Haynes:LitReviewMay2016

<- Back to Publications

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	Ben N.
Journal of Biological Engineering	http://www.jbioleng.org	Ben N.
Journal of Cell Biology	http://jcb.rupress.org	Daniel V.
Molecular Biology of the Cell	http://www.molbiolcell.org	Rene D.
Molecular and Cellular Biology	http://mcb.asm.org	Rene D.
Nature	http://www.nature.com/nature/index.html	Cassandra B.
Nature Biotechnology	http://www.nature.com/nbt/index.html	Stefan T.
Nature Methods	http://www.nature.com/nmeth/index.html	Daniel V.
Public Library of Science Biology (PLoS Biology)	http://journals.plos.org/plosbiology/	Rene D.
Proceedings of the National Academy of Sciences	http://www.pnas.org	Stefan T.
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

No relevant articles found in the past 5 months.

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: Authors tried to reduce cross-talk for quorum sensing bacteria by manipulating the promoter region.

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: Researchers attempted to look at a higher order of chromatin compaction in cells that were differentiating. They used a Hi-C to look at the three-dimensional structure of the chromatin, this was to see if there are domains within domains and the changes that occur during differentiation. They noticed that these topologically associated domains (TAD) will associate with other TADs creating a metaTAD which they described as "tree-like hierarchy." These metaTAD features are correlated with genetic, epigenomic and expression features that will rearrange during differentiation for differences in transcriptional states.

Frontiers in Bioengineering and Biotechnology

No relevant articles were found within the last 5 months.

Journal of Biological Engineering

No relevant articles found in the past 5 months.

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. (2016) Oakes et al. Profiling of engineering hotspots identifies an allosteric CRISPR-Cas9 switch Link
   Summary: SUMMARY GOES HERE.
   
2. (2016) Weiner et al. Co-ChIP enables genome-wide mapping of histone mark co-occurrence at single-molecule resolution Link.
   Summary: SUMMARY GOES HERE
3. (2016) Morita et al. Targeted DNA demethylation in vivo using dCas9–peptide repeat and scFv–TET1 catalytic domain fusions Link.
   Summary: SUMMARY GOES HERE

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: The authors use four different epigenetic silencing modifications to look at how chromosome regulator recruitment alters gene expression on the single cell level. EED (H3K27me3), KRAB(H3K9me3), DNMT3B(CpG methylation), and HDAC4 (H3 H4 deacetylation) were tested, and all silenced in an all or none fashion. Although the all or none silencing was similar in the cells, the timing of silencing was highly varied, and the rate of silencing was dependent on the regulator used. KRAB and HDAC4 quickly silenced cells within a single cell cycle, while EED and DNMT3B silenced at a slower rate, with only 50% of the cells silenced by 35 hrs and 62 hrs. This indicates that the silencing is a stochastic process. To test epigenetic memory, the CR activator was washed out after 5 days of recruitment. EED, KRAB, and HDAC4 reactivated in an all-or-none fashion, mimicking the silencing. The DNMT3B did not reactivate up to 80 hours after washing. Overall, HDAC4 achieved short term memory, losing all silencing within 5 days of CR removal. DNMT3B were stably silenced for over 30 days. EED and KRAB imparted a hybrid memory, with a fraction of cells reactivating in 2-3 weeks, while the rest were silent for at least a month.

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: Ants were tested for epigenetically controlled behavioral states. When treated with HDAC inhibitors, the ants exhibited increased foraging and scouting behavior. The increase was suppressed when treated with HAT inhibitors. Analysis of the chromatin in the brains showed changes in genes linked to H3K27!!!

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.
3. (2016) Polkade AV, Mantri SS, Patwekar UJ, Jangid K. Quorum Sensing: An Under-Explored Phenomenon in the Phylum Actinobacteria. Front Microbiol. 7:131. Link.
   Summary: Review mentions under-explored AHL quorum sensing homologues in Actinobacteria (typically gram-positive).
4. (2016) Haynes KA. Synthetic biology: Building genetic containment. Nat Chem Biol. 12:55-56. Link

News

1. 03.30.16 - Minimal Synthetic Bacterial Cell Engineered With Just 473 Genes. SynBioBeta. Link.
   Research article: (2016) Hutchison CA 3rd, Chuang RY, Noskov VN, Assad-Garcia N, Deerinck TJ, Ellisman MH, Gill J, Kannan K, Karas BJ, Ma L, Pelletier JF, Qi ZQ, Richter RA, Strychalski EA, Sun L, Suzuki Y, Tsvetanova B, Wise KS, Smith HO, Glass JI, Merryman C, Gibson DG, Venter JC. Design and synthesis of a minimal bacterial genome. Science. 351:aad6253.

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.