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Tata Institute of Fundamental Research

7 ARTICLES PUBLISHED IN JoVE

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Developmental Biology

Functional Manipulation of Maternal Gene Products Using In Vitro Oocyte Maturation in Zebrafish
Elaine L. Welch *1, Celeste C. Eno *1, Sreelaja Nair 2, Robin E. Lindeman 3, Francisco Pelegri 1
1Laboratory of Genetics, University of Wisconsin-Madison, 2Department of Biological Sciences, Tata Institute of Fundamental Research, 3Department of Genetics, Cell Biology, and Development, University of Minnesota

An optimized protocol for the in vitro maturation of zebrafish oocytes used for the manipulation of maternal gene products is presented here.

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Biochemistry

RNA Blot Analysis for the Detection and Quantification of Plant MicroRNAs
Varsha Tirumalai 1,2, Melvin Prasad 1, P. V. Shivaprasad 1
1National Centre for Biological Sciences, Tata Institute of Fundamental Research, 2SASTRA University

This method demonstrates use of the northern hybridization technique to detect miRNAs from total RNA extract.

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Biology

Reconstitution of Membrane-Tethered Minimal Actin Cortices on Supported Lipid Bilayers
Darius Vasco Köster 1, Abrar Bhat 2, Sankarshan Talluri 2, Satyajit Mayor 2
1Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, University of Warwick, 2National Centre for Biological Sciences, Tata Institute of Fundamental Research

This protocol describes the formation of supported lipid bilayers and the addition of cytoskeletal filaments and motor proteins to study the dynamics of reconstituted, membrane-tethered cytoskeletal networks using fluorescence microscopy.

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Developmental Biology

In Ovo and Ex Ovo Methods to Study Avian Inner Ear Development
Nishant Singh *1,2, Anubhav Prakash *1, Suraj Ranganath Chakravarthy *1, Raman Kaushik *1, Raj K. Ladher 1
1National Centre for Biological Sciences, Tata Institute of Fundamental Research, 2The University of Trans-Disciplinary Health Sciences and Technology

The chick is a cost-effective, accessible, and widely available model organism for a variety of studies. Here, a series of protocols is detailed to understand the molecular mechanisms underlying avian inner ear development and regeneration.

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Biochemistry

Modeling Ligands into Maps Derived from Electron Cryomicroscopy
Shaileshanand Jha *1, Sucharita Bose *2, Kutti R. Vinothkumar 1
1National Centre for Biological Sciences, Tata Institute of Fundamental Research, 2Institute for Stem Cell Science and Regenerative Medicine

This protocol introduces the tools available for modeling small-molecule ligands in cryoEM maps of macromolecules.

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Biology

Growing Mycobacterial Biofilm as a Model to Study Antimicrobial Resistance
Kaushik Poddar 1, Amitesh Anand 1
1Department of Biological Sciences, Tata Institute of Fundamental Research

This protocol describes a robust method for developing pellicle biofilm. The method is scalable to different culture volumes, allowing easy adoption for various experimental objectives. The method's design enables qualitative or quantitative assessment of the biofilm-forming potential of several mycobacterial species.

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Developmental Biology

Light Sheet Microscopy Imaging and Mounting Strategies for Early Zebrafish Embryos
Swetha Nagarajan *1, Siddhartha Bardhan *1, Sundar Ram Naganathan 1
1Department of Biological Sciences, Tata Institute of Fundamental Research

A sample preparation strategy for imaging early zebrafish embryos within an intact chorion using a light-sheet microscope is described. It analyzes the different orientations that embryos acquire within the chorion at the 70% epiboly and bud stages and details imaging strategies for obtaining cellular-scale resolution throughout the embryo using the light-sheet system.

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