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Team:TUDelft/Papers
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Some review papers on RNA switches. | Some review papers on RNA switches. | ||
| - | + | * RNA dynamics: it is about time - Al-Hashimi et al., April 2008 [http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6VS6-4SPV149-1-9&_cdi=6254&_user=499885&_orig=search&_coverDate=06%2F30%2F2008&_sk=999819996&view=c&wchp=dGLbVzb-zSkWA&md5=0fba1ad96c9780db45aa96dd764933d7&ie=/sdarticle.pdf] | |
| - | + | * mRNA-mediated detection of environmental conditions - Narberhaus, August 2002 [http://www.springerlink.com/content/dv19jt8aw0vdm0ff/fulltext.pdf] | |
| - | + | * RNA switches regulate initiation of translation in bacteria - Stefano Marzi, Pierre Fechter, Cle´ment Chevalier, Pascale Romby and Thomas Geissmann - Biol. Chem., Vol. 389, pp. 585–598, May 2008 | |
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===RNA thermometers=== | ===RNA thermometers=== | ||
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* RNA thermometers - Narberhaus et al., May 2005 [http://www3.interscience.wiley.com/cgi-bin/fulltext/118587582/PDFSTART] | * RNA thermometers - Narberhaus et al., May 2005 [http://www3.interscience.wiley.com/cgi-bin/fulltext/118587582/PDFSTART] | ||
| - | *Molecular basis for temperature sensing by an RNA thermometer - Saheli Chowdhury, Christophe Maris, Frederic Allain and Franz Narberhaus - The EMBO Journal (2006) 25, 2487–2497 | + | * Molecular basis for temperature sensing by an RNA thermometer - Saheli Chowdhury, Christophe Maris, Frederic Allain and Franz Narberhaus - The EMBO Journal (2006) 25, 2487–2497 |
| - | *An RNA Thermosensor Controls Expression of Virulence Genes in Listeria monocytogenes - Chowdhurry et al., 2006 [http://rnaworld.bio.ku.edu/class/biol599/sp08/reprints/thermometer/Johansson(2002)Cell_110,551.pdf] | + | * An RNA Thermosensor Controls Expression of Virulence Genes in Listeria monocytogenes - Chowdhurry et al., 2006 [http://rnaworld.bio.ku.edu/class/biol599/sp08/reprints/thermometer/Johansson(2002)Cell_110,551.pdf] |
| - | *FourU: a novel type of RNA thermometer in Salmonella - Waldminghaus, 2007 [http://www3.interscience.wiley.com/cgi-bin/fulltext/118542064/PDFSTART] | + | * FourU: a novel type of RNA thermometer in Salmonella - Waldminghaus, 2007 [http://www3.interscience.wiley.com/cgi-bin/fulltext/118542064/PDFSTART] |
| - | *RNA Quadruplex-Based Modulation of Gene Expression - Wieland et al., June 2007 [http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6VRP-4P8YWVM-7-8&_cdi=6240&_user=499885&_orig=search&_coverDate=07%2F30%2F2007&_sk=999859992&view=c&wchp=dGLbVzz-zSkzS&md5=97741390ae4ff0d9a8c4d5f41beb0f1d&ie=/sdarticle.pdf] | + | * RNA Quadruplex-Based Modulation of Gene Expression - Wieland et al., June 2007 [http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6VRP-4P8YWVM-7-8&_cdi=6240&_user=499885&_orig=search&_coverDate=07%2F30%2F2007&_sk=999859992&view=c&wchp=dGLbVzz-zSkzS&md5=97741390ae4ff0d9a8c4d5f41beb0f1d&ie=/sdarticle.pdf] |
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| + | * A mRNA-based thermosensor controls expression of rhizobial heat shock genes - Nocker et al., October 2001 [http://nar.oxfordjournals.org/cgi/reprint/29/23/4800] | ||
| + | * Molecular Processes in Biological Thermosensation - Digel et al., April 2008 [http://hindawi.com/Getpdf.aspx?doi=10.1155/2008/602870] | ||
===Bioinformatics=== | ===Bioinformatics=== | ||
Papers on bioinformatic approaches used to search for potential RNA thermometers. | Papers on bioinformatic approaches used to search for potential RNA thermometers. | ||
