Aindrila Mukhopadhyay

Aindrila Mukhopadhyay

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Aindrila Mukhopadhyay

Aindrila Mukhopadhyay

Publications by authors named "Aindrila Mukhopadhyay"

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Engineering Robust Production Microbes for Large-Scale Cultivation.

Trends Microbiol 2019 Jun 25;27(6):524-537. Epub 2019 Feb 25.

Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S0966842X193001
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http://dx.doi.org/10.1016/j.tim.2019.01.006DOI Listing
June 2019

Rhizobacteria mediate the phytotoxicity of a range of biorefinery-relevant compounds.

Environ Toxicol Chem 2019 May 20. Epub 2019 May 20.

Biological Systems and Engineering Division, Biosciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.

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http://dx.doi.org/10.1002/etc.4501DOI Listing
May 2019

LurR is a regulator of the central lactate oxidation pathway in sulfate-reducing Desulfovibrio species.

PLoS One 2019 9;14(4):e0214960. Epub 2019 Apr 9.

Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0214960PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6456213PMC
April 2019

Multiple signaling systems target a core set of transition metal homeostasis genes using similar binding motifs.

Mol Microbiol 2018 03 23;107(6):704-717. Epub 2018 Jan 23.

Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.

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http://dx.doi.org/10.1111/mmi.13909DOI Listing
March 2018

Intracellular cellobiose metabolism and its applications in lignocellulose-based biorefineries.

Bioresour Technol 2017 Sep 4;239:496-506. Epub 2017 May 4.

Joint BioEnergy Institute, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Chemical and Biomolecular Engineering & Department of Bioengineering, UC Berkeley, Berkeley, CA 94720, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, KogleAllé, DK2970 Hørsholm, Denmark; Synthetic Biology Engineering Research Center (Synberc), Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1016/j.biortech.2017.05.001DOI Listing
September 2017

Engineering high-level production of fatty alcohols by Saccharomyces cerevisiae from lignocellulosic feedstocks.

Metab Eng 2017 07 10;42:115-125. Epub 2017 Jun 10.

DOE Joint BioEnergy Institute, Emeryville, CA 94608, United States; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA 94720, United States; Department of Bioengineering, University of California, Berkeley, CA 94720, United States; The Novo Nordisk Foundation Center for Sustainability, Technical University of Denmark, Denmark. Electronic address:

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http://dx.doi.org/10.1016/j.ymben.2017.06.004DOI Listing
July 2017

Endoribonuclease-Based Two-Component Repressor Systems for Tight Gene Expression Control in Plants.

ACS Synth Biol 2017 05 8;6(5):806-816. Epub 2017 Feb 8.

Joint BioEnergy Institute, EmeryStation East, 5885 Hollis Street, 4th Floor, Emeryville, California 94608, United States.

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http://dx.doi.org/10.1021/acssynbio.6b00295DOI Listing
May 2017

Flux-Enabled Exploration of the Role of Sip1 in Galactose Yeast Metabolism.

Front Bioeng Biotechnol 2017 24;5:31. Epub 2017 May 24.

Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.

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http://dx.doi.org/10.3389/fbioe.2017.00031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5443151PMC
May 2017

A Highly Expressed High-Molecular-Weight S-Layer Complex of Pelosinus sp. Strain UFO1 Binds Uranium.

Appl Environ Microbiol 2017 02 1;83(4). Epub 2017 Feb 1.

Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA

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http://dx.doi.org/10.1128/AEM.03044-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5288816PMC
February 2017

Engineering Bacteria to Catabolize the Carbonaceous Component of Sarin: Teaching E. coli to Eat Isopropanol.

ACS Synth Biol 2016 12 27;5(12):1485-1496. Epub 2016 Jul 27.

Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States.

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http://dx.doi.org/10.1021/acssynbio.6b00115DOI Listing
December 2016

The Future of Antibiotics: Emerging Technologies and Stewardship.

Trends Microbiol 2016 07 24;24(7):515-517. Epub 2016 May 24.

Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Electronic address:

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http://dx.doi.org/10.1016/j.tim.2016.04.003DOI Listing
July 2016

Development of a native Escherichia coli induction system for ionic liquid tolerance.

