Pratik Kumar, PhD

Pratik Kumar, PhD

HHMI Postdoctoral Associate

Janelia Research Campus

  I am an HHMI postdoc with Luke Lavis (Janelia). I use fluorescent dyes to make reagents for cell biology, neuroscience, pharmacology, and imaging.
  During my PhD with Scott Laughlin, I made light and enzyme-controlled cyclopropenes for bioorthogonal labeling/imaging in cellular systems. Before coming to the US, as an undergrad, I worked on bactericidal, cationic gemini surfactants with Jayanta Haldar.
  I strongly care about effective mentoring, diversity in academia, awareness about “alternative” career options, and communicating my science to public.

Interests

  • Fluorescent Tools
  • Bioorthogonal Reagents
  • Biological Imaging
  • Biomolecule Manipulation
  • Effective Mentoring
  • Diversity in Science
  • Scientific Awareness

Education

  • PhD, Chemistry, 2019

    Stony Brook University, New York, US

  • MS and BS, Chemistry, 2013

    IISER-K, Kolkata, IN

  • Diploma, Chemistry, 2009-11

    JNCASR, Bangalore, IN

  • Scientists Teaching Science, 2020

    Certificate

  • OMIBS, 2018

    Marine Biological Laboratory, Woods Hole, US

Research Experience

 
 
 
 
 

HHMI Postdoctoral Associate w/ Luke Lavis

HHMI-Janelia Research Campus

Jul 2019 – Present Virginia, USA
 
 
 
 
 

Graduate Student w/ Scott Laughlin

Stony Brook University

Aug 2013 – May 2019 New York, USA
 
 
 
 
 

POCE Fellowship w/ Jayanta Haldar

JNCASR

Aug 2010 – May 2012 Bangalore, India

Research Summary

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Postdoc PhD Undergrad All

Caged Cyclopropenes

Using light or enzymes to control the bioorthogonal reactions of cyclopropenes

Bioorthogonal Neurotransmitters

Bringing bioorthogonal chemistry to the realm of neuroscience

Lipidated Spirocyclopropyls

Synthesis of spirocyclic systems, cyclic enamines, and their conjugation to lipids

Olfactory Circuit Labeling

Testing fluorescent boronic acid probes as tracers of neural circuitry

Bactericidal Gemini Surfactants

Biodegradable cationic surfactants that kill bacterial cells but not mammalian cells

Multiclick dyes

Far-red emitting dyes that fluoresce upon bioorthogonal activation

Multifunctional dyes

Visualizing and manipulating biomolecules

Single-molecule imaging dyes

Novel photoactivatable rhodamine dyes for single particle tracking

Publications

Live imaging of the extracellular matrix with a glycan-binding fluorophore

Antonio Fiore, Guoqiang Yu, Jason J. Northey, Ronak Patel, Thomas A. Ravenscroft, Richard Ikegami, Wiert Kolkman, Pratik Kumar, Tanya L. Dilan, Virginia M.S. Ruetten, Misha B. Ahrens, Hari Shroff, Shaohe Wang, Valerie M. Weaver, Kayvon Pedram
November 2024 Nature Methods, Accepted in principle
All multicellular systems produce and dynamically regulate extracellular matrices (ECM) that play essential roles in both biochemical and mechanical signaling. Though the spatial arrangement of these …
DOI

Transforming chemigenetic bimolecular fluorescence complementation systems into chemical dimerizers using chemistry

Pratik Kumar, Alina Gutu, Amelia Waring, Timothy A. Brown, Luke D. Lavis, Alison G. Tebo
January 2024 In Review
Chemigenetic tags are versatile labels for fluorescence microscopy that combine some of the advantages of genetically encoded tags with small molecule fluorophores. The Fluorescence Activating and …
PDF Project DOI

Single-cell synaptome mapping of endogenous protein subpopulations in mammalian brain

Motokazu Uchigashima, Risa Iguchi, Kazuma Fujii, Pratik Kumar, Xinyi Liu, Manabu Abe, Motohiro Nozumi, Yosuke Okamura, Michihiro Igarashi, Kenji Sakimura, Ryoma Bise, Luke Lavis, Takayasu Mikuni
September 2023 In Review
Different spatial or temporal protein populations, such as cell-surface/intracellular or pre-existing/nascent subpopulations, determine the basal and activity-induced functions of individual synapses …
Project

