Team:TUDelft/Papers

Temperature

• 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

• The NMR structure of a well known heat shock protein
  • 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

• 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

• A paper about RNA thermometers
  • RNA thermometers - Narberhaus et al., May 2005 [http://www3.interscience.wiley.com/cgi-bin/fulltext/118587582/PDFSTART]

• 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 [http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6WBK-4N67NVV-5-C&_cdi=6713&_user=499885&_orig=search&_coverDate=04%2F27%2F2007&_sk=996439998&view=c&wchp=dGLbVlz-zSkWA&md5=571d5d21c20c71f0567f2ae53ee0e2ea&ie=/sdarticle.pdf]

• Papers about ROSE
  • 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]
  • Temperature-controlled Structural Alterations of an RNA Thermometer - Chowdhury et al., June 2003 [http://www.jbc.org/cgi/reprint/278/48/47915]

• Some general papers
  • Molecular Processes in Biological Thermosensation - Digel et al., April 2008 [http://hindawi.com/Getpdf.aspx?doi=10.1155/2008/602870]
  • Thermometer design at the nanoscale - Lee et al., February 2007 [http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B82X8-4N13BB2-N-1&_cdi=33024&_user=499885&_orig=search&_coverDate=02%2F28%2F2007&_sk=999979998&view=c&wchp=dGLbVlz-zSkzS&md5=02d4712f0e1ba955f322b80941b09106&ie=/sdarticle.pdf]
  • RNA dynamics: it is about time - Al-Hashimi et al., April 2008 [http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6VS6-4SPV149-1-9&_cdi=6254&_user=499885&_orig=search&_coverDate=06%2F30%2F2008&_sk=999819996&view=c&wchp=dGLbVzb-zSkWA&md5=0fba1ad96c9780db45aa96dd764933d7&ie=/sdarticle.pdf]
  • mRNA-mediated detection of environmental conditions - Narberhaus, August 2002 [http://www.springerlink.com/content/dv19jt8aw0vdm0ff/fulltext.pdf]

• Working thermosensor
  • 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]

• Temperature perception in plants [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VS4-4GR8NCH-5&_user=499885&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000024500&_version=1&_urlVersion=0&_userid=499885&md5=bf9f1315fa5e719feb6fb433cc31c8b5]

• RNA thermometer in salmonella
  • FourU: a novel type of RNA thermometer in Salmonella - Waldminghaus, 2007 [http://www3.interscience.wiley.com/cgi-bin/fulltext/118542064/PDFSTART]

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 [http://parts.mit.edu/igem07/index.php/Edinburgh/Yoghurt/References]

• 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]

Modeling

• Some papers on modeling regulation by small RNA
  • Quantitative characteristics of gene regulation by small RNA. Levine et al., September 2007 [http://biology.plosjournals.org/archive/1545-7885/5/9/pdf/10.1371_journal.pbio.0050229-L.pdf]
  • Regulation of gene expression by small non-coding RNAs: a quantitative view. Shimoni et al., August 2007 [http://www.nature.com/msb/journal/v3/n1/pdf/msb4100181.pdf]
  • Computational modeling of post-transcriptional gene regulation by microRNAs, Khanin et al., 2008 [http://www.liebertonline.com/doi/pdfplus/10.1089/cmb.2007.0184]
  • Bifurcations in the interplay of messenger RNA, protein and nonprotein coding RNA, Zhdanov, M [http://www.iop.org/EJ/article/1751-8121/41/28/285101/a8_28_285101.pdf?request-id=fda8e7bc-1319-441e-832d-0132cc42e83f]