomyces cerevisiae cells on growth rate. (1978) PMID 374379
Transcriptional/translational control
- Gudrun Bjornsdottir and Lawrence C. Myers. Minimal components of the RNA polymerase II transcription apparatus determine the consensus TATA box. (2008) PMID 18385157
- Wei Zhouet al. Isolation and identification of short nucleotide sequences that affect translation initiation in Saccharomyces cerevisiae. (2002) PMID 12679518
- Thomas Masek et al. Hepatitis C virus internal ribosome entry site initiates protein synthesis at the authentic initiation codon in yeast. (2007) PMID 17554033
Eukaryotic activation/repression domains
- Gerald Thiel et al. How mammalian transcriptional repressors work. (2004) PMID: 15233782
- Gemma Bellí et al. An activator/repressor dual system allows tight tetracycline-regulated gene expression in budding yeast. (1998) PMID 9461451
- Jae-Ryeon Ryu et al. Cell-type specificity of short-range transcriptional repressors. (2001) PMID 11687630
- Tania M. Malavé and Sharon Y.R. Dent. Transcriptional repression by Tup1-Ssn6. (2006) PMID 16936817
Prokaryotic DNA binding domains (+ affinity mutations)
- M. Madan Babu and Sarah A. Teichmann. Functional determinants of transcription factors in Escherichia coli: protein families and binding sites. (2003) PMID 12547514
- Christian Berens and Wolfgang Hillen. Gene regulation by tetracyclines. Constraints of resistance regulation in bacteria shape TetR for application in eukaryotes. (2003) PMID 12869186
- A. Wissmann et al. Amino acids determining operator binding specificity in the helix-turn-helix motif of Tn10 Tet repressor. (1991) PMID 1756721
Protein degradation motifs
- Emily R. Hildebrandt and M. Andrew Hoyt. Cell cycle-dependent degradation of the Saccharomyces cerevisiae spindle motor Cin8p requires APC(Cdh1) and a bipartite destruction sequence. (2001) PMID 11694576
- Janet L. Burton and Mark Solomon. D box and KEN box motifs in budding yeast Hsl1p are required for APC-mediated degradation and direct binding to Cdc20p and Cdh1p. (2001) PMID 11562348
- Sofie R. Salama. G1 cyclin degradation: the PEST motif of yeast Cln2 is necessary, but not sufficient, for rapid protein turnover. (1994) PMID 7969135
- Carolina Mateus and Simon V. Avery. Destabilized green fluorescent protein for monitoring dynamic changes in yeast gene expression with flow cytometry. (2000) PMID 11015728
- Catherine Berset et al. Transferable domain in the G(1) cyclin Cln2 sufficient to switch degradation of Sic1 from the E3 ubiquitin ligase SCF(Cdc4) to SCF(Grr1). (2002) PMID 12052857
- Matthew D. Petroski and Raymond J. Deshaies. Redundant degrons ensure the rapid destruction of Sic1 at the G1/S transition of the budding yeast cell cycle. (2003) PMID 12963827
Nuclear localistation
- Gabriel Schlenstedt et al. Reconstitution of nuclear protein transport with semi-intact yeast cells. (1993) PMID: 8227140
- Julia M. Sidorova et al. Cell cycle-regulated phosphorylation of Swi6 controls its nuclear localization. (1995) PMID 8590795
- Michelle T. Harreman. Regulation of nuclear import by phosphorylation adjacent to nuclear localization signals. (2004) PMID 14998990
Site-specific proteases
- Sung Yun Kim et al. In vivo determination of substrate specificity of hepatitis C virus NS3 protease: genetic assay for site-specific proteolysis. (2000) PMID 10933854
- Hara Kang et al. An improved strategy for a genetic assay for site-specific proteolysis. (2001) PMID 11355710
mRNA instability
- Reut Shalgi et al. A catalog of stability-associated sequence elements in 3'UTRs of yeast mRNAs. (2005) PMID 16207357
BioBrick assembly
- Tom Knight. Idempotent Vector Design for Standard Assembly of Biobricks (2003) [http://web.mit.edu/synbio/release/docs/biobricks.pdf]
- Ira E. Philips and Pamels A. Silver. A New Biobrick Assembly Strategy Designed for Facile Protein Engineering (2006) [http://dspace.mit.edu/bitstream/handle/1721.1/32535/PhillipsSilverFusion.pdf?sequence=1]
Toggle switches
- Timothy S. Gardner et al. Construction of a genetic toggle switch in Escherichia coli. (2000) PMID 10659857
- Beat P. Kramer and Martin Fussenegger. Hysteresis in a synthetic mammalian gene network. (2005) PMID 15972812
Fluorescent proteins
- Nathan C. Shaner et al. A guide to choosing fluorescent proteins. (2005) PMID 16299475
