Have you ever wondered why astronauts float in their spacecraft or outside, during a spacewalk? The reason behind this is due to microgravity. Microgravity is a phenomenon where the gravity seems very small causing the people and objects to appear weightless. The human body undergoes dramatic changes during a long term space flight. To further understand these changes, a group research project was carried out by two of our Research Fellows at Pine Biotech - Shubham Kumar and Ojasvi Dutta on the effects of microgravity on Human-induced Pluripotent Stem Cells and to understand the change in the activity of cardiac and muscle cells.
Shubham Kumar and Ojasvi Dutta are the students of M.Sc. Bioinformatics from Panjab University, Chandigarh, India. After joining the Bioinformatics Research Fellowship Program, the team worked under the guidance of Dr. Raghavendran Lakshminarayanan, Research Consultant and Mentor at Pine Biotech and Mr. Elia Brodsky, CEO of Pine Biotech.
To refresh their memory on the basic concepts of bioinformatics, the team started learning the two introductory courses on bioinformatics — Course 1: Introduction to Bioinformatics and Course 2: Bytes and Molecules. After gaining a concrete background knowledge of bioinformatics, the team further completed several intermediated courses related to biomedical data science:
- Course 3: Genomics
- Course 5: Transcriptomics
- Python Course 1: Getting Started with Bioinformatics
- Python Course 2: Introduction to Data Science (BioML)
- R-Coding Course 1: Getting Started with Bioinformatics
- R-Coding Course 2: Introduction to Data Science (BioML)
- Course 9: Designing a Bioinformatics Research Project
All these courses helped them to develop a strong theoretical and practical knowledge in bioinformatics which further guided the team to complete an example project on Project 01: COVID-19 Origin & Pathogenesis of SARS-COV2.
To view their OmicsLogic student profile and learn more about the various courses and example projects they have completed, visit the links -
Shubham Kumar - https://learn.omicslogic.com/user/rUhpNZ5Zgof9Y63cLbU9raHaEZb2
Ojasvi Dutta - https://learn.omicslogic.com/user/YOuVgBvD9CVRsmoiDYPCQgtPWRI3
The dataset used for the project is available under the GEO Accession ID: GSE137081. To conduct the analysis, 18 samples of Human-induced Pluripotent Stem Cell (hiPSC) lines were subdivided into two groups: Ground vs Flight and Ground vs Post-Flight. Expression count analysis and the mapping of transcripts were performed using RNA-Seq Pipeline; normalization of the count was performed using Quantile Normalization Pipeline Analysis along with PCA and differential gene expression analysis was done using the Differential Expression Pipeline on the T-BioInfo server.
Fig - Quantile Normalization Pipeline Analysis along with PCA on the Tauber Bioinformatics Server
After analyzing and interpreting the results, two unique pathways were observed related to pluripotency of stem cells and muscle contraction. Signaling pathways regulating pluripotency of stem cells were observed in the Ground vs Flight condition but not in the Ground vs Post-Flight condition. Pathways related to muscle were not obtained in KEGG analysis of the Ground vs Flight condition, whereas in the Ground vs Post-Flight condition Vascular Smooth Muscle contraction pathway was observed.
Their research project was also presented at the Omics Research Symposium 2022 for which they won the second prize for the title “Promising Research Direction For Future Potential”.
Let us hear what Shubham and Ojasvi had to say about their research fellowship experience:
“I joined Pine Biotech in May 2021 as a Campus Ambassador and I am having a great time working in this company. I started working here with very little experience but over time, with guidance and training, I was able to develop my skills in Data Science, Bioinformatics and Space Omics. I had the opportunity to go through several courses available on the OmicsLogic platform and I appreciate the way the courses have been designed to cover all the topics in-depth. The sample projects provided in the program were very helpful and gave me ideas to come up with my own research project.
I completed the Research Fellowship program under the mentorship of Mr. Elia Brodsky and Dr. Raghavendran Lakshminarayanan on the topic “Effects Of Microgravity On HiPSCs-CMs (Cardiac And Muscle Activity)”. During the fellowship program, we received a constant source of support and help from our mentors in completing our research project. I have not received this much guidance and support anywhere else. The steady mentor guidance while doing our own research project was worth it.
If anyone wishes to explore the field of bioinformatics research I would highly recommend them to join the Research Fellowship program at Pine Biotech.”
“I enrolled in the Research Fellowship Program at Pine Biotech on August 2021. It was an extraordinary experience for me from the start. After enrolling, I started studying the courses on the OmicsLogic Platform including Introduction to Bioinformatics, Bioinfo for Python, and Transcriptomics, to name a few. These courses helped me gain a concrete knowledge of the subjects which further helped me in finishing my research project on “Effects Of Microgravity On HiPSCs-CMs (Cardiac And Muscle Activity)” under the mentorship of Mr. Elia Brodsky and Dr. Raghavendran Lakshminarayanan.
The OmicsLogic support team were very understanding and cooperative from the beginning of the Research Fellowship Program till I completed my research project. I really enjoyed being a part of this program as it helped me to work on a project of my research interest. I would actively encourage anyone who is interested in the field of biomedical data science to join the research fellowship program.”
To learn more about their research project, visit the link - https://learn.omicslogic.com/projects/rUhpNZ5Zgof9Y63cLbU9raHaEZb2/effects-of-microgravity-on-hipscs-cmscardiac-and-muscle-activity
Feeling motivated to work on your own research project? Then don't miss the chance to register yourself for the Bioinformatics Research Fellowship Program!
The Bioinformatics Research Fellowship Program is a structured program that guides students through various areas of Big Data Bioinformatics Research using practical examples. During this program, we go through several high-quality research publications and learn about applications of computational biology in projects these publications describe. This allows beginners to try computational biology techniques on public domain data, making it possible to work with large files and extract meaningful information from patient samples, animal models, cell lines, and microbiota. The program provides support and mentorship, therefore it is an intensive research program involving training tasks, access to our online sessions and a guide on the implementation of learned skills to proposed research ideas.
To learn more about the program, please visit the link: https://learn.omicslogic.com/blog/post/research-fellowship-with-pine-biotech-independent-research-projects-using-bioinformatics