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  • 1
    Publication Date: 2012-09-27
    Description: Genome-scale engineering of living organisms requires precise and economical methods to efficiently modify many loci within chromosomes. One such example is the directed integration of chemically synthesized single-stranded deoxyribonucleic acid (oligonucleotides) into the chromosome of Escherichia coli during replication. Herein, we present a general co-selection strategy in multiplex genome engineering that yields highly modified cells. We demonstrate that disparate sites throughout the genome can be easily modified simultaneously by leveraging selectable markers within 500 kb of the target sites. We apply this technique to the modification of 80 sites in the E. coli genome.
    Keywords: Synthetic Biology and Assembly Cloning
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 2
    Publication Date: 2013-10-19
    Description: Efficient strategies for precise genome editing in human-induced pluripotent cells (hiPSCs) will enable sophisticated genome engineering for research and clinical purposes. The development of programmable sequence-specific nucleases such as Transcription Activator-Like Effectors Nucleases (TALENs) and Cas9-gRNA allows genetic modifications to be made more efficiently at targeted sites of interest. However, many opportunities remain to optimize these tools and to enlarge their spheres of application. We present several improvements: First, we developed functional re-coded TALEs (reTALEs), which not only enable simple one-pot TALE synthesis but also allow TALE-based applications to be performed using lentiviral vectors. We then compared genome-editing efficiencies in hiPSCs mediated by 15 pairs of reTALENs and Cas9-gRNA targeting CCR5 and optimized ssODN design in conjunction with both methods for introducing specific mutations. We found Cas9-gRNA achieved 7–8 x higher non-homologous end joining efficiencies (3%) than reTALENs (0.4%) and moderately superior homology-directed repair efficiencies (1.0 versus 0.6%) when combined with ssODN donors in hiPSCs. Using the optimal design, we demonstrated a streamlined process to generated seamlessly genome corrected hiPSCs within 3 weeks.
    Keywords: Synthetic Biology and Assembly Cloning, Genomics
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 3
    Publication Date: 2010-05-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bedau, Mark -- Church, George -- Rasmussen, Steen -- Caplan, Arthur -- Benner, Steven -- Fussenegger, Martin -- Collins, Jim -- Deamer, David -- England -- Nature. 2010 May 27;465(7297):422-4. doi: 10.1038/465422a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20495545" target="_blank"〉PubMed〈/a〉
    Keywords: Bioengineering/methods/trends ; Biotechnology/methods/*trends ; DNA, Recombinant/biosynthesis/*genetics ; Genetic Engineering/methods/*trends ; Genome, Bacterial/*genetics ; *Life ; Mycoplasma mycoides/*genetics ; Transformation, Bacterial/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2009-05-30
    Description: Synthetic gene networks can be constructed to emulate digital circuits and devices, giving one the ability to program and design cells with some of the principles of modern computing, such as counting. A cellular counter would enable complex synthetic programming and a variety of biotechnology applications. Here, we report two complementary synthetic genetic counters in Escherichia coli that can count up to three induction events: the first, a riboregulated transcriptional cascade, and the second, a recombinase-based cascade of memory units. These modular devices permit counting of varied user-defined inputs over a range of frequencies and can be expanded to count higher numbers.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2690711/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2690711/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Friedland, Ari E -- Lu, Timothy K -- Wang, Xiao -- Shi, David -- Church, George -- Collins, James J -- DP1 OD003644/OD/NIH HHS/ -- DP1 OD003644-01/OD/NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2009 May 29;324(5931):1199-202. doi: 10.1126/science.1172005.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Biomedical Engineering, Center for BioDynamics and Center for Advanced Biotechnology, Boston University, Boston, MA 02215, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19478183" target="_blank"〉PubMed〈/a〉