| - | *Genome-wide bioinformatic prediction and experimental evaluation of potential RNA thermometers - Torsten Waldminghaus · Lena C. Gaubig · Franz Narberhaus - Mol Genet Genomics (2007) 278:555–564 | + | * Genome-wide bioinformatic prediction and experimental evaluation of potential RNA thermometers - Torsten Waldminghaus · Lena C. Gaubig · Franz Narberhaus - Mol Genet Genomics (2007) 278:555–564 |
===Modeling=== | ===Modeling=== | ||
Some papers that can be used for the modeling part. | Some papers that can be used for the modeling part. | ||
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* RNA synthetic biology - F.J. Isaacs et al., 2006 [http://knowledgecontext.org/COSMOS/RNA_synthetic_biology.pdf] | * RNA synthetic biology - F.J. Isaacs et al., 2006 [http://knowledgecontext.org/COSMOS/RNA_synthetic_biology.pdf] | ||
| + | * Design of 5'-untranslated region variants for tunable expression in Escherichia coli - Park et al., February 2007 [http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6WBK-4N67NVV-5-C&_cdi=6713&_user=499885&_orig=search&_coverDate=04%2F27%2F2007&_sk=996439998&view=c&wchp=dGLbVlz-zSkWA&md5=571d5d21c20c71f0567f2ae53ee0e2ea&ie=/sdarticle.pdf] | ||
| + | * Engineered riboregulators enable post-transcriptional control of gene expression - G. Isaacs, D. Dqyer, C. Ding, D. Pervouchine, C. Cantor & J. Collins - Nature Biotechnology (2004) volume 7 number 22. | ||
| + | * Temperature-controlled Structural Alterations of an RNA Thermometer - Chowdhury et al., June 2003 [http://www.jbc.org/cgi/reprint/278/48/47915] | ||
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===Color=== | ===Color=== | ||
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* Identification of genes for bacterial bioluminescence [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=345387&blobtype=pdf] | * Identification of genes for bacterial bioluminescence [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=345387&blobtype=pdf] | ||
* Group in Leiden working with the Soil Bacterium Streptomyces [http://wwwchem.gorlaeus.net/micdev/micdev_pages/vanwezel.html] | * Group in Leiden working with the Soil Bacterium Streptomyces [http://wwwchem.gorlaeus.net/micdev/micdev_pages/vanwezel.html] | ||
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Revision as of 09:48, 1 August 2008
[http://www.tudelft.nl ]
[http://www.tudelft.nl ]
- Thermometer design at the nanoscale - Lee et al., February 2007 [http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B82X8-4N13BB2-N-1&_cdi=33024&_user=499885&_orig=search&_coverDate=02%2F28%2F2007&_sk=999979998&view=c&wchp=dGLbVlz-zSkzS&md5=02d4712f0e1ba955f322b80941b09106&ie=/sdarticle.pdf]
Contents |
Temperature
RNA switches
Some review papers on RNA switches.
- RNA dynamics: it is about time - Al-Hashimi et al., April 2008 [http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6VS6-4SPV149-1-9&_cdi=6254&_user=499885&_orig=search&_coverDate=06%2F30%2F2008&_sk=999819996&view=c&wchp=dGLbVzb-zSkWA&md5=0fba1ad96c9780db45aa96dd764933d7&ie=/sdarticle.pdf]
- mRNA-mediated detection of environmental conditions - Narberhaus, August 2002 [http://www.springerlink.com/content/dv19jt8aw0vdm0ff/fulltext.pdf]
- RNA switches regulate initiation of translation in bacteria - Stefano Marzi, Pierre Fechter, Cle´ment Chevalier, Pascale Romby and Thomas Geissmann - Biol. Chem., Vol. 389, pp. 585–598, May 2008
RNA thermometers
Some papers aimed at RNA thermometers, a special type of RNA switch that we are going to use for our project.
