Team:TUDelft/Papers

From 2008.igem.org

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==Temperature==
==Temperature==
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===RNA switches===
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====RNA switches====
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Some papers on RNA switches in general.
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<ul class="references">
<ul class="references">
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<li>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 </li>
 
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<li>mRNA-mediated detection of environmental conditions - Narberhaus, August 2002 [http://www.springerlink.com/content/dv19jt8aw0vdm0ff/fulltext.pdf]</li>
 
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</ul>
 
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A paper on RNA switch engineering
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<li>Marzi S, Fechter P, Chevalier C, Romby P, Geissmann T. RNA switches regulate initiation of translation in bacteria. ''Biological Chemistry'', 389(5):585-598, 2008. [http://www.ncbi.nlm.nih.gov/pubmed/18953726 PMID:18953726]</li>
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<ul class="references">
+
 
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<li>RNA synthetic biology - F.J. Isaacs et al., 2006 [http://knowledgecontext.org/COSMOS/RNA_synthetic_biology.pdf]</li>
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<li>Narberhaus F. mRNA-mediated detection of environmental conditions. ''Archives of Microbiology'', 178(6):404-410, 2002. [http://www.ncbi.nlm.nih.gov/pubmed/16680139 PMID:16680139]</li>
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</ul>
+
 
 +
<li>Isaacs FJ, Dwyer DJ, Collins JJ. RNA synthetic biology. ''Nature Biology'', 24(5):545-554, 2006. [http://www.ncbi.nlm.nih.gov/pubmed/16680139 PMID:16680139]</li>
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===RNA thermometers===
 
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<ul class="references">
 
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<li>RNA thermometers - Narberhaus et al., May 2005 [http://www3.interscience.wiley.com/cgi-bin/fulltext/118587582/PDFSTART]</li>
 
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<li>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 </li>
 
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<li>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]</li>
 
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<li>FourU: a novel type of RNA thermometer in Salmonella - Waldminghaus, 2007 [http://www3.interscience.wiley.com/cgi-bin/fulltext/118542064/PDFSTART]</li>
 
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<li>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]</li>
 
-
<li>Temperature-controlled Structural Alterations of an RNA Thermometer - Chowdhury et al., June 2003 [http://www.jbc.org/cgi/reprint/278/48/47915]</li>
 
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<li>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]</li>
 
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<li>Molecular Processes in Biological Thermosensation - Digel et al., April 2008 [http://hindawi.com/Getpdf.aspx?doi=10.1155/2008/602870]</li>
 
</ul>
</ul>
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===Bioinformatics===
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====RNA thermometers====
<ul class="references">
<ul class="references">
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<li>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</li>
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<li>F. Narberhaus, T. Waldminghaus & S. Chowdhury. RNA thermometers. ''FEMS Microbiol Rev'', 30(1):3-16, 2006. [http://www.ncbi.nlm.nih.gov/pubmed/16438677 PMID:16438677]</li>
 +
<li>Saheli Chowdhury, Christophe Maris, Frédéric H-T Allain, and Franz Narberhaus. Molecular basis for temperature sensing by an RNA thermometer. ''The EMBO Journal'', 25:2487–2497, 2006. [http://www.ncbi.nlm.nih.gov/pubmed/16710302 PMID:16710302] </li>
 +
<li>J . Johansson, P . Mandin, A . Renzoni, C . Chiaruttini, M . Springer, and P . Cossart. An RNA thermosensor controls expression of virulance genes in Listeria monocytogenes. ''Cell'' , 110(5):551-561, 2002. [http://www.ncbi.nlm.nih.gov/pubmed/12230973 PMID:12230973]</li>
 +
<li>Torsten Waldminghaus, Nadja Heidrich, Sabine Brantl, and Franz Narberhaus. FourU: a novel type of RNA thermometer in Salmonella. ''Molecular Microbiology'', 65(2):413-424, 2007. [http://www.ncbi.nlm.nih.gov/pubmed/17630972 PMID:17630972]</li>
 +
<li>M. Wieland and J.S. Hartig. RNA Quadruplex-Based Modulation of Gene Expression.  ''Chemistry & Biology'', 14(7):757–763, 2007. [http://www.ncbi.nlm.nih.gov/pubmed/17656312 PMID:17656312]</li>
 +
<li>Saheli Chowdhury, Curdin Ragaz, Emma Kreuger, and Franz Narberhaus. Temperature-controlled Structural Alterations of an RNA Thermometer. ''The Journal of Biological Chemistry'', 278(48):47915-47921, 2003. [http://www.ncbi.nlm.nih.gov/pubmed/12963744 PMID:12963744]</li>
 +
<li>Nocker A, Hausherr T, Balsiger S, Krstulovic NP, Hennecke H, Narberhaus F. A mRNA-based thermosensor controls expression of rhizobial heat shock genes. 29(23):4800-4807, 2001 [http://www.ncbi.nlm.nih.gov/pubmed/11726689 PMID:11726689]</li>
</ul>
</ul>
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<ul class="references">
<ul class="references">
<li>A general text on using micro-organisms for flavor production [http://www.springerlink.com/content/k8m037341x701594/fulltext.pdf]</li>
<li>A general text on using micro-organisms for flavor production [http://www.springerlink.com/content/k8m037341x701594/fulltext.pdf]</li>
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<li>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]</li>
+
<li>The references page on the edinburgh 2007 wiki, several references on color and flavor are present [https://2007.igem.org/Edinburgh/Yoghurt/References]</li>
</ul>
</ul>

