Haynes:LitReviewNov2013

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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. (2013) Generic Metric to Quantify Quorum Sensing Activation Dynamics. Anand Pai, Jaydeep Srimani, Yu Tanouchi, et. al. ACS Synthetic Biology. ePub ahead of print. Link.
   Summary: Attempt to represent temporal and dose-dependent quorum sensing behavior with a single metric. Only use Lux system, perturb system to represent diversity.
   
   
2. (2013) Quorum sensing-modulated AND-gate promoters control gene expression in response to a combination of endogenous and exogenous signals. Jasmine Shong, Cynthia H. Collins. ACS Synthetic Biology. ePub ahead of print. Link.
   Summary: Device that is activated with IPTG or Tet and AHL. Use Esa system in combination with well-studied Lac or Tet promoter system.
   
   
3. (2013) A fluorogenic TMP-tag for high signal-to-background intracellular live cell imaging. Jing C, Cornish VW. ACS Synthetic Biology. 8:1704−1712. Link.
   Summary: Possible replacement for luciferase.
   
   
4. (2013) The Spinach RNA Aptamer as a Characterization Tool for Synthetic Biology. Georgios Pothoulakis,†,‡ Francesca Ceroni,†,‡ Benjamin Reeve, et. al.. ACS Synthetic Biology. ePub ahead of print. Link.
   Summary: Learn more about spinach as a reporter.
   
   

Cell

1. (2013) Transcription Recovery after DNA Damage Requires Chromatin Priming by the H3.3 Histone Chaperone HIRA. Salome Adams, Sophie Polo, and Genevieve Almouzni. Cell. 155:963. Link.
   Summary: A group from Institut Curie Research Centre in France studied the chromatin actions in restoring transcription function after UV damage to DNA. The chaperon protein HIRA moderates placement of new H3.3 histones to replace damage histones in the affected chromatin through ubiquitylation events.

Frontiers in Microbiotechnology

1. (2013) Ex vivo DNA assembly. Adam B. Fisher, Zachary B. Canfield, Laura C. Hayward, Stephen S. Fong and George H. McArthur IV. Frontiers in Microbiotechnology. 1:12. Link Summary: This article summarizes attempts to assemble DNA using cell lysates for E. coli to join double-stranded DNA. Generally good paper for creating efficient methods for dsDNA end joining ex vivo. Comparative to Gibson Assemblies, ex vivo assemblies of linear or circular constructs should take a few hours. Most tested times were under a few hours.

1. (2013) Metabolic analyses elucidate non-trivial gene targets for amplifying dihydroartemisinic acid production in yeast. Ashish Misra, Matthew F. Conway, Joseph Johnnie, Tabish M. Qureshi, Bao Lige, Anne M. Derrick, Eddy C. Agbo and Ganesh Sriram. Frontiers in Microbiotechnology. 4:200. Link. This article uses application of metabolic pathway analysis of yeast to find most efficient ways to produce DHA. Using engineering of certain genetic sequences can allow for better and more efficient synthesis of DHA in yeast. The authors point that similar mechanisms can be used to improve yields of certain products in cells. Analyses include FBA and Carbon 13 flux analysis.

Journal of Biological Engineering

1. (2013) Hidden hysteresis – population dynamics can obscure gene network dynamics. Phillip Poisson and Kaustubh D Bhalerao Journal of Biological Engineering . 7:16. Link.
   Summary: They use a bistable gene network in E-coli to show that the cells concentration will affect the hysteresis and change the steady state level of gene expression. Higher cell concentration show higher hysteresis due to positive feedback loop effects. This research shows that cell concentration should be considered in designing the synthetic gene circuit for long term application.
   
   
2. (2013) A survey of enabling technologies in synthetic biology. Linda J Kahl and Drew Endy Journal of Biological Engineering . 7:13. Link.
   Summary: This is a survey that they did between synthetic biology researchers to find out their opinions and experiences with available technologies such as public and private registries of biological parts, standard methods for physical assembly of DNA constructs, genomic databases that they've used to move forward they researches. This survey try to show the real potential of these technologies and their actual impacts on synthetic biology researches.
   