- RNA thermometers - Narberhaus et al., May 2005 [http://www3.interscience.wiley.com/cgi-bin/fulltext/118587582/PDFSTART]
- Molecular basis for temperature sensing by an RNA thermometer - Saheli Chowdhury, Christophe Maris, Frederic Allain and Franz Narberhaus - The EMBO Journal (2006) 25, 2487–2497
- An RNA Thermosensor Controls Expression of Virulence Genes in Listeria monocytogenes - Chowdhurry et al., 2006 [http://rnaworld.bio.ku.edu/class/biol599/sp08/reprints/thermometer/Johansson(2002)Cell_110,551.pdf]
- FourU: a novel type of RNA thermometer in Salmonella - Waldminghaus, 2007 [http://www3.interscience.wiley.com/cgi-bin/fulltext/118542064/PDFSTART]
- RNA Quadruplex-Based Modulation of Gene Expression - Wieland et al., June 2007 [http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6VRP-4P8YWVM-7-8&_cdi=6240&_user=499885&_orig=search&_coverDate=07%2F30%2F2007&_sk=999859992&view=c&wchp=dGLbVzz-zSkzS&md5=97741390ae4ff0d9a8c4d5f41beb0f1d&ie=/sdarticle.pdf]
- A mRNA-based thermosensor controls expression of rhizobial heat shock genes - Nocker et al., October 2001 [http://nar.oxfordjournals.org/cgi/reprint/29/23/4800]
- Molecular Processes in Biological Thermosensation - Digel et al., April 2008 [http://hindawi.com/Getpdf.aspx?doi=10.1155/2008/602870]
Bioinformatics
Papers on bioinformatic approaches used to search for potential RNA thermometers.
- Genome-wide bioinformatic prediction and experimental evaluation of potential RNA thermometers - Torsten Waldminghaus · Lena C. Gaubig · Franz Narberhaus - Mol Genet Genomics (2007) 278:555–564
Modeling
Some papers that can be used for the modeling part.
- RNA synthetic biology - F.J. Isaacs et al., 2006 [http://knowledgecontext.org/COSMOS/RNA_synthetic_biology.pdf]
- Design of 5'-untranslated region variants for tunable expression in Escherichia coli - Park et al., February 2007 [http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6WBK-4N67NVV-5-C&_cdi=6713&_user=499885&_orig=search&_coverDate=04%2F27%2F2007&_sk=996439998&view=c&wchp=dGLbVlz-zSkWA&md5=571d5d21c20c71f0567f2ae53ee0e2ea&ie=/sdarticle.pdf]
- Engineered riboregulators enable post-transcriptional control of gene expression - G. Isaacs, D. Dqyer, C. Ding, D. Pervouchine, C. Cantor & J. Collins - Nature Biotechnology (2004) volume 7 number 22.
- Temperature-controlled Structural Alterations of an RNA Thermometer - Chowdhury et al., June 2003 [http://www.jbc.org/cgi/reprint/278/48/47915]
Color
- A general text on using micro-organisms for flavor production [http://www.springerlink.com/content/k8m037341x701594/fulltext.pdf]
- The references page on the edinburgh 2007 wiki, several references on color and flavor are present [http://parts.mit.edu/igem07/index.php/Edinburgh/Yoghurt/References]
- Two papers on Geosmin biosynthesis (an earthy odorant):
- Biosynthesis of the earthy odorant geosmin by a bifunctional Streptomyces coelicolor enzyme, Jiang et al.[http://www.nature.com/nchembio/journal/v3/n11/pdf/nchembio.2007.29.pdf]
- A Novel Type of Geosmin Biosynthesis in Myxobacteria, Dickschat et al. [http://pubs.acs.org/cgi-bin/article.cgi/joceah/2005/70/i13/pdf/jo050449g.pdf]
- Papers on plant volatile production:
- Biosynthesis of Plant Volatiles: Nature’s Diversity and Ingenuity, Pichersky et al. [http://www.sciencemag.org/cgi/reprint/311/5762/808.pdf]
- Biosynthesis of plant-derived flavor compounds, Schwab et al. [http://www3.interscience.wiley.com/cgi-bin/fulltext/120090045/PDFSTART]
- Rose Scent [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=151220]
- Stable-light producing E. coli [http://www.springerlink.com/index/P145100J28J0122H.pdf]
- Identification of genes for bacterial bioluminescence [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=345387&blobtype=pdf]
- Group in Leiden working with the Soil Bacterium Streptomyces [http://wwwchem.gorlaeus.net/micdev/micdev_pages/vanwezel.html]
