Department of Bioengineering

MTech program in Bioengineering
2023-03-15 08:00 - 17:00 UTC
Unlock your potential with our MTech program in Bioengineering. Apply now to gain expertise, industry connections, and become a leader in this transformative field. Submission deadline : 23rd March 2023 Eligibility criteria and how to apply: https://iisc.ac.in/admissions/

Seminar by Dr. Somenath Bakshi on "Connecting the dynamics of microbial systems across scales"
2023-03-13 16:00 - 17:00 UTC | Online
Title: Connecting the dynamics of microbial systems across scales
Abstract:
Biological reactions often involve low-copy molecular reactants, leading to stochastic outcomes. As a result, there is substantial heterogeneity among cells, even when they experience the same external conditions. Recent theoretical and experimental investigations have demonstrated that for microbial systems such heterogeneity is of important consequence to the population fitness and therefore also important for their evolution. We are establishing an experimental framework to connect the single-cell level picture of microbes to the short-term and long-term behaviours of their populations. We are using this approach to analyse the extent and role of cellular heterogeneity in determining the population dynamics of microbial systems in the context of – 1. Emergence of antibiotic persistence 2. Fitness costs of plasmids carrying antibiotic resistance genes and 3. The arms race between bacteria and bacteriophages. In this talk I will describe the background and motivation for this approach, the key challenges, the necessary technical advancements, and illustrate its potential with selected key findings
About the Speaker:
Somenath Bakshi is an Assistant Professor in the Department of Engineering at the University of Cambridge. He did his PhD in University of Wisconsin Madison under Professor James Weisshaar – developing super-resolution imaging technologies to study central cellular processes in microbes. After finishing his PhD, he moved to Harvard University for his postdoc with Professor Johan Paulsson in the Department of Systems Biology. During his postdoc Somenath developed high-throughput timelapse imaging technologies to study stress-response in bacteria. In 2019, he moved to Cambridge, and established the Laboratory of Systems and Synthetic Microbiology. His work focuses on the analysis of the genetic and metabolic factors underlying the emergence of antibiotic resistance, and engineering diagnostic and therapeutic strategies to combat the spread of antibiotic resistance. He is also the head of the recently established Smart Microscopy Laboratory, which is a cross-school platform for bringing together engineers, computer scientists, and biologists to develop targeted imaging solutions for specific biological problems.
Platform: MS Teams (Online)
link for the Seminar: https://tinyurl.com/3vcsm2jt

BSSE Lecture by Prof. Joachim Spatz on "Matter to Life: Bottom-Up Assembly of Synthetic Cells".
2023-03-13 11:30 - 12:30 UTC
Register here: https://forms.gle/kf1cYCUB6wcydwe8A

Seminar by Prof. Anup Singh on "Molecular Imaging using CEST MRI: Acquisition, Analysis and Applications"
2023-03-07 16:00 - 17:00 UTC | CES Seminar Hall, CES Seminar Hall, 3rd Floor, Biological Science Building
Title: Molecular Imaging using CEST MRI: Acquisition, Analysis and Applications
Abstract:
MRI is routinely being used to obtain different types of images that are sensitive to structural, functional, and physiological information. The use of MRI in disease diagnosis, treatment planning, and treatment monitoring is rapidly growing. Chemical-exchange-saturation-transfer (CEST) is an advanced MRI techniques which provides high resolution molecular information. CEST MRI of multiple in vivo molecules has been demonstrated and research studies are being carried out to evaluate their clinical potential. In this talk, an overview of the molecular imaging using CEST MRI shall be presented, including data acquisition approaches, quantitative analysis and some applications.
About the Speaker:
Dr. Anup Singh is currently an Associate Professor at the Centre for Biomedical Engineering (CBME), IIT-Delhi and is associated as a faculty with the Department of Biomedical Engineering, All India Institute of Medical Sciences, AIIMS, New Delhi. Dr. Singh received a PhD degree from the Department of Mathematics and Statistics, Indian Institute of Technology Kanpur (IIT-Kanpur) in 2008. Dr. Singh has worked as a Postdoctoral Researcher (Aug 2008 – March 2013) in the Center for Magnetic Resonance and Optical Imaging (CMROI), Department of Radiology at University of Pennsylvania(UPENN) and then as a Research Associate (April 2013 – March 2014) in the same Center. His group is pursuing multiple research projects on the development of the methodology of quantitative multi-parametric MRI and evaluating its potential applications to cancer (brain tumor, breast cancer and prostate cancer) diagnosis and treatment monitoring.

