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George Church

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https://www.readbyqxmd.com/read/28933153/rapid-sequential-in-situ-multiplexing-with-dna-exchange-imaging-in-neuronal-cells-and-tissues
#1
Yu Wang, Johannes B Woehrstein, Noah Donoghue, Mingjie Dai, Maier S Avendano, Ron C J Schackmann, Jason Zoeller, Shan Shan H Wang, Paul W Tillberg, Demian Park, Sylvain W Lapan, Edward S Boyden, Joan S Brugge, Pascal S Kaeser, George Church, Sarit S Agasti, Ralf Jungmann, Peng Yin
To decipher the molecular mechanism of biological function, it is critical to map the molecular composition of individual cells or even more importantly tissue samples in the context of their biological environment in situ. Immunofluorescence (IF) provides specific labeling for molecular profiling. However, conventional IF methods have finite multiplexing capabilities due to spectral overlap of the fluorophores. Various sequential imaging methods have been developed to circumvent this spectral limit, but are not widely adopted due to the common limitation of requiring multi-rounds of slow (typically over 2 hours at room temperature to overnight at 4 °C in practice) immunostaining...
September 21, 2017: Nano Letters
https://www.readbyqxmd.com/read/28911123/a-systematic-comparison-of-error-correction-enzymes-by-next-generation-sequencing
#2
Nathan B Lubock, Di Zhang, Angus M Sidore, George M Church, Sriram Kosuri
Gene synthesis, the process of assembling gene-length fragments from shorter groups of oligonucleotides (oligos), is becoming an increasingly important tool in molecular and synthetic biology. The length, quality and cost of gene synthesis are limited by errors produced during oligo synthesis and subsequent assembly. Enzymatic error correction methods are cost-effective means to ameliorate errors in gene synthesis. Previous analyses of these methods relied on cloning and Sanger sequencing to evaluate their efficiencies, limiting quantitative assessment...
September 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28852223/beyond-editing-to-writing-large-genomes
#3
REVIEW
Raj Chari, George M Church
Recent exponential advances in genome sequencing and engineering technologies have enabled an unprecedented level of interrogation into the impact of DNA variation (genotype) on cellular function (phenotype). Furthermore, these advances have also prompted realistic discussion of writing and radically re-writing complex genomes. In this Perspective, we detail the motivation for large-scale engineering, discuss the progress made from such projects in bacteria and yeast and describe how various genome-engineering technologies will contribute to this effort...
August 30, 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28828661/imaging-of-isolated-extracellular-vesicles-using-fluorescence-microscopy
#4
Dmitry Ter-Ovanesyan, Emma J K Kowal, Aviv Regev, George M Church, Emanuele Cocucci
High-resolution fluorescence microscopy approaches enable the study of single objects or biological complexes. Single object studies have the general advantage of uncovering heterogeneity that may be hidden during the ensemble averaging which is common in any bulk conventional biochemical analysis. The implementation of single object analysis in the study of extracellular vesicles (EVs) may therefore be used to characterize specific properties of vesicle subsets which would be otherwise undetectable. We present a protocol for staining isolated EVs with a fluorescent lipid dye and attaching them onto a glass slide in preparation for imaging with total internal reflection fluorescence microscopy (TIRF-M) or other high-resolution microscopy techniques...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28828654/extracellular-vesicle-isolation-and-analysis-by-western-blotting
#5
Emma J K Kowal, Dmitry Ter-Ovanesyan, Aviv Regev, George M Church
Extracellular vesicles (EVs) are released by mammalian cells and are thought to be important mediators of intercellular communication. There are many methods for isolating EVs from cell culture media, but the most popular methods involve purification based on ultracentrifugation . Here, we provide a detailed protocol for isolating EVs by differential ultracentrifugation and analyzing EV proteins (such as the tetraspanins CD9 , CD63 and CD81 ) by western blotting.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28807739/community-based-participatory-research-to-design-a-faith-enhanced-diabetes-prevention-program-the-better-me-within-randomized-trial
#6
Heather Kitzman, Leilani Dodgen, Abdullah Mamun, J Lee Slater, George King, Donna Slater, Alene King, Surendra Mandapati, Mark DeHaven
Reducing obesity positively impacts diabetes and cardiovascular risk; however, evidence-based lifestyle programs, such as the diabetes prevention program (DPP), show reduced effectiveness in African American (AA) women. In addition to an attenuated response to lifestyle programs, AA women also demonstrate high rates of obesity, diabetes, and cardiovascular disease. To address these disparities, enhancements to evidence-based lifestyle programs for AA women need to be developed and evaluated with culturally relevant and rigorous study designs...
