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845 results on '"Mukhopadhyay, Aindrila"'

201. Ecogenomics of groundwater viruses suggests niche differentiation linked to specific environmental tolerance

Author

Kothari, Ankita, primary, Roux, Simon, additional, Zhang, Hanqiao, additional, Prieto, Anatori, additional, Soneja, Drishti, additional, Chandonia, John-Marc, additional, Spencer, Sarah, additional, Wu, Xiaoqin, additional, Altenburg, Sara, additional, Fields, Matthew W., additional, Deutschbauer, Adam M., additional, Arkin, Adam P., additional, Alm, Eric J., additional, Chakraborty, Romy, additional, and Mukhopadhyay, Aindrila, additional

Published
2020
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202. Functional analysis of the fatty acid and alcohol metabolism ofPseudomonas putidausing RB-TnSeq

Author

Thompson, Mitchell G., primary, Incha, Matthew R., additional, Pearson, Allison N., additional, Schmidt, Matthias, additional, Sharpless, William A., additional, Eiben, Christopher B., additional, Cruz-Morales, Pablo, additional, Blake-Hedges, Jacquelyn M., additional, Liu, Yuzhong, additional, Adams, Catharine A., additional, Haushalter, Robert W., additional, Krishna, Rohith N., additional, Lichtner, Patrick, additional, Blank, Lars M., additional, Mukhopadhyay, Aindrila, additional, Deutschbauer, Adam M., additional, Shih, Patrick M., additional, and Keasling, Jay D., additional

Published
2020
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205. Chemoinformatic-Guided Engineering of Polyketide Synthases

Author

Zargar, Amin, primary, Lal, Ravi, additional, Valencia, Luis, additional, Wang, Jessica, additional, Backman, Tyler William H., additional, Cruz-Morales, Pablo, additional, Kothari, Ankita, additional, Werts, Miranda, additional, Wong, Andrew R., additional, Bailey, Constance B., additional, Loubat, Arthur, additional, Liu, Yuzhong, additional, Chen, Yan, additional, Chang, Samantha, additional, Benites, Veronica T., additional, Hernández, Amanda C., additional, Barajas, Jesus F., additional, Thompson, Mitchell G., additional, Barcelos, Carolina, additional, Anayah, Rasha, additional, Martin, Hector Garcia, additional, Mukhopadhyay, Aindrila, additional, Petzold, Christopher J., additional, Baidoo, Edward E. K., additional, Katz, Leonard, additional, and Keasling, Jay D., additional

Published
2020
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206. Population dynamics analysis ofSaccharomyces cerevisiaedeletion library during fed-batch cultivation using Bar-seq

Author

Wehrs, Maren, primary, Thompson, Mitchell G., additional, Banerjee, Deepanwita, additional, Prahl, Jan-Philip, additional, Barcelos, Carolina A., additional, Moon, Jadie, additional, Morella, Norma M., additional, Costello, Zak, additional, Keasling, Jay D., additional, Shih, Patrick M., additional, Tanjore, Deepti, additional, and Mukhopadhyay, Aindrila, additional

Published
2020
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209. Genome-scale metabolic rewiring to achieve predictable titers rates and yield of a non-native product at scale

Author

Banerjee, Deepanwita, primary, Eng, Thomas, additional, Lau, Andrew K., additional, Wang, Brenda, additional, Sasaki, Yusuke, additional, Herbert, Robin A., additional, Chen, Yan, additional, Liu, Yuzhong, additional, Prahl, Jan-Philip, additional, Singan, Vasanth R., additional, Tanjore, Deepti, additional, Petzold, Christopher J., additional, Keasling, Jay D., additional, and Mukhopadhyay, Aindrila, additional

Published
2020
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211. Generation of ionic liquid tolerant Pseudomonas putida KT2440 strains via adaptive laboratory evolution