Lipid Expansion Microscopy

Brittany M. White, Pratik Kumar, Amanda N. Conwell, Kane Wu, Jeremy M. Baskin
October 2022 Journal of the American Chemical Society, 144, 40, 18212-18217
Strategies to visualize cellular membranes with light microscopy are restricted by the diffraction limit of light, which far exceeds the dimensions of lipid bilayers. Here, we describe a method for …
Dataset Project DOI Cornell News

Multifunctional Fluorophores for Live-Cell Imaging and Affinity Capture of Proteins

Pratik Kumar, Jason D. Vevea, Edwin R. Chapman, Luke D. Lavis
July 2022 In Review
The development of enzyme-based self-labeling tags allow the labeling of proteins in living cells with synthetic small-molecules. Use of a fluorophore-containing ligand enables the visualization of …
Dataset Project DOI preLights

Melding Synthetic Molecules and Genetically Encoded Proteins to Forge New Tools for Neuroscience

Pratik Kumar, Luke D. Lavis
February 2022 Annual Review of Neuroscience, 45, 131-150
Unraveling the complexity of the brain requires sophisticated methods to probe and perturb neurobiological processes with high spatiotemporal control. The field of chemical biology has produced …
PDF Project DOI

2,7-Diaminobenzopyrylium Dyes are Live-Cell Mitochondrial Stains

Sambashiva Banala, Ariana Tkachuk, Ronak Patel, Pratik Kumar, Timothy Brown, Luke D. Lavis
February 2022 ACS Bio & Med Chem Au, 2(3), 307-312
Small-molecule fluorescent stains enable the imaging of cellular structures without the need for genetic manipulation. Here, we introduce 2,7-diaminobenzopyrylium (DAB) dyes as live-cell mitochondrial …
Dataset DOI

Modular Enzyme- and Light-Based Activation of Cyclopropene-Tetrazine Ligation

Ting Jiang, Pratik Kumar, Wei Huang, Wei-Siang Kao, Adrian O. Thompson, Frank M. Camarda, Scott T. Laughlin
September 2019 ChemBioChem, 20(17), 2222-2226
We describe a modular activation strategy for cyclopropene-tetrazine ligation. This activation strategy uses chemically diverse enzyme- or photolabile protecting groups as cyclopropene reactivity …
Dataset Project DOI

Stable Cyclopropene-Containing Analogs of the Amino Acid Neurotransmitter Glutamate

Pratik Kumar, Wei Huang, David Shukhman, Frank M. Camarda, Scott T. Laughlin
May 2019 Tetrahedron Letters, 60(22), 1476-1480
As a neurotransmitter, the amino acid glutamate has been the subject of efforts to generate structural analogs with unique properties. Here we report a practical, half-gram synthesis of two …
Dataset Project DOI

Caged Cyclopropenes with Improved Tetrazine Ligation Kinetics

Pratik Kumar, Omar Zainul, Frank M. Camarda, Ting Jiang, John A. Mannone, Wei Huang, Scott T. Laughlin
May 2019 Organic Letters, 21(10), 3721-3725
Activatable cyclopropenes are unreactive toward their inverse electron demand Diels-Alder reaction partner (e.g., s-tetrazines) until they are activated. The activation strategy is highly modular due …
Dataset Project DOI

Modular Activatable Bioorthogonal Reagents

Pratik Kumar, Scott T. Laughlin
March 2019 Methods in Enzymology, 622(1), 153-182
The bioorthogonal reaction toolbox contains approximately two-dozen unique chemistries that permit selective tagging and probing of biomolecules. Over the past two decades, significant effort has been …
Project DOI

Lipidated Cyclopropenes via a Stable 3-N Spirocyclopropene Scaffold

Pratik Kumar, Ting Jiang, Omar Zainul, Alyssa N. Preston, Sining Li, Joshua D. Farr, Pavit Suri, Scott T. Laughlin
August 2018 Tetrahedron Letters, 59(37), 3435-3438
Lipidated cyclopropenes serve as useful bioorthogonal reagents for imaging cell membranes due to the cyclopropene’s small size and ability to ligate with pro-fluorescent tetrazines. Previously, …
PDF Dataset Project Project DOI

Caged Cyclopropenes for Controlling Bioorthogonal Reactivity

Pratik Kumar, Ting Jiang, Sining Li, Omar Zainul, Scott T. Laughlin
July 2018 Organic and Biomolecular Chemistry, 16(22), 4081-4085
Bioorthogonal ligations have been designed and optimized to provide new experimental avenues for understanding biological systems. Generally, these optimizations have focused on improving reaction …
Dataset Project DOI RSC Blog
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