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George Church

Tara Rheault, Sanjeev Khindri, Mitra Vahdati-Bolouri, Alison Church, William A Fahy
This study compared the efficacy and safety of once-daily umeclidinium 62.5 µg with once-daily glycopyrronium 50 µg in patients with moderate-to-severe chronic obstructive pulmonary disease. This was a 12-week, multicentre, randomised, open-label, parallel-group study ( NCT02236611). Patients were randomised 1:1 to umeclidinium 62.5 µg or glycopyrronium 50 µg administered via Ellipta or Breezhaler dry powder inhaler, respectively. The primary endpoint was trough forced expiratory volume in 1 s (FEV1) at day 85 in the per-protocol population...
April 2016: ERJ Open Research
P Benjamin Stranges, Mirkó Palla, Sergey Kalachikov, Jeff Nivala, Michael Dorwart, Andrew Trans, Shiv Kumar, Mintu Porel, Minchen Chien, Chuanjuan Tao, Irina Morozova, Zengmin Li, Shundi Shi, Aman Aberra, Cleoma Arnold, Alexander Yang, Anne Aguirre, Eric T Harada, Daniel Korenblum, James Pollard, Ashwini Bhat, Dmitriy Gremyachinskiy, Arek Bibillo, Roger Chen, Randy Davis, James J Russo, Carl W Fuller, Stefan Roever, Jingyue Ju, George M Church
Scalable, high-throughput DNA sequencing is a prerequisite for precision medicine and biomedical research. Recently, we presented a nanopore-based sequencing-by-synthesis (Nanopore-SBS) approach, which used a set of nucleotides with polymer tags that allow discrimination of the nucleotides in a biological nanopore. Here, we designed and covalently coupled a DNA polymerase to an α-hemolysin (αHL) heptamer using the SpyCatcher/SpyTag conjugation approach. These porin-polymerase conjugates were inserted into lipid bilayers on a complementary metal oxide semiconductor (CMOS)-based electrode array for high-throughput electrical recording of DNA synthesis...
October 11, 2016: Proceedings of the National Academy of Sciences of the United States of America
Qing Mao, Serban Ciotlos, Rebecca Yu Zhang, Madeleine P Ball, Robert Chin, Paolo Carnevali, Nina Barua, Staci Nguyen, Misha R Agarwal, Tom Clegg, Abram Connelly, Ward Vandewege, Alexander Wait Zaranek, Preston W Estep, George M Church, Radoje Drmanac, Brock A Peters
BACKGROUND: Since the completion of the Human Genome Project in 2003, it is estimated that more than 200,000 individual whole human genomes have been sequenced. A stunning accomplishment in such a short period of time. However, most of these were sequenced without experimental haplotype data and are therefore missing an important aspect of genome biology. In addition, much of the genomic data is not available to the public and lacks phenotypic information. FINDINGS: As part of the Personal Genome Project, blood samples from 184 participants were collected and processed using Complete Genomics' Long Fragment Read technology...
October 11, 2016: GigaScience
Katherine M Livingstone, Carlos Celis-Morales, George D Papandonatos, Bahar Erar, Jose C Florez, Kathleen A Jablonski, Cristina Razquin, Amelia Marti, Yoriko Heianza, Tao Huang, Frank M Sacks, Mathilde Svendstrup, Xuemei Sui, Timothy S Church, Tiina Jääskeläinen, Jaana Lindström, Jaakko Tuomilehto, Matti Uusitupa, Tuomo Rankinen, Wim H M Saris, Torben Hansen, Oluf Pedersen, Arne Astrup, Thorkild I A Sørensen, Lu Qi, George A Bray, Miguel A Martinez-Gonzalez, J Alfredo Martinez, Paul W Franks, Jeanne M McCaffery, Jose Lara, John C Mathers
OBJECTIVE:  To assess the effect of the FTO genotype on weight loss after dietary, physical activity, or drug based interventions in randomised controlled trials. DESIGN:  Systematic review and random effects meta-analysis of individual participant data from randomised controlled trials. DATA SOURCES:  Ovid Medline, Scopus, Embase, and Cochrane from inception to November 2015. ELIGIBILITY CRITERIA FOR STUDY SELECTION:  Randomised controlled trials in overweight or obese adults reporting reduction in body mass index, body weight, or waist circumference by FTO genotype (rs9939609 or a proxy) after dietary, physical activity, or drug based interventions...