Author

Lim, Hyun Gyu, primary, Fong, Bonnie, additional, Alarcon, Geovanni, additional, Magurudeniya, Harsha D., additional, Eng, Thomas, additional, Szubin, Richard, additional, Olson, Connor A., additional, Palsson, Bernhard O., additional, Gladden, John M., additional, Simmons, Blake A., additional, Mukhopadhyay, Aindrila, additional, Singer, Steven W., additional, and Feist, Adam M., additional

Published
2020
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214. Identification, Characterization, and Application of a Highly Sensitive Lactam Biosensor from Pseudomonas putida

Author

Thompson, Mitchell G., primary, Pearson, Allison N., additional, Barajas, Jesus F., additional, Cruz-Morales, Pablo, additional, Sedaghatian, Nima, additional, Costello, Zak, additional, Garber, Megan E., additional, Incha, Matthew R., additional, Valencia, Luis E., additional, Baidoo, Edward E. K., additional, Martin, Hector Garcia, additional, Mukhopadhyay, Aindrila, additional, and Keasling, Jay D., additional

Published
2019
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217. Evaluating Protic Ionic Liquid for Woody Biomass One-Pot Pretreatment + Saccharification, Followed by Rhodosporidium toruloides Cultivation

Author

Rigual, Victoria, primary, Papa, Gabriella, additional, Rodriguez, Alberto, additional, Wehrs, Maren, additional, Kim, Kwang Ho, additional, Oliet, Mercedes, additional, Alonso, M. Virginia, additional, Gladden, John M., additional, Mukhopadhyay, Aindrila, additional, Simmons, Blake A., additional, and Singh, Seema, additional

Published
2019
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219. Chemoinformatic-guided engineering of polyketide synthases

Author

Zargar, Amin, primary, Lal, Ravi, additional, Valencia, Luis, additional, Wang, Jessica, additional, Backman, Tyler William H., additional, Cruz-Morales, Pablo, additional, Kothari, Ankita, additional, Werts, Miranda, additional, Wong, Andrew R., additional, Bailey, Constance B., additional, Loubat, Arthur, additional, Liu, Yuzhong, additional, Chen, Yan, additional, Benites, Veronica T., additional, Chang, Samantha, additional, Hernández, Amanda C., additional, Barajas, Jesus F., additional, Thompson, Mitchell G., additional, Barcelos, Carolina, additional, Anayah, Rasha, additional, Martin, Hector Garcia, additional, Mukhopadhyay, Aindrila, additional, Petzold, Christopher J., additional, Baidoo, Edward E.K., additional, Katz, Leonard, additional, and Keasling, Jay D., additional

Published
2019
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222. Development of dual‐inducible duet‐expression vectors for tunable gene expression control and CRISPR interference‐based gene repression in Pseudomonas putida KT2440.

Author

Gauttam, Rahul, Mukhopadhyay, Aindrila, Simmons, Blake A., and Singer, Steven W.

Subjects
*GENE expression, *PSEUDOMONAS putida, *CRISPRS, *GENES, *PHENOTYPES
Abstract

Summary: The development of P. putida as an industrial host requires a sophisticated molecular toolbox for strain improvement, including vectors for gene expression and repression. To augment existing expression plasmids for metabolic engineering, we developed a series of dual‐inducible duet‐expression vectors for P. putida KT2440. A number of inducible promoters (Plac, Ptac, PtetR/tetA and Pbad) were used in different combinations to differentially regulate the expression of individual genes. Protein expression was evaluated by measuring the fluorescence of reporter proteins (GFP and RFP). Our experiments demonstrated the use of compatible plasmids, a useful approach to coexpress multiple genes in P. putida KT2440. These duet vectors were modified to generate a fully inducible CRISPR interference system using two catalytically inactive Cas9 variants from S. pasteurianus (dCas9) and S. pyogenes (spdCas9). The utility of developed CRISPRi system(s) was demonstrated by repressing the expression of nine conditionally essential genes, resulting in growth impairment and prolonged lag phase for P. putida KT2440 growth on glucose. Furthermore, the system was shown to be tightly regulated, tunable and to provide a simple way to identify essential genes with an observable phenotype. [ABSTRACT FROM AUTHOR]

