Namrata

I am currently pursuing PhD at Institut de Génomique Fonctionnelle de Lyon (IGFL), as part of the ANR RePlay project, which investigates whether leg regeneration reuses developmental gene regulatory networks (GRNs). Using the crustacean Parhyale hawaiensis as a model organism, I integrate single-nuclei RNA-seq and ATAC-seq (snMultiome) data to reconstruct GRNs at cell-type resolution during leg development and regeneration. My research combines molecular and computational approaches, using tools such as single-nuceli multiome sequencing and SCENIC+ to identify shared and regeneration-specific regulatory modules and validate key nodes through transgenic reporter assays.

I hold a Master’s degree in Bioinformatics from KU Leuven and have a strong interest in interdisciplinary research that integrates laboratory and computational approaches. My master’s thesis was focussed on the characterization of microproteins in the proteome landscape. Additionally, I am committed to promoting environmental sustainability.

Previously, I worked as a Bio-Lab manager in a non-profit organization called Center for Sustainable Agriculture (CSA), Hyderabad. There I established a bio-lab to produce and maintain mother-cultures of beneficial soil microbes and test the quality of liquid biofertilizers. I also trained farmers across several villages in Andhra Pradesh, India, to become bio-entrepreneurs by self-producing and marketing biofertilizers.

Before joining CSA, I worked in the RNA Biology Lab under the supervision of Dr. Debojyoti Chakraborty at CSIR-IGIB, New Delhi. My work included purification of Cas9 protein variants, comparison of off-target activities of SpCas9 (Streptococcus pyogenes Cas9) and FnCas9 (Francisella novicida Cas9 ) proteins, and identification of position-specific mismatch detection property of FnCas9 protein. I also discerned the staggered pattern of DNA cleavage produced by FnCas9. This work resulted in the development of an inexpensive paper-based COVID diagnostic kit named FELUDA. See my publications in this area.

I have earned my BSc and MSc in Zoology from the University of Delhi with summa cum laude.

My hobbies are cooking, dancing, singing, yoga, and reading (non-fiction). I was born in Siwan, the birthplace of the first President of India, Dr. Rajendra Prasad.

selected publications

Biosens. Bioelect.

Rapid and accurate nucleobase detection using FnCas9 and its application in COVID-19 diagnosis

Mohd Azhar , Rhythm Phutela , Manoj Kumar , and 24 more authors

Biosensors and Bioelectronics, 2021

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Rapid detection of DNA/RNA pathogenic sequences or variants through point-of-care diagnostics is valuable for accelerated clinical prognosis, as witnessed during the recent COVID-19 outbreak. Traditional methods relying on qPCR or sequencing are tough to implement with limited resources, necessitating the development of accurate and robust alternative strategies. Here, we report FnCas9 Editor Linked Uniform Detection Assay (FELUDA) that utilizes a direct Cas9 based enzymatic readout for detecting nucleobase and nucleotide sequences without trans-cleavage of reporter molecules. We also demonstrate that FELUDA is 100% accurate in detecting single nucleotide variants (SNVs), including heterozygous carriers, and present a simple web-tool JATAYU to aid end-users. FELUDA is semi-quantitative, can adapt to multiple signal detection platforms, and deploy for versatile applications such as molecular diagnosis during infectious disease outbreaks like COVID-19. Employing a lateral flow readout, FELUDA shows 100% sensitivity and 97% specificity across all ranges of viral loads in clinical samples within 1hr. In combination with RT-RPA and a smartphone application True Outcome Predicted via Strip Evaluation (TOPSE), we present a prototype for FELUDA for CoV-2 detection closer to home.
PNAS

Francisella novicida Cas9 interrogates genomic DNA with very high specificity and can be used for mammalian genome editing

Sundaram Acharya , Arpit Mishra , Deepanjan Paul , and 14 more authors

Proceedings of the National Academy of Sciences, 2019

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Genome editing using the CRISPR/Cas9 system has been used to make precise heritable changes in the DNA of organisms. Although the widely used Streptococcus pyogenes Cas9 (SpCas9) and its engineered variants have been efficiently harnessed for numerous gene-editing applications across different platforms, concerns remain regarding their putative off-targeting at multiple loci across the genome. Here we report that Francisella novicida Cas9 (FnCas9) shows a very high specificity of binding to its intended targets and negligible binding to off-target loci. The specificity is determined by its minimal binding affinity with DNA when mismatches to the target single-guide RNA (sgRNA) are present in the sgRNA:DNA heteroduplex. FnCas9 produces staggered cleavage, higher homology-directed repair rates, and very low nonspecific genome editing compared to SpCas9. We demonstrate FnCas9-mediated correction of the sickle cell mutation in patient-derived induced pluripotent stem cells and propose that it can be used for precise therapeutic genome editing for a wide variety of genetic disorders.