   
3. (2013) A standard vector for the chromosomal integration and characterization of BioBrick™ parts in Escherichia coli . Susanna Zucca12, Lorenzo Pasotti and et al. Journal of Biological Engineering . 7:12. Link.
   Summary: In this research they designed an integrative vector which has the BioBricks standard restriction sites and be able to integrate the designed part to the target site in E-coli genome with bacteriophage integration mechanism or homologous recombination.
   
   

Journal of Cell Biology

1. (2013) Whole-genome screening identifies proteins localized to distinct nuclear bodies. Ka-wing Fong, Yujing Li, Wenqi Wang et al. Journal of Cell Biology. 203 (1): 149. Link.
   Summary: Fong et al. performed a genome-wide microscopy-based screening for proteins that form nuclear foci and characterized their localizations using markers of known nuclear bodies. In total, they identified 325 proteins localized to distinct nuclear bodies, including Polycomb Repressive Complex(PRC1 & PRC2)
   
   

1. (2013) The histone demethylase LSD1/KDM1A promotes the DNA damage response. Nima Mosammaparast1, Haeyoung Kim, Benoit Laurent et al. Journal of Cell Biology. 203 (3): 457. Link.
   Summary: They report a role for the histone demethylase LSD1/KDM1A in the DNA damage response (DDR). They show that LSD1 is recruited directly to sites of DNA damage.
   
   

Molecular Biology of the Cell

1. # 2013 A short carboxyl-terminal tail is required for single-stranded DNA binding, higher-order structural organization, and stability of the mitochondrial single-stranded annealing protein Mgm101. MacMillan Mbantenkhu*, Sara Wierzbicki, Xiaowen Wang, Shangdong Guo, Stephan Wilkens, and Xin Jie Chen. Molecular Biology of the Cell. Link 24: 1507-1518. Summary: This article goes over the carboxyl-terminal tail on the annealing protein Mgm101. Mgm101 is a single-stranded annealing protein (SSAP) that is required for mitochondrial DNA repair. The c-tail is required for the binding of the protein to DNA, stability of the protein and structural organization. The studies on the c-tail could have better implications for how SSAPs help with DNA repair and maintenance.

Molecular and Cellular Biology

1. (2013) Expression of Polycomb Targets Predicts Breast Cancer Prognosis. Alba Jene-Sanz, Renáta Váraljai, Alexandra V. Vilkova, et. al.. Molecular and Cellular Biology. 33:3951-3961. Link.
   Mix of analysis of human tissue samples, publicly available ChIP-seq and microarray data, and cell culture experiments to understand how EZH2 expression, a protein subunit of PRC2, can modify cancer cell behavior and predict patient outcomes. They conclude high expression of EZH2 predicts aggressive phenotype, high expression of PRC2 predicts better patient outcome, low expression of PRC2 predicts metastasis..
   
   
2. (2013) Variable requirements for DNA-binding proteins at polycomb-dependent repressive regions in human HOX clusters. Woo CJ, Kharchenko PV, Daheron L, et. al. Molecular and Cellular Biology. 33:3274-3285. Link.
   Found new target sites from HOXB and HOXC that recruit PcG by using a reporter construct. Experiments done in mesenchymal stem cells. Discovered two DNA-binding proteins, JARID2 and YY1, possibly regulate PcG.
   
   

Nature

1. (2013) Effect of natural genetic variation on enhancer selection and function. S. Heinz, C. Benner, and E. Romanoski et al. Nature. Epub ahead of print. Link.
   Summary: The study found Inter-individual genetic variation was highly defined by the functioning of lineage determining transcription factors signal-specific binding to enhancer-like regions of the genome. This helps define epigentic and transcriptomic states and prioritizing regulator variants.
   
   

Nature Biotechnology

1. (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. Link
   Group from University of Washington developed improved method of generating contiguous sequencing results by aligning chromosome conformation capture with shotgun sequencing results.

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

Science

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.
   
   

News

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.