Team:TUDelft/Papers
From 2008.igem.org
(Difference between revisions)
Bavandenberg (Talk | contribs) (→Temperature) |
Bavandenberg (Talk | contribs) (→RNA switches) |
||
Line 17: | Line 17: | ||
* 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 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 | ||
* mRNA-mediated detection of environmental conditions - Narberhaus, August 2002 [http://www.springerlink.com/content/dv19jt8aw0vdm0ff/fulltext.pdf] | * mRNA-mediated detection of environmental conditions - Narberhaus, August 2002 [http://www.springerlink.com/content/dv19jt8aw0vdm0ff/fulltext.pdf] | ||
+ | |||
+ | A paper on RNA switch engineering | ||
+ | |||
* 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] | ||
Revision as of 08:46, 3 August 2008
Contents |
Thermometer
- Thermometer design at the nanoscale - Lee et al., February 2007 [1]
Temperature
RNA switches
Some papers on RNA switches in general.
- RNA dynamics: it is about time - Al-Hashimi et al., April 2008 [2]
- 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
- mRNA-mediated detection of environmental conditions - Narberhaus, August 2002 [3]
A paper on RNA switch engineering
- RNA synthetic biology - F.J. Isaacs et al., 2006 [4]
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 [5]
- 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 [6]
- FourU: a novel type of RNA thermometer in Salmonella - Waldminghaus, 2007 [7]
- RNA Quadruplex-Based Modulation of Gene Expression - Wieland et al., June 2007 [8]
- A mRNA-based thermosensor controls expression of rhizobial heat shock genes - Nocker et al., October 2001 [9]
- Molecular Processes in Biological Thermosensation - Digel et al., April 2008 [10]
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.
- Design of 5'-untranslated region variants for tunable expression in Escherichia coli - Park et al., February 2007 [11]
- 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 [12]
Color
- A general text on using micro-organisms for flavor production [13]
- The references page on the edinburgh 2007 wiki, several references on color and flavor are present [14]
- Two papers on Geosmin biosynthesis (an earthy odorant):
- Papers on plant volatile production:
- Rose Scent [19]
- Stable-light producing E. coli [20]
- Identification of genes for bacterial bioluminescence [21]
- Group in Leiden working with the Soil Bacterium Streptomyces [22]