Published
2021
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223. Rhizobacteria Mediate the Phytotoxicity of a Range of Biorefinery-Relevant Compounds

Author

Herbert, Robin A, Eng, Thomas, Martinez, Uriel, Wang, Brenda, Langley, Sasha, Wan, Kenneth, Pidatala, Venkataramana, Hoffman, Elijah, Chen, Joseph C, Bissell, Mina J, Brown, James B, Mukhopadhyay, Aindrila, and Mortimer, Jenny C

Subjects
plants, fungi, Arabidopsis, food and beverages, microbiome, Agriculture, Toxicology screening, Biological Sciences, Ecotoxicology, Plant Roots, biofuels, Ionic liquids, Climate Action, Affordable and Clean Energy, Chemical Sciences, Soil Pollutants, Biomass, Sorghum, Environmental Sciences, Rhizobium
Abstract

Advances in engineering biology have expanded the list of renewable compounds that can be produced at scale via biological routes from plant biomass. In most cases, these chemical products have not been evaluated for effects on biological systems, defined in the present study as bioactivity, that may be relevant to their manufacture. For sustainable chemical and fuel production, the industry needs to transition from fossil to renewable carbon sources, resulting in unprecedented expansion in the production and environmental distribution of chemicals used in biomanufacturing. Further, although some chemicals have been assessed for mammalian toxicity, environmental and agricultural hazards are largely unknown. We assessed 6 compounds that are representative of the emerging biofuel and bioproduct manufacturing process for their effect on model plants (Arabidopsis thaliana, Sorghum bicolor) and show that several alter plant seedling physiology at submillimolar concentrations. However, these responses change in the presence of individual bacterial species from the A. thaliana root microbiome. We identified 2 individual microbes that change the effect of chemical treatment on root architecture and a pooled microbial community with different effects relative to its constituents individually. The present study indicates that screening industrial chemicals for bioactivity on model organisms in the presence of their microbiomes is important for biologically and ecologically relevant risk analyses. Environ Toxicol Chem 2019;38:1911-1922. © 2019 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals, Inc. on behalf of SETAC.

Published
2019

224. Engineering Robust Production Microbes for Large-Scale Cultivation

Author

Wehrs, Maren, Tanjore, Deepti, Eng, Thomas, Lievense, Jeff, Pray, Todd R, and Mukhopadhyay, Aindrila

Subjects
Microbiological Techniques, scale-up, Systems Biology, Bioengineering, bioproduct, Microbiology, strain selection, bioreactor, Bioreactors, Medical Microbiology, Fermentation, microbial hosts, biofuel, mixing, heterogeneity, Genetic Association Studies
Abstract

Systems biology and synthetic biology are increasingly used to examine and modulate complex biological systems. As such, many issues arising during scaling-up microbial production processes can be addressed using these approaches. We review differences between laboratory-scale cultures and larger-scale processes to provide a perspective on those strain characteristics that are especially important during scaling. Systems biology has been used to examine a range of microbial systems for their response in bioreactors to fluctuations in nutrients, dissolved gases, and other stresses. Synthetic biology has been used both to assess and modulate strain response, and to engineer strains to improve production. We discuss these approaches and tools in the context of their use in engineering robust microbes for applications in large-scale production.

Published
2019

225. Integration of Genome-Scale Metabolic Model with Biorefinery Process Model Reveals Market-Competitive Carbon-Negative Sustainable Aviation Fuel Utilizing Microbial Cell Mass Lipids and Biogenic CO2.

Author

Baral, Nawa Raj, Banerjee, Deepanwita, Mukhopadhyay, Aindrila, Simmons, Blake A., Singer, Steven W., and Scown, Corinne D.

