Aindrila Mukhopadhyay

This study improves acetate tolerance in Pseudomonas putida through adaptive laboratory evolution and identifies gacA and fabB as key targets for efficient acetate assimilation.

The paper identifies target genes for 31 transcription factors in two Rhodanobacter strains using DAP-seq and comparative genomics, revealing conserved regulatory networks and a key global regulator Clp.

This study identifies distinct TNT bioremediation strategies in Pantoea sp. MT58 and P. putida KT2440 using proteomics and RB-TnSeq, revealing nitrogen assimilation versus stress tolerance mechanisms.

This study evolves a microbial strain under dynamic conditions to optimize sugar catabolism, finding that mixed-sugar environments promote stable retention and coordinated optimization of multiple pathways.

This study identifies tolerance mechanisms in Paraburkholderia graminis OAS925 to alcohol and salt stress using RB-TnSeq, revealing key genes involved in membrane transport, efflux systems, signaling, and oxidative stress response.

The paper uses a biosensor-driven strategy to enhance isoprenol production in Pseudomonas putida through combinatorial strain engineering and omics analysis.

This study compares GenBank and RefSeq annotations for Pseudomonas putida KT2440, showing 16% of ORFs differ in genomic position and highlighting potential impacts on RNA-seq analysis.

This study uses RB-TnSeq to identify genetic basis of dicarboxylic acid metabolism in β-proteobacteria, revealing distinct metabolic pathways and enabling plastic waste upcycling.

This study shows that modifying lignin composition in Brachypodium distachyon changes root exudates and microbiome composition, affecting microbial colonization and community structure.

This study uses adaptive laboratory evolution and rational engineering to improve Pseudomonas putida's tolerance to isoprenol, enhancing its production of a sustainable aviation fuel precursor.

The paper identifies and validates novel plasmid origins of replication from an environmental Pantoea strain, enabling expression of heterologous proteins and pathways in both model and non-model bacteria.

This study introduces two methods, FluxRETAP and VAMMPIRE, to improve CRISPRi-mediated gene downregulation for bioproduction by enhancing target identification and multiplexed construct assembly.

This paper develops acetate-tolerant Pseudomonas putida strains for isoprenol production using mixed carbon sources and identifies molecular mechanisms underlying tolerance and production.

This study identifies fumarate hydratase activity as a bottleneck in a genome-scale metabolic model design for bioproduction from para-coumarate, requiring optimization for growth and product formation.

BioPKS Pipeline automates the design of chimeric type I polyketide synthases and enzymatic pathways to synthesize target chemicals, achieving exact designs for 93 of 155 tested molecules and proposing routes for complex natural products.

This study demonstrates the use of EcoFABs to measure horizontal gene transfer frequency in the rhizosphere of Brachypodium distachyon, showing dependencies on plant stage, root exudates, donor cell numbers, and environmental stress.

This paper engineers Corynebacterium glutamicum to produce 2,3,5,6-tetramethylpyrazine (TMP) at high titer using statistical design of experiments to optimize media composition.

The paper develops growth-coupled microbial strains for high-yield indigoidine production using iterative engineering and computational evaluation.

This paper engineers Pseudomonas putida for isoprenol production using computational modeling and strain optimization, achieving a titer of 3.5 g/L.

The paper optimizes a P. putida strain for indigoidine production using 13C-MFA and metabolomics, identifying key metabolic bottlenecks and engineering improvements.

The paper describes a microfluidic system for high-throughput CRISPR-based gene editing and screening, demonstrating its ability to perform parallel genetic modifications in E. coli.

The paper resequences and analyzes transcriptomic changes in an engineered C. glutamicum strain under bioreactor conditions with and without ionic liquid stress.

The paper identifies gene deletions that enhance indigoidine production in Pseudomonas putida using fitness profiling and bioreactor experiments.

The paper develops a highly sensitive biosensor for caprolactam and valerolactam from Pseudomonas putida, capable of detecting product titers above background at ~6 g/L.

The paper validates a native plasmid-encoded mercury resistance operon in groundwater bacteria and identifies strains capable of natural transformation.

The paper identifies and characterizes 20 constitutive promoters in Rhodosporidium toruloides for use in genetic engineering and metabolic pathway optimization.

The paper analyzes plasmid DNA from groundwater to identify metal resistance genes, finding abundant mercury resistance genes despite low mercury levels.