2016: BMJ: British Medical Journal
Michael G Napolitano, Matthieu Landon, Christopher J Gregg, Marc J Lajoie, Lakshmi Govindarajan, Joshua A Mosberg, Gleb Kuznetsov, Daniel B Goodman, Oscar Vargas-Rodriguez, Farren J Isaacs, Dieter Söll, George M Church
The degeneracy of the genetic code allows nucleic acids to encode amino acid identity as well as noncoding information for gene regulation and genome maintenance. The rare arginine codons AGA and AGG (AGR) present a case study in codon choice, with AGRs encoding important transcriptional and translational properties distinct from the other synonymous alternatives (CGN). We created a strain of Escherichia coli with all 123 instances of AGR codons removed from all essential genes. We readily replaced 110 AGR codons with the synonymous CGU codons, but the remaining 13 "recalcitrant" AGRs required diversification to identify viable alternatives...
September 20, 2016: Proceedings of the National Academy of Sciences of the United States of America
Wei Leong Chew, Mohammadsharif Tabebordbar, Jason K W Cheng, Prashant Mali, Elizabeth Y Wu, Alex H M Ng, Kexian Zhu, Amy J Wagers, George M Church
CRISPR-Cas9 delivery by adeno-associated virus (AAV) holds promise for gene therapy but faces critical barriers on account of its potential immunogenicity and limited payload capacity. Here, we demonstrate genome engineering in postnatal mice using AAV-split-Cas9, a multifunctional platform customizable for genome editing, transcriptional regulation, and other previously impracticable applications of AAV-CRISPR-Cas9. We identify crucial parameters that impact efficacy and clinical translation of our platform, including viral biodistribution, editing efficiencies in various organs, antigenicity, immunological reactions, and physiological outcomes...
October 2016: Nature Methods
Stella K Vasiliou, Eleftherios P Diamandis, George M Church, Henry T Greely, Françoise Baylis, Charis Thompson, Gerold Schmitt-Ulms
No abstract text is available yet for this article.
October 2016: Clinical Chemistry
Nili Ostrov, Matthieu Landon, Marc Guell, Gleb Kuznetsov, Jun Teramoto, Natalie Cervantes, Minerva Zhou, Kerry Singh, Michael G Napolitano, Mark Moosburner, Ellen Shrock, Benjamin W Pruitt, Nicholas Conway, Daniel B Goodman, Cameron L Gardner, Gary Tyree, Alexandra Gonzales, Barry L Wanner, Julie E Norville, Marc J Lajoie, George M Church
Recoding--the repurposing of genetic codons--is a powerful strategy for enhancing genomes with functions not commonly found in nature. Here, we report computational design, synthesis, and progress toward assembly of a 3.97-megabase, 57-codon Escherichia coli genome in which all 62,214 instances of seven codons were replaced with synonymous alternatives across all protein-coding genes. We have validated 63% of recoded genes by individually testing 55 segments of 50 kilobases each. We observed that 91% of tested essential genes retained functionality with limited fitness effect...
August 19, 2016: Science
Fei Chen, Asmamaw T Wassie, Allison J Cote, Anubhav Sinha, Shahar Alon, Shoh Asano, Evan R Daugharthy, Jae-Byum Chang, Adam Marblestone, George M Church, Arjun Raj, Edward S Boyden
The ability to image RNA identity and location with nanoscale precision in intact tissues is of great interest for defining cell types and states in normal and pathological biological settings. Here, we present a strategy for expansion microscopy of RNA. We developed a small-molecule linker that enables RNA to be covalently attached to a swellable polyelectrolyte gel synthesized throughout a biological specimen. Then, postexpansion, fluorescent in situ hybridization (FISH) imaging of RNA can be performed with high yield and specificity as well as single-molecule precision in both cultured cells and intact brain tissue...
August 2016: Nature Methods
Seth L Shipman, Jeff Nivala, Jeffrey D Macklis, George M Church
The ability to write a stable record of identified molecular events into a specific genomic locus would enable the examination of long cellular histories and have many applications, ranging from developmental biology to synthetic devices. We show that the type I-E CRISPR (clustered regularly interspaced short palindromic repeats)-Cas system of Escherichia coli can mediate acquisition of defined pieces of synthetic DNA. We harnessed this feature to generate records of specific DNA sequences into a population of bacterial genomes...