Latest revision as of 15:18, 29 October 2008

Contents

References

Thermometer

  • J. Lee & N.A. Kotov. Thermometer design at the nanoscale. Nano Today, 2(1):48-51, 2007. [http://dx.doi.org/10.1016/S1748-0132(07)70019-1 doi:10.1016/S1748-0132(07)70019-1]

Temperature

RNA switches

  • Marzi S, Fechter P, Chevalier C, Romby P, Geissmann T. RNA switches regulate initiation of translation in bacteria. Biological Chemistry, 389(5):585-598, 2008. [http://www.ncbi.nlm.nih.gov/pubmed/18953726 PMID:18953726]
  • Narberhaus F. mRNA-mediated detection of environmental conditions. Archives of Microbiology, 178(6):404-410, 2002. [http://www.ncbi.nlm.nih.gov/pubmed/16680139 PMID:16680139]
  • Isaacs FJ, Dwyer DJ, Collins JJ. RNA synthetic biology. Nature Biology, 24(5):545-554, 2006. [http://www.ncbi.nlm.nih.gov/pubmed/16680139 PMID:16680139]

RNA thermometers

  • F. Narberhaus, T. Waldminghaus & S. Chowdhury. RNA thermometers. FEMS Microbiol Rev, 30(1):3-16, 2006. [http://www.ncbi.nlm.nih.gov/pubmed/16438677 PMID:16438677]
  • Saheli Chowdhury, Christophe Maris, Frédéric H-T Allain, and Franz Narberhaus. Molecular basis for temperature sensing by an RNA thermometer. The EMBO Journal, 25:2487–2497, 2006. [http://www.ncbi.nlm.nih.gov/pubmed/16710302 PMID:16710302]
  • J . Johansson, P . Mandin, A . Renzoni, C . Chiaruttini, M . Springer, and P . Cossart. An RNA thermosensor controls expression of virulance genes in Listeria monocytogenes. Cell , 110(5):551-561, 2002. [http://www.ncbi.nlm.nih.gov/pubmed/12230973 PMID:12230973]
  • Torsten Waldminghaus, Nadja Heidrich, Sabine Brantl, and Franz Narberhaus. FourU: a novel type of RNA thermometer in Salmonella. Molecular Microbiology, 65(2):413-424, 2007. [http://www.ncbi.nlm.nih.gov/pubmed/17630972 PMID:17630972]
  • M. Wieland and J.S. Hartig. RNA Quadruplex-Based Modulation of Gene Expression. Chemistry & Biology, 14(7):757–763, 2007. [http://www.ncbi.nlm.nih.gov/pubmed/17656312 PMID:17656312]
  • Saheli Chowdhury, Curdin Ragaz, Emma Kreuger, and Franz Narberhaus. Temperature-controlled Structural Alterations of an RNA Thermometer. The Journal of Biological Chemistry, 278(48):47915-47921, 2003. [http://www.ncbi.nlm.nih.gov/pubmed/12963744 PMID:12963744]
  • Nocker A, Hausherr T, Balsiger S, Krstulovic NP, Hennecke H, Narberhaus F. A mRNA-based thermosensor controls expression of rhizobial heat shock genes. 29(23):4800-4807, 2001 [http://www.ncbi.nlm.nih.gov/pubmed/11726689 PMID:11726689]

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 [1]

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]
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