Research Areas

Yeast in space:

This project is a launchpad to understand how radiation works on the human body both in space and earth. The yeast and alge samples sent as probes will help understand which mutants thrive the best and which don't, and in turn elucidate which genes are most important for surviving cosmic radiation.

Chemogenomic Screens in Yeast:

Variant profiling in humanized yeast

This research involves designing an approach to link genetic variations to drug response and in the process translate variants of unknown significance into actionable variants especially those that affect phenotype using humanize yeast. The objective is to use this strategy to quantitate all variants by capturing drug response in the target gene, leading to their functional characterization in terms of drug resistance and sensitivity.

Single-cell variation response to drug perturbation

This research focuses on single cell variation response to drugs to investigate how genetically identical yeast cells respond differently to drugs at the DNA, transcription, and translation level. Our goal is to establish a baseline, by creating a collection of barcoded genetically identical yeast cells, to address fundamental questions about the role of non-genomic factors affecting various responses to drugs and ultimately other environmental stressors.

Developing high-throughput method to assess retrotransposon insertion frequency

Transposable elements are mobile DNA elements comprising repeated sequences that can change their location within a genome. Retrotransposons mobilize via RNA intermediates and their mobilization in the human genome can cause various diseases. In Saccharomyces cerevisiae, the most abundant retrotransposon is called Ty1 which is present at ~ 32 copies in the S.cerevisiae S288c genome. Ty1 is ~6kb long, and often integrates within a 1kb window upstream of diverse genes that are transcribed by RNA Polymerase III, such as transferRNA (tRNA) genes. The aim of my project is to develop and validate a high-throughput, genome-wide method to assess Ty1 insertion frequency upstream of tRNA genes in S. cerevisiae. My goal is to multiplex my PCR reactions to interrogate multiple tRNA insertion events at once and testing different analytical methods to measure any qualitative and quantitative differences between wildtype and mutant that are suspected to be involved in the aspects of retrotransposon biology.

Investigating the mechanism of anthracycline by manipulating variants of pharmacogenomic importance

Anthracyclines are among the most effective anticancer treatments developed so far. The broad use of these chemotherapeutic agents in different types of cancer has dramatically improved the overall cancer survival statistics. But, in many cases, the development of drug resistance may render anthracyclines ineffective. Through this work, the goal is to identify novel variants that confer resistance to these cancer drugs and characterize the underlying mechanism by utilizing several doxorubicin-resistant yeast strains.

Understanding the role and mechanisms of mycoparasitism through mutant analysis

We are using a parallel mutant analysis to identify hit deletion mutants of S. cerevisiae that could be susceptible or resistant to S. schoenii. Genes, by virtue of their deletion mutants and complexity of yeast-yeast interaction genetics, involved in diverse cell processes could be involved in the prey-predator interaction during predation. This study will provide important insights on predation biology.

Spinpods: Utilizing 3D-cell culture:

This research is to make spheroids from different mammalian cell lines using Spinpod which can simulate low-shear modeled microgravity to investigate its effect on gene expression. These cell spinpods are injection-molded polystyrene and polycarbonate cylinders acting as suspension culture devices to deliver fluid shear stress to cells. It's components include CAD renderings and a cell/media chamber sandwiched between two breathable membranes. They also possess two surface-bonded self-sealing silicone rubber needle ports for loading cells/media and for bleeding the air during loading.

Single-Cell based assays:

Antibody secreting cells are rare (≈0.01 to 1% of circulating and lymphoid cells), differentiated cells that are hard to culture in native state. Mature ASCs have minimal or complete absence of B cell receptors (BCRs) on their surface due to its release in form of secreting antibodies. Most of antibody discovery platforms highly rely on hybridomas that have their own shortcomings. Here, we are combining our present knowledge of ASCs with the resources available in form of flow-cytometers, transgenic mice, microencapsulation devices and state of the art single cell screening platforms to decipher the best enrichment strategy for ASCs with improved cell recovery and viability. This will enable next-generation sequencing (NGS) based screening of rare ASCs clones with their antibody repertoire more efficiently.

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