    Keywords: Arabinose/metabolism ; DNA, Bacterial/*genetics ; DNA-Directed RNA Polymerases/genetics/metabolism ; Escherichia coli K12/*genetics ; Gene Expression Regulation, Bacterial ; *Gene Regulatory Networks ; Genetic Engineering ; Green Fluorescent Proteins/biosynthesis ; Models, Genetic ; Plasmids ; Promoter Regions, Genetic ; *Protein Biosynthesis ; RNA, Bacterial/genetics/metabolism ; Recombinases/genetics/*metabolism ; *Regulatory Elements, Transcriptional ; *Transcription, Genetic ; Viral Proteins/genetics/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
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    Nature Publishing Group (NPG)
    Publication Date: 2013-10-11
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Church, George -- England -- Nature. 2013 Oct 10;502(7470):143. doi: 10.1038/502143a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Harvard Medical School, Boston, Massachusetts, USA. gmc@harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24108012" target="_blank"〉PubMed〈/a〉
    Keywords: Confidentiality ; Disease/genetics ; Genome/*ethics/*genetics ; Genomics/*economics/ethics/*standards/trends ; High-Throughput Nucleotide Sequencing ; Humans
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 6
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    Nature Publishing Group (NPG)
    Publication Date: 2015-12-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Church, George -- England -- Nature. 2015 Dec 3;528(7580):S7. doi: 10.1038/528S7a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Harvard Medical School in Boston, Massachusetts.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26630599" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; CRISPR-Cas Systems/*genetics ; Congresses as Topic ; Genetic Engineering/*ethics ; Genome/*genetics ; Germ-Line Mutation/*genetics ; Humans ; Preventive Medicine/methods ; Public Opinion ; Risk Assessment ; *Safety
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 2018-10-24
    Description: “[Everyone has] the right to enjoy the benefits of scientific progress and its applications.” Article 15(1)(b), International Covenant on Economic, Social and Cultural Rights (1) We all have a human right to enjoy the benefits of scientific progress (the Right to Science [RtS]).* The right has its origins in Article...
    Keywords: Opinions, Front Matter
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 8
    Publication Date: 2007-06-26
    Description: Although classical genetic and biochemical approaches have identified hundreds of proteins that function in the dynamic remodeling of cell shape in response to upstream signals, there is currently little systems-level understanding of the organization and composition of signaling networks that regulate cell morphology. We have developed quantitative morphological profiling methods to systematically investigate the role of individual genes in the regulation of cell morphology in a fast, robust, and cost-efficient manner. We analyzed a compendium of quantitative morphological signatures and described the existence of local signaling networks that act to regulate cell protrusion, adhesion, and tension.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bakal, Chris -- Aach, John -- Church, George -- Perrimon, Norbert -- New York, N.Y. -- Science. 2007 Jun 22;316(5832):1753-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17588932" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Cell Movement/genetics/physiology ; Cell Shape/*genetics/physiology ; Drosophila ; Green Fluorescent Proteins ; Metabolic Networks and Pathways/*genetics ; Phenotype ; RNA Interference ; Signal Transduction/*genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
    Publication Date: 2014-07-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Oye, Kenneth A -- Esvelt, Kevin -- Appleton, Evan -- Catteruccia, Flaminia -- Church, George -- Kuiken, Todd -- Lightfoot, Shlomiya Bar-Yam -- McNamara, Julie -- Smidler, Andrea -- Collins, James P -- New York, N.Y. -- Science. 2014 Aug 8;345(6197):626-8. doi: 10.1126/science.1254287. Epub 2014 Jul 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Political Science Department, Massachusetts Institute of Technology. Engineering Systems Division, Massachusetts Institute of Technology. oye@mit.edu. ; Wyss Institute, Harvard University. ; Bioinformatics, Boston University. ; Harvard School of Public Health. University of Perugia, Italy. ; Woodrow Wilson International Center for Scholars. ; Engineering Systems Division, Massachusetts Institute of Technology. ; Harvard School of Public Health. Harvard Medical School. ; School of Life Sciences, Arizona State University.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25035410" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Animals, Genetically Modified/*genetics ; Caspase 9/genetics ; *Clustered Regularly Interspaced Short Palindromic Repeats ; Communicable Disease Control/*methods ; Culicidae/*genetics ; Dengue/prevention & control ; *Gene Expression Regulation ; Gene Targeting/methods ; Genetic Engineering/*methods ; Humans ; Malaria/parasitology/prevention & control ; Mosquito Control/*methods ; RNA/genetics ; Reproduction/genetics ; Risk Management
