Haynes:LitReviewApr2013

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Spring 2013, 04/09/13

Use the following text format...

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 2012 1.3:75-82. Link. Summary: Group from University of Toronto developed protein that causes rapid cell apotosis (cell death) of targeted cells.
   
   

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ACS Synthetic Biology

1. (2012) Stable Maintenance of Multiple Plasmids in E. coli Using a Single Selective Marker. Calvin Schmidt, David Shis, Truong Nguyen-Huu et.al. ACS Synthetic Biology. 1:445-450. link Method for selecting for up to three plasmids using a single antibiotic. One has T7 polymerase, one has protein A for kan resistance, third has protein B for kan resistance, both under control of T7 promoters
2. (2013) Promoter Element Arising from the Fusion of Standard BioBrick Parts. Andrew Yao, Timothy Fenton, Keegan Owsley, et. al. ACS Synthetic Biology. 2:111-120. link Found that adding short parts like tags and barcodes can lead to unexpected activity. In their example, they found that a barcode added to a particular part gave the part a new promoter.
3. (2013) Engineered Quorum Sensing Using Pheromone-Mediated Cell-to-Cell Communication in Saccharomyces cerevisiae. Thomas Williams, Lars Nielsen, Claudia Vickers. ACS Synthetic Biology. 2:136-149. link Interesting because they engineered quorum sensing in yeast but used peptide signaling, not AHL. They added a positive feedback loop by having the peptide signal controlled by a promoter that's repressed by a repressor that is deactivated by MAP kinase, which is activated by the peptide signal. Interesting that the circuits are fairly complicated (high stress levels) but seem to work. could be because peptides are less energetically taxing than a full protein that acts on a substrate.

Cell

1. 2013 Chromatin Remodeling at DNA Double-Strand Breaks. Brendan Price, Alan D'Andrea, et al. Cell 152: 1344-1354.link. Summary: DNA double-stranded breaks can occur from natural mutations, the dysfunction of the replication for, and ionizing radiation. With the use of chromatin and nucleosome packing to potentially fix these breaks.

1. 2013 Chromatin Movement in the Maintenance of Genome Stability. Vincent Dion, Susan Gasser, et al. Cell 152: 1355-1364. link. Summary: This article describes the use of mathematical modeling to understand and predict the random or non-random movement of chromatin.

Frontiers in Microbiotechnology

1. (2012) Engineering microbial consortia to enhance biomining and bioremediation. Karl D. Brune, and Travis D. Bayer. Frontiers in Microbiotechnology. 3:203. Link Summary: This review looks into the use of microbial consortia - different species of microbes - in in bioremediation techniques. The argument presented is that consortia are more able to survive in extreme environments, an important feature when launching a bioremediation strategy in mine waste or acid pools. Mentions Hg.

1. (2013) Quantifying heavy metals sequestrtion by sulfate-reducing bacteria in an acid mine drainage-contaminated natural world. John W. Moreau, John H. Fournelle, and Jillian F. Banfield. Frontiers in Microbiotechnology. 4:43. Link Summary: This article may be a little off topic for research and development of microbes for bioremediation. It does however address some of the issues regarding toxins in acid ponds and slough. Not a good article for methods, but helps create a foundation. Useful paragraph regarding Hg in the fourth to last paragraph in the discussion section.

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) 2ab assembly: a methodology for automatable, high-throughput assembly of standard biological partsMariana Leguia, Jennifer AN Brophy,Douglas Densmore, et al. 7:1754-1611.[1]. They integrate a new software tool chain with 2ab assembly and show that it is robust enough to generate 528 distinct composite parts. They assembly strategy is based on two antibiotic resistance genes. 2ab assembly is a single iterative process, based on the BglBricks standard. The resulting composite part contains unique BglII and BamHI sites flanking the 5′ and 3′ ends, respectively.

Journal of Cell Biology

1. (2013) Global analysis of SUMO chain function reveals multiple roles in chromatin regulation. Tharan Srikumar, Megan C. Lewicki, and Michael Costanzo et al. Journal of Cell Biology. 201:145-163. Link Summary: The paper demonstrates that the small ubiquitin-related modifier (SUMO) protein chains are required for the maintenance of normal higher-order chromatin structure and transcriptional repression of environmental stress response genes in budding yeast.
   
