Haynes:LitReviewNov2013: Difference between revisions
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==ACS Synthetic Biology== | ==ACS Synthetic Biology== | ||
# (2013) '''A fluorogenic TMP-tag for high signal-to-background intracellular live cell imaging.''' Jing C, Cornish VW. ACS Synthetic Biology. 8:1704−1712. [http://www-ncbi-nlm-nih-gov.ezproxy1.lib.asu.edu/pubmed/23745575 Link]. <br>'''Possible replacement for luciferase.'''<br><br> | #(2013) '''Generic Metric to Quantify Quorum Sensing Activation Dynamics.''' Anand Pai, Jaydeep Srimani, Yu Tanouchi, ''et. al''. ACS Synthetic Biology. ePub ahead of print. [http://www-ncbi-nlm-nih-gov.ezproxy1.lib.asu.edu/pubmed/?term=Generic+Metric+to+Quantify+Quorum+Sensing+Activation+Dynamics Link]. <br> '''Summary:''' Attempt to represent temporal and dose-dependent quorum sensing behavior with a single metric. Only use Lux system, perturb system to represent diversity. <br><br> | ||
#(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. [http://www-ncbi-nlm-nih-gov.ezproxy1.lib.asu.edu/pubmed/24175658 Link]. <br> '''Summary:''' Device that is activated with IPTG or Tet and AHL. Use Esa system in combination with well-studied Lac or Tet promoter system. <br><br> | |||
# (2013) '''A fluorogenic TMP-tag for high signal-to-background intracellular live cell imaging.''' Jing C, Cornish VW. ACS Synthetic Biology. 8:1704−1712. [http://www-ncbi-nlm-nih-gov.ezproxy1.lib.asu.edu/pubmed/23745575 Link]. <br>'''Summary:''' Possible replacement for luciferase.<br><br> | |||
# (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. [http://www.ncbi.nlm.nih.gov/pubmed/23991760 Link]. <br>'''Summary:''' Learn more about spinach as a reporter.<br><br> | |||
==Cell== | ==Cell== | ||
# | # (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. [http://www.sciencedirect.com.ezproxy1.lib.asu.edu/science/article/pii/S0092867413010234# Link]. <br>'''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. | ||
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==Frontiers in Microbiotechnology== | ==Frontiers in Microbiotechnology== | ||
# | # (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. [http://www.frontiersin.org/synthetic_biology/10.3389/fbioe.2013.00012/abstract 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. | ||
# (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. [http://www.frontiersin.org/Journal/10.3389/fmicb.2013.00200/abstract 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== | ==Journal of Biological Engineering== | ||
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==Molecular Biology of the Cell== | ==Molecular Biology of the Cell== | ||
# | # # 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. [http://www.molbiolcell.org/content/24/10/1507.full.pdf+html 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. | ||
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==Nature== | ==Nature== | ||
# | # (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. [http://www.nature.com.ezproxy1.lib.asu.edu/nature/journal/vaop/ncurrent/full/nature12615.html Link]. <br>'''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. <br><br> | ||
==Nature Biotechnology== | ==Nature Biotechnology== | ||
#( | #(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. [http://www.nature.com/nbt/journal/vaop/ncurrent/pdf/nbt.2727.pdf Link] <br> '''Group from University of Washington developed improved method of generating contiguous sequencing results by aligning chromosome conformation capture with shotgun sequencing results.''' | ||
==Nature Methods== | ==Nature Methods== | ||
# (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]. [http://www.nature.com.ezproxy1.lib.asu.edu/nmeth/journal/vaop/ncurrent/full/nmeth.2701.html Link]. <br>'''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.<br><br> | # (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]. [http://www.nature.com.ezproxy1.lib.asu.edu/nmeth/journal/vaop/ncurrent/full/nmeth.2701.html Link]. <br>'''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.<br><br> | ||
# (2013) '''Cas9 as a versatile tool for engineering biology''' Mali P, Esvelt KM, Church GM. Nature Methods. 10:957-63. [http://www.nature.com.ezproxy1.lib.asu.edu/nmeth/journal/v10/n10/full/nmeth.2649.html Link]. <br>'''Summary''': This article is a perspective piece on the Cas9-guide-RNA methodology.<br><br> | |||
# (2013) '''ExpressionBlast: mining large, unstructured expression databases''' Zinman GE, Naiman S, Kanfi Y, Cohen H, Bar-Joseph Z. 10:925-6. [http://www.nature.com.ezproxy1.lib.asu.edu/nmeth/journal/v10/n10/full/nmeth.2630.html Link]. <br>'''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).<br><br> | |||
==Nature Molecular Systems Biology== | ==Nature Molecular Systems Biology== | ||
#( | # (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 [http://www.nature.com/msb/journal/v9/n1/pdf/msb201358.pdf Link] <br> '''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.''' | ||
# (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 [http://www.nature.com/msb/journal/v9/n1/pdf/msb201355.pdf Link] <br> '''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)== | ==Public Library of Science Biology (PLoS Biology)== | ||
# (2013) '''Chromatin-Specific Regulation of Mammalian rDNA Transcription by Clustered TTF-I Binding Sites'''. PLoS Genetics 9:9: 1-12. [http://www.plosgenetics.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pgen.1003786&representation=PDF Link] | # (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. [http://www.plosgenetics.org/article/fetchObject.action?uri=info%3Adoi%2F10.1371%2Fjournal.pgen.1003786&representation=PDF Link] | ||
Determined that clustered binding sites increase the binding affinity of transcription factors in chromatin. | Determined that clustered binding sites increase the binding affinity of transcription factors in chromatin. | ||
==Proceedings of the National Academy of Sciences | ==Proceedings of the National Academy of Sciences== | ||
#(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. [http://www.pnas.org/content/110/19/7772.full Link] | |||
# (2013) ''' | |||
==Science== | ==Science== | ||
# | #(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. [http://www-ncbi-nlm-nih-gov.ezproxy1.lib.asu.edu/pubmed/23539183 Link]<br>'''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.<br><br> | ||
==Miscellaneous Reviews and Media== | ==Miscellaneous Reviews and Media== | ||
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# (2013) '''Exosome mediated mammalian cell-cell communication.''' MIT iGEM Team. iGEM World Championship. [http://2013.igem.org/Team:MIT Link]. <br>'''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).<br><br> | # (2013) '''Exosome mediated mammalian cell-cell communication.''' MIT iGEM Team. iGEM World Championship. [http://2013.igem.org/Team:MIT Link]. <br>'''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).<br><br> | ||
# (2013) '''The uniCAS toolkit for gene regulation.''' Freiburg iGEM Team. iGEM World Championship. [http://2013.igem.org/Team:Freiburg Link]. <br>'''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.<br><br> | # (2013) '''The uniCAS toolkit for gene regulation.''' Freiburg iGEM Team. iGEM World Championship. [http://2013.igem.org/Team:Freiburg Link]. <br>'''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.<br><br> | ||
'''News''' | |||
# November 6, 2013. '''BBSRC Invests $16M in Synthetic Biology Startup Fund.''' GenomeWeb Staff Reporter. GenomeWeb Daily News. [http://www.genomeweb.com/bbsrc-invests-16m-synthetic-biology-startup-fund Link]. <br>'''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<br><br> | |||
# October 24, 2013. '''SRC launches synthetic biology research effort at six universities.''' Semiconductor Research Corp. R&D Magazine. [http://www.rdmag.com/news/2013/10/src-launches-synthetic-biology-research-effort-six-universities Link]. <br>'''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.<br><br> | |||