August 12, 2017: Contemporary Clinical Trials
https://www.readbyqxmd.com/read/28798043/inactivation-of-porcine-endogenous-retrovirus-in-pigs-using-crispr-cas9
#7
Dong Niu, Hong-Jiang Wei, Lin Lin, Haydy George, Tao Wang, I-Hsiu Lee, Hong-Ye Zhao, Yong Wang, Yinan Kan, Ellen Shrock, Emal Lesha, Gang Wang, Yonglun Luo, Yubo Qing, Deling Jiao, Heng Zhao, Xiaoyang Zhou, Shouqi Wang, Hong Wei, Marc Güell, George M Church, Luhan Yang
Xenotransplantation is a promising strategy to alleviate the shortage of organs for human transplantation. In addition to the concern on pig-to-human immunological compatibility, the risk of cross-species transmission of porcine endogenous retroviruses (PERVs) has impeded the clinical application of this approach. Earlier, we demonstrated the feasibility of inactivating PERV activity in an immortalized pig cell line. Here, we confirmed that PERVs infect human cells, and observed the horizontal transfer of PERVs among human cells...
August 10, 2017: Science
https://www.readbyqxmd.com/read/28714951/rates-distribution-and-implications-of-postzygotic-mosaic-mutations-in-autism-spectrum-disorder
#8
Elaine T Lim, Mohammed Uddin, Silvia De Rubeis, Yingleong Chan, Anne S Kamumbu, Xiaochang Zhang, Alissa M D'Gama, Sonia N Kim, Robert Sean Hill, Arthur P Goldberg, Christopher Poultney, Nancy J Minshew, Itaru Kushima, Branko Aleksic, Norio Ozaki, Mara Parellada, Celso Arango, Maria J Penzol, Angel Carracedo, Alexander Kolevzon, Christina M Hultman, Lauren A Weiss, Menachem Fromer, Andreas G Chiocchetti, Christine M Freitag, George M Church, Stephen W Scherer, Joseph D Buxbaum, Christopher A Walsh
We systematically analyzed postzygotic mutations (PZMs) in whole-exome sequences from the largest collection of trios (5,947) with autism spectrum disorder (ASD) available, including 282 unpublished trios, and performed resequencing using multiple independent technologies. We identified 7.5% of de novo mutations as PZMs, 83.3% of which were not described in previous studies. Damaging, nonsynonymous PZMs within critical exons of prenatally expressed genes were more common in ASD probands than controls (P < 1 × 10(-6)), and genes carrying these PZMs were enriched for expression in the amygdala (P = 5...
September 2017: Nature Neuroscience
https://www.readbyqxmd.com/read/28707856/science-and-orthodox-christianity-an-overview
#9
REVIEW
Efthymios Nicolaidis, Eudoxie Delli, Nikolaos Livanos, Kostas Tampakis, George Vlahakis
This essay offers an overview of the history of the relations between science and Eastern Christianity based on Greek-language sources. The civilizations concerned are the Byzantine Empire, the Christian Orthodox communities of the Ottoman Empire, and modern Greece, as a case study of a national state. Beginning with the Greek Church Fathers, the essay investigates the ideas of theologians and scholars on nature. Neoplatonism, the theological debates of Iconoclasm and Hesychasm, the proposed union of the Eastern and Western Churches, and the complex relations with the Hellenic past all had notable impacts on the conception of science held by the Byzantine Orthodox...
September 2016: Isis; An International Review Devoted to the History of Science and its Cultural Influences
https://www.readbyqxmd.com/read/28702280/dissecting-limiting-factors-of-the-protein-synthesis-using-recombinant-elements-pure-system
#10
Jun Li, Chi Zhang, Poyi Huang, Erkin Kuru, Eliot T C Forster-Benson, Taibo Li, George M Church
Reconstituted cell-free protein synthesis systems such as the Protein synthesis Using Recombinant Elements (PURE) system give high-throughput and controlled access to in vitro protein synthesis. Here we show that compared with the commercial S30 crude extract based RTS 100 E. coli HY system, the PURE system has less mRNA degradation and produces up to ∼6-fold full-length proteins. However the majority of polypeptides PURE produces are partially translated or inactive since the signal from firefly luciferase (Fluc) translated in PURE is only ∼2/3(rd) of that measured using the RTS 100 E...
