Biology & Life Sciences

Synthetic Biology: Methods & Instruments

Published January 30, 2017 Curated Collections

Synthetic Biology is an emerging, trans-disciplinary field at the intersection between many engineering and scientific disciplines such as biology, chemical engineering, chemistry, electrical engineering, and computer science. This section of the Synthetic Biology Collection details papers related to Methods & Instruments.

Image Credit: Ivan Morozov (Virginia Bioinformatics Institute) / PLOS

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Research Articles

Research Articles

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10.1371/journal.pone.0154765

PLOS ONE Directed Chemical Evolution with an Outsized Genetic Code
August 10, 2016 Casey J. Krusemark, Nicolas P. Tilmans, Patrick O. Brown, Pehr B. Harbury
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10.1371/journal.pone.0159777

PLOS ONE On-Flow Synthesis of Co-Polymerizable Oligo-Microspheres and Application in ssDNA Amplification
July 22, 2016 Se Hee Lee, Jae Ha Lee, Ho Won Lee, Yang-Hoon Kim, Ok Chan Jeong, Ji-Young Ahn
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10.1371/journal.pcbi.1004995

PLOS Computational Biology Cellular Interrogation: Exploiting Cell-to-Cell Variability to Discriminate Regulatory Mechanisms in Oscillatory Signalling
July 1, 2016 Javier Estrada, Natalie Andrew, Daniel Gibson, Frederick Chang, Florian Gnad, Jeremy Gunawardena
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10.1371/journal.pone.0157603

PLOS ONE Chondroitin Sulfate- and Decorin-Based Self-Assembling Scaffolds for Cartilage Tissue Engineering
June 17, 2016 Lourdes Recha-Sancho, Carlos E. Semino
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10.1371/journal.ppat.1005641

PLOS Pathogens Receptor-Targeted Nipah Virus Glycoproteins Improve Cell-Type Selective Gene Delivery and Reveal a Preference for Membrane-Proximal Cell Attachment
June 9, 2016 Ruben R. Bender, Anke Muth, Irene C. Schneider, Thorsten Friedel, Jessica Hartmann, Andreas Plückthun, Andrea Maisner, Christian J. Buchholz
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10.1371/journal.pone.0157187

PLOS ONE Highly Efficient Transfer of Chromosomes to a Broad Range of Target Cells Using Chinese Hamster Ovary Cells Expressing Murine Leukemia Virus-Derived Envelope Proteins
June 7, 2016 Teruhiko Suzuki, Yasuhiro Kazuki, Mitsuo Oshimura, Takahiko Hara
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10.1371/journal.pone.0155625

PLOS ONE Fibrous Hydrogels for Cell Encapsulation: A Modular and Supramolecular Approach
May 25, 2016 Małgorzata K. Włodarczyk-Biegun, Kambiz Farbod, Marc W. T. Werten, Cornelis J. Slingerland, Frits A. de Wolf, Jeroen J. J. P. van den Beucken, Sander C. G. Leeuwenburgh, Martien A. Cohen Stuart, Marleen Kamperman
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10.1371/journal.pone.0156341

PLOS ONE A Reversibly Sealed, Easy Access, Modular (SEAM) Microfluidic Architecture to Establish In Vitro Tissue Interfaces
May 26, 2016 Vinay V. Abhyankar, Meiye Wu, Chung-Yan Koh, Anson V. Hatch
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10.1371/journal.pone.0154634

PLOS ONE Targeted Mutagenesis in Plant Cells through Transformation of Sequence-Specific Nuclease mRNA
May 13, 2016 Thomas J. Stoddard, Benjamin M. Clasen, Nicholas J. Baltes, Zachary L. Demorest, Daniel F. Voytas, Feng Zhang, Song Luo
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10.1371/journal.pone.0155359

PLOS ONE A Novel Method for Gene-Specific Enhancement of Protein Translation by Targeting 5’UTRs of Selected Tumor Suppressors
May 12, 2016 Adam Master, Anna Wójcicka, Kamilla Giżewska, Piotr Popławski, Graham R. Williams, Alicja Nauman
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10.1371/journal.pone.0154303

