Haynes:LitReviewOct2012

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(Nature Molecular Systems Biology)
(Nature Molecular Systems Biology)
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# (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) '''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.
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# (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.
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# (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)==

Revision as of 20:14, 15 November 2012

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Contents

Fall 2012, 10/8/12

ACS Synthetic Biology

Example:

  1. (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

  1. None


Frontiers in Microbiotechnology

  1. None


Journal of Biological Engineering

  1. (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.

  2. (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.

  3. (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

  4. (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

  5. (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

  1. None


Molecular Biology of the Cell

  1. None


Molecular and Cellular Biology

  1. (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.
  2. (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

  1. (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.
  2. (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

  1. None


Nature Molecular Systems Biology

  1. (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.
  2. (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)

  1. (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)

  1. None


Science

  1. None


Miscellaneous Reviews and Media

  1. (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

  2. (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

  3. (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
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