Department of Bioengineering

Seminar by Dr. Tarini Shankar Ghosh on The gut microbiome and biological aging
2023-01-02 16:00 - 17:00 UTC | CES Seminar Hall, CES Seminar Hall, 3rd Floor, Biological Science Building
Speaker: Dr. Tarini Shankar Ghosh (Indraprastha Institute of Information Technology, IIIT-Delhi)
Title: The gut microbiome and biological aging
Abstract:
“The gut harbours one of the largest microbial communities found in human body, with more than 1.3 trillion microbial cells encoding a functional capacity estimated to be more than 150 times the coding capacity of our own. Alterations in the gut microbiome have been associated with many aspects of human physiology, some of the medically and economically significant multifactorial non-communicable diseases as well as with the treatment responses of individuals to different therapeutic interventions.
Age is one such aspect of host physiology having one of the strongest associations with the composition of the gut microbiome. Aging is associated with a progressive decline in multiple bodily functions and an onset of low-grade inflammation (referred to as ‘Inflammaging’). But even in healthy people, the gut microbiome alters with age. Are age-associated gut microbiome alterations a cause or a mere consequence of a declining state of human health? Or do these alterations indicate a transition to an even more vicious cycle of deterioration in host physiology? Can these alterations in a host be ‘reset’ using microbiome-targeted therapeutics to delay the transition to an unhealthy aging trajectory? In this talk, I will some of the recent genomic and metagenomic studies (including some of my previous works) that have attempted to answer the above questions. I will also briefly describe specific examples, where in we observed the gut microbiome to be a key transducer of the beneficial signals of diet on health of older people. Finally, my talk will provide implications for future, including the prospects of devising microbiome-targeted diagnostic/therapeutic strategies specifically customized for societies like India for improving human health.”
About the Speaker:
Tarini Shankar Ghosh is an Assistant Professor of Computational Biology at the Indraprastha Institute of Information Technology Delhi (IIIT-Delhi). He received his B.Tech from Indian Institute of Technology (IIT) Kharagpur, his M.Tech from IIT Kanpur and his Ph.D from the University of Hyderabad. After completing his PhD, he first moved to the Genome Institute of Singapore (as a post-doctoral researcher) and then to his current institute APC Microbiome Ireland at Cork. His core research focus is to understand gut microbial ecology using an in-silico approach. He uses a combination of metagenome informatics, machine learning and statistical approaches to identify the generic microbial markers of health, their variation across various population-strata, their alterations in different disease conditions and finally the formulation of personalized diet/symbiotic-based microbiome restoration strategies for improving human health. He has published more than 50 research papers in notable journals including Nature Medicine, Nature Reviews Gastroenterology and Hepatology, Nature Aging, Nature Ecology and Evolution, Gut (British Medical Journals), Gastroenterology (American Gastroenterological Association) and Cell hosts and microbes. He has 8 US/EU based patents pertaining to metagenomic data analysis algorithms and design of microbial consortia targeted to ameliorate frailty and colorectal cancer. Dr. Ghosh was also selected for the Pathway Investigator Award by the Science Foundation of Ireland and the Irish Research Council for the year 2022. He has also been a recipient of the Yakult Young Investigator Award in the year 2014 and the Torrent Pharmaceuticals – ISHR Young Investigator Award in the year 2017.

9th Annual Symposium, BSSE 2023 (19th-21st Jan 2023)
2022-12-29 08:00 - 17:00 UTC

