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Team:ESBS-Strasbourg/Essential publications
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| - | + | =Reading= | |
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<br> | <br> | ||
== Project essentials == | == Project essentials == | ||
| - | * ''Caroline M. Ajo-Franklin et al. Rational design of memory in eukaryotic cells. (2007) | + | * ''Caroline M. Ajo-Franklin et al.'' Rational design of memory in eukaryotic cells. (2007) PMID 17875664 |
| - | * ''Attila Becskei et al. Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion. (2001) | + | * ''Attila Becskei et al.'' Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion. (2001) PMID 11350942 |
| - | * ''Christina B. Tyson et al. Dependency of size of Saccharomyces cerevisiae cells on growth rate. (1978) | + | * ''Christina B. Tyson et al.'' Dependency of size of Saccharomyces cerevisiae cells on growth rate. (1978) PMID 374379 |
| - | * ''Nathan C. Shaner et al. A guide to choosing fluorescent proteins. (2005) | + | * ''Nathan C. Shaner et al.'' A guide to choosing fluorescent proteins. (2005) PMID 16299475 |
<br> | <br> | ||
== Transcriptional/translational control == | == Transcriptional/translational control == | ||
| - | * ''Gudrun Bjornsdottir and Lawrence C. Myers. Minimal components of the RNA polymerase II transcription apparatus determine the consensus TATA box. (2008) | + | * ''Gudrun Bjornsdottir and Lawrence C. Myers.'' Minimal components of the RNA polymerase II transcription apparatus determine the consensus TATA box. (2008) PMID 18385157 |
| - | + | * ''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 | + | * ''Wei Zhouet et al.'' Isolation and identification of short nucleotide sequences that affect translation initiation in Saccharomyces cerevisiae. (2002) PMID 12679518 |
<br> | <br> | ||
== Eukaryotic activation/repression domains == | == Eukaryotic activation/repression domains == | ||
| - | * ''Gerald Thiel et al. How mammalian transcriptional repressors work. (2004) | + | * ''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) | + | * ''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) | + | * ''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) | + | * ''Tania M. Malavé and Sharon Y.R. Dent.'' Transcriptional repression by Tup1-Ssn6. (2006) PMID 16936817 |
<br> | <br> | ||
== 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) | + | * ''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) | + | * ''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 | + | * ''A. Wissmann et al.'' Amino acids determining operator binding specificity in the helix-turn-helix motif of Tn10 Tet repressor. (1991) PMID 1756721 |
| + | * ''Hillary C.M. Nelson and Robert T. Sauer.'' Lambda repressor mutations that increase the affinity and specificity of operator binding. (1985) PMID 3161621 | ||
| + | * ''Nicholas Benson et al.'' Mutant lambda repressors with increased operator affinities reveal new, specific protein-DNA contacts. (1992) PMID 1531047 | ||
| + | * ''P. Oertel-Buchheit et al.'' Isolation and characterization of LexA mutant repressors with enhanced DNA binding affinity. (1992) PMID 1602473 | ||
| + | * ''Liskin Swint-Kruse et al.'' Perturbation from a distance: mutations that alter LacI function through long-range effects. (2003) PMID 14636069 | ||
<br> | <br> | ||
== Protein degradation motifs == | == 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) | + | * ''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) | + | * ''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 et al. G1 cyclin degradation: the PEST motif of yeast Cln2 is necessary, but not sufficient, for rapid protein turnover. (1994) | + | * ''Sofie R. Salama et al.'' 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) | + | * ''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) | + | * ''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) | + | * ''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 |
| - | * ''Alexander Varshavsky. The N-end rule: functions, mysteries, uses. (1996) | + | * ''Alexander Varshavsky.'' The N-end rule: functions, mysteries, uses. (1996) PMID 8901547 |
<br> | <br> | ||
== Nuclear localistation == | == Nuclear localistation == | ||
| - | * ''Gabriel Schlenstedt et al. Reconstitution of nuclear protein transport with semi-intact yeast cells. (1993) | + | * ''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) | + | * ''Julia M. Sidorova et al.'' Cell cycle-regulated phosphorylation of Swi6 controls its nuclear localization. (1995) PMID 8590795 |
| - | * ''Michelle T. Harreman et al. Regulation of nuclear import by phosphorylation adjacent to nuclear localization signals. (2004) | + | * ''Michelle T. Harreman et al.'' Regulation of nuclear import by phosphorylation adjacent to nuclear localization signals. (2004) PMID 14998990 |
<br> | <br> | ||