2017: Translation
https://www.readbyqxmd.com/read/28700573/crispr-cas-encoding-of-a-digital-movie-into-the-genomes-of-a-population-of-living-bacteria
#11
Seth L Shipman, Jeff Nivala, Jeffrey D Macklis, George M Church
DNA is an excellent medium for archiving data. Recent efforts have illustrated the potential for information storage in DNA using synthesized oligonucleotides assembled in vitro. A relatively unexplored avenue of information storage in DNA is the ability to write information into the genome of a living cell by the addition of nucleotides over time. Using the Cas1-Cas2 integrase, the CRISPR-Cas microbial immune system stores the nucleotide content of invading viruses to confer adaptive immunity. When harnessed, this system has the potential to write arbitrary information into the genome...
July 20, 2017: Nature
https://www.readbyqxmd.com/read/28591112/the-promise-of-organ-and-tissue-preservation-to-transform-medicine
#12
REVIEW
Sebastian Giwa, Jedediah K Lewis, Luis Alvarez, Robert Langer, Alvin E Roth, George M Church, James F Markmann, David H Sachs, Anil Chandraker, Jason A Wertheim, Martine Rothblatt, Edward S Boyden, Elling Eidbo, W P Andrew Lee, Bohdan Pomahac, Gerald Brandacher, David M Weinstock, Gloria Elliott, David Nelson, Jason P Acker, Korkut Uygun, Boris Schmalz, Brad P Weegman, Alessandro Tocchio, Greg M Fahy, Kenneth B Storey, Boris Rubinsky, John Bischof, Janet A W Elliott, Teresa K Woodruff, G John Morris, Utkan Demirci, Kelvin G M Brockbank, Erik J Woods, Robert N Ben, John G Baust, Dayong Gao, Barry Fuller, Yoed Rabin, David C Kravitz, Michael J Taylor, Mehmet Toner
The ability to replace organs and tissues on demand could save or improve millions of lives each year globally and create public health benefits on par with curing cancer. Unmet needs for organ and tissue preservation place enormous logistical limitations on transplantation, regenerative medicine, drug discovery, and a variety of rapidly advancing areas spanning biomedicine. A growing coalition of researchers, clinicians, advocacy organizations, academic institutions, and other stakeholders has assembled to address the unmet need for preservation advances, outlining remaining challenges and identifying areas of underinvestment and untapped opportunities...
June 7, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28569062/scalable-device-for-automated-microbial-electroporation-in-a-digital-microfluidic-platform
#13
Andrew C Madison, Matthew W Royal, Frederic Vigneault, Liji Chen, Peter B Griffin, Mark Horowitz, George M Church, Richard B Fair
Electrowetting-on-dielectric (EWD) digital microfluidic laboratory-on-a-chip platforms demonstrate excellent performance in automating labor-intensive protocols. When coupled with an on-chip electroporation capability, these systems hold promise for streamlining cumbersome processes such as multiplex automated genome engineering (MAGE). We integrated a single Ti:Au electroporation electrode into an otherwise standard parallel-plate EWD geometry to enable high-efficiency transformation of Escherichia coli with reporter plasmid DNA in a 200 nL droplet...
September 15, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28559321/qnas-with-alta-charo-and-george-church
#14
Prashant Nair
No abstract text is available yet for this article.
June 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28545559/millstone-software-for-multiplex-microbial-genome-analysis-and-engineering
#15
Daniel B Goodman, Gleb Kuznetsov, Marc J Lajoie, Brian W Ahern, Michael G Napolitano, Kevin Y Chen, Changping Chen, George M Church
Inexpensive DNA sequencing and advances in genome editing have made computational analysis a major rate-limiting step in adaptive laboratory evolution and microbial genome engineering. We describe Millstone, a web-based platform that automates genotype comparison and visualization for projects with up to hundreds of genomic samples. To enable iterative genome engineering, Millstone allows users to design oligonucleotide libraries and create successive versions of reference genomes. Millstone is open source and easily deployable to a cloud platform, local cluster, or desktop, making it a scalable solution for any lab...