Seminar by Dr. Rati Sharma on "Systems Biology In Action: A dive into signaling pathways and behavioral dynamics"
2023-02-27 16:00 - 17:00 UTC | CES Seminar Hall, CES Seminar Hall, 3rd Floor, Biological Science Building
Speaker: Dr. Rati Sharma
Title: Systems Biology In Action: A dive into signaling pathways and behavioral dynamics
Abstract:
“Systems Biology” refers to the study of biological systems through modeling, experiments and computational tools. In particular, the workings and implications of genetic networks, behavior and signal-response can be studied through the tools and techniques adapted from the field of systems biology. This field, therefore, has an important role to play in the understanding of biological entities, be it at the level of the cell, tissue or organism. In this talk, I will discuss our work in the area of systems biology along four major themes, namely, (i) theoretical and computational modeling of signaling pathways using concepts from chemical kinetics and non-equilibrium statistical mechanics; (ii) signal response studies in the nematode (roundworm) C. elegans; (iii) development of microfluidics devices and (iv) development of machine learning tools for the study of biological systems.
In the first part of my talk, I will discuss one example of a cellular pathway, viz. the immune response pathway, where noise or fluctuations plays an important role. Through the analysis of this system and upon comparing the theoretically predicted average virus levels to those of COVID-19 patients, we hypothesize that the long lived viral dynamics are due to the long range correlations in the temporal fluctuations of the virion [1, 2]. Next, I will discuss the sensation and behavioral aspects of the model organism C. elegans in response to a heat shock and chemical stimuli [3]. Third, I will talk about the development of microfluidics devices that can aid in performing controlled experiments with these model organisms [4]. And finally, given the need for automation in labor intensive behavioral studies in C. elegans, I will also discuss our efforts in this direction and talk about the recently developed Deep-Worm-Tracker from our lab [5]. I will, therefore, provide an overview of the kind of important biological questions that can be addressed through a combination of modeling, computational and experimental studies.
References:

Persistent correlation in cellular noise determines longevity of viral infections. Abhilasha Batra, Shoubhik Banerjee and Rati Sharma*, J. Phys. Chem. Lett. 13, 7252 (2022). https://doi.org/10.1021/acs.jpclett.2c01875
A near analytic solution of a stochastic immune response model considering variability in virus and T-cell dynamics. Abhilasha Batra and Rati Sharma*, J. Chem. Phys. 154, 195104 (2021). https://doi.org/10.1063/5.0047442
Lessons learned from two decades of modeling the heat shock response. Ayush Ranawade, Rati Sharma and Erel Levine, Biomolecules 12, 1645 (2022).https://doi.org/10.3390/biom12111645
Microfluidics based bioimaging with cost-efficient fabrication of multi-level micron sized trenches. A Anand, Abhilasha Batra, Santanu Talukder and Rati Sharma*, Submitted.
Deep-Worm-Tracker: Deep Learning Methods for Accurate Detection and Tracking for Behavioral Studies in C. elegans.Shoubhik Chandan Banerjee, Khursheed Ahmad Khan and Rati Sharma*, Under review. (bioRxiv preprint: https://doi.org/10.1101/2022.08.18.504475)

About the Speaker:
Dr. Rati Sharma is an Assistant Professor in the Dept. of Chemistry at Indian Institute of Science Education and Research (IISER) Bhopal. She graduated in Chemistry from Stella Maris College, Madras University in 2007. Following this, she joined the Integrated PhD program of the Division of Chemical Sciences at Indian Institute of Science, Bangalore, where she completed her MS and PhD in 2013 under the guidance of Prof. Binny J. Cherayil. Her PhD thesis primarily focussed on questions in theoretical biophysics and polymer physics. She then pursued postdoctoral research at the Dept. of Biophysics, Johns Hopkins University, USA from 2013-2016 and at the Dept. of Physics, Harvard University, USA from 2016 to 2018. Her postdoctoral research training encompassed a variety of topics in systems biology. She moved back to India in 2019 where she has steadily established her group. She has received research grants from both DST-SERB and DBT since she joined IISER Bhopal. Her current research interests focus on computational and experimental biophysics, ranging from topics such as stress response dynamics in C. