Haynes:LitReviewOct2012: Difference between revisions
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==Journal of Biological Engineering== | ==Journal of Biological Engineering== | ||
# | # (2012) '''Engineered cell-cell communication via DNA messaging'''. Monica Ortiz, Drew Endy at Stanford (No permanent link yet). Summary: Used bacteriophage M13 gene products to send DNA messages that encoded different messages to F+ bacteria. Could be useful if you could control when the message is sent, like in the presence of some compound.<br><br> | ||
#(2012) '''A genetic bistable switch utilizing nonlinear protein degradation'''. Daniel Huang, William Holtz, Michel Maharbiz from Department of Electrical Engineering and Computer Science at Berkeley [http://www.jbioleng.org/content/6/1/9 Link]. Summary: Made a bistable switch where the bistability depends on protein degradation. Used Lon protease which will not interfere with endogenous E. coli that targets a specific degradation tag that will not be targeted by endogenous E. coli proteases (no cross talk). Argue that using protein degradation to flip a switch is better than heat shock and UV because it won't damage the rest of the cell.<br><br> | |||
# (2012) '''A synthetic biology approach to self-regulatory recombinant protein production in Escherichia coli'''. Martin Dragosits, Daniel Nicklas, Ilias Tagkopoulos from UC Davis Genome Center, University of California, Davis [http://www.jbioleng.org/content/6/1/2 Link]<br><br> | |||
# (2012) '''DeviceEditor visual biological CAD canvas'''. Joanna Chen, Douglas Densmore, Timothy S Ham, Jay D Keasling, Nathan J Hillson from Joint BioEnergy Institute, Emeryville, CA [http://www.jbioleng.org/content/6/1/1 Link]<br><br> | |||
# (2012) '''The Constructor: a web application optimizing cloning strategies based on modules from the registry of standard biological parts'''. Matthijn C Hesselman, Jasper J Koehorst, Thijs Slijkhuis, Floor Hugenholtz, Dorett I Odoni, Mark WJ van Passel from Wageningen University, The Netherlands. Based on an iGEM project. (No permanent link yet)<br><br> | |||
==Journal of Cell Biology== | ==Journal of Cell Biology== | ||
Line 30: | Line 33: | ||
==Molecular Biology of the Cell== | ==Molecular Biology of the Cell== | ||
# | # | ||
==Molecular and Cellular Biology== | ==Molecular and Cellular Biology== | ||
# (2012) Activating Transcription Factor 3 Regulates Immune and Metabolic Homeostasis. Jan Rynesa | # (2012) Activating Transcription Factor 3 Regulates Immune and Metabolic Homeostasis. Jan Rynesa, Colin D. Donohoea, Peter Frommoltc, Susanne Brodesserd, Marek Jindrae and Mirka Uhlirovaa. MCB Molecular and Cellular Biology 2012 32.19:3949-3962. Link. Summary: Group studying the loss of Atf3 within Drosophila and how it affects the metabolic, immunity, and other related systems. | ||
#(2012) Origins and Formation of Histone Methylation across the Human Cell Cycle. Barry M. Zeea, Laura-Mae P. Brittona, Daniel Wollea, Devorah M. Habermanb and Benjamin A. Garciaa. MCB Molecular and Cellular Biology 2012 32.21: 2503-2514. Link. Summary: The connections between various nuclear processes and specific histone posttranslational modifications are dependent to a large extent on the acquisition of those modifications after histone synthesis. | |||
==Nature== | ==Nature== | ||
# | # (2012) '''A map of nucleosome positions in yeast at base-pair resolution.''' Kristin Brogaard, Liqun Xi, Ji-Ping Wang, and Jonathan Widom. Nature 2012 0:1-6. [http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11142.html Link]. Summary: A more accurate method developed for mapping nucleosome centers based on chemically modifying engineered histones. | ||
# (2012) '''Chromatin organization is a major influence on regional mutation rates in human cancer cells.''' Benjamine Schuster-Bockler and Ben Lehner. Nature 2012 488: 504-507. [http://www.nature.com/nature/journal/vaop/ncurrent/full/nature11273.html Link]. Summary: There is a strong relationship between chromatin organization and mutation rates. The amount of somatic mutations correlates to histone modification levels and anti-correlates with open chromatin's genomic features. | |||
==Nature Biotechnology== | ==Nature Biotechnology== | ||
Line 49: | Line 52: | ||
==Nature Molecular Systems Biology== | ==Nature Molecular Systems Biology== | ||