July 29, 2016: Science
Thomas M Siler, Alison C Donald, Dianne O'Dell, Alison Church, William A Fahy
BACKGROUND: The combination of the inhaled muscarinic antagonist umeclidinium (UMEC) with the long-acting β2-agonist vilanterol (VI) has been shown to provide significant improvements in lung function compared with UMEC, VI, or placebo (PBO) in patients with chronic obstructive pulmonary disease (COPD). This study was specifically designed to support these findings by assessing health-related quality of life and symptomatic outcomes in a similar population. METHODS: This was a 12-week multicenter, randomized, double-blind, parallel-group, placebo-controlled study...
2016: International Journal of Chronic Obstructive Pulmonary Disease
Justin M Zook, David Catoe, Jennifer McDaniel, Lindsay Vang, Noah Spies, Arend Sidow, Ziming Weng, Yuling Liu, Christopher E Mason, Noah Alexander, Elizabeth Henaff, Alexa B R McIntyre, Dhruva Chandramohan, Feng Chen, Erich Jaeger, Ali Moshrefi, Khoa Pham, William Stedman, Tiffany Liang, Michael Saghbini, Zeljko Dzakula, Alex Hastie, Han Cao, Gintaras Deikus, Eric Schadt, Robert Sebra, Ali Bashir, Rebecca M Truty, Christopher C Chang, Natali Gulbahce, Keyan Zhao, Srinka Ghosh, Fiona Hyland, Yutao Fu, Mark Chaisson, Chunlin Xiao, Jonathan Trow, Stephen T Sherry, Alexander W Zaranek, Madeleine Ball, Jason Bobe, Preston Estep, George M Church, Patrick Marks, Sofia Kyriazopoulou-Panagiotopoulou, Grace X Y Zheng, Michael Schnall-Levin, Heather S Ordonez, Patrice A Mudivarti, Kristina Giorda, Ying Sheng, Karoline Bjarnesdatter Rypdal, Marc Salit
The Genome in a Bottle Consortium, hosted by the National Institute of Standards and Technology (NIST) is creating reference materials and data for human genome sequencing, as well as methods for genome comparison and benchmarking. Here, we describe a large, diverse set of sequencing data for seven human genomes; five are current or candidate NIST Reference Materials. The pilot genome, NA12878, has been released as NIST RM 8398. We also describe data from two Personal Genome Project trios, one of Ashkenazim Jewish ancestry and one of Chinese ancestry...
2016: Scientific Data
Jef D Boeke, George Church, Andrew Hessel, Nancy J Kelley, Adam Arkin, Yizhi Cai, Rob Carlson, Aravinda Chakravarti, Virginia W Cornish, Liam Holt, Farren J Isaacs, Todd Kuiken, Marc Lajoie, Tracy Lessor, Jeantine Lunshof, Matthew T Maurano, Leslie A Mitchell, Jasper Rine, Susan Rosser, Neville E Sanjana, Pamela A Silver, David Valle, Harris Wang, Jeffrey C Way, Luhan Yang
No abstract text is available yet for this article.
July 8, 2016: Science
Suhani Vora, Marcelle Tuttle, Jenny Cheng, George Church
Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins offer a breakthrough platform for cheap, programmable, and effective sequence-specific DNA targeting. The CRISPR-Cas system is naturally equipped for targeted DNA cutting through its native nuclease activity. As such, groups researching a broad spectrum of biological organisms have quickly adopted the technology with groundbreaking applications to genomic sequence editing in over 20 different species. However, the biological code of life is not only encoded in genetics but also in epigenetics as well...
September 2016: FEBS Journal
Alejandro Chavez, Marcelle Tuttle, Benjamin W Pruitt, Ben Ewen-Campen, Raj Chari, Dmitry Ter-Ovanesyan, Sabina J Haque, Ryan J Cecchi, Emma J K Kowal, Joanna Buchthal, Benjamin E Housden, Norbert Perrimon, James J Collins, George Church
Several programmable transcription factors exist based on the versatile Cas9 protein, yet their relative potency and effectiveness across various cell types and species remain unexplored. Here, we compare Cas9 activator systems and examine their ability to induce robust gene expression in several human, mouse, and fly cell lines. We also explore the potential for improved activation through the combination of the most potent activator systems, and we assess the role of cooperativity in maximizing gene expression...