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 10
    Publication Date: 2015-09-01
    Description: Human mutations that truncate the massive sarcomere protein titin [TTN-truncating variants (TTNtvs)] are the most common genetic cause for dilated cardiomyopathy (DCM), a major cause of heart failure and premature death. Here we show that cardiac microtissues engineered from human induced pluripotent stem (iPS) cells are a powerful system for evaluating the pathogenicity of titin gene variants. We found that certain missense mutations, like TTNtvs, diminish contractile performance and are pathogenic. By combining functional analyses with RNA sequencing, we explain why truncations in the A-band domain of TTN cause DCM, whereas truncations in the I band are better tolerated. Finally, we demonstrate that mutant titin protein in iPS cell-derived cardiomyocytes results in sarcomere insufficiency, impaired responses to mechanical and beta-adrenergic stress, and attenuated growth factor and cell signaling activation. Our findings indicate that titin mutations cause DCM by disrupting critical linkages between sarcomerogenesis and adaptive remodeling.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4618316/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4618316/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hinson, John T -- Chopra, Anant -- Nafissi, Navid -- Polacheck, William J -- Benson, Craig C -- Swist, Sandra -- Gorham, Joshua -- Yang, Luhan -- Schafer, Sebastian -- Sheng, Calvin C -- Haghighi, Alireza -- Homsy, Jason -- Hubner, Norbert -- Church, George -- Cook, Stuart A -- Linke, Wolfgang A -- Chen, Christopher S -- Seidman, J G -- Seidman, Christine E -- EB017103/EB/NIBIB NIH HHS/ -- HG005550/HG/NHGRI NIH HHS/ -- HL007374/HL/NHLBI NIH HHS/ -- HL115553/HL/NHLBI NIH HHS/ -- HL125807/HL/NHLBI NIH HHS/ -- K08 HL125807/HL/NHLBI NIH HHS/ -- T32 HL007208/HL/NHLBI NIH HHS/ -- Department of Health/United Kingdom -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2015 Aug 28;349(6251):982-6. doi: 10.1126/science.aaa5458.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA. jthinson@partners.org cseidman@genetics.med.harvard.edu. ; Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA. The Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA 02115, USA. ; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. ; Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215, USA. ; Department of Cardiovascular Physiology, Ruhr University Bochum, MA 3/56 D-44780, Bochum, Germany. ; The Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA 02115, USA. Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. ; Cardiovascular and Metabolic Sciences, Max Delbruck Center for Molecular Medicine, Berlin, Germany. ; Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA. Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA. ; Cardiovascular and Metabolic Sciences, Max Delbruck Center for Molecular Medicine, Berlin, Germany. DZHK (German Center for Cardiovascular Research), Partner Site Berlin, Berlin, Germany. ; National Institute for Health Research (NIHR) Biomedical Research Unit in Cardiovascular Disease at Royal Brompton and Harefield National Health Service (NHS) Foundation Trust, Imperial College London, London, UK. National Heart Centre and Duke-National University, Singapore, Singapore. ; Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA. Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA. jthinson@partners.org cseidman@genetics.med.harvard.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26315439" target="_blank"〉PubMed〈/a〉
    Keywords: Adrenergic beta-Agonists/pharmacology ; Cardiomyopathy, Dilated/*genetics/pathology/*physiopathology ; Cells, Cultured ; Connectin/chemistry/*genetics/*physiology ; Heart Rate ; Humans ; Induced Pluripotent Stem Cells/*physiology ; Isoproterenol/pharmacology ; Mutant Proteins/chemistry/physiology ; *Mutation, Missense ; Myocardial Contraction ; Myocytes, Cardiac/*physiology ; RNA/genetics/metabolism ; Sarcomeres/*physiology/ultrastructure ; Sequence Analysis, RNA ; Signal Transduction ; Stress, Physiological
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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