Subjects
*MICROBIAL lipids, *FOSSIL fuels, *CARBON sequestration, *MICROBIAL fuel cells, *AIRCRAFT fuels, *BIOCONVERSION
Abstract

Producing scalable, economically viable, low-carbon biofuels or biochemicals hinges on more efficient bioconversion processes. While microbial conversion can offer robust solutions, the native microbial growth process often redirects a large fraction of carbon to CO2 and cell mass. By integrating genome-scale metabolic models with techno-economic and life cycle assessment models, this study analyzes the effects of converting cell mass lipids to hydrocarbon fuels, and CO2 to methanol on the facility's costs and life-cycle carbon footprint. Results show that upgrading microbial lipids or both microbial lipids and CO2 using renewable hydrogen produces carbon-negative bisabolene. Additionally, on-site electrolytic hydrogen production offers a supply of pure oxygen to use in place of air for bioconversion and fuel combustion in the boiler. To reach cost parity with conventional jet fuel, renewable hydrogen needs to be produced at less than $2.2 to $3.1/kg, with a bisabolene yield of 80% of the theoretical yield, along with cell mass and CO2 yields of 22 wt% and 54 wt%, respectively. The economic combination of cell mass, CO2, and bisabolene yields demonstrated in this study provides practical insights for prioritizing research, selecting suitable hosts, and determining necessary engineered production levels. [ABSTRACT FROM AUTHOR]

Published
2024
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226. Assembly and Evolution of Artificial Metalloenzymes within E. coliNissle 1917 for Enantioselective and Site-Selective Functionalization of C─H and C═C Bonds

Author

Liu, Zhennan, Huang, Jing, Gu, Yang, Clark, Douglas S., Mukhopadhyay, Aindrila, Keasling, Jay D., and Hartwig, John F.

Abstract

The potential applications afforded by the generation and reactivity of artificial metalloenzymes (ArMs) in microorganisms are vast. We show that a non-pathogenic E. colistrain, Nissle 1917 (EcN), is a suitable host for the creation of ArMs from cytochrome P450s and artificial heme cofactors. An outer-membrane receptor in EcN transports an iridium porphyrin into the cell, and the Ir-CYP119 (CYP119 containing iridium porphyrin) assembled in vivocatalyzes carbene insertions into benzylic C–H bonds enantioselectively and site-selectively. The application of EcN as a whole-cell screening platform eliminates the need for laborious processing procedures, drastically increases the ease and throughput of screening, and accelerates the development of Ir-CYP119 with improved catalytic properties. Studies to identify the transport machinery suggest that a transporter different from the previously assumed ChuA receptor serves to usher the iridium porphyrin into the cytoplasm.

Published
2022
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228. Multiple signaling systems target a core set of transition metal homeostasis genes using similar binding motifs

Author

Garber, Megan E, Rajeev, Lara, Kazakov, Alexey E, Trinh, Jessica, Masuno, Duy, Thompson, Mitchell G, Kaplan, Nurgul, Luk, Joyce, Novichkov, Pavel S, and Mukhopadhyay, Aindrila

Subjects
Pseudomonas stutzeri, Agricultural and Veterinary Sciences, Human Genome, Bacterial, DNA, Biological Sciences, Microbiology, Medical and Health Sciences, Zinc, Bacterial Proteins, Gene Expression Regulation, Operon, Genetics, Homeostasis, Copper, Molecular Chaperones, Signal Transduction, Protein Binding, Biotechnology
Abstract

© 2018 John Wiley & Sons Ltd Bacterial response to metals can require complex regulation. We report an overlapping regulation for copper and zinc resistance genes in the denitrifying bacterium, Pseudomonas stutzeri RCH2, by three two-component regulatory proteins CopR1, CopR2 and CzcR. We conducted genome-wide evaluations to identify gene targets of two paralogous regulators, CopR1 and CopR2, annotated for copper signaling, and compared the results with the gene targets for CzcR, implicated in zinc signaling. We discovered that the CopRs and CzcR have largely common targets, and crossregulate a core set of P. stutzeri copper and zinc responsive genes. We established that this crossregulation is enabled by a conserved binding motif in the upstream regulatory regions of the target genes. The crossregulation is physiologically relevant as these regulators synergistically and antagonistically target multicopper oxidases, metal efflux and sequestration systems. CopR1 and CopR2 upregulate two cop operons encoding copper tolerance genes, while all three regulators downregulate a putative copper chaperone, Psest_1595. CzcR also upregulated the oprD gene and the CzcIABC Zn2+efflux system, while CopR1 and CopR2 downregulated these genes. Our study suggests that crossregulation of copper and zinc homeostasis can be advantageous, and in P. stutzeri this is enabled by shared binding motifs for multiple response regulators.