   
2. (2012) The chromatin remodeler p400 ATPase facilitates Rad51-mediated repair of DNA double-strand breaks. Céline Courilleau, Catherine Chailleux, and Alain Jauneau et al. Journal of Cell Biology. 199:1067-1081. Link Summary: The paper demonstrates that p400 ATPase is required for double stranded DNA breaks (DSBs) repair by homologous recombination because the enzyme recruits Rad51 (a key component of homologous recombination) to the DNA break site, supports homology-directed repair, and helps survival after DNA damage. According to the data attained, p400 and Rad51 are present in the same complex and both favor chromatin remodeling around DSBs, reflecting a direct molecular link between the two.

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.

1. 2012 Myosin Vs organize actin cables in fission yeast, Libera Lo Presti, Fred Chang, and Sophie G. Martin et al. Molecular Biology of the Cell. Link 23: 4579-91. Summary: Actin filaments serve as tracks for myosin motors. Evidence suggests that myosin contribute to the organization of these actin filaments. Using a synthetic biology approach, they separated the two distinct elements of cargo transport. First, They created a kinesin-myosin chimera, which delivers myosin cargoes across microtubule networks. Second, they linked the nucleus to the myosin motor traveling along actin cables partly restores cable organization. It was determined that the tethering the motor domain of Myo52 to the nucleus increases retrograde flow and cable extension. The in vivo data reveals that there is evidence of a self-organizing system in which myosin motor proteins shape their own tracks.

1. 2011 Coiled-coil networking shapes cell molecular machinery Yongqiang Wanga, Xinlei Zhanga, Hong Zhang et al. Molecular Biology of the Cell. 23: 3911-22 Link Summary: An understanding of the coiled-coil interactions would help reveal the potential for exploration of its function and use in therapeutics. In Saccharomyces cerevisiae (yeast), it is revealed that CCI is functionally involved in cell machinery organization. CCI also plays an important role in the formation of kinetochore, which means that disruption of CCI leads to a defect in the kinetochore assembly. The study characterizes the CCI as a valuable component for shaping and regulation.

Molecular and Cellular Biology

1. (2012) Geminin Regulates the Transcriptional and Epigenetic Status of Neuronal Fate-Promoting Genes during Mammalian Neurogenesis. Dhananjay Yellajoshyula, Jong-won Lim, Dominic M. Thompson, Jr. et al. Molecular and Cellular Biology. 32:4549-4560. link Nucleoprotein Geminin plays a role in maintaining the bivalent state of genes involved in differentiation. Gem keeps PcG around and keeps up H3K27me3. Important (not sure if necessary) to keep embryonic stem cells to undergo terminal differentiation. Gem is not sufficient to prevent differentiation. Interesting for future applications in engineering stem cells. Studies done in Xenopus and the mammalian P19 cells (mouse teratocarcinoma cell line)
2. (2013) Scmh1 has E3 ubiquitin ligase activity for geminin and histone H2A and regulates geminin stability directly or indirectly via transcriptional repression of Hoxa9 and Hoxb4. Shin’ichiro Yasunaga, Motoaki Ohtsubo, Yoshinori Ohno et al. Molecular and Cellular Biology. 33:644-660. link Schm1 is a part of PcG complex 1 that interacts with geminin. Made a mouse Schm2 knockout. Without Scmh1, PcG complex 1 was not sufficient to repress Hoxa9 and Hoxb4 in hematopoietic cells. Conclude that PcG and some Hox genes regulate geminin. Interesting for future applications in engineering stem cells.