PLOS ONE Germline Gene Editing in Chickens by Efficient CRISPR-Mediated Homologous Recombination in Primordial Germ Cells
April 21, 2016 Lazar Dimitrov, Darlene Pedersen, Kathryn H. Ching, Henry Yi, Ellen J. Collarini, Shelley Izquierdo, Marie-Cecile van de Lavoir, Philip A. Leighton
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10.1371/journal.pone.0153901

PLOS ONE A Digital PCR-Based Method for Efficient and Highly Specific Screening of Genome Edited Cells
April 18, 2016 Scott D. Findlay, Krista M. Vincent, Jennifer R. Berman, Lynne-Marie Postovit
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10.1371/journal.pone.0153437

PLOS ONE Mapping of Enzyme Kinetics on a Microfluidic Device
April 15, 2016 Hoon Suk Rho, Alexander Thomas Hanke, Marcel Ottens, Han Gardeniers
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10.1371/journal.pone.0152774

PLOS ONE Multiplexed Sequence Encoding: A Framework for DNA Communication
April 6, 2016 Bijan Zakeri, Peter A. Carr, Timothy K. Lu
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10.1371/journal.pone.0152023

PLOS ONE Simple and Versatile 3D Printed Microfluidics Using Fused Filament Fabrication
April 6, 2016 Alex J. L. Morgan, Lorena Hidalgo San Jose, William D. Jamieson, Jennifer M. Wymant, Bing Song, Phil Stephens, David A. Barrow, Oliver K. Castell
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10.1371/journal.pone.0152666

PLOS ONE Design of Novel Relaxase Substrates Based on Rolling Circle Replicases for Bioconjugation to DNA Nanostructures
March 30, 2016 Sandra Sagredo, Fernando de la Cruz, Gabriel Moncalián
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10.1371/journal.pone.0151740

PLOS ONE SiteOut: An Online Tool to Design Binding Site-Free DNA Sequences
March 17, 2016 Javier Estrada, Teresa Ruiz-Herrero, Clarissa Scholes, Zeba Wunderlich, Angela DePace
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10.1371/journal.pone.0150037

PLOS ONE Reactivation of Latent HIV-1 Expression by Engineered TALE Transcription Factors
March 2, 2016 Pedro Perdigão, Thomas Gaj, Mariana Santa-Marta, Carlos F. Barbas, Joao Goncalves
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10.1371/journal.pntd.0004484

PLOS Neglected Tropical Diseases A Heterologous Multiepitope DNA Prime/Recombinant Protein Boost Immunisation Strategy for the Development of an Antiserum against Micrurus corallinus (Coral Snake) Venom
March 3, 2016 Henrique Ramos, Inacio de Loiola Junqueira-de-Azevedo, Juliana Novo, Karen Castro, Clara Duarte, Ricardo Machado-de-Ávila, Carlos Chavez-Olortegui, Paulo Ho
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10.1371/journal.pone.0150360

PLOS ONE Distinct Contributions of Astrocytes and Pericytes to Neuroinflammation Identified in a 3D Human Blood-Brain Barrier on a Chip
March 1, 2016 Anna Herland, Andries van der Meer, Edward FitzGerald, Tae-Eun Park, Jelle Sleeboom, Donald Ingber
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10.1371/journal.ppat.1005360

PLOS Pathogens Yeast as a Heterologous Model System to Uncover Type III Effector Function
February 25, 2016 Crina Popa, Núria S. Coll, Marc Valls, Guido Sessa
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10.1371/journal.pone.0146415

PLOS ONE Angiotensin II Induced Cardiac Dysfunction on a Chip
January 25, 2016 Renita E. Horton, Moran Yadid, Megan L. McCain, Sean P. Sheehy, Francesco S. Pasqualini, Sung-Jin Park, Alexander Cho, Patrick Campbell, Kevin Kit Parker
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10.1371/journal.pone.0146919

PLOS ONE Production of Biologically Active Cecropin A Peptide in Rice Seed Oil Bodies
January 13, 2016 Laura Montesinos, Mireia Bundó, Esther Izquierdo, Sonia Campo, Esther Badosa, Michel Rossignol, Emilio Montesinos, Blanca San Segundo, María Coca
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10.1371/journal.pone.0149667