Published
2018

231. Rhizobacteria Mediate the Phytotoxicity of a Range of Biorefinery‐Relevant Compounds

Author

Herbert, Robin A., primary, Eng, Thomas, additional, Martinez, Uriel, additional, Wang, Brenda, additional, Langley, Sasha, additional, Wan, Kenneth, additional, Pidatala, Venkataramana, additional, Hoffman, Elijah, additional, Chen, Joseph C., additional, Bissell, Mina J., additional, Brown, James B., additional, Mukhopadhyay, Aindrila, additional, and Mortimer, Jenny C., additional

Published
2019
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232. Identification, characterization, and application of a highly sensitive lactam biosensor fromPseudomonas putida

Author

Thompson, Mitchell G., primary, Pearson, Allison N., additional, Barajas, Jesus F., additional, Cruz-Morales, Pablo, additional, Sedaghatian, Nima, additional, Costello, Zak, additional, Garber, Megan E., additional, Incha, Matthew R., additional, Valencia, Luis E., additional, Baidoo, Edward E. K., additional, Martin, Hector Garcia, additional, Mukhopadhyay, Aindrila, additional, and Keasling, Jay D., additional

Published
2019
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233. A toolset of constitutive promoters for metabolic engineering of Rhodosporidium toruloides

Author

Nora, Luísa Czamanski, primary, Wehrs, Maren, additional, Kim, Joonhoon, additional, Cheng, Jan-Fang, additional, Tarver, Angela, additional, Simmons, Blake A., additional, Magnuson, Jon, additional, Harmon-Smith, Miranda, additional, Silva-Rocha, Rafael, additional, Gladden, John M., additional, Mukhopadhyay, Aindrila, additional, Skerker, Jeffrey M., additional, and Kirby, James, additional

Published
2019
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236. Methyl ketone production by Pseudomonas putida is enhanced by plant‐derived amino acids

Author

Dong, Jie, primary, Chen, Yan, additional, Benites, Veronica Teixeira, additional, Baidoo, Edward E.K., additional, Petzold, Christopher J., additional, Beller, Harry R., additional, Eudes, Aymerick, additional, Scheller, Henrik V., additional, Adams, Paul D., additional, Mukhopadhyay, Aindrila, additional, Simmons, Blake A., additional, and Singer, Steven W., additional

Published
2019
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238. A toolset of constitutive promoters for metabolic engineering ofRhodosporidium toruloides

Author

Nora, Luísa Czamanski, primary, Wehrs, Maren, additional, Kim, Joonhoon, additional, Cheng, Jan-Fang, additional, Tarver, Angela, additional, Simmons, Blake A., additional, Magnuson, Jon, additional, Harmon-Smith, Miranda, additional, Silva-Rocha, Rafael, additional, Gladden, John M., additional, Mukhopadhyay, Aindrila, additional, Skerker, Jeffrey M., additional, and Kirby, James, additional

Published
2019
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241. Correction: Sustainable bioproduction of the blue pigment indigoidine: Expanding the range of heterologous products in R. toruloides to include non-ribosomal peptides

Author

Wehrs, Maren, primary, Gladden, John M., additional, Liu, Yuzhong, additional, Platz, Lukas, additional, Prahl, Jan-Philip, additional, Moon, Jadie, additional, Papa, Gabriella, additional, Sundstrom, Eric, additional, Geiselman, Gina M., additional, Tanjore, Deepti, additional, Keasling, Jay D., additional, Pray, Todd R., additional, Simmons, Blake A., additional, and Mukhopadhyay, Aindrila, additional

Published
2019
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242. Sustainable bioproduction of the blue pigment indigoidine: Expanding the range of heterologous products inR. toruloidesto include non-ribosomal peptides

Author

Wehrs, Maren, primary, Gladden, John M., additional, Liu, Yuzhong, additional, Platz, Lukas, additional, Prahl, Jan-Philip, additional, Moon, Jadie, additional, Papa, Gabriella, additional, Sundstrom, Eric, additional, Geiselman, Gina M., additional, Tanjore, Deepti, additional, Keasling, Jay D., additional, Pray, Todd R., additional, Simmons, Blake A., additional, and Mukhopadhyay, Aindrila, additional

Published
2019
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243. Isolation and Characterization of Bacterial Cellulase Producers for Biomass Deconstruction: A Microbiology Laboratory Course

Author

Barajas, Jesus F., primary, Wehrs, Maren, additional, To, Milton, additional, Cruickshanks, Lauchlin, additional, Urban, Rochelle, additional, McKee, Adrienne, additional, Gladden, John, additional, Goh, Ee-Been, additional, Brown, Margaret E., additional, Pierotti, Diane, additional, Carothers, James M., additional, Mukhopadhyay, Aindrila, additional, Keasling, Jay D., additional, Fortman, Jeffrey L., additional, Singer, Steven W., additional, and Bailey, Constance B., additional

Published
2019
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245. Methyl ketone production byPseudomonas putidais enhanced by plant-derived amino acids

Author

Dong, Jie, primary, Chen, Yan, additional, Benites, Veronica Teixeira, additional, Baidoo, Edward E.K., additional, Petzold, Christopher J., additional, Beller, Harry R., additional, Eudes, Aymerick, additional, Scheller, Henrik V., additional, Adams, Paul D., additional, Mukhopadhyay, Aindrila, additional, Simmons, Blake A., additional, and Singer, Steven W., additional

Published
2018
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248. Restoration of biofuel production levels and increased tolerance under ionic liquid stress is enabled by a mutation in the essential Escherichia coli gene cydC

Author

Eng, Thomas, primary, Demling, Philipp, additional, Herbert, Robin A., additional, Chen, Yan, additional, Benites, Veronica, additional, Martin, Joel, additional, Lipzen, Anna, additional, Baidoo, Edward E. K., additional, Blank, Lars M., additional, Petzold, Christopher J., additional, and Mukhopadhyay, Aindrila, additional

Published
2018
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249. A rapid and inexpensive labeling method for microarray gene expression analysis

Author

Adams Paul D, Ouellet Mario, Keasling Jay D, and Mukhopadhyay Aindrila

Subjects
Biotechnology, TP248.13-248.65
Abstract

Abstract Background Global gene expression profiling by DNA microarrays is an invaluable tool in biological research. However, existing labeling methods are time consuming and costly and therefore often limit the scale of microarray experiments and sample throughput. Here we introduce a new, fast, inexpensive method for direct random-primed fluorescent labeling of eukaryotic cDNA for gene expression analysis and compare the results obtained on the NimbleGen microarray platform with two other widely-used labeling methods, namely the NimbleGen-recommended double-stranded cDNA protocol and the indirect (aminoallyl) method. Results Two total RNA samples were labeled with each method and hybridized to NimbleGen expression arrays. Although all methods tested here provided similar global results and biological conclusions, the new direct random-primed cDNA labeling method provided slightly better correlation between replicates compared to the other methods and thus increased ability to find statistically significant differentially expressed genes. Conclusion The new direct random-primed cDNA labeling method introduced here is suitable for gene expression microarrays and provides a rapid, inexpensive alternative to existing methods. Using NimbleGen microarrays, the method produced excellent results comparable to those obtained with other methods. However, the simplicity and cost-effectiveness of the new method allows for increased sample throughput in microarray experiments and makes the process amenable to automation with a relatively simple liquid handling system.

Published
2009
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