Building novel high-throughput technologies with the ability to transform the design and development of protein-based drugswww.protillion.com

Lead Assay Development efforts towards detecting and serotyping Salmonella in a single testAm also involved in building a completely automated 3-in-1 Listeria detection, speciation and mapping test.

There are over 2500 serotypes of Salmonella! Determining the serotype of the Salmonella in food is a tedious, slow and subjective process. I currently lead the effort to develop an automated molecular serotyping solution for Salmonella.

Food safety is a prime concern for manufacturers and producers in the food industry. We have developed a fully automated NGS-based platform to detect and serotype Salmonella in different food matrices. My main contributions are towards the development of the molecular biology workflow that powers the assay.

Towards a quantitative, predictive understanding of RNA-protein interactions - How do RNA binding proteins recognize and bind their RNA targets? Initiated and completed an ambitious project to systematically and accurately measure biophysical parameters of binding of 6 eukaryotic Pumilio RBPs to a library of >25,000 unique RNA sequences on a novel, massively parallel, Illumina-based microfluidics platform Helped develop custom software in Python for the analysis and visualization of resultant multi-dimensional datasets and for modeling the binding of protein to RNA on the flow-cell Developed an accurate affinity-based model to describe RNA-Pumilio binding interactions Have also shown that common mRNA modifications alter protein:RNA interactions suggesting important functional roles for the RNA epitranscriptome in the regulation of gene expression- What factors regulate protein recognition of and occupancy on mRNA targets?Building on our in vitro thermodynamic and kinetic measurements of protein binding to RNA, we are developing a quantitative model to predict RNA-protein interactions in human cells.

How is gene-specific translational regulation achieved in eukaryotes?- I initiated and led a project to measure genome-wide protein translation at single codon resolution using ribosome footprint profiling (Ribo-seq) and RNA-seq in glucose-fed and glucose-starved yeast- I showed that prolonged glucose withdrawal dramatically alters the translational efficiency of a large number of yeast genes via a PKA-mediated mechanism. - Developed custom Python pipelines for analysis and visualization of sequencing data How do ribosome-associated proteins regulate gene expression at the level of protein translation?- Using ribosome footprint profiling, I studied the gene expression regulatory roles of Translation Machinery Associated (TMA) proteins that are upregulated in response to a variety of environmental stresses - Using mass spectrometry, we also identified two novel proteins that are specifically enriched on actively translating ribosomes from glucose-starved cells. A graduate student in the lab is further characterizing these proteins

Provided leadership and vision for the Boston chapter of Association for India's Development (AID), helped coordinate 4 major fundraisers in 2012, ran the Bay State marathon in 2012 and raised $3400 for AID. Was recognized by India New England online paper for my volunteering efforts

Designed, developed and taught one molecular biology class on the fundamentals of ribosome biogenesis and RNA modification.

Trained undergraduate and graduate students in basic molecular biology techniques employed in protein purification for X-ray crystallography and in RNA modification.

Arun Malhotra Ph.D. and Murray P Deutscher Ph.D. (Advisors)Research focused on the substrate specificity of 6 23S RNA pseudouridine synthases (RluA - RluF) and the role of pseudouridines in ribosome biogenesis. Discovered that RluD, an important 23S RNA pseudouridine synthase in E. coli, chooses its three target uridines on Helix 69 for modification in the context of the 50S subunit rather than on free RNA. In an effort to understand the roles of some of the 23S RNA pseudouridine synthases, we constructed a quintuple deletion strain lacking these 5 enzymes and their 7 pseudouridines. Surprisingly, although the mutant strain is viable, it fares more poorly than wild-type in high-salt media suggesting that these 23S RNA pseudouridines may be involved in protecting the ribosome from salinity stress.

Designed, developed and tested software in an Enterprise Java project that aimed at internet enabling legacy banking software. Responsibilities included, among others, coordinating the on-site and off-shore development teams, developing model code templates for the development team to utilize, exploration of new technologies and their incorporation into existing frameworks, peer reviews and unit-level, performance, integration and functional testing of code.