PLOS ONE Logic Gate Operation by DNA Translocation through Biological Nanopores
February 18, 2016 Hiroki Yasuga, Ryuji Kawano, Masahiro Takinoue, Yutaro Tsuji, Toshihisa Osaki, Koki Kamiya, Norihisa Miki, Shoji Takeuchi
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10.1371/journal.pone.0149522

PLOS ONE Isolating Influenza RNA from Clinical Samples Using Microfluidic Oil-Water Interfaces
February 17, 2016 Francis R. Cui, Jingjing Wang, Steven M. Opal, Anubhav Tripathi
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10.1371/journal.pone.0148797

PLOS ONE A Microfluidic Channel Method for Rapid Drug-Susceptibility Testing of Pseudomonas aeruginosa
February 12, 2016 Yoshimi Matsumoto, Shouichi Sakakihara, Andrey Grushnikov, Kazuma Kikuchi, Hiroyuki Noji, Akihito Yamaguchi, Ryota Iino, Yasushi Yagi, Kunihiko Nishino
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10.1371/journal.pone.0149150

PLOS ONE A Rapid and Low-Cost PCR Thermal Cycler for Infectious Disease Diagnostics
February 12, 2016 Kamfai Chan, Pui-Yan Wong, Peter Yu, Justin Hardick, Kah-Yat Wong, Scott Wilson, Tiffany Wu, Zoe Hui, Charlotte Gaydos, Season Wong
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10.1371/journal.pone.0148559

PLOS ONE In Vitro Reconstruction of Neuronal Networks Derived from Human iPS Cells Using Microfabricated Devices
February 5, 2016 Yuzo Takayama, Yasuyuki S. Kida
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10.1371/journal.pone.0143636

PLOS ONE DNA Assembly in 3D Printed Fluidics
December 30, 2015 William G. Patrick, Alec A. K. Nielsen, Steven J. Keating, Taylor J. Levy, Che-Wei Wang, Jaime J. Rivera, Octavio Mondragón-Palomino, Peter A. Carr, Christopher A. Voigt, Neri Oxman, David S. Kong
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10.1371/journal.pone.0147801

PLOS ONE A Unidirectional Cell Switching Gate by Engineering Grating Length and Bending Angle
January 28, 2016 Shu Fan Zhou, Singaram Gopalakrishnan, Yuan Hao Xu, Jie Yang, Yun Wah Lam, Stella W. Pang
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10.1371/journal.pone.0141640

PLOS ONE Customizable 3D Printed ‘Plug and Play’ Millifluidic Devices for Programmable Fluidics
November 11, 2015 Soichiro Tsuda, Hussain Jaffery, David Doran, Mohammad Hezwani, Phillip J. Robbins, Mari Yoshida, Leroy Cronin
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10.1371/journal.pone.0000663

PLOS ONE Printing Multistrain Bacterial Patterns with a Piezoelectric Inkjet Printer
July 25, 2007 Jack Merrin, Stanislas Leibler, John S. Chuang
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10.1371/journal.pone.0001468

PLOS ONE A Microfluidic Device for Temporally Controlled Gene Expression and Long-Term Fluorescent Imaging in Unperturbed Dividing Yeast Cells
January 23, 2008 Gilles Charvin, Frederick R. Cross, Eric D. Siggia
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10.1371/journal.pone.0007086

PLOS ONE A Modified Consumer Inkjet for Spatiotemporal Control of Gene Expression
September 18, 2009 Daniel J. Cohen, Roberto C. Morfino, Michel M. Maharbiz
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10.1371/journal.pone.0036982

PLOS ONE A Multi-Platform Flow Device for Microbial (Co-) Cultivation and Microscopic Analysis
May 14, 2012 Matthijn Hesselman, Dorett Odoni, Brendan Ryback, Suzette de Groot, Ruben van Heck, Jaap Keijsers, Pim Kolkman, David Nieuwenhuijse, Youri van Nuland, Erik Sebus, Rob Spee, Hugo de Vries, Marten Wapenaar, Colin Ingham, Karin Schroën, Vítor Martins dos Santos, Sebastiaan Spaans, Floor Hugenholtz, Mark van Passel

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