Nature

1. (2012) Genetic programs constructed from layered logic gates in single cells Tae Seok Moon, Chunbo Lou, Alvin Tamsir, et al. Nature 491, 249–253 Link Summary: Building more challenging and bigger genetic circuits is a constant challenge for synthetic biology. Moon et al. developed a system of logical AND gates based on two input promoters regulating one output promoter. The regulatory effect is based on transcription of an activator and its needed chaperone protein. The resulting AND gates are small in metabolic load and exhibit a rather stable behavior. They developed their regulators by directed evolution based on existing parts, therefore increasing their part library should be feasible while maintaining stability and orthogonality.
2. (2012) DAXX envelops a histone H3.3–H4 dimer for H3.3-specific recognition Simon J. Elsässer, Hongda Huang, Peter W. Lewis, et al. Nature 491, 560–565 Link Summary: The authors examined DAXX a histone chaperone involved in processing of the histone variant H3.3 prior to assembly into chromatin. For the first time the complete 3D structure of DAXX is reported including 3D structures of DAXX binding to its substrate. Further structure analysis are reported on DAXX mutations and functional binding analyses are performed in vitro and in vivo. For all these assays 3D structures are reported.
3. (2012) Principles for designing ideal protein structures Nobuyasu Koga, Rie Tatsumi-Koga, Gaohua Liu, et al. Nature 491, 222–227 Link Summary: Until now synthetic biology is restricted to reproducing existing or modified proteins. Though it might be of future interest to design a protein de novo. Koga et al. determined from existing protein data rules that govern the formation of tertiary motifs based on secondary structures. With the help of these rules and their data mining they could compute energy landscapes of proteins. They then designed tertiary protein foldings from scratch and simulated the needed secondary structure and amino acid sequence. In vitro produced amino acid sequences did fold into the predicted tertiary structures.
4. (2012) Synthesis: A constructive debate Jay D. Keasling, Abraham Mendoza and Phil S. Baran. Nature 492, 188–189 Link Summary: This is not a scientific article but a debate! The authors are debating on the possibility of synthetic biology to overcome synthetic chemistry as the main supplier of synthetic molecules. Keasling advocates synthetic biology by showing recent success to produce important drugs in synthetic organism cost effective and reliable from simple compounds like sugar. Though he also address issues synthetic biology has to resolve like enzyme design from scratch and more reliable pathways with high output. Mendoza and Baran therefore claim synthetic chemistry will continue to dominate production of synthetic molecules. Especially due to it's better ability to scale up, it's faster design of new compounds and it's better understood mechanism.

Nature Biotechnology

1. (2013) A ligation-independent cloning technique for high-throughput assembly of transcription activator-like effector genes. Jonathan Schmid-Burgk, Tobias Schmidt, Vera Kaiser, Klara Honing, and Veit Hornung. Nature Biotechnology 2013 31.1:76-81. Link. Summary: Transcription-activator-like (TAL) effector proteins are secreted by Xanthomonas bacteria and can enter the nucleus of an infected host plant cell, bind to the DNA, and regulate expression of the host genes. The most widely used assembly method for TAL effector proteins is Golden Gate cloning but this requires much hands on time and quality control. Ligation independent cloning (LIC) relies on 10-30 bp nonpalindromic single strand overhangs. E. coli can be transformed by annealing the reaction without prior ligation because long overhangs do not dissociate during transformation and can be ligated by bacterial ligases.

1. (2013) Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in rheumatoid arthritis. Yun Lieu, Martin Aryee, Leonid Padyukov, et. al. Nature Biotechnology 2013 31.2:142-147. Link. Summary: There has not been robust association of epigenetic modifications to common diseases. A comprehensive genome-wide analysis was performed using arrays and protein antibody-associated rheumatoid arthritis cases to find two clulsters in the major histocompatibility complex region with different methylation that potentially mediate genetic risk. Leukocytes are involved in the disease and are readily available for DNA methylation analysis, so the disease state can be determined by the presence of antibodies to protein antigens.

Nature Methods

1. (2013) Quantitative estimation of activity and quality for collections of functional genetic elements. Mutalik, V. K., Guimaraes, J. C., Cambray, G., Mai, Q.-A., Christoffersen, M. J., Martin, L., et al (incl. Drew Endy, Adam Arkin, & Jay Keasling). Nature Methods. 10:347-353. Link.
   SUMMARY: Group from the BIOFAB, JBEI, UC Berkeley, Stanford, and the Fred Hutchinson Institute (Seattle) measure the contextual behavior of promoters and propose to use this as a metric/ score for "part quality." Some results show that the downstream ORF influences promoter-RBS activity (Fig. 2).
   