PLoS One 2014 1;9(7):e101115. Epub 2014 Jul 1.

Joint BioEnergy Institute, Emeryville, California, United States of America; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0101115PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4077768PMC
December 2015

Regulation of Nitrite Stress Response in Desulfovibrio vulgaris Hildenborough, a Model Sulfate-Reducing Bacterium.

J Bacteriol 2015 Nov 17;197(21):3400-8. Epub 2015 Aug 17.

Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA

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http://dx.doi.org/10.1128/JB.00319-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4621071PMC
November 2015

σ54-dependent regulome in Desulfovibrio vulgaris Hildenborough.

BMC Genomics 2015 Nov 10;16:919. Epub 2015 Nov 10.

Lawrence Berkeley National Laboratory, Berkeley, CA, 94710, USA.

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http://dx.doi.org/10.1186/s12864-015-2176-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4641369PMC
November 2015

A Method to Constrain Genome-Scale Models with 13C Labeling Data.

PLoS Comput Biol 2015 Sep 17;11(9):e1004363. Epub 2015 Sep 17.

Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States of America; Joint BioEnergy Institute, Emeryville, United States of America; Department of Bioengineering, University of California, Berkeley, Berkely, United States of America; Department of Chemical Engineering, University of California, Berkeley, Berkeley, United States of America.

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https://dx.plos.org/10.1371/journal.pcbi.1004363
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http://dx.doi.org/10.1371/journal.pcbi.1004363DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4574858PMC
September 2015

Tolerance engineering in bacteria for the production of advanced biofuels and chemicals.

Trends Microbiol 2015 Aug 26;23(8):498-508. Epub 2015 May 26.

Joint BioEnergy Institute, 5885 Hollis St, Emeryville, CA 94608, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Electronic address:

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http://dx.doi.org/10.1016/j.tim.2015.04.008DOI Listing
August 2015

Acute Limonene Toxicity in Escherichia coli Is Caused by Limonene Hydroperoxide and Alleviated by a Point Mutation in Alkyl Hydroperoxidase AhpC.

Appl Environ Microbiol 2015 Jul 1;81(14):4690-6. Epub 2015 May 1.

Joint BioEnergy Institute, Emeryville, California, USA Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA

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http://dx.doi.org/10.1128/AEM.01102-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4551201PMC
July 2015

Isolation of a significant fraction of non-phototroph diversity from a desert Biological Soil Crust.

Front Microbiol 2015 14;6:277. Epub 2015 Apr 14.

Lawrence Berkeley National Laboratory, Earth Sciences Division Berkeley, CA, USA ; Department of Environmental Science, Policy and Management, University of California, Berkeley Berkeley, CA, USA.

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http://dx.doi.org/10.3389/fmicb.2015.00277DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4396413PMC
April 2015

A peptide-based method for 13C Metabolic Flux Analysis in microbial communities.

PLoS Comput Biol 2014 Sep 4;10(9):e1003827. Epub 2014 Sep 4.

Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America; Joint BioEnergy Institute, Emeryville, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1003827DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4154649PMC
September 2014

DNA-affinity-purified chip (DAP-chip) method to determine gene targets for bacterial two component regulatory systems.

J Vis Exp 2014 Jul 21(89). Epub 2014 Jul 21.

Physical Biosciences Division, Lawrence Berkeley National Laboratory.

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http://dx.doi.org/10.3791/51715DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4233932PMC
July 2014

Engineering dynamic pathway regulation using stress-response promoters.

Nat Biotechnol 2013 Nov 20;31(11):1039-46. Epub 2013 Oct 20.

1] Joint BioEnergy Institute, Emeryville, California, USA. [2] Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA. [3] Department of Chemical & Biomolecular Engineering, University of California, Berkeley, California, USA.

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http://dx.doi.org/10.1038/nbt.2689DOI Listing
November 2013

New family of tungstate-responsive transcriptional regulators in sulfate-reducing bacteria.

J Bacteriol 2013 Oct 2;195(19):4466-75. Epub 2013 Aug 2.

Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.

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http://dx.doi.org/10.1128/JB.00679-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3807478PMC
October 2013

Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution.

ISME J 2013 Sep 11;7(9):1790-802. Epub 2013 Apr 11.

Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA.

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http://dx.doi.org/10.1038/ismej.2013.60DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3749499PMC
September 2013

Enhancing fatty acid production by the expression of the regulatory transcription factor FadR.

Metab Eng 2012 Nov 28;14(6):653-60. Epub 2012 Sep 28.

Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA.

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http://dx.doi.org/10.1016/j.ymben.2012.08.009DOI Listing
November 2012

Modular engineering of L-tyrosine production in Escherichia coli.

Appl Environ Microbiol 2012 Jan 21;78(1):89-98. Epub 2011 Oct 21.

California Institute for Quantitative Biosciences and Berkeley Center for Synthetic Biology, University of California, Berkeley, California, USA.

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http://dx.doi.org/10.1128/AEM.06017-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3255607PMC
January 2012

Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium.

Genome Biol 2011 Oct 12;12(10):R99. Epub 2011 Oct 12.

Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1186/gb-2011-12-10-r99DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3333781PMC
October 2011

Identification and microbial production of a terpene-based advanced biofuel.

Nat Commun 2011 Sep 27;2:483. Epub 2011 Sep 27.

Joint BioEnergy Institute, 5885 Hollis Avenue, Emeryville, California 94608, USA.

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http://dx.doi.org/10.1038/ncomms1494DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3195254PMC
September 2011

How sulphate-reducing microorganisms cope with stress: lessons from systems biology.

Nat Rev Microbiol 2011 Jun 16;9(6):452-66. Epub 2011 May 16.

Stephenson Research & Technology Center, 101 David L. Boren Blvd., Institut for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma 73019, USA.

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http://dx.doi.org/10.1038/nrmicro2575DOI Listing
June 2011

Analysis of the Arabidopsis cytosolic proteome highlights subcellular partitioning of central plant metabolism.

J Proteome Res 2011 Apr 28;10(4):1571-82. Epub 2011 Feb 28.

Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road MS978-4101, Berkeley, California 94720, United States.

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http://dx.doi.org/10.1021/pr1009433DOI Listing
April 2011

The interconversion of UDP-arabinopyranose and UDP-arabinofuranose is indispensable for plant development in Arabidopsis.

Plant Cell 2011 Apr 8;23(4):1373-90. Epub 2011 Apr 8.

Joint BioEnergy Institute, Feedstocks Division, Lawrence Berkeley National Laboratory, Emeryville, California 94608, USA.

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http://dx.doi.org/10.1105/tpc.111.083931DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3101560PMC
April 2011

Targeted proteomics for metabolic pathway optimization: application to terpene production.

Metab Eng 2011 Mar 5;13(2):194-203. Epub 2011 Jan 5.

Lawrence Berkeley National Laboratory, Physical Biosciences Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA.

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http://dx.doi.org/10.1016/j.ymben.2010.12.005DOI Listing
March 2011

Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough.

Environ Microbiol 2010 Oct;12(10):2645-57

Virtual Institute of Microbial Stress and Survival, Department of Botany and Microbiology, University of Oklahoma, Norman, OK 73019, USA.

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http://dx.doi.org/10.1111/j.1462-2920.2010.02234.xDOI Listing
October 2010

Study of stationary phase metabolism via isotopomer analysis of amino acids from an isolated protein.

Biotechnol Prog 2010 Jan-Feb;26(1):52-6

Dept. of Chemical Engineering, University of California, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1002/btpr.325DOI Listing
May 2010

Functional genomic study of exogenous n-butanol stress in Escherichia coli.

Appl Environ Microbiol 2010 Mar 29;76(6):1935-45. Epub 2010 Jan 29.

Department of Chemical Engineering, University of California, Berkeley, CA 94720, USA.

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http://aem.asm.org/cgi/doi/10.1128/AEM.02323-09
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http://dx.doi.org/10.1128/AEM.02323-09DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2838030PMC
March 2010

4.0-A resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement.

Proc Natl Acad Sci U S A 2010 Mar 1;107(11):4967-72. Epub 2010 Mar 1.

National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemsitry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030.

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http://dx.doi.org/10.1073/pnas.0913774107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2841888PMC
March 2010

A rapid and inexpensive labeling method for microarray gene expression analysis.

