Mukhopadhyay:Publications: Difference between revisions
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==Refereed Publications== | ==Refereed Publications== | ||
===M group pubs=== | ===M group pubs=== | ||
#Mingardon F, Clement C, Hirano K, Nhan M, Luning EG, Chanal A, Mukhopadhyay A* Improving olefin tolerance and production in E. coli using native and evolved AcrB. ''Biotechnology and Bioengineering''. '''2014''' (accepted) | |||
#Foo JL, Jensen HM, Dahl RH, George K, Keasling JD, Lee TS,Leong SSJ, Mukhopadhyay A*. Improving microbial bio-gasoline production in ''Escherichia coli'' using tolerance engineering. ''mBio'' '''2014''' [http://mbio.asm.org/content/5/6/e01932-14 open access] | |||
#Rajeev L, Luning,EG, Altenburg S, Zane GM, Baidoo EE, Catena M, Keasling JD, Wall JD, Fields MW, Mukhopadhyay A. Identification of a cyclic-di-GMP-modulating response regulator that impacts biofilm formation in a model sulfate reducing bacterium. ''Frontiers in Microbiology 5.'' '''2014''' [http://journal.frontiersin.org/Journal/10.3389/fmicb.2014.00382/abstract open access] | |||
#Frederix M, Hutter K, Leu J, Batth TS, Turner WJ, Rüegg TL, Blanch H, Simmons BA, Adams PD, Keasling JD, Thelen MP, Dunlop MJ, Petzold CJ, Mukhopadhyay A* Development of a native Escherichia coli induction system for ionic liquid tolerance ''Plos One'' '''2014''' [http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0101115 online] | |||
#Rajeev, L., Luning, E. G., Mukhopadhyay, A. DNA-affinity-purified Chip (DAP-chip) Method to Determine Gene Targets for Bacterial Two component Regulatory Systems. ''J. Vis. Exp.'' '''2014''' | |||
#Ray J, Keller KL, Catena M, Juba TR, Zemla M, Rajeev L, Knierim B, Zane GM, Robertson J, Auer M, Wall JD, Mukhopadhyay A* Exploring the role of CheA3 in Desulfovibrio vulgaris Hildenborough motility ''Frontiers in Microbiology'' '''2014'''[http://journal.frontiersin.org/Journal/10.3389/fmicb.2014.00077/abstract open access] | |||
# Szmidt-Middleton HL, Ouellet M, Adams PD, Keasling JD, Mukhopadhyay A*. Utilizing a highly responsive gene, ''yhjX'', in ''E. coli'' based production of 1,4-Butanediol ''CES'' '''2013''' [http://www.sciencedirect.com/science/article/pii/S0009250913004673 open access] | |||
#Rajeev L, da Rocha U, Klitgord N, Luning E, Fortney J, Axen S, Shih P, Bouskill N, Bowen B, Kerfeld C, Garcia-Pichel F, Brodie E, Northen T*, Mukhopadhyay A*. Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust. ''ISME J'' '''2013''' [http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej201383a.html open access] | |||
#Walker CB, Redding-Johanson AM, Baidoo EE, Rajeev L, He Z, Hendrickson EL, Joachimiak MP, Stolyar S, Arkin AP, Leigh JA, Zhou J, Keasling JD, Mukhopadhyay A* and Stahl DA. Functional Responses of Methanogenic Archaea to Syntrophic Growth. ''ISME J'' '''2012''' [http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej201260a.html open access] | |||
#Rajeev L, Luning EG, Dehal PS, Price MN, Arkin AP, Mukhopadhyay A* Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium. ''Genome Biology'' '''2011''' [http://genomebiology.com/2011/12/10/R99/abstract open access] | #Rajeev L, Luning EG, Dehal PS, Price MN, Arkin AP, Mukhopadhyay A* Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium. ''Genome Biology'' '''2011''' [http://genomebiology.com/2011/12/10/R99/abstract open access] | ||
