Difference between revisions of "Haynes:LitReviewMay2014"

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(Nature Biotechnology)
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==Nature Biotechnology==
==Nature Biotechnology==
#(2013) '''Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions'''. Joshua N Burton, Andrew Adey, Rupali P Patwardhan, et al. Nature Biotechnology. advance online publication: 1-7. [http://www.nature.com/nbt/journal/vaop/ncurrent/pdf/nbt.2727.pdf Link] <br> '''Group from University of Washington developed improved method of generating contiguous sequencing results by aligning chromosome conformation capture with shotgun sequencing results.'''
# Item
==Nature Methods==
==Nature Methods==

Revision as of 12:07, 25 April 2014

<- Back to Publications


  • ACS Synthetic Biology - Rene
  • Cell - Brendan
  • Frontiers in Microbiotechnology – David
  • Journal of Biological Engineering - Behzad
  • Journal of Cell Biology - Behzad
  • Molecular Biology of the Cell - David
  • Molecular and Cellular Biology - Rene
  • Nature - Brendan
  • Nature Biotechnology - Ryan
  • Nature Methods - Dr. Haynes
  • Nature Molecular Systems Biology - Ryan
  • Public Library of Science Biology (PLoS Biology) - Cameron
  • Proceedings of the National Academy of Sciences - (orphaned)
  • Science - Cameron
  • Miscellaneous Reviews and Media - Dr. Haynes

INSTRUCTIONS: Please search for lab-relevant articles dated November 11, 2013 up to today.

Fall 2013, 11/11/13

Use the following text format EXACTLY as it is shown below...

  1. (year) Title. Author One, Author Two, and Author Three et al. Journal. Volume:pages. Link.
    Summary: Very short explanation of why this paper is relevant/ interesting.

  2. (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, 1.3:75-82. Link.
    Summary: A group from University of Toronto developed a protein that causes rapid apotosis (cell death) of targeted cells.

Open edit mode and copy the example list above. Do not erase the <br><br> tags. Do not use keyboard line returns to space out the numbered list, or else each item will start with the number 1.

ACS Synthetic Biology

  1. Item


  1. Item

Frontiers in Microbiotechnology

  1. Item

Journal of Biological Engineering

  1. Item

Journal of Cell Biology

  1. Item

Molecular Biology of the Cell

  1. Item

Molecular and Cellular Biology

  1. Item


  1. Item

Nature Biotechnology

  1. Item

Nature Methods

  1. (2013) A superfolding Spinach2 reveals the dynamic nature of trinucleotide repeat-containing RNA Strack RL, Disney MD, Jaffrey SR. Nature Methods. [Epub ahead of print]. Link.
    Summary: The Jaffrey group was the first to develop and test an RNA that folds into a structure that produces green fluorescence ("Spinach"). In this paper, they report a more stable version, Spinach2, with shows a brighter signal. They used the tag to study the dynamics of "toxic RNA" that is associated with FragileX syndrome.

  2. (2013) Cas9 as a versatile tool for engineering biology Mali P, Esvelt KM, Church GM. Nature Methods. 10:957-63. Link.
    Summary: This article is a perspective piece on the Cas9-guide-RNA methodology.

  3. (2013) ExpressionBlast: mining large, unstructured expression databases Zinman GE, Naiman S, Kanfi Y, Cohen H, Bar-Joseph Z. 10:925-6. Link.
    Summary: This article is a correspondence piece that describes a convenient tool for finding out how your gene of interest is expressed. The data are extracted from the NCBI Gene Expression Omnibus (which is usually very difficult to navigate).

Nature Molecular Systems Biology

  1. (2013) Design of orthogonal genetic switches based on a crosstalk map of sigma s, anti-sigma s, and promoters. Virgil A Rhodius, Thomas H Segall-Shapiro, Brian D Sharon, et al. Nature Molecular Systems Biology. 9.702:1-13 Link
    A group from the University of California, San Francisco tested 86 extracytoplasmic function sigma factors and 62 anti sigma factors and identified a subset of 20 sigma factors and promoters highly orthogonal to each other.
  2. (2013) Temporal control of self-organized pattern formation without morphogen gradients in bacteria. Stephen Payne, Bochong Li, Yangxiaolu Cao, et al. Nature Molecular Systems Biology. 9.697:1-10 Link
    The majority of biological pattern formation requires morphogens as a spatial cue. A group at Duke University programmed E.coli to instead create a self-organized ring pattern, using the morphogen as a timing cue.

