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Interactomics : Basics & Applications

By Prof. Sanjeeva Srivastava   |   IIT Bombay
Learners enrolled: 133
Proteins are the key effectors of any living system and are largely responsible for the functioning of a cell. Intricate cell signaling and molecular triggers are dependent on interactions involving proteins at the cellular level. It is due to this very reason that, in an age where clinical biology is thriving to make an impact in global health-care and biomedical diagnostics, there has been a surge of interest in the area of Interactomics. Interactomics essentially involves the study of interactions between biomolecules, particularly proteins and the consequences of those interactions in a biosystem.

Due to rapidly evolving technological platforms in biology, there is a need to keep pace with latest developments in field to explore their versatile applications. Interactions resulting from protein-protein, protein-peptide, protein-RNA, protein-DNA or protein- small molecule have immense application in life-sciences and translational biology. Through this course, we aim to provide an interface between distinguished scientists involved in interactomics research, industrial partners, faculties and students. This course would feature an intensive lecture series followed by some demonstrations designed to provide the much needed training required to explore the endless possibilities in interactomics research using genomics and proteomics approach, that can be useful for a researcher at any stage.

Various technology platforms such as Protein microarrays, Label-free biosensors and Next-Generation Sequencing (NGS) Technology will be discussed. The students/participants will gain exposure to the above mentioned technologies and its applications from some of the experts in the field, from both- academia and industry perspective.
INTENDED AUDIENCE : Biology or biotechnology background students having interest in latest technologies, (BE/B.Tech) Biotechnology Students, B.Sc. students science background but course is open to all
PREREQUISITES : None
INDUSTRY SUPPORT : GE Healthcare, Pall Life Sciences, Thermofisher Scientific, Illumina
Summary
Course Status : Upcoming
Course Type : Elective
Duration : 12 weeks
Start Date : 24 Jan 2022
End Date : 15 Apr 2022
Exam Date : 23 Apr 2022 IST
Category :
  • Biological Sciences & Bioengineering
  • Biosciences
Credit Points : 3
Level : Undergraduate/Postgraduate



Course layout

Week 1- Interactomics: Basics and Applications
Lecture 1: Introduction to Proteomics
Lecture 2: Introduction to Interactomics
Lecture 3: High throughput platforms of interactomics: Protein arrays
Lecture 4: Cell-free expression based protein microarrays
Lecture 5: NAPPA: Recombinational Cloning, Basic workflow, Surface Chemistry, Printing and Assessment

Week 2- Interactomics: Basics and Applications
Lecture 6: NAPPA Technology and Protein Arrays-I
Lecture 7: NAPPA Technology and Protein Arrays-II
Lecture 8: Biomarkers: Harnessing the immune system for early detection of disease-I
Lecture 9: Biomarkers: Harnessing the immune system for early detection of disease-II
Lecture 10: Biomarkers: Harnessing the immune system for early detection of disease-III

Week 3- Interactomics: Basics and Applications
Lecture11: NAPPA & its applications in study of antibody immune response in disease & in drug screening-I
Lecture12: NAPPA & its applications in study of antibody immune response in disease & in drug screening-II
Lecture13: NAPPA & its applications in study of antibody immune response in disease & in drug screening-III
Lecture 14: Using functional proteomics to identify biomarkers and therapeutic targets-I
Lecture 15: Using functional proteomics to identify biomarkers and therapeutic targets-II

Week 4- Interactomics: Basics and Applications
Lecture 16: Applications of protein microarrays in Malaria Research-I
Lecture 17: Applications of protein microarrays in Malaria Research-II
Lecture 18: Introduction to Bioprinting and Iris™ Optical QC Benefits-I
Lecture 19: Introduction to Bioprinting and Iris™ Optical QC Benefits-II
Lecture 20: Screening of autoantibody signatures in cancer patients: Lab demonstration

Week 5- Interactomics: Basics and Applications
Lecture-21: Basics of Image Scanning and data acquisition
Lecture-22: Applications of protein arrays in the identification of autoantibody signatures-I
Lecture-23: Applications of protein arrays in the identification of autoantibody signatures-II
Lecture-24: Applications of protein microarrays in deciphering PTMs and biological networks
Lecture-25: Basics and Applications of Reverse Phase Protein Arrays-I

Week 6- Interactomics: Basics and Applications
Lecture-26: Basics and Applications of Reverse Phase Protein Arrays-II
Lecture-27: Basics and Applications of Reverse Phase Protein Arrays-III
Lecture-28: An overview of label-free technologies
Lecture-29: An overview of label-free technologies
Lecture-30: Surface Plasmon Resonance- Principles and Assays-II

Week 7- Interactomics: Basics and Applications
Lecture-31: Basics of SPR: Surface chemistry
Lecture-32: Basics of SPR: Experimental design
Lecture-33: Protein immobilization for protein-protein interaction studies
Lecture-34: Protein-protein interaction study: Binding analysis
Lecture-35: Protein-protein interaction study: Kinetic analysis

Week 8- Interactomics: Basics and Applications
Lecture-36: Use of SPR in unravelling domain motif interactions of proteasomal assembly chaperones
Lecture-37: Protein-small molecule interaction study: Immobilization Immobilisation & binding analysis
Lecture-38: Protein-small molecule interaction study: Kinetic analysis
Lecture-39: An introduction to biolayer interferometry (BLI) and its applications in protein research
Lecture-40: Biomolecular interactions using Bio-Layer Interferometry (BLI)-I