#Dunlop MJ, Dossani ZY, Szmidt HL, Chu HC, Lee TS, Keasling JD, Hadi MZ, Mukhopadhyay A*. Engineering microbial biofuel tolerance and export using efflux pumps. ''Mol Syst Biol.'' '''2011''' ([http://www.nature.com/msb/journal/v7/n1/full/msb201121.html Feature Article]) | #Dunlop MJ, Dossani ZY, Szmidt HL, Chu HC, Lee TS, Keasling JD, Hadi MZ, Mukhopadhyay A*. Engineering microbial biofuel tolerance and export using efflux pumps. ''Mol Syst Biol.'' '''2011''' ([http://www.nature.com/msb/journal/v7/n1/full/msb201121.html Feature Article]) | ||
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#A. Mukhopadhyay#, A.M. Redding#, B.J. Rutherford, J.D. Keasling. Importance of systems biology in engineering microbes for biofuel production. Curr Opin Biotechnol. '''2008''' [http://www.sciencedirect.com/science/article/pii/S0958166908000566 link] | #A. Mukhopadhyay#, A.M. Redding#, B.J. Rutherford, J.D. Keasling. Importance of systems biology in engineering microbes for biofuel production. Curr Opin Biotechnol. '''2008''' [http://www.sciencedirect.com/science/article/pii/S0958166908000566 link] | ||
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===Collaborations=== | ===Collaborations=== | ||
#Park JI, Steen EJ, Burd H, Evans SS, Redding-Johnson AM, et al. | #Ghosh A, Nilmeier J, Weaver D, Adams PD, Keasling JD, Mukhopadhyay A, Petzold CJ, García-Martín H.A Peptide-Based Method for 13C Metabolic Flux Analysis in Microbial Communities. ''PLoS Comput Biol'' '''2014''' | ||
#Dahl RH, Zhang F, Alonso-Gutierrez J, Baidoo E, Batth TS, Redding-Johanson AM, Petzold CJ, Mukhopadhyay A, Lee TS, Adams PD et al: Engineering dynamic pathway regulation using stress-response promoters. ''Nat Biotechnol'' '''2013'''. | |||
#Kazakov A, Rajeev L, Luning EG, Zane G, Siddartha K, Rodionov D, Dubchak I, Arkin A, Wall J, Mukhopadhyay A, Novichkov P. A new family of tungstate-responsive transcriptional regulators in sulfate-reducing bacteria" ''J Bact'' '''2013''' | |||
#Zhou A, Baidoo E E, He Z, Mukhopadhyay A, Baumohl J, Benke P I, Joachimiak M, Xie M, Song R, Arkin A, Hazen T, Keasling J, Wall J, Stahl D, Zhou J Characterization of NaCl-tolerance in ''Desulfovibrio vulagris'' Hildenborough through experimental evolution ''ISME J'' '''2013''' | |||
#Zhang F, Ouellet M, Batth TS, Adams PD, Petzold CJ, Mukhopadhyay A, Keasling J Enhancing fatty acid production by the expression of the regulatory transcription factor FadR. Metab Eng '''2012''' | |||
#Park JI, Steen EJ, Burd H, Evans SS, Redding-Johnson AM, et al. A Thermophilic Ionic Liquid-Tolerant Cellulase Cocktail for the Production of Cellulosic Biofuels. PLoS ONE '''2012''' | |||
#Clark ME, He Z, Redding AM, Joachimiak MP, Keasling JD, Zhou J, Arkin AP, Mukhopadhyay A, Fields MW. Transcriptomic and Proteomic Analyses of Desulfovibrio vulgaris Biofilms: Carbon and Energy Flow Contribute to the Distinct Biofilm Growth State. BMC Genomics. '''2012''' | #Clark ME, He Z, Redding AM, Joachimiak MP, Keasling JD, Zhou J, Arkin AP, Mukhopadhyay A, Fields MW. Transcriptomic and Proteomic Analyses of Desulfovibrio vulgaris Biofilms: Carbon and Energy Flow Contribute to the Distinct Biofilm Growth State. BMC Genomics. '''2012''' | ||
#Eudes A, George A, Mukerjee P, et al, Mukhopadhyay A, Keasling JD, Simmons BA, Lapierre C, Ralph J, Loque D. Biosynthesis and incorporation of side-chain-truncated lignin monomers to reduce lignin polymerization and enhance saccharification. Plant Biotechnol J. '''2012''' | #Eudes A, George A, Mukerjee P, et al, Mukhopadhyay A, Keasling JD, Simmons BA, Lapierre C, Ralph J, Loque D. Biosynthesis and incorporation of side-chain-truncated lignin monomers to reduce lignin polymerization and enhance saccharification. Plant Biotechnol J. '''2012''' | ||
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#Y. Cong, M. Baker, J. Jakana, D. Woolford, E. Miller, S. Reissmann, R. Kumar, A. Redding-Johanson, T. Batth, A. Mukhopadhyay, S. Ludtke, J. Frydman, W. Chiu. 4.0 Å Resolution Cryo-EM Structure of the Mammalian Chaperonin TRiC/CCT Reveals its Unique Subunit Arrangement. ''PNAS.'' '''2010''' | #Y. Cong, M. Baker, J. Jakana, D. Woolford, E. Miller, S. Reissmann, R. Kumar, A. Redding-Johanson, T. Batth, A. Mukhopadhyay, S. Ludtke, J. Frydman, W. Chiu. 4.0 Å Resolution Cryo-EM Structure of the Mammalian Chaperonin TRiC/CCT Reveals its Unique Subunit Arrangement. ''PNAS.'' '''2010''' | ||
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===M Postdoc and Graduate Research=== | ===M Postdoc and Graduate Research=== | ||
#A Zhou, Z He, AM Redding-Johanson, A Mukhopadhyay, CL Hemme, MP Joachimiak, F Luo, Y Deng, KS Bender, Q He, JD Keasling, DA Stahl, MW Fields, TC Hazen, AP Arkin, JD Wall, J Zhou. Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough. ''Environ Microbiol.'' '''2010''' | #A Zhou, Z He, AM Redding-Johanson, A Mukhopadhyay, CL Hemme, MP Joachimiak, F Luo, Y Deng, KS Bender, Q He, JD Keasling, DA Stahl, MW Fields, TC Hazen, AP Arkin, JD Wall, J Zhou. Hydrogen peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough. ''Environ Microbiol.'' '''2010''' | ||
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#Mukhopadhyay A, Hillson NJ, Keasling JD* Control of Stress tolerance in bacterial host organisms for bioproduction of fuels '''2012''' Microbial Stress Tolerance: From Genomics to Biofuels, Microbiology Monographs. ed. Z. Lewis Liu, Springer Berlin / Heidelberg. 22: 209-238 [http://www.springerlink.com/content/r381461g42l3566g/ link] | #Mukhopadhyay A, Hillson NJ, Keasling JD* Control of Stress tolerance in bacterial host organisms for bioproduction of fuels '''2012''' Microbial Stress Tolerance: From Genomics to Biofuels, Microbiology Monographs. ed. Z. Lewis Liu, Springer Berlin / Heidelberg. 22: 209-238 [http://www.springerlink.com/content/r381461g42l3566g/ link] | ||
#Rutherford, B.J and Mukhopadhyay, A. '''2012''' Engineering Stress Tolerance in Microbial Systems for Bioproduction of Fuels. In: Arora, R. (ed) Microbial Biotechnology: Energy and Environment. CABI, Wallingford, UK. | #Rutherford, B.J and Mukhopadhyay, A. '''2012''' Engineering Stress Tolerance in Microbial Systems for Bioproduction of Fuels. In: Arora, R. (ed) Microbial Biotechnology: Energy and Environment. CABI, Wallingford, UK. | ||
#Mukhopadhyay A, Hauser Loren Workflow 4: Signaling, in the DOE Systems Biology Knowledgebase Implementation Plan. U.S. Department of Energy Office of Science. DOE Genomic Science Microbial Systems Biology Knowledgebase Workshop, Feb. 9–10, 2010 | #Mukhopadhyay A, Hauser Loren Workflow 4: Signaling, in the DOE Systems Biology Knowledgebase Implementation Plan. U.S. Department of Energy Office of Science. DOE Genomic Science Microbial Systems Biology Knowledgebase Workshop, Feb. 9–10, 2010 [http://www.genomicscience.energy.gov/compbio/kbase_plan/workshop3.pdf pdf] | ||