# | # (2012) '''Asymmetric positive feedback loops reliably control biological responses.''' Alexander V Ratushny, Ramsey A Saleem, Katherine Sitko, Stephen A Ramsey & John D Aitchison. Nature Molecular Systems Biology 2012 8:577. [http://www.ncbi.nlm.nih.gov/pubmed?term=Asymmetric%20positive%20feedback%20loops%20reliably%20control%20biological%20responses Link]. Summary: They studied both experimentally and using computational modeling, the behavior of systems controlled by the ASSURE I or II motif and systems in which both regulatory molecules in the pair are self-upregulated. | ||
# (2012) '''A regulatory role for repeated decoy transcription factor binding sites in target gene expression.''' Lee TH, Maheshri N. Nature Molecular Systems Biology 2012 8:576. [http://www.ncbi.nlm.nih.gov/pubmed?term=A%20regulatory%20role%20for%20repeated%20decoy%20transcription%20factor%20binding%20sites%20in%20target%20gene%20expression Link]. Summary: They used the synthetic tet–OFF system in budding yeast to study how repeated arrays of tetO decoy sites influenced expression of tTA-inducible tetO promoters. | |||
==Public Library of Science Biology (PLoS Biology)== | ==Public Library of Science Biology (PLoS Biology)== | ||
# | #(2012) Systematic Dissection of Roles for Chromatin Regulators in a Yeast Stress Response. Assaf Weiner, Hsiuyi Chen, Chih Long Liu, and Ayelet Rahat et al. PLOS Biology 2012 10.7: [http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001369 Link] Summary: Gene expression is tested in 200 chromatin mutants during a yeast stress response. Studies indicate that gene expression is greatly affected compared to steady-state transcription. | ||
==Proceedings of the National Academy of Sciences (PNAS)== | ==Proceedings of the National Academy of Sciences (PNAS)== | ||
Line 69: | Line 71: | ||
==Miscellaneous Reviews and Media== | ==Miscellaneous Reviews and Media== | ||
# | # (10/04/12) '''Colbert Report: George Church'''. The Colbert Report. Summary: Molecular geneticist George Church shares his book, "Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves." [http://www.colbertnation.com/the-colbert-report-videos/419824/october-04-2012/george-church Video]<br><br> | ||
# (10/11/12) '''Nobel Prize in medicine awarded to Sir John Gurdon and Shinya Yamanaka''' CNN Wire Staff. Summary: 2012 Nobel prize in medicine was awarded to work on induced pluripotent stem cells, research that began in 1962 with Xenopus (frog) developmental biology experiments. [http://www.cnn.com/2012/10/08/world/europe/sweden-nobel-prize-medicine/index.html Link]<br><br> | |||
# (10/11/12) '''Americans win Nobel Prize in chemistry for revealing gateway to cells''' Ben Brumfeld, CNN. Summary: 2012 Nobel prize in chemistry was awarded for the characterization of GPCRs. [http://www.cnn.com/2012/10/10/world/sweden-nobel-prize-chemisty/index.html Link] |
Latest revision as of 18:19, 15 November 2012
Fall 2012, 10/8/12
ACS Synthetic Biology
Example:
- (2011) Engineering a Photoactivated Caspase-7 for Rapid Induction of Apoptosis. Evan Mills, Xi Chen, Elizabeth Pham, Stanley Wong, and Kevin Truong et al. ACS Synthetic Biology 2012 1.3:75-82. Link. Summary: Group from University of Toronto developed protein that causes rapid cell apotosis (cell death) of targeted cells.
Cell
- None
Frontiers in Microbiotechnology
- None
Journal of Biological Engineering
- (2012) Engineered cell-cell communication via DNA messaging. Monica Ortiz, Drew Endy at Stanford (No permanent link yet). Summary: Used bacteriophage M13 gene products to send DNA messages that encoded different messages to F+ bacteria. Could be useful if you could control when the message is sent, like in the presence of some compound.
- (2012) A genetic bistable switch utilizing nonlinear protein degradation. Daniel Huang, William Holtz, Michel Maharbiz from Department of Electrical Engineering and Computer Science at Berkeley Link. Summary: Made a bistable switch where the bistability depends on protein degradation. Used Lon protease which will not interfere with endogenous E. coli that targets a specific degradation tag that will not be targeted by endogenous E. coli proteases (no cross talk). Argue that using protein degradation to flip a switch is better than heat shock and UV because it won't damage the rest of the cell.