== Site-specific proteases == | == 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) | + | * ''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) | + | * ''Hara Kang et al.'' An improved strategy for a genetic assay for site-specific proteolysis. (2001) PMID 11355710 |
| - | * ''Sung Yun Kim et al. Detection of site-specific proteolysis in secretory pathways. (2002) | + | * ''Sung Yun Kim et al.'' Detection of site-specific proteolysis in secretory pathways. (2002) PMID 12163035 |
<br> | <br> | ||
== mRNA instability == | == mRNA instability == | ||
| - | * ''Reut Shalgi et al. A catalog of stability-associated sequence elements in 3'UTRs of yeast mRNAs. (2005) | + | * ''T. Chinnappan Santiago et al.'' The relationship between mRNA stability and length in Saccharomyces cerevisiae. (1986) PMID 3537957 |
| - | * ''Tina Gill et al. RNase MRP cleaves the CLB2 mRNA to promote cell cycle progression: novel method of mRNA degradation. (2003)'' PMID | + | * ''Reut Shalgi et al.'' A catalog of stability-associated sequence elements in 3'UTRs of yeast mRNAs. (2005) PMID 16207357 |
| + | * ''Tina Gill et al.'' RNase MRP cleaves the CLB2 mRNA to promote cell cycle progression: novel method of mRNA degradation. (2003) PMID 14729943 | ||
| + | * ''Bernard J. de la Cruz et al.'' The role of the 5' untranslated region (UTR) in glucose-dependent mRNA decay. (2002) PMID 12112242 | ||
| + | * ''Benoit Pierrat et al.'' The 5' untranslated region of the PPR1 regulatory gene dictates rapid mRNA decay in yeast. (1993) PMID 8370540 | ||
<br> | <br> | ||
| - | == | + | == 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 |
<br> | <br> | ||
| - | == | + | == BioBrick assembly == |
| - | * '' | + | * ''Tom Knight.'' Idempotent Vector Design for Standard Assembly of Biobricks (2003) [http://web.mit.edu/synbio/release/docs/biobricks.pdf] |
| - | * '' | + | * ''Ira E. Phillips and Pamela 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] |
| - | |||
| - | + | ||
| + | == Miscellaneous == | ||
| + | * ''Pawan K. Dhar.'' The next step in biology: a periodic table? (2007) PMID 17914242 | ||
| + | |||
| + | <br><br> | ||
Latest revision as of 21:20, 29 October 2008
|
Reading
Project essentials
- Caroline M. Ajo-Franklin et al. Rational design of memory in eukaryotic cells. (2007) PMID 17875664
- Attila Becskei et al. Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion. (2001) PMID 11350942
- Christina B. Tyson et al. Dependency of size of Saccharomyces cerevisiae cells on growth rate. (1978) PMID 374379
- Nathan C. Shaner et al. A guide to choosing fluorescent proteins. (2005) PMID 16299475
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
- Thomas Masek et al. Hepatitis C virus internal ribosome entry site initiates protein synthesis at the authentic initiation codon in yeast. (2007) PMID 17554033
- Wei Zhouet et al. Isolation and identification of short nucleotide sequences that affect translation initiation in Saccharomyces cerevisiae. (2002) PMID 12679518
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
- Hillary C.M. Nelson and Robert T. Sauer. Lambda repressor mutations that increase the affinity and specificity of operator binding. (1985) PMID 3161621
- Nicholas Benson et al. Mutant lambda repressors with increased operator affinities reveal new, specific protein-DNA contacts. (1992) PMID 1531047
- P. Oertel-Buchheit et al. Isolation and characterization of LexA mutant repressors with enhanced DNA binding affinity. (1992) PMID 1602473
- Liskin Swint-Kruse et al. Perturbation from a distance: mutations that alter LacI function through long-range effects. (2003) PMID 14636069
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 et al. 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
- Alexander Varshavsky. The N-end rule: functions, mysteries, uses. (1996) PMID 8901547
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 et al. 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
- Sung Yun Kim et al. Detection of site-specific proteolysis in secretory pathways. (2002) PMID 12163035
mRNA instability
- T. Chinnappan Santiago et al. The relationship between mRNA stability and length in Saccharomyces cerevisiae. (1986) PMID 3537957
- Reut Shalgi et al. A catalog of stability-associated sequence elements in 3'UTRs of yeast mRNAs. (2005) PMID 16207357
- Tina Gill et al. RNase MRP cleaves the CLB2 mRNA to promote cell cycle progression: novel method of mRNA degradation. (2003) PMID 14729943
- Bernard J. de la Cruz et al. The role of the 5' untranslated region (UTR) in glucose-dependent mRNA decay. (2002) PMID 12112242
- Benoit Pierrat et al. The 5' untranslated region of the PPR1 regulatory gene dictates rapid mRNA decay in yeast. (1993) PMID 8370540
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
BioBrick assembly
- Tom Knight. Idempotent Vector Design for Standard Assembly of Biobricks (2003) [http://web.mit.edu/synbio/release/docs/biobricks.pdf]
- Ira E. Phillips and Pamela 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]
Miscellaneous
- Pawan K. Dhar. The next step in biology: a periodic table? (2007) PMID 17914242