Seminar (Talk-2) by Dr. Shyni Varghese on Ex vivo 3D tumor models to study cancer cell invasion and T cell recruitment
2022-12-14 16:00 - 17:00 UTC | CES Seminar Hall, CES Seminar Hall, 3rd Floor, Biological Science Building
Title: Ex vivo 3D tumor models to study cancer cell invasion and T cell recruitment
Abstract:
“Advancement in three-dimensional (3D) cell cultures and microfabrication has led to the development of physiologically relevant ex vivo models to understand the interdependency between cells and their microenvironment as well as various cellular functions involved in development and pathogenesis. In this talk, I will discuss about our efforts on understanding the role of physical properties of the matrix in disease progression such as cancer metastasis. Metastatic dissemination of cancer cells is a key contributor to >90% of cancer-related mortality. Though metastasis involves multiple steps, the ability of cancer cells to invade and traverse through dense 3D structures (i.e., extracellular matrix such as collagen network) is a crucial manifestation of cancer malignancy. In order to understand cancer cell invasion and migration, we have developed a single cell resolution quantitative assay to estimate the three-dimensional (3D) traction stresses generated by the cancer cells during their migration. We also examined the effect of material properties on protease independent vs. dependent mode of migration of cancer cells. Such quantitative analysis would lead to identification of new pathways that might be targeted to develop therapies to treat cancer metastasis. I will also talk about the application of tumor-on-chip platform involving heterotypic cells to study tumor associated microenvironment on cell recruitment.”
About the Speaker:
Shyni Varghese, Ph.D., is a Professor of Biomedical Engineering, Mechanical Engineering & Materials Science, and Orthopaedics Surgery at Duke University. She is the inaugural MEDx Investigator at Duke University. Prior to moving to Duke, she was a Professor of Bioengineering at University of California, San Diego. Dr. Varghese’s research covers a broad range of topics including stem cells, biomaterials, biologically inspired systems, tissue chips, and regenerative medicine. Her research activities have resulted in over 100 publications and over a dozen patent disclosures. Examples of ongoing research activities in her laboratory involve developing functional biomaterials such as self-healing hydrogels and biomineralized matrices; technologies to improve cell-based therapies including stem-cell differentiation, cell transplantation, activating endogenous stem cells, and engineered functional tissue grafts; and organ-on-a-chip technologies. She is a fellow of AIMBE and Royal Society of Chemistry. She is currently serving as an Associate Editor of Biomaterials Science (an RSC journal).

Seminar by Dr. Shyni Varghese on Engineering the interface: From smart materials to devices to cell transplantation
2022-12-12 16:00 - 17:00 UTC | CES Seminar Hall, CES Seminar Hall, 3rd Floor, Biological Science Building
Title: Engineering the interface: From smart materials to devices to cell transplantation
Abstract:
“In this talk, I will discuss our efforts in engineering the bio-material interface to achieve unique biological functions and medical applications. First, I will talk about design of hydrogel matrices to control stem cell fate in vitro and in vivo and use of such engineered matrices to understand the molecular mechanism underlying stem cell differentiation (Ayala et al., Biomaterials, 2011; Shih et al., PNAS 2014; Zeng et al., Adv. Mater. 2020). I will next talk about developing biomaterial interfaces to support xenogeneic transplantation of cells, where the transplanted cells act as a “drug store” for biomolecules (Kumar et al., Adv. Funct. Mater., 2021). Finally, I will talk about how interfacial engineering can be exploited to creating materials with “living” functions such as self-healing along with their applications in cartilage tissue repair and soft robotics (Phadke et al., PNAS, 2012; Kumar et al., Adv. Int. Syst. 2021; Gilpin et al., Adv. Healthc. Mater. 2021).”
About the Speaker:
Shyni Varghese, Ph.D., is a Professor of Biomedical Engineering, Mechanical Engineering & Materials Science, and Orthopaedics Surgery at Duke University. She is the inaugural MEDx Investigator at Duke University. Prior to moving to Duke, she was a Professor of Bioengineering at University of California, San Diego. Dr. Varghese’s research covers a broad range of topics including stem cells, biomaterials, biologically inspired systems, tissue chips, and regenerative medicine. Her research activities have resulted in over 100 publications and over a dozen patent disclosures. Examples of ongoing research activities in her laboratory involve developing functional biomaterials such as self-healing hydrogels and biomineralized matrices; technologies to improve cell-based therapies including stem-cell differentiation, cell transplantation, activating endogenous stem cells, and engineered functional tissue grafts; and organ-on-a-chip technologies. She is a fellow of AIMBE and Royal Society of Chemistry. She is currently serving as an Associate Editor of Biomaterials Science (an RSC journal).