May 25, 2017: Genome Biology
https://www.readbyqxmd.com/read/28545477/optimizing-complex-phenotypes-through-model-guided-multiplex-genome-engineering
#16
Gleb Kuznetsov, Daniel B Goodman, Gabriel T Filsinger, Matthieu Landon, Nadin Rohland, John Aach, Marc J Lajoie, George M Church
We present a method for identifying genomic modifications that optimize a complex phenotype through multiplex genome engineering and predictive modeling. We apply our method to identify six single nucleotide mutations that recover 59% of the fitness defect exhibited by the 63-codon E. coli strain C321.∆A. By introducing targeted combinations of changes in multiplex we generate rich genotypic and phenotypic diversity and characterize clones using whole-genome sequencing and doubling time measurements. Regularized multivariate linear regression accurately quantifies individual allelic effects and overcomes bias from hitchhiking mutations and context-dependence of genome editing efficiency that would confound other strategies...
May 25, 2017: Genome Biology
https://www.readbyqxmd.com/read/28544481/matching-phenotypes-to-whole-genomes-lessons-learned-from-four-iterations-of-the-personal-genome-project-community-challenges
#17
Binghuang Cai, Biao Li, Nikki Kiga, Janita Thusberg, Timothy Bergquist, Yun-Ching Chen, Noushin Niknafs, Hannah Carter, Collin Tokheim, Violeta Beleva-Guthrie, Christopher Douville, Rohit Bhattacharya, Hui Ting Grace Yeo, Jean Fan, Sohini Sengupta, Dewey Kim, Melissa Cline, Tychele Turner, Mark Diekhans, Jan Zaucha, Lipika R Pal, Chen Cao, Chen-Hsin Yu, Yizhou Yin, Marco Carraro, Manuel Giollo, Carlo Ferrari, Emanuela Leonardi, Silvio C E Tosatto, Jason Bobe, Madeleine Ball, Roger A Hoskins, Susanna Repo, George Church, Steven E Brenner, John Moult, Julian Gough, Mario Stanke, Rachel Karchin, Sean D Mooney
The advent of next-generation sequencing has dramatically decreased the cost for whole-genome sequencing and increased the viability for its application in research and clinical care. The Personal Genome Project (PGP) provides unrestricted access to genomes of individuals and their associated phenotypes. This resource enabled the Critical Assessment of Genome Interpretation (CAGI) to create a community challenge to assess the bioinformatics community's ability to predict traits from whole genomes. In the CAGI PGP challenge, researchers were asked to predict whether an individual had a particular trait or profile based on their whole genome...
September 2017: Human Mutation
https://www.readbyqxmd.com/read/28494857/correction-addressing-the-ethical-issues-raised-by-synthetic-human-entities-with-embryo-like-features
#18
John Aach, Jeantine Lunshof, Eswar Iyer, George M Church
No abstract text is available yet for this article.
April 13, 2017: ELife
https://www.readbyqxmd.com/read/28494856/addressing-the-ethical-issues-raised-by-synthetic-human-entities-with-embryo-like-features
#19
John Aach, Jeantine Lunshof, Eswar Iyer, George M Church
The "14-day rule" for embryo research stipulates that experiments with intact human embryos must not allow them to develop beyond 14 days or the appearance of the primitive streak. However, recent experiments showing that suitably cultured human pluripotent stem cells can self-organize and recapitulate embryonic features have highlighted difficulties with the 14-day rule and led to calls for its reassessment. Here we argue that these and related experiments raise more foundational issues that cannot be fixed by adjusting the 14-day rule, because the framework underlying the rule cannot adequately describe the ways by which synthetic human entities with embryo-like features (SHEEFs) might develop morally concerning features through altered forms of development...
March 21, 2017: ELife
https://www.readbyqxmd.com/read/28470971/impact-of-integrated-services-on-hiv-testing-a-nonrandomized-trial-among-kenyan-family-planning-clients
#20
Kathryn Church, Charlotte E Warren, Isolde Birdthistle, George B Ploubidis, Keith Tomlin, Weiwei Zhou, James Kimani, Timothy Abuya, Charity Ndwiga, Sedona Sweeney, Susannah H Mayhew
The impact of integrated reproductive health and HIV services on HIV testing and counseling (HTC) uptake was assessed among 882 Kenyan family planning clients using a nonrandomized cohort design within six intervention and six "comparison" facilities. The effect of integration on HTC goals (two tests over two years) was assessed using conditional logistic regression to test four "integration" exposures: a training and reorganization intervention; receipt of reproductive health and HIV services at recruitment; a functional measure of facility integration at recruitment; and a woman's cumulative exposure to functionally integrated care across different facilities over time...
June 2017: Studies in Family Planning
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