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References

Thermometer

1. 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):
  • Biosynthesis of the earthy odorant geosmin by a bifunctional Streptomyces coelicolor enzyme, Jiang et al.[15]
  • A Novel Type of Geosmin Biosynthesis in Myxobacteria, Dickschat et al. [16]

• Papers on plant volatile production:
  • Biosynthesis of Plant Volatiles: Nature’s Diversity and Ingenuity, Pichersky et al. [17]
  • Biosynthesis of plant-derived flavor compounds, Schwab et al. [18]
• 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]