Seminar by Dr. Parag Katira on Mechanics of Cancer
2022-12-05 16:00 - 17:00 UTC | M Tech Classroom, BSSE Annex
Title: Mechanics of Cancer
Abstract:
Cancer is a disease rooted in genetic mutations and epigenetic regulation of cell biology. There is extensive heterogeneity in the biological drivers of this disease across cancer types, across patients with one type of cancer, and even within tumors within a single patient, making early cancer diagnosis, accurate prognosis and treatment challenging. We take the view that all the varying biological factors influencing cancer ultimately lead to similar mechanical outcomes that define the disease – uncontrolled cell proliferation and tumor growth within the host tissue environment, cell migration and invasion of neighboring tissues, and formation of secondary neoplasms within the invaded tissues. Can the mechanics of these physical processes then shed light on key elements of cancer occurrence and progression? Can these mechanistic insights provide avenues for better prognosis and treatments of cancer? This talk will describe our efforts to understand the role of mechanics in cancer progression, some interesting physical paradoxes that cancer progression presents and what biological insights if any can be gained from such understanding.
About the Speaker:
Dr. Parag Katira is an Associate Professor in Mechanical Engineering and Associate Director of the Computational Sciences Research Center at San Diego State University. He is also the program coordinator for the Bioengineering Graduate Program at San Diego State University. Prior to his current position, he was a Research Scientist at Columbia University in New York from 2013-2015 and a Postdoctoral Fellow at the University of Texas at Austin from 2009-2013. He completed his PhD. in Materials Science and Engineering from the University of Florida in 2009. His current research focuses on modeling active matter systems such as assemblies of driven cytoskeletal filaments, cellular collectives on 2D and in 3D environments, and tissue dynamics during processes such as wound-healing and cancer. His research is funded by grants from the US National Science Foundation, Department of Defence Army Research Office and the National Institutes of Health. He was awarded the 2021 Outstanding Leadership in Engineering Award by the San Diego County Engineering Council for his efforts on transforming engineering education and training at San Diego State University.

Seminar by Dr. Vinaya Simha on Lipodystrophy and Insulin Resistance
2022-12-05 11:00 - 12:00 UTC | CES Seminar Hall, CES Seminar Hall, 3rd Floor, Biological Science Building
Speaker Name and Affiliation: Dr. Vinaya Simha, Mayo Clinic (currently Satish Dhawan visiting professor at IISc)
Seminar Title: Lipodystrophy and Insulin Resistance: Lessons learned and to be learned
Abstract: Lipodystrophy syndromes are a diverse group of congenital and acquired disorders characterized by selective fat loss and features of marked insulin resistance including early-onset diabetes, hyperlipidemia and hepatic steatosis. Much progress has been made recently in understanding the molecular basis of fat loss and metabolic complications. It has also thrown light on the pathogenesis of insulin resistance in obesity and metabolic syndrome and the importance of adipocyte endocrine function. Recent studies focusing on muscle mitochondrial dysfunction in lipodystrophy may help to further elucidate mechanisms of insulin resistance contributing to diabetes and dyslipidemia.
Brief Bio of Speaker: Prof. Simha is an Associate Professor of Medicine at the Mayo Clinic College of Medicine and Science and a Consultant in Endocrinology in the Department of Internal Medicine at Mayo Clinic, Rochester, Minnesota. He has won numerous awards, the latest of which is the 2018 Laureate Award from the Mayo Clinic. He has been an active clinical practitioner and researcher, specializing in diabetes and other endocrine disorders and their complications. He has been and is currently an investigator on several NIH grants and the lead investigator/director on clinical trials supported by the pharmaceutical industry.

