"It is not because things are difficult that we do not dare; it is because we do not dare that things are difficult" Seneca
- tanmay.tanna@ inf.ethz.ch
My research focuses on creating computational tools for synthetic biology, metagenomics and transcriptomics. I am also interested in integrating different types of omics data for health and diagnostic applications.
I am a joint doctoral student at Prof. Gunnar Rätsch’s group at the D-INFK and Prof. Randall Platt’s group at the D-BSSE.
I completed my MSc in Biology with a major in Molecular Health Sciences at the ETH on an Inlaks foundation fellowship. During my MSc, I focused on computational biology, testing algorithms for the analysis of time-series transcriptomic data or working on the prediction of protein structural changes by applying machine learning to NMR spectra. As part of my master’s thesis at Prof. Platt’s group, I was involved in developing the statistical and computational framework for analyzing data generated by a novel transcriptomic technology, Record-seq.
Prior to joining ETH, I completed a Bachelor of Technology in Biotechnology at the National Institute of Technology, Warangal, India. During my bachelor’s, I spent some time at the University of Tokyo working with ChIP-seq data analysis, and undertook my thesis as an Erasmus exchange fellow at the Warsaw University of Life Sciences.
Abstract Engineered microbes show potential for diagnosing and treating diseases. In this issue of Cell Host & Microbe, Zou et al. develop an “intelligent” bacterial strain that detects and monitors an inflammation biomarker in the gut and responds by releasing an immunomodulator, thereby combining diagnosis and therapy for intestinal inflammation.
Authors Tanmay Tanna, Randall J. Platt
Submitted Cell Host and Microbe
Abstract Transcriptional recording by CRISPR spacer acquisition from RNA endows engineered Escherichia coli with synthetic memory, which through Record-seq reveals transcriptome-scale records. Microbial sentinels that traverse the gastrointestinal tract capture a wide range of genes and pathways that describe interactions with the host, including quantitative shifts in the molecular environment that result from alterations in the host diet, induced inflammation, and microbiome complexity. We demonstrate multiplexed recording using barcoded CRISPR arrays, enabling the reconstruction of transcriptional histories of isogenic bacterial strains in vivo. Record-seq therefore provides a scalable, noninvasive platform for interrogating intestinal and microbial physiology throughout the length of the intestine without manipulations to host physiology and can determine how single microbial genetic differences alter the way in which the microbe adapts to the host intestinal environment.
Authors Florian Schmidt, Jakob Zimmermann, Tanmay Tanna, Rick Farouni, Tyrell Conway, Andrew J Macpherson, and Randall J Platt
Engineered bacteria to report gut function: technologies and implementation Current Opinion in Microbiology
Abstract Advances in synthetic biology and microbiology have enabled the creation of engineered bacteria which can sense and report on intracellular and extracellular signals. When deployed in vivo these whole-cell bacterial biosensors can act as sentinels to monitor biomolecules of interest in human health and disease settings. This is particularly interesting in the context of the gut microbiota, which interacts extensively with the human host throughout time and transit of the gut and can be accessed from feces without requiring invasive collection. Leveraging rational engineering approaches for genetic circuits as well as an expanding catalog of disease-associated biomarkers, bacterial biosensors can act as non-invasive and easy-to-monitor reporters of the gut. Here, we summarize recent engineering approaches applied in vivo in animal models and then highlight promising technologies for designing the next generation of bacterial biosensors.
Authors Tanmay Tanna, Raghavendra Ramachanderan, Randall J Platt
Submitted Current Opinion in Microbiology
Abstract It is difficult to elucidate the transcriptional history of a cell using current experimental approaches, as they are destructive in nature and therefore describe only a moment in time. To overcome these limitations, we recently established Record-seq, a technology that enables transcriptional recording by CRISPR spacer acquisition from RNA. The recorded transcriptomes are recovered by SENECA, a method that selectively amplifies expanded CRISPR arrays, followed by deep sequencing. The resulting CRISPR spacers are aligned to the host genome, thereby enabling transcript quantification and associated analyses. Here, we describe the experimental procedures of the Record-seq workflow as well as subsequent data analysis. Beginning with the experimental design, Record-seq data can be obtained and analyzed within 1–2 weeks.
Authors Tanmay Tanna, Florian Schmidt, Mariia Y. Cherepkova, Michal Okoniewski, Randall J. Platt
Submitted Nature Protocols