Literature DB >> 19668248

Microfluidic devices for measuring gene network dynamics in single cells.

Matthew R Bennett1, Jeff Hasty.   

Abstract

The dynamics governing gene regulation have an important role in determining the phenotype of a cell or organism. From processing extracellular signals to generating internal rhythms, gene networks are central to many time-dependent cellular processes. Recent technological advances now make it possible to track the dynamics of gene networks in single cells under various environmental conditions using microfluidic 'lab-on-a-chip' devices, and researchers are using these new techniques to analyse cellular dynamics and discover regulatory mechanisms. These technologies are expected to yield novel insights and allow the construction of mathematical models that more accurately describe the complex dynamics of gene regulation.

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Year:  2009        PMID: 19668248      PMCID: PMC2931582          DOI: 10.1038/nrg2625

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  119 in total

1.  Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations.

Authors:  T B Kepler; T C Elston
Journal:  Biophys J       Date:  2001-12       Impact factor: 4.033

2.  Microfluidic devices for the high-throughput chemical analysis of cells.

Authors:  Maxine A McClain; Christopher T Culbertson; Stephen C Jacobson; Nancy L Allbritton; Christopher E Sims; J Michael Ramsey
Journal:  Anal Chem       Date:  2003-11-01       Impact factor: 6.986

3.  Bacterial persistence as a phenotypic switch.

Authors:  Nathalie Q Balaban; Jack Merrin; Remy Chait; Lukasz Kowalik; Stanislas Leibler
Journal:  Science       Date:  2004-08-12       Impact factor: 47.728

4.  Delay-induced stochastic oscillations in gene regulation.

Authors:  Dmitri Bratsun; Dmitri Volfson; Lev S Tsimring; Jeff Hasty
Journal:  Proc Natl Acad Sci U S A       Date:  2005-09-30       Impact factor: 11.205

5.  A microfluidic chemostat for experiments with bacterial and yeast cells.

Authors:  Alex Groisman; Caroline Lobo; HoJung Cho; J Kyle Campbell; Yann S Dufour; Ann M Stevens; Andre Levchenko
Journal:  Nat Methods       Date:  2005-09       Impact factor: 28.547

6.  Integration of biological networks and gene expression data using Cytoscape.

Authors:  Melissa S Cline; Michael Smoot; Ethan Cerami; Allan Kuchinsky; Nerius Landys; Chris Workman; Rowan Christmas; Iliana Avila-Campilo; Michael Creech; Benjamin Gross; Kristina Hanspers; Ruth Isserlin; Ryan Kelley; Sarah Killcoyne; Samad Lotia; Steven Maere; John Morris; Keiichiro Ono; Vuk Pavlovic; Alexander R Pico; Aditya Vailaya; Peng-Liang Wang; Annette Adler; Bruce R Conklin; Leroy Hood; Martin Kuiper; Chris Sander; Ilya Schmulevich; Benno Schwikowski; Guy J Warner; Trey Ideker; Gary D Bader
Journal:  Nat Protoc       Date:  2007       Impact factor: 13.491

7.  The chemistrode: a droplet-based microfluidic device for stimulation and recording with high temporal, spatial, and chemical resolution.

Authors:  Delai Chen; Wenbin Du; Ying Liu; Weishan Liu; Andrey Kuznetsov; Felipe E Mendez; Louis H Philipson; Rustem F Ismagilov
Journal:  Proc Natl Acad Sci U S A       Date:  2008-10-30       Impact factor: 11.205

Review 8.  Engineered gene circuits.

Authors:  Jeff Hasty; David McMillen; J J Collins
Journal:  Nature       Date:  2002-11-14       Impact factor: 49.962

9.  Designer gene networks: Towards fundamental cellular control.

Authors:  Jeff Hasty; Farren Isaacs; Milos Dolnik; David McMillen; J. J. Collins
Journal:  Chaos       Date:  2001-03       Impact factor: 3.642

10.  Frequency-modulated nuclear localization bursts coordinate gene regulation.

Authors:  Long Cai; Chiraj K Dalal; Michael B Elowitz
Journal:  Nature       Date:  2008-09-25       Impact factor: 49.962

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  99 in total

Review 1.  Microfluidic technologies for temporal perturbations of chemotaxis.

Authors:  Daniel Irimia
Journal:  Annu Rev Biomed Eng       Date:  2010-08-15       Impact factor: 9.590

2.  Antagonistic gene transcripts regulate adaptation to new growth environments.

Authors:  Bridget L Baumgartner; Matthew R Bennett; Michael Ferry; Tracy L Johnson; Lev S Tsimring; Jeff Hasty
Journal:  Proc Natl Acad Sci U S A       Date:  2011-12-12       Impact factor: 11.205

Review 3.  Heterogeneous bacterial persisters and engineering approaches to eliminate them.

Authors:  Kyle R Allison; Mark P Brynildsen; James J Collins
Journal:  Curr Opin Microbiol       Date:  2011-09-19       Impact factor: 7.934

4.  Growth propagation of yeast in linear arrays of microfluidic chambers over many generations.

Authors:  Li Wang; Jiaji Liu; Xin Li; Jian Shi; Jie Hu; Ran Cui; Zhi-Ling Zhang; Dai-Wen Pang; Yong Chen
Journal:  Biomicrofluidics       Date:  2011-12-16       Impact factor: 2.800

Review 5.  Measurement of single-cell dynamics.

Authors:  David G Spiller; Christopher D Wood; David A Rand; Michael R H White
Journal:  Nature       Date:  2010-06-10       Impact factor: 49.962

Review 6.  Signal Transduction at the Single-Cell Level: Approaches to Study the Dynamic Nature of Signaling Networks.

Authors:  L Naomi Handly; Jason Yao; Roy Wollman
Journal:  J Mol Biol       Date:  2016-07-16       Impact factor: 5.469

7.  SYNTHETIC BIOLOGY. Emergent genetic oscillations in a synthetic microbial consortium.

Authors:  Ye Chen; Jae Kyoung Kim; Andrew J Hirning; Krešimir Josić; Matthew R Bennett
Journal:  Science       Date:  2015-08-28       Impact factor: 47.728

Review 8.  Genetic design automation: engineering fantasy or scientific renewal?

Authors:  Matthew W Lux; Brian W Bramlett; David A Ball; Jean Peccoud
Journal:  Trends Biotechnol       Date:  2011-10-14       Impact factor: 19.536

9.  Bistability and oscillations in co-repressive synthetic microbial consortia.

Authors:  Mehdi Sadeghpour; Alan Veliz-Cuba; Gábor Orosz; Krešimir Josić; Matthew R Bennett
Journal:  Quant Biol       Date:  2017-03-30

Review 10.  Microfluidics expanding the frontiers of microbial ecology.

Authors:  Roberto Rusconi; Melissa Garren; Roman Stocker
Journal:  Annu Rev Biophys       Date:  2014       Impact factor: 12.981

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