Guest Lecture by Dr. Andrew Holle on "Tight squeeze: Engineering confinement for mechanobiology research"
2022-12-02 15:00 - 16:00 UTC | M Tech Classroom, BSSE Annex
Abstract:
Self-induced cellular confinement has been shown to play a role in a wide variety of biological processes, including cancer invasion and metastasis, immune cell navigation, and mechanosensitive gene expression and localization. However, the ability of adult stem cells to enter tight confinements has been less studied, despite the fact that stem cells are capable of finely tuned mechano-transduction, must migrate from their home niche to their regenerative niche, and have been shown to integrate past stimuli in a form of ‘mechanical memory’. Here, we characterize the interstitial spaces in cleared tissue, providing a physiological basis for the design of biomimetic microchannel devices. Next, we show that adipose-derived stem cells (ASCs) and bone marrow stem cells (hMSCs) are capable of entering and permeating PDMS-based microchannels as narrow as 3 µm. Patterns of microchannel permeation as a function of width are similar to those found in cancer cells, despite the fact that these stem cells are more well-spread and exhibit higher cell diameters. Both narrow and wide confinements were shown to induce an upregulation of the osteogenic differentiation marker CBFA1. Interestingly, narrow confinements led to enhanced CBFA1 nuclear localization compared to wide channels, suggesting that the level of confinement imposed upon a stem cell via its extracellular environment ultimately plays a role in differentiation. In conjunction with these changes in fate, stem cells exposed to confinement also showed significant changes in epigenetic state as measured by H3K9Ac localization. Future work will ultimately discern if the migratory journey a stem cell undergoes during development and regeneration, and the confinement it experiences along the way, drive tissue-specific stem cell differentiation
About the Speaker:
Dr. Andrew Holle is currently an Assistant Professor at the Department of Biomedical Engineering, National University of Singapore (NUS) and the Principal Investigator at the Mechanobiology Institute, NUS. He received Ph.D. at the University of California, San Diego, where he worked in Prof. Adam Engler’s Stem Cell Biology and Bioengineering group. He identified the mechanosensitive role of the focal adhesion protein vinculin in substrate stiffness-induced stem cell differentiation. Looking to explore the commonalities between stem cells and cancer mechanobiology, he then joined Prof. Joachim Spatz’s Cellular Biophysics group at the Max Planck Institute for Medical Research (Stuttgart, Germany). He used photolithography and microfluidics to build microchannel assays better to characterize cancer cell invasion and migration in confinement. His current work at the Mechanobiology Institute and in the NUS Biomedical Engineering department is focused on the role of confinement in mechanobiology, with an emphasis on novel strategies for controlling stem cell differentiation.

Guest Lecture by Dr. Jason T. George on "Stochastic modeling of the tumor-immune interaction"
2022-09-26 14:30 - 15:30 (Asia/Kolkata) | M Tech Classroom, BSSE Annex
Abstract: “Harnessing the adaptive immune system to recognize and eliminate cancer cells has ushered in T cell-based immunotherapies, which have revolutionized cancer treatment by inducing durable remission for many patients. Due to the immense complexity of T cell immunotherapy, nearly all attempts to improve these approaches and to expand their applications have been driven empirically. To predict treatment failure and optimize current therapies, we must understand the dynamic interplay between an adaptive immune system and an evolving cancer population. My talk will describe stochastic modeling that our group has been actively developing, which include random energy models of the T cell receptor-antigen interface developed to characterize immune recognition potential against tumor antigens, and dynamical models of the interaction between an evolving cancer population and an adaptive immune system.
About the speaker: Jason T. George is an assistant professor in the Department of Biomedical Engineering at Texas A&M University. His research interests lie at the intersection of engineering and applied mathematics, where he focuses on developing dual theoretical and data-driven mathematical models to characterize cancer development and evasion with the goal of improving treatment outcomes. Prior to joining A&M, Dr. George was a postdoctoral fellow in the Center for Theoretical Biological Physics at Rice University. He was a student in the Medical Scientist Training Program where he earned his M.D. at Baylor College of Medicine and Ph.D. in the Department of Bioengineering at Rice University under the mentorship of Herbert Levine. Prior to this, Dr. George completed his undergraduate training at Texas A&M University, where he earned a B.S. in Biomedical Engineering and a B.A. in Mathematics. Dr. George is the recipient of the CPRIT First-Time Tenure-Track Faculty Recruitment Award. His graduate thesis work was funded by a Ruth L. Kirschstein Fellowship through the NIH National Cancer Institute.

Seminar: Microenvironment regulation of metastasis
2022-03-28 16:30 - 17:30 UTC | Online
The Centre for BioSystems Science and Engineering (BSSE) cordially invites you to attend a departmental seminar.

Speaker: Dr. Kandice Tanner, National Cancer Institute, NIH

Discoveries in natural light sensing and probing cellular dynamics: an interdisciplinary approach and a need for engineering in biology
2022-03-07 16:00 - 17:00 UTC | Online
The Centre for BioSystems Science and Engineering (BSSE) cordially invites you to attend a departmental seminar.Speaker: Dr. Akash Gulyani, Department of Biochemistry, School of Life Sciences, University of Hyderabad

Mechanobiology of Liver Cirrhosis: The Role of Hepatocytes in Fibrosis Progression
2022-02-23 16:00 - 18:00 UTC | Online
The Centre for BioSystems Science and Engineering (BSSE) cordially invites you to attend an Annual Work Presentation.
Student: Anwesha Barua (BSSE)
Advisors: Prof. G.K. Ananthasuresh (ME) and Prof. Saumitra Das (MCB)