July 2016: Nature Methods
Jonathan L Braff, Stephanie J Yaung, Kevin M Esvelt, George M Church
In light of the multitude of new Cas9-mediated functionalities, the ability to carry out multiple Cas9-enabled processes simultaneously and in a single cell is becoming increasingly valuable. Accomplishing this aim requires a set of Cas9-guide RNA (gRNA) pairings that are functionally independent and insulated from one another. For instance, two such protein-gRNA complexes would allow for concurrent activation and editing at independent target sites in the same cell. The problem of establishing orthogonal CRISPR systems can be decomposed into three stages...
2016: Cold Spring Harbor Protocols
Jonathan L Braff, Stephanie J Yaung, Kevin M Esvelt, George M Church
This protocol outlines a general approach for characterizing the protospacer-adjacent motifs (PAMs) of Cas9 orthologs. It uses a three-plasmid system: One plasmid carries Cas9 and its tracrRNA, a second targeting vector contains the spacer and repeat, and the third plasmid encodes the targeted sequence (as the protospacer) with varying PAM sequences. It leverages the Cas9 nuclease activity to cleave and destroy plasmids that bear a compatible PAM. The level of depletion of a library of targeted plasmids after Cas9-mediated selection can then be assessed by deep sequencing to reveal candidate PAMs for downstream validation...
2016: Cold Spring Harbor Protocols
Gregory Feldman, François Maltais, Sanjeev Khindri, Mitra Vahdati-Bolouri, Alison Church, William A Fahy, Roopa Trivedi
BACKGROUND: The long-acting muscarinic antagonists umeclidinium (UMEC) and tiotropium (TIO) are approved once-daily maintenance therapies for COPD. This study investigated the efficacy and safety of UMEC versus TIO in COPD. METHODS: This was a 12-week, multicenter, randomized, blinded, double-dummy, parallel-group, non-inferiority study. Patients were randomized 1:1 to UMEC 62.5 μg plus placebo or TIO 18 μg plus placebo. The primary end point was trough forced expiratory volume in 1 second (FEV1) at day 85 (non-inferiority margin -50 mL; per-protocol [PP] population)...
2016: International Journal of Chronic Obstructive Pulmonary Disease
Carl W Fuller, Shiv Kumar, Mintu Porel, Minchen Chien, Arek Bibillo, P Benjamin Stranges, Michael Dorwart, Chuanjuan Tao, Zengmin Li, Wenjing Guo, Shundi Shi, Daniel Korenblum, Andrew Trans, Anne Aguirre, Edward Liu, Eric T Harada, James Pollard, Ashwini Bhat, Cynthia Cech, Alexander Yang, Cleoma Arnold, Mirkó Palla, Jennifer Hovis, Roger Chen, Irina Morozova, Sergey Kalachikov, James J Russo, John J Kasianowicz, Randy Davis, Stefan Roever, George M Church, Jingyue Ju
DNA sequencing by synthesis (SBS) offers a robust platform to decipher nucleic acid sequences. Recently, we reported a single-molecule nanopore-based SBS strategy that accurately distinguishes four bases by electronically detecting and differentiating four different polymer tags attached to the 5'-phosphate of the nucleotides during their incorporation into a growing DNA strand catalyzed by DNA polymerase. Further developing this approach, we report here the use of nucleotides tagged at the terminal phosphate with oligonucleotide-based polymers to perform nanopore SBS on an α-hemolysin nanopore array platform...
May 10, 2016: Proceedings of the National Academy of Sciences of the United States of America
Yunan Zheng, Marc J Lajoie, James S Italia, Melissa A Chin, George M Church, Abhishek Chatterjee
Site-specific incorporation of noncanonical amino acids (ncAAs) into proteins expressed in E. coli using UAG-suppression competes with termination mediated by release factor 1 (RF1). Recently, unconditional deletion of RF1 was achieved in a genomically recoded E. coli (C321), devoid of all endogenous UAG stop codons. Here we evaluate the efficiency of ncAA incorporation in this strain using optimized suppression vectors. Even though the absence of RF1 does not benefit the suppression efficiency of a single UAG codon, multi-site incorporation of a series of chemically distinct ncAAs was significantly improved...
May 24, 2016: Molecular BioSystems
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