BMC Biotechnol 2009 Nov 25;9:97. Epub 2009 Nov 25.

The Joint Bioenergy Institute, Lawrence Berkeley National Laboratory, Emeryville, USA.

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http://dx.doi.org/10.1186/1472-6750-9-97DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2790446PMC
November 2009

Expression profiling of hypothetical genes in Desulfovibrio vulgaris leads to improved functional annotation.

Nucleic Acids Res 2009 May 17;37(9):2926-39. Epub 2009 Mar 17.

Department of Biochemistry, Virtual Institute for Microbial Stress and Survival, University of Missouri-Columbia, Columbia, MO 65211, USA.

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http://dx.doi.org/10.1093/nar/gkp164DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2685097PMC
May 2009

Overcoming the anaerobic hurdle in phenotypic microarrays: generation and visualization of growth curve data for Desulfovibrio vulgaris Hildenborough.

J Microbiol Methods 2009 Feb 22;76(2):159-68. Epub 2008 Oct 22.

Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1016/j.mimet.2008.10.003DOI Listing
February 2009

Biofuel alternatives to ethanol: pumping the microbial well.

Trends Biotechnol 2008 Jul 28;26(7):375-81. Epub 2008 May 28.

Department of Chemical Engineering, University of California, 717 Potter Street, Building 977, Mail code 3224 Berkeley, CA 94720-3224, USA.

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http://linkinghub.elsevier.com/retrieve/pii/S016777990800112
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http://dx.doi.org/10.1016/j.tibtech.2008.03.008DOI Listing
July 2008

Post-translational modifications of Desulfovibrio vulgaris Hildenborough sulfate reduction pathway proteins.

J Proteome Res 2008 Jun 17;7(6):2320-31. Epub 2008 Apr 17.

Sandia National Laboratory, Livermore, California 94550, USA.

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http://dx.doi.org/10.1021/pr700772sDOI Listing
June 2008

Importance of systems biology in engineering microbes for biofuel production.

Curr Opin Biotechnol 2008 Jun;19(3):228-34

Joint BioEnergy Institute, Emeryville, CA 95608, United States.

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http://dx.doi.org/10.1016/j.copbio.2008.05.003DOI Listing
June 2008

Isotopomer distributions in amino acids from a highly expressed protein as a proxy for those from total protein.

Anal Chem 2008 Feb 8;80(3):886-90. Epub 2008 Jan 8.

Department of Chemical Engineering, University of California, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1021/ac071445+DOI Listing
February 2008

Pathway confirmation and flux analysis of central metabolic pathways in Desulfovibrio vulgaris hildenborough using gas chromatography-mass spectrometry and Fourier transform-ion cyclotron resonance mass spectrometry.

J Bacteriol 2007 Feb 17;189(3):940-9. Epub 2006 Nov 17.

Virtual Institute of Microbial Stress and Survival, Department of Chemical Engineering and Bioengineering, University of California, Berkeley, California, USA.

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http://dx.doi.org/10.1128/JB.00948-06DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1797301PMC
February 2007

Constitutive activation of two-component response regulators: characterization of VirG activation in Agrobacterium tumefaciens.

J Bacteriol 2006 Jul;188(14):5204-11

Center for Fundamental and Applied Molecular Evolution, Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA.

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http://dx.doi.org/10.1128/JB.00387-06DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1539974PMC
July 2006

Study of nitrate stress in Desulfovibrio vulgaris Hildenborough using iTRAQ proteomics.

Brief Funct Genomic Proteomic 2006 Jun 23;5(2):133-43. Epub 2006 May 23.

Department of Chemical Engineering, University of California, Berkeley, CA 94720-3224, USA.

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http://dx.doi.org/10.1093/bfgp/ell025DOI Listing
June 2006

Integrating input from multiple signals: the VirA/VirG two-component system of Agrobacterium tumefaciens.

Chembiochem 2004 Nov;5(11):1535-42

Center for Fundamental and Applied Molecular Evolution, Department of Chemistry and Biology, Emory University, Atlanta, GA 30322, USA.

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http://doi.wiley.com/10.1002/cbic.200300828
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http://dx.doi.org/10.1002/cbic.200300828DOI Listing
November 2004