Team:TUDelft/Papers

From 2008.igem.org

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=References=
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===Temperature===
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==Thermometer==
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*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
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** On database searching for thermo-sensitive RNA sequences
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*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
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<ul class="references">
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** The NMR structure of a well known heat shock protein
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<li> 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]</li>
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</ul>
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*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.
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==Temperature==
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** Well more on RNA-translation regulation, so I thought let's post it.
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* 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 switches====
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** A very recent review on RNA-translation regulation
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<ul class="references">
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===Color===
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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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</div>
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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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<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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</ul>
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====RNA thermometers====
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<ul class="references">
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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>
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<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>
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<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>
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<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>
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<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>
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<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>
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</ul>
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==Color==
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<ul class="references">
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<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 [https://2007.igem.org/Edinburgh/Yoghurt/References]</li>
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</ul>
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Two papers on Geosmin biosynthesis (an earthy odorant):
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<ul class="references">
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<li>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]</li>
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<li>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]</li>
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</ul>
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Papers on plant volatile production:
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<ul class="references">
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<li>Biosynthesis of Plant Volatiles: Nature’s Diversity and Ingenuity, Pichersky et al. [http://www.sciencemag.org/cgi/reprint/311/5762/808.pdf]</li>
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<li>Biosynthesis of plant-derived flavor compounds, Schwab et al. [http://www3.interscience.wiley.com/cgi-bin/fulltext/120090045/PDFSTART]</li>
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<li>Rose Scent [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=151220]</li>
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<li>Stable-light producing E. coli [http://www.springerlink.com/index/P145100J28J0122H.pdf]</li>
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<li>Identification of genes for bacterial bioluminescence [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=345387&blobtype=pdf]</li>
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<li>Group in Leiden working with the Soil Bacterium Streptomyces [http://wwwchem.gorlaeus.net/micdev/micdev_pages/vanwezel.html]</li>
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</ul>
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{{Template:TUDelftiGEM2008_sidebar}}

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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