- (2012) A synthetic biology approach to self-regulatory recombinant protein production in Escherichia coli. Martin Dragosits, Daniel Nicklas, Ilias Tagkopoulos from UC Davis Genome Center, University of California, Davis Link
- (2012) DeviceEditor visual biological CAD canvas. Joanna Chen, Douglas Densmore, Timothy S Ham, Jay D Keasling, Nathan J Hillson from Joint BioEnergy Institute, Emeryville, CA Link
- (2012) The Constructor: a web application optimizing cloning strategies based on modules from the registry of standard biological parts. Matthijn C Hesselman, Jasper J Koehorst, Thijs Slijkhuis, Floor Hugenholtz, Dorett I Odoni, Mark WJ van Passel from Wageningen University, The Netherlands. Based on an iGEM project. (No permanent link yet)
Journal of Cell Biology
- None
Molecular Biology of the Cell
Molecular and Cellular Biology
- (2012) Activating Transcription Factor 3 Regulates Immune and Metabolic Homeostasis. Jan Rynesa, Colin D. Donohoea, Peter Frommoltc, Susanne Brodesserd, Marek Jindrae and Mirka Uhlirovaa. MCB Molecular and Cellular Biology 2012 32.19:3949-3962. Link. Summary: Group studying the loss of Atf3 within Drosophila and how it affects the metabolic, immunity, and other related systems.
- (2012) Origins and Formation of Histone Methylation across the Human Cell Cycle. Barry M. Zeea, Laura-Mae P. Brittona, Daniel Wollea, Devorah M. Habermanb and Benjamin A. Garciaa. MCB Molecular and Cellular Biology 2012 32.21: 2503-2514. Link. Summary: The connections between various nuclear processes and specific histone posttranslational modifications are dependent to a large extent on the acquisition of those modifications after histone synthesis.
Nature
- (2012) A map of nucleosome positions in yeast at base-pair resolution. Kristin Brogaard, Liqun Xi, Ji-Ping Wang, and Jonathan Widom. Nature 2012 0:1-6. Link. Summary: A more accurate method developed for mapping nucleosome centers based on chemically modifying engineered histones.
- (2012) Chromatin organization is a major influence on regional mutation rates in human cancer cells. Benjamine Schuster-Bockler and Ben Lehner. Nature 2012 488: 504-507. Link. Summary: There is a strong relationship between chromatin organization and mutation rates. The amount of somatic mutations correlates to histone modification levels and anti-correlates with open chromatin's genomic features.
Nature Biotechnology
- None
Nature Molecular Systems Biology
- (2012) Asymmetric positive feedback loops reliably control biological responses. Alexander V Ratushny, Ramsey A Saleem, Katherine Sitko, Stephen A Ramsey & John D Aitchison. Nature Molecular Systems Biology 2012 8:577. Link. Summary: They studied both experimentally and using computational modeling, the behavior of systems controlled by the ASSURE I or II motif and systems in which both regulatory molecules in the pair are self-upregulated.
- (2012) A regulatory role for repeated decoy transcription factor binding sites in target gene expression. Lee TH, Maheshri N. Nature Molecular Systems Biology 2012 8:576. Link. Summary: They used the synthetic tet–OFF system in budding yeast to study how repeated arrays of tetO decoy sites influenced expression of tTA-inducible tetO promoters.
Public Library of Science Biology (PLoS Biology)
- (2012) Systematic Dissection of Roles for Chromatin Regulators in a Yeast Stress Response. Assaf Weiner, Hsiuyi Chen, Chih Long Liu, and Ayelet Rahat et al. PLOS Biology 2012 10.7: Link Summary: Gene expression is tested in 200 chromatin mutants during a yeast stress response. Studies indicate that gene expression is greatly affected compared to steady-state transcription.
Proceedings of the National Academy of Sciences (PNAS)
- None
Science
- None
Miscellaneous Reviews and Media
- (10/04/12) Colbert Report: George Church. The Colbert Report. Summary: Molecular geneticist George Church shares his book, "Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves." Video
- (10/11/12) Nobel Prize in medicine awarded to Sir John Gurdon and Shinya Yamanaka CNN Wire Staff. Summary: 2012 Nobel prize in medicine was awarded to work on induced pluripotent stem cells, research that began in 1962 with Xenopus (frog) developmental biology experiments. Link
- (10/11/12) Americans win Nobel Prize in chemistry for revealing gateway to cells Ben Brumfeld, CNN. Summary: 2012 Nobel prize in chemistry was awarded for the characterization of GPCRs. Link