Team:TUDelft/Papers

Temperature

• • Thermometer design at the nanoscale - Lee et al., February 2007 [1]

• • RNA thermometers - Narberhaus et al., May 2005 [2]
  • 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 [3]
  • FourU: a novel type of RNA thermometer in Salmonella - Waldminghaus, 2007 [4]
  • RNA Quadruplex-Based Modulation of Gene Expression - Wieland et al., June 2007 [5]

• On database searching for thermo-sensitive RNA sequences
  • 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

• Well more on RNA-translation regulation, so I thought let's post it.
  • 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.

• A very recent review on RNA-translation regulation
  • 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

• Tuning the expression by altering the RNA sequence
  • Design of 5'-untranslated region variants for tunable expression in Escherichia coli - Park et al., February 2007 [6]

• Papers about ROSE
  • A mRNA-based thermosensor controls expression of rhizobial heat shock genes - Nocker et al., October 2001 [7]
  • Temperature-controlled Structural Alterations of an RNA Thermometer - Chowdhury et al., June 2003 [8]

• Some general papers
  • Molecular Processes in Biological Thermosensation - Digel et al., April 2008 [9]
  • RNA dynamics: it is about time - Al-Hashimi et al., April 2008 [10]
  • mRNA-mediated detection of environmental conditions - Narberhaus, August 2002 [11]

• Temperature perception in plants [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]

Modeling