Indian Institute of Technology Bombay

6 ARTICLES PUBLISHED IN JoVE

Biology

Comprehensive Workflow of Mass Spectrometry-based Shotgun Proteomics of Tissue Samples

Ayushi Verma^*1, Vipin Kumar^*1, Saicharan Ghantasala¹, Shuvolina Mukherjee¹, Sanjeeva Srivastava¹

¹Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay

The described protocol provides an optimized quantitative proteomics analysis of tissue samples using two approaches: label-based and label free quantitation. Label-based approaches have the advantage of more accurate quantitation of proteins, while a label-free approach is more cost-effective and used to analyze hundreds of samples of a cohort.

Biology

Quantitative Proteomics Workflow using Multiple Reaction Monitoring Based Detection of Proteins from Human Brain Tissue

Saicharan Ghantasala^*1, Medha Gayathri J Pai^*2, Sanjeeva Srivastava²

¹Centre for Research in Nanotechnology and Science, Indian Institute of Technology Bombay, ²Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay

The protocol aims to introduce the use of a triple quadrupole mass spectrometer for Multiple Reaction Monitoring (MRM) of proteins from clinical samples. We have provided a systematic workflow starting from sample preparation to data analysis for clinical samples with all the necessary precautions to be taken.

Biology

Determination of the Mating Efficiency of Haploids in Saccharomyces cerevisiae

Anjali Mahilkar^*1,2, Prachitha Nagendra^*1, Supreet Saini¹

¹Department of Chemical Engineering, Indian Institute of Technology Bombay, ²Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor

In this work, a robust method for the quantification of mating efficiency in the yeast Saccharomyces cerevisiae is described. This method is particularly useful for the quantification of pre-zygotic barriers in speciation studies.

Biochemistry

"Cell Surface Capture" Workflow for Label-Free Quantification of the Cell Surface Proteome

Akul Naik¹, Sanjeeva Srivastava^1,2, Arun P. Wiita^1,3,4

¹Department of Laboratory Medicine, University of California, San Francisco, ²Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, ³Deptartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, ⁴Chan Zuckerberg Biohub

Here, we describe a proteomics workflow for characterization of the cell surface proteome of various cell types. This workflow includes cell surface protein enrichment, subsequent sample preparation, analysis using an LC-MS/MS platform, and data processing with specialized software.

Behavior

A Modified Mirror Test as a Visual Guide for the Self-awareness Trait in Wild Antarctica Penguins, Pygoscelis adeliae

Prabir G Dastidar¹, Azizuddin Khan², Anindya Sinha^3,4,5

¹Polar Science Division, Ministry of Earth Sciences (MoES), Government of India, ²Psychophysiology Laboratory, Humanities and Social Sciences, Indian Institute of Technology Bombay, ³Animal Behavior and Cognition Programme, National Institute of Advanced Studies, ⁴Centre for Neuroscience, Indian Institute of Science, ⁵Department of Environmental Sciences and Wildlife Biology, Cotton University

A specially devised Modified Mirror Test has been used to find the traits of self-awareness in wild Adelie penguins. The experiment, conducted in different terrains of Antarctica during January-February 2020, is probably the first attempt to report the presence of these characteristics in penguins.

Bioengineering

Synthesis of Compound Giant Unilamellar Vesicles: A Biomimetic Model of Nucleate Cells

Rupesh Kumar¹, Rajarshi Chakrabarti², Rochish M. Thaokar³

¹Centre for Research in Nanotechnology & Science, Indian Institute of Technology Bombay, ²Department of Chemistry, Indian Institute of Technology Bombay, ³Department of Chemical Engineering, Indian Institute of Technology Bombay

This article presents a method for preparing compound Giant Unilamellar Vesicles (cGUVs) with a vesicle-in-vesicle structure, with customized electrical conductivity in inner, annular, and outer regions. Electroformation synthesizes simple GUVs, which are transformed into stomatocytes and cGUVs via osmotic shock, providing a valuable model for studying the biophysics of nucleated cells.