==Patents== | ==Patents== | ||
#Dunlop, Mary J.; Keasling, Jay D.; Mukhopadhyay, Aindrila Modified Host Cells with Efflux Pumps U.S. Patent Application Ser. No: 13/115,925 25-May-2011. [http://www.freepatentsonline.com/y2011/0294183.html online] or Go to Berkeley lab [http://www.lbl.gov/Tech-Transfer/techs/lbnl2845.html Tech Transfer] | #Dunlop, Mary J.; Keasling, Jay D.; Mukhopadhyay, Aindrila Modified Host Cells with Efflux Pumps U.S. Patent Application Ser. No: 13/115,925 25-May-2011. [http://www.freepatentsonline.com/y2011/0294183.html online] or Go to Berkeley lab [http://www.lbl.gov/Tech-Transfer/techs/lbnl2845.html Tech Transfer] | ||
#Mukhopadhyay, Aindrila; Mingardon, Florence; Chanal, Angelique. Modified Host Cells Having tolerance to α-Olefins. U.S. Patent Application Ser. No: 61/986,669 30-Apr-2014. | |||
==Recent invited talks== | ==Recent invited talks== | ||
#Mukhopadhyay A Engineering microbes for advanced biofuel production Genomic Science Awardee Meeting X Bethesda, Maryland
, February 26-29, 2012 [https://www.orau.gov/gtl2012/agenda.htm Plenary session] | #Mukhopadhyay A, Engineering Microbial Solvent Tolerance, Indo-US Conference and Workshop in Systems and Synthetic Biology, New Delhi, India, Nov 9-12 2014 [https://icares.wustl.edu/programs/Pages/Indo-US-Workshop-on-Synthetic-and-Systems-Biology.aspx link] | ||
#Mukhopadhyay A Engineering Solvent tolerant microbes for biofuel production. Invited talk, Society for Industrial Microbiology Annual Meeting, New Orleans, July 27th 2011 [http://sim.confex.com/sim/2011/webprogram/Paper19968.html Link] | #Mukhopadhyay A, Engineering Microbial Solvent Tolerance, SIMB, St Louise MO, USA, Jul 24th 2014 | ||
#Mukhopadhyay A. Study of yeast transcription factors as a strategy to discover new parts for cellular and metabolic engineering. Invited Talk, Yeast Synthetic biology Workshop, UC Mission Bay Campus, San Francisco, Oct 16th 2010. [http://vimeo.com/17126215 video] | #Mukhopadhyay A, Engineering Microbial Solvent Tolerance, Bioenergy and Photosynthesis Seminar, ASU, Tempe, AZ USA Feb 20th 2014 | ||
#Mukhopadhyay A Engineering Solvent tolerance using Efflux Pumps. Invited talk, Society for Industrial Microbiology Annual Meeting, San Francisco, CA, August 5, 2010. | #Mukhopadhyay A, Dynamic response of biological soil crust to wetting and drying events, 12th Biennial Conference of Science and Management on the Colorado Plateau Northern Arizona University, Flagstaff, Sept 18th 2013 | ||
#Mukhopadhyay A, Production of biofuels from lignocellulosic biomass using microbial systems. Invited Speaker, Indo-American Frontiers of Engineering Symposium, Jaypee Palace Hotel, Agra, India, March 10-13, 2010 [http://www.naefrontiers.org/Symposia/IAFOE/IA-PastSymposia/2010IAFOE.aspx link] | # Mukhopadhyay A, Engineering Microbial Solvent Tolerance, Energy Biosciences Institute Seminar Series, Berkeley CA, USA Sept 3rd 2013 [https://cc.readytalk.com/cc/playback/Playback.do?id=3jyojd see talk] | ||
