Haynes:LitReviewMay2016

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JOURNAL ASSIGNMENTS:

JOURNAL	WEBSITE	Assigned to…
ACS Synthetic Biology	http://pubs.acs.org/journal/asbcd6	Cassandra B.
Cell	http://www.cell.com	Ben N.
EMBO Molecular Systems Biology	http://msb.embopress.org	Daniel V.
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	Dr. Haynes
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 November 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.

SPRING 2016, 05/16/2015

ACS Synthetic Biology

1. (2016) FlowCal: A user-friendly, open source software tool for automatically converting flow cytometry data from arbitrary to calibrated units. Sebastian Martin Castillo-Hair, John Thomas Sexton, Brian Landry, Evan James Olson, Oleg A Igoshin, and Jeffrey J. Tabor et al. ACS Synthetic Biology. NA. Link. Summary: The authors present an open-source software to convert arbitrary units into calibrated unit molecules of equivalent fluorophore (MEF) for flow cytometry data. Using either an Excel interface or Python script, the software additionally performs basic statistical analyses, automatically gates data, and produces plots. The software has been validated and optimized across several cell types, days, and machines.

Cell

1. tba

EMBO Molecular Systems Biology

1. (2016) Orthogonal intercellular signaling for programmed spatial behavior. Paul K Grant, Neil Dalchau, James R Brown, Fernan Federici, Timothy J Rudge, Boyan Yordanov, Om Patange, Andrew Phillips, Jim Haseloff. Molecular Systems Biology. Link. Summary:

1. (2015) Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation. James Fraser, Carmelo Ferrai, Andrea M Chiariello, Markus Schueler, Tiago Rito, Giovanni Laudanno, Mariano Barbieri, Benjamin L Moore, Dorothee CA Kraemer, Stuart Aitken, Sheila Q Xie, Kelly J Morris, Masayoshi Itoh, Hideya Kawaji, Ines Jaeger, Yoshihide Hayashizaki, Piero Carninci, Alistair RR Forrest, , Colin A Semple, Josée Dostie, Ana Pombo, Mario Nicodemi. Molecular Systems Biology. Link. Summary:

Frontiers in Microbiotechnology

1. tba

Journal of Biological Engineering

1. tba

Journal of Cell Biology

1. (2016) Mardaryev AN, Liu B, Rapisarda V, Poterlowicz K, Malashchuk I, Rudolf J, Sharov AA, Jahoda CA, Fessing MY, Benitah SA, Xu GL, Botchkarev VA. Cbx4 maintains the epithelial lineage identity and cell proliferation in the developing stratified epithelium. J Cell Biol. 212:77-89. Link.
   Summary: Cbx4 is a Polycomb protein, a homologue of Cbx8, which is the protein we used to design PcTF. This paper describes the role of Cbx4 in the repression of nonepidermal lineage and cell cycle inhibitor genes in epidermal, proliferating cells.
   

Molecular Biology of the Cell

1. tba

Molecular and Cellular Biology

1. (2016) The Overlooked Fact: Fundamental Need for Spike-In Control for Virtually All Genome-Wide Analyses. Kaifu Chen, Zheng Hu, Zheng Xia, Dongyu Zhao, Wei Li, and Jessica K. Tyler. Molecular and Cellular Biology, 36.5:662-667. Link
   Summary: Authors found they had drawn incorrect conclusions from genome-wide sequencing studies because they didn’t include a spike-in control. Suggest all researchers use spike-ins to avoid incorrectly normalizing away differences resulting in incorrect conclusions.

Nature

1. (2016) Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells. Maud de Dieuleveult, Kuangyu Yen, Isabelle Hmitou et al. Nature. 530:113–116. Link. Summary: This article explains how mammalian chromatin remodellers target specific nucleosomes at the edge nucleosome-free promoter regions to regulate transcription.

Nature Biotechnology

1. tba

Nature Methods

1. (2016) Genetic code expansion in stable cell lines enables encoded chromatin modification. Simon J Elsässer, Russell J Ernst, Olivia S Walker & Jason W Chin. Nature Methods. Volume 13 No. 2:158-170. Link.
   Summary: The researchers stably integrated a synthetic tRNA-synthetase into mouse ESCs and were able to insert unnatural amino acids into target proteins to study histone acetylation. Not too relevant to any work being done in the lab but I just found it a cool concept to consider.
   
   

1. (2016) Editing the epigenome: technologies for programmable transcription and epigenetic modulation. Pratiksha I Thakore, Joshua B Black, Isaac B Hilton & Charles A Gersbach. Nature Methods. Volume 13 No. 2:127-137. Link.
   Summary: A review paper that mostly talks about recent advances in CRISPR-Cas9 technology but also talks about zinc finger proteins and transcription activator-like effectors. Potentially interesting for anyone doing CRISPR work.
   
   

Nature Molecular Systems Biology

1. tba

Public Library of Science Biology (PLoS Biology)

1. (2016) ""Social Evolution Selects for Redundancy in Bacterial Quorum Sensing"". PLOS Biology. http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002386 ""Summary:"" Bacteria frequently use multiple quorum-sensing systems to control group behaviors. The benefits of utilizing multiple QS inducer—receptor pairs are unclear and mysterious, because these signals seem redundant. It appears that when in low abundance, a strain with additional QS networks can avoid cooperating with its ancestor strain (which does not have the extra QS networks), only to return to its cooperative state when it is abundant. This paper demonstrates that "increased complexity in QS signaling circuits can evolve without providing adaptive advantage in a clonal population". The QS/iGEM subgroup should definitely look into the paper's methods and data reporting because they seem relevant to our project.

Proceedings of the National Academy of Sciences

No relevant articles found in the past 5 months.

Science

1. (2016) Bintu, L. Dynamics of epigenetic regulation at the single-cell level. Science (80-. ). 351, (2016). Link.
   Summary: Put Summary Here

1. (2016) Simola, D. F. et al. Epigenetic (re)programming of caste-specific behavior in the ant Camponotus floridanus. Science (80-. ). 351, (2016). [Link goes here Link].
   Summary: Summary here

1. (Year) Journal info goes here . [Link goes here Link].
   Summary: Summary goes here

Miscellaneous Reviews and Media

Reviews

1. (2016) Bhattacharjee D, Shenoy S, Bairy KL. DNA Methylation and Chromatin Remodeling: The Blueprint of Cancer Epigenetics. Scientifica (Cairo). Epub 2016 Mar 28. Link
   Summary: Current review on epigenetic drugs used to treat cancer.
   
2. (2016) Mahmoud F, Shields B, Makhoul I, Hutchins LF, Shalin SC, Tackett AJ. Role of EZH2 histone methyltrasferase in melanoma progression and metastasis. Cancer Biol

Ther. Epub ahead of print. Link.
Summary: Review of EZH2 inhibitors to treant melanoma.

News

1. tba

Researcher Profiles

1. (2016) Sedwick C. Jim Kadonaga: Exploring transcription and chromatin. J Cell Biol. 212:608-9. Link Summary: Profile on Jim Kadonaga, a scientist who is well known for discovering many basic mechanisms of gene regulation and chromatin, including core promoters in eukaryotes. Currently located at UCSD.