Public Library of Science Biology (PLoS Biology)

  1. (2013) Chromatin-Specific Regulation of Mammalian rDNA Transcription by Clustered TTF-I Binding Sites. Sarah D. Diermeier, Attila Németh, Michael Rehli,Ingrid Grummt, Gernot Längst. PLoS Genetics 9:9: 1-12. Link

Determined that clustered binding sites increase the binding affinity of transcription factors in chromatin.

Proceedings of the National Academy of Sciences

  1. (2013) Single-molecule analysis of combinatorial epigenomic states in normal and tumor cells. Patrick Murphy et. al. Proceedings of the National Academy of Sciences. 110: 19: 7772-7777. Link


  1. (2013) Inhibition of PRC2 Activity by a Gain-of-Function H3 Mutation Found in Pediatric Glioblastoma. Peter W. Lewis, Manuel M. Müller, Matthew S. Koletsky, et. al.. Science 340:857-61. Link
    Summary: Found that Lys27Met mutations in histone tails inhibit PRC2 activity in a specific child cancer. Somewhat novel application of therapies being explored in our lab.

Miscellaneous Reviews and Media

2013 iGEM World Championship - Projects of Interest

  1. (2013) COLISWEEPER: The world's first bacterial minesweeper game. ETH Zurich iGEM Team. iGEM World Championship. Link.
    Summary: Biological version of the Minesweeper game. Bacterial spot-cultures (spaced on a grid on agar) represented either mines or number clues (via expression of some combination of colorimetric enzymes). Quorum sensing (Lux) was used to enable the number clue spots to create a certain color depending upon their positioning near one, two, or more mines. Their data included a nice demonstration of AHL-concentration-dependent gene induction.

  2. (2013) E. teamwork: Engineering a synthetic microbial consortium. Braunschweig iGEM Team. iGEM World Championship. Link.
    Summary: Quroum sensing (Las and Rhl) was used to cross-induce ampicillin resistance in cells so that the survival of each relied on eachother. Cell types were "tagged" with pigment expression (blue and pink) in order to quantify the proportion of each in co-culture. The team reported a third strain (labeled yellow) but I only saw data for a two-strain blue/ pink co-culture on their poster.

  3. (2013) Exosome mediated mammalian cell-cell communication. MIT iGEM Team. iGEM World Championship. Link.
    Summary: The Acyl-TyA peptide tag was used to incorporate proteins into mammalian exosomes, which are vesicles that carry "cargo" from one mammalian cell to another. There is data that suggests that cell membrane localization worked, but no data for actual protein delivery (just tests to see if the tag disrupted protein function).

  4. (2013) The uniCAS toolkit for gene regulation. Freiburg iGEM Team. iGEM World Championship. Link.
    Summary: The team used the Cas9 protein/ guide-RNA system to target various transcriptional regulators to genes in mammalian cells. One very cool, straight-forward application was a split transcription activator: Cas9+CRY2 binds DNA, and CIB1+VP16 is required to activate transcription. Blue light stimulates CRY2-CIB1 interaction; as a result, VP16 recruitment to a gene is controlled by light. Note: the Cas9+Vp16 has been published recently.


  1. November 6, 2013. BBSRC Invests $16M in Synthetic Biology Startup Fund. GenomeWeb Staff Reporter. GenomeWeb Daily News. Link.
    Summary: Biotechnology and Biological Science Research Council (BBRC) said today that it has provided £10 million ($16.1 million USD) to launch an investment fund that will fund early-stage companies in the United Kingdom that are focused on commercializing synthetic biology technologies

  2. October 24, 2013. SRC launches synthetic biology research effort at six universities. Semiconductor Research Corp. R&D Magazine. Link.
    Summary: Semiconductor Research Corporation (SRC) launched the Semiconductor Synthetic Biology (SSB) research program on hybrid bio-semiconductor systems. The program will initially fund research at six universities: Massachusetts Institute of Technology, the Univ. of Massachusetts at Amherst, Yale, Georgia Tech, Brigham Young, and the Univ. of Washington.