#Mukhopadhyay A, Production of biofuels from lignocellulosic biomass using microbial systems. Invited Speaker, Special Departmental Seminar, Department of Chemistry, Indian Institute of Technology, Mumbai, India March 8th, 2010. | # Mukhopadhyay A Presenting at Science at the Theater event, [http://today.lbl.gov/2013/05/16/lab-researchers-discuss-their-%E2%80%98big-ideas%E2%80%99-at-recent-science-at-the-theater-talk/ Eight Big Ideas], Berkeley Repertory Theater, Berkeley CA USA May 13th 2013 | ||
# Mukhopadhyay A Lecture to ChemE Students (Biofuel production and processing, ChemE 437; Unit Ops II), invited by Prof James Carothers, University of Washington Seattle, USA, Feb 8th 2013 | |||
# Mukhopadhyay A Advances in Host Engineering for the production of Chemicals and Fuels, Bioenergy and Biotechnology Team, Reliance India Limited, Mumbai, India Jan 3rd 2013 | |||
# Mukhopadhyay A Advances in Host Engineering for production of Chemicals and Fuels, Special Seminar, DBT-ICT Center for Energy Biosciences, Mumbai, India, Dec 31st 2012 | |||
# Mukhopadhyay A Signaling and stress in natural and engineered microbes, Departmental Seminar, Washington University at St Louis, Missouri, Sept 21, 2012 | |||
# Mukhopadhyay A Society for General Microbiology, Fall Conference, Warwick, UK, Sept 3-5 2012 [http://www.sgm.ac.uk/meetings/past.cfm link] | |||
# Mukhopadhyay A Engineering Solvent Tolerant Microbes for Biofuel production, ITRI forum 2012, Milpitas, CA June 25th 2012 | |||
# Mukhopadhyay A Resolving Community and Metabolic Dynamics in Colorado Plateau Biological Soil Crusts, ASMCUE, San Mateo, June 15th 2012 [http://www.asmcue.org/page02c.shtml link] | |||
# Mukhopadhyay A Engineering microbes for advanced biofuel production Genomic Science Awardee Meeting X Bethesda, Maryland
, February 26-29, 2012 [https://www.orau.gov/gtl2012/agenda.htm Plenary session] | |||
# Mukhopadhyay A Engineering Solvent tolerant microbes for biofuel production. Invited talk, Society for Industrial Microbiology Annual Meeting, New Orleans, July 27th 2011 [http://sim.confex.com/sim/2011/webprogram/Paper19968.html Link] | |||
# Mukhopadhyay A. Study of yeast transcription factors as a strategy to discover new parts for cellular and metabolic engineering. Invited Talk, Yeast Synthetic biology Workshop, UC Mission Bay Campus, San Francisco, Oct 16th 2010. [http://vimeo.com/17126215 video] | |||
# Mukhopadhyay A Engineering Solvent tolerance using Efflux Pumps. Invited talk, Society for Industrial Microbiology Annual Meeting, San Francisco, CA, August 5, 2010. | |||
# Mukhopadhyay A, Production of biofuels from lignocellulosic biomass using microbial systems. Invited Speaker, Indo-American Frontiers of Engineering Symposium, Jaypee Palace Hotel, Agra, India, March 10-13, 2010 [http://www.naefrontiers.org/Symposia/IAFOE/IA-PastSymposia/2010IAFOE.aspx link] | |||
# Mukhopadhyay A, Production of biofuels from lignocellulosic biomass using microbial systems. Invited Speaker, Special Departmental Seminar, Department of Chemistry, Indian Institute of Technology, Mumbai, India March 8th, 2010. |
Revision as of 08:44, 26 November 2014
Refereed PublicationsM group pubs
Collaborations
M Postdoc and Graduate Research
Book Chapters, Invited articles and Reports
Patents
Recent invited talks
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