   
2. (2013) Precise and reliable gene expression via standard transcription and translation initiation elements. Mutalik, V. K., Guimaraes, J. C., Cambray, G., Lam, C., Christoffersen, M. J., Mai, Q.-A., et al. Nature Methods. E-pub ahead of print.
   SUMMARY: Same group as above developed a set of gene transcription/ translation parts to mitigate context-dependent behavior. Creating a standard 5'UTR upstream of the start codon seems to help (Fig. 2). They even designed some elements to aid consistent two-peptide expression from a single mRNA (bicistronic).

Nature Molecular Systems Biology

1. (2013) A fluorescent reporter for mapping cellular protein-protein interactions in time and space Daniel Moreno, Joachim Neller, Hans A Kestler, et al. Molecular Systems Biology. 9.647:1-13. Link. Summary: A group from Ulm University in Germany was able to construct a fluorescent reporter to monitor protein-protein interactions in vivo by utilizing the ratio of two auto-fluorescent proteins.

Public Library of Science Biology (PLoS Biology)

1. (2012) Epigenetic Editing: Targeted Rewriting of Epigenetic Marks to Modulate Expression of Selected Targeted Genes. de Groote, ML, Verschure PJ ,Rote, MG. Nucleic Acids Research, 40:10596-10613. Link This paper talks about the use of the DNA binding domain to deliberately cause changes to histone tails and affect regulation of gene expression. This article can help with a solid development of a introduction or background or broadening a literature search.
   
   

Proceedings of the National Academy of Sciences (PNAS)

1. TBA

Science

1. (2013) Epigenetic reprogramming in cancer. Suvà ML, Riggi N, Bernstein BE.. Science. 339:1567-1571. Link. Summary: In this review they highlight important interrelationships among transcription factors, chromatin regulators, and preexisting epigenetic states. TFs recruit chromatin regulators (CRs) that modulate the accessibility of target DNA and impart specific chromatin states characterized by signature histone modifications and common functional roles. They also discuss the accessibility of the chromatin in Stem cells and Differential cells. A differentiated cell can be directly reprogrammed into an induced pluripotent stem (iPS) cell by a defined set of TFs.
   
   

1. (2013) Bacterial Quorum Sensing and Metabolic Incentives to Cooperate Ajai A. Dandekar, Sudha Chugani,E. Peter Greenberg2 [2]

Miscellaneous Reviews and Media

1. (Oct 7 2012) MIT team builds most complex synthetic biology circuit yet A. Trafton. MIT News. http://web.mit.edu/newsoffice/2012/complex-biological-circuit-1007.html
   SUMMARY: Article about the Nature paper from Voigt's group (referenced in this round of lit. review).
   
   
2. (Feb 28 2013) Why Synthetic Biology Is the Field of the Future. J. Keasling. PBS Nova Next. http://www.pbs.org/wgbh/nova/next/tech/why-synthetic-biology-is-the-field-of-the-future/
   SUMMARY: Tech+Engineering blog by Jay Keasling, explaining why his field is the field of the future. Includes a nice video, narrated by Neil DeGrasse Tyson, about Jay, the "tough Nebraska farm boy."
   
   
3. (Apr 9 2013) Ziopharm Goes Lean to Stretch Funds for New Synthetic Biology Focus B. Tansey. Xconomy. http://www.xconomy.com/new-york/2013/04/09/ziopharm-goes-lean-to-stretch-funds-for-new-synthetic-biology-focus/
   SUMMARY: Biotech company uses a synthetic switch that is designed to express IL-12 to treat cancer. Nice. interesting story of a synthetic device going to market. Note: IL-12 expression has made appearances in iGEM at least twice.
   
   
4. (Apr 12 2013) Will Synthetic Biology Benefit or Threaten Wild Things? A. Revkin. New York Times. http://dotearth.blogs.nytimes.com/2013/04/12/will-synthetic-biology-benefit-or-threaten-wild-things/
   SUMMARY: Article summarizing a recent meeting/ debate, between synthetic biologists and conservationists, held at Cambridge University (U.K.).
   
   
5. (Apr 16 2013) Synthetic biologists and conservationists open talks. E. Callaway. Nature News. http://www.nature.com/news/synthetic-biologists-and-conservationists-open-talks-1.12807
   SUMMARY: Another article summarizing a recent meeting/ debate, between synthetic biologists and conservationists, held at Cambridge University (U.K.). Drew Endy and Jay Keasling weigh in.