Haynes:LitReviewNov2015

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JOURNAL ASSIGNMENTS:

JOURNAL	WEBSITE	Assigned to…
ACS Synthetic Biology	http://pubs.acs.org/journal/asbcd6	Rene D.
Cell	http://www.cell.com	Ben N.
EMBO Molecular Systems Biology	http://msb.embopress.org	Brady D.
Frontiers in Bioengineering and Biotechnology	http://journal.frontiersin.org/journal/bioengineering-and-biotechnology	David B.
Journal of Biological Engineering	http://www.jbioleng.org	Ben N.
Journal of Cell Biology	http://jcb.rupress.org	David T.
Molecular Biology of the Cell	http://www.molbiolcell.org	David B.
Molecular and Cellular Biology	http://mcb.asm.org	Rene D.
Nature	http://www.nature.com/nature/index.html	Ted K.
Nature Biotechnology	http://www.nature.com/nbt/index.html	Stefan T.
Nature Methods	http://www.nature.com/nmeth/index.html	Jan S.
Public Library of Science Biology (PLoS Biology)	http://journals.plos.org/plosbiology/	Jiaqi W.
Proceedings of the National Academy of Sciences	http://www.pnas.org	Jan S.
Science	http://www.sciencemag.org/journals	Stefan T.
Miscellaneous Reviews and Media	N/A	Dr. Haynes

INSTRUCTIONS

• Search for lab-relevant articles dated May 2015 up to today. You can use PubMed or go directly to the journal's website.
• Be prepared to give a 3-minute summary of why the article should be read by the group.

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

# (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 THEN copy the template that is shown below. Do not use keyboard line returns to space out the numbered list, or else each item will start with the number 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.

FALL 2015, 11/16/2015

ACS Synthetic Biology

1. (2015) BASIC: A New Biopart Assembly Standard for Idempotent Cloning Provides Accurate, Single-Tier DNA Assembly for Synthetic Biology. Storch M, Casini A, and Fleming T et al. ACS Synth Biol. 4(7):781-7. http://pubs.acs.org.ezproxy1.lib.asu.edu/doi/abs/10.1021/sb500356d. Summary: The authors propose a type IIs restriction enzyme based cloning standard, BASIC (Biopart Assembly Standard for Idempotent Cloning), that utilizes orthogonal linkers to build multi-gene constructs. A unique element of this strategy is the use of the linkers as small parts such as RBS sequences or fusion protein linkers.
2. (2015) CRISPathBrick: Modular Combinatorial Assembly of Type II-A CRISPR Arrays for dCas9-Mediate Multiplex Transcriptional Repression in E. coli. Brady F. Cress, O. Duhan Toparlak, and Mattheos A. G. Koffas et al. ACS Synth Biol. 4(9):987-1000. http://pubs.acs.org.ezproxy1.lib.asu.edu/doi/10.1021/acssynbio.5b00012.Summary: This paper describes a vector system with rapid modular assembly that allows for the use of type II-A CRISPR arrays to simultaneously repress multiple gene loci in E. coli. Repression in the system is based on dCas9 binding.

Cell

1. (2015) A CRISPR View of Cleavage. Weinberger AD, Gilmore MS. Cell. 161(5):964-6. Link.
   Summary: Very short explanation of why this paper is relevant/ interesting.

EMBO Molecular Systems Biology

1. tba

Frontiers in Microbiotechnology

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Journal of Biological Engineering

1. (2015) Artificial cell-cell communication as an emerging tool in synthetic biology applications. Stefan Hennig,corresponding author Gerhard Rödel, and Kai Ostermann. J Biol Eng. 9:13. Link.
   Summary: Review paper on cell signaling of interest to synthetic biologists, including quorum sensing, fungal pheromones, and communication systems in mammalian systems. Emphasis is on multiple cell subtypes within a networked population to reduce crosstalk and metabolic load of cell-cell communication system.
2. (2015) No training required: experimental tests support homology-based DNA assembly as a best practice in synthetic biology. Afnan Azizi, Wilson Lam, and Hilary Phenix, et al. J Biol Eng. 9:8. Link.
   Summary: A bit of insider baseball, but the paper argues that the registry for standard biological parts and iGEM should include homology-based assembly methods in addition to the standard 3 antibiotic (3A) assembly method, due to the ease of setting up homology-based assembly.

Journal of Cell Biology

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Molecular Biology of the Cell

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Molecular and Cellular Biology

1. (2015) The Lineage-Specific Transcription Factor PU.1 Prevents Polycomb Mediated Heterochromatin Formation at Macrophage-Specific Genes. Mohita Tagore, Michael J. McAndrew, Alison Gjidoda et al. Molecular and Cellular Biology. 35.22:3841-3853. Link.
   Summary: This paper argues that the pioneer transcription factor PU.1 is able to displace nucleosomes at its binding sites and prevent further nucleosome formation and PRC2 mediated silencing. They use a quantitative nucleosome occupancy assay to map nucleosomes to ~60bp resolution. This type of transcription factor could be useful for the openchrom project and the nucleosome assay could be used for many projects in the lab.
   
   
2. (2015) Pluripotency and Epigenetic Factors in Mouse Embryonic Stem Cell Fate Regulation. Lluis Morey, Alexandra Santanach, and Luciano Di Croce. Molecular and Cellular Biology. 35.16:2716-2728. Link.
   Summary: Review on the roles of PRC1 and 2 complexes in mouse stem cell maintenance and differentiation. Discussion of non-canonical PRC1 (ncPRC1) and some mechanisms for mcPRC1 recruitment of PRC2. .
   
   

Nature

1. (2015) Targeting Polycomb systems to regulate gene expression: modifications to a complex story. Neil Blackledge, Nathan Rose, Robert Kloseet et al. Nature. 16: 643-649 Link.
   Summary: A group from University of Oxford, UK have an alternative model for the Polyomb Repressive Complex, where initially complexes in PRC1 apart from chromobox (CBX) bind to chromatin, which then promotes the binding of PRC2. This initial process of binding is then independent from PRC2 and H3K27me3.
   
   
2. (2015) Epigenetic regulation of ageing: linking environmental inputs to genomic stability. Elizabeth Pollina, Berenice Benayoun, Anne Brunet et al. Nature, 16:593-610. Link.
   Summary: A group from Stanford University finds that changes in H3K27me3 are correlated to longevity. Although in in different cells, up-regulation or down-regulation was needed to achieve longevity.

Nature Biotechnology

1. (2015) Hilton, I. B., D’Ippolito, A. M., Vockley, C. M., Thakore, P. I., Crawford, G. E., Reddy, T. E., & Gersbach, C. A. (2015). Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Nature Biotechnology, 33(5), 510–517. Link.
   Summary: ADD SUMMARY HERE.

Nature Methods

1. tba

Nature Molecular Systems Biology

1. tba

Public Library of Science Biology (PLoS Biology)

1. tba

Proceedings of the National Academy of Sciences

1. tba

Science

1. (2015) Jiao, L., & Liu, X. (2015). Structural basis of histone H3K27 trimethylation by an active polycomb repressive complex 2. Science, 350(6258), aac4383-1 – aac4383-8. Link.
   Summary: ADD SUMMARY HERE.
   
   

1. (2015) Audergon, P. N. C. B., Catania, S., Kagansky, A., Tong, P., Shukla, M., Pidoux, A. L., & Allshire, R. C. (2015). Epigenetics. Restricted epigenetic inheritance of H3K9 methylation. Science (New York, NY), 348(6230), 132–135. . Link.
   Summary: ADD SUMMARY HERE
   
   

1. (2015) Ragunathan, K., Jih, G., & Moazed, D. (2015). Epigenetic inheritance uncoupled from sequence-specific recruitment. Science, 348(6230),1258699-1 - 1258699-8 . Link.
   Summary: ADD SUMMARY HERE
   
   

Miscellaneous Reviews and Media

Reviews

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News

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iGEM 2015

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