Week 9- Interactomics: Basics and Applications
Lecture 41: Biomolecular interactions using Bio-Layer Interferometry (BLI)-II
Lecture 42: Lab session- An introduction to Bio-Layer Interferometry (BLI) and its applications in protein research
Lecture 43: Applications of label-free technologies-II
Lecture 44: Biomolecular interaction analytics using MicroScale Thermophoresis
Lecture 45: Mass Spectrometry coupled Interactomics-I

Week 10- Interactomics: Basics and Applications
Lecture 46: Mass Spectrometry coupled Interactomics-II
Lecture 47: Next-Generation Sequencing Technology- Ion Torrent™
Lecture 48: NGS Technology - Bioinformatics and data analysis-I
Lecture 49: NGS Technology - Bioinformatics and data analysis-II
Lecture 50: Next-Generation Sequencing Technology- Illumina

Week 11- Interactomics: Basics and Applications
Lecture 51: Agilent complete NGS target enrichment workflow for exomes, targeted panels and beyond
Lecture 52: The Human Pathology Atlas: A Pathology Atlas of the Human Transcriptome-I
Lecture 53: The Human Pathology Atlas: A Pathology Atlas of the Human Transcriptome-II
Lecture 54: Statistical Analysis-I
Lecture 55: Statistical Analysis-II

Week 12- Interactomics: Basics and Applications
Lecture 56: Secondary Data Analysis
Lecture 57: Pathway Enrichment and Network Analysis
Lecture 58: Data Repositories and Databases
Lecture 59: Application of multi-omics approach for better understanding of cancers
Lecture 60: Integrated Omics and Systems Biology- Conclusion

Books and references

Proteomics: A Cold Spring Harbor Laboratory Course Manual, A.J. Link and J. LaBaer, Cold Spring Harbor Laboratory Press, 2009.
Selected papers from scientific journals

Instructor bio

Prof. Sanjeeva Srivastava

IIT Bombay
Prof. Sanjeeva Srivastava Dr. Sanjeeva Srivastava is a Professor and group head of proteomics laboratory at the Indian Institute of Technology, Bombay. He obtained his Ph.D. from the University of Alberta and post-doc from the Harvard Medical School in the area of proteomics, stress physiology and has specialized expertise in applications of data enabled sciences in global health, developing country and resource limited settings. He joined IIT Bombay in 2009 as an Assistant Professor and currently working as Professor. Current research in his group centers on biomarker and drug target discovery and deciphering the protein interaction networks in complex human diseases (gliomas) and infectious diseases (malaria) using high throughput proteomics, protein microarrays and mass spectrometry. Dr. Srivastava is an active contributor to global proteomics science and innovation. He serves on the Executive Council of Human Proteome Organization (HUPO) and Proteomics Society, India (PSI). He has organized three successful international conferences & workshops at IIT Bombay PSI-2014, Targeted Proteomics International Symposium in 2015 and 2018. He has published four special issues as editor, Proteomics in India for Journal of Proteomics; Proteomics Research in India for Nature India, Protein Arrays for Proteomics and Neglected Tropical Infectious Diseases for Proteomics Clinical Applications. Having an extensive teaching experience at IITB and experience of conducting proteomics courses at CSHL, New York provided him with the background to increase proteomics education for the global community. One of his special contributions has been the development of e-learning resources (MOOC mass spectrometry and interactomics courses; Virtual Proteomics Laboratory). He has made first ever proteomics documentaries Proteomics: Translating the Code of Life and Human Proteome Project (HPP). He has directed HUPO Perspective in Proteomics video interview series, which is hosted on HUPO website. Recently we have signed a MOU on clinical proteogenomics cancer research with National Cancer Institute, along with Tata Memorial Centre and India has now become 12th country to join the International Cancer Proteogenome Consortium (ICPC). Dr. Srivastava continues to develop proteomics & omics science and innovation together with and for the next generation of keen students, researchers and the research and education commons in Asia and global OMICS community. Click here to view Faculty Profile: http://www.bio.iitb.ac.in/~sanjeeva/ About the Instructor: https://youtu.be/sb4faypvWwk


Course certificate

The course is free to enroll and learn from. But if you want a certificate, you have to register and write the proctored exam conducted by us in person at any of the designated exam centres.
The exam is optional for a fee of Rs 1000/- (Rupees one thousand only).
Date and Time of Exams: 23 April 2022 Morning session 9am to 12 noon; Afternoon Session 2pm to 5pm.
Registration url: Announcements will be made when the registration form is open for registrations.
The online registration form has to be filled and the certification exam fee needs to be paid. More details will be made available when the exam registration form is published. If there are any changes, it will be mentioned then.
Please check the form for more details on the cities where the exams will be held, the conditions you agree to when you fill the form etc.

CRITERIA TO GET A CERTIFICATE

Average assignment score = 25% of average of best 8 assignments out of the total 12 assignments given in the course.
Exam score = 75% of the proctored certification exam score out of 100

Final score = Average assignment score + Exam score

YOU WILL BE ELIGIBLE FOR A CERTIFICATE ONLY IF AVERAGE ASSIGNMENT SCORE >=10/25 AND EXAM SCORE >= 30/75. If one of the 2 criteria is not met, you will not get the certificate even if the Final score >= 40/100.

Certificate will have your name, photograph and the score in the final exam with the breakup.It will have the logos of NPTEL and IIT Bombay.It will be e-verifiable at nptel.ac.in/noc.

Only the e-certificate will be made available. Hard copies will not be dispatched.

Once again, thanks for your interest in our online courses and certification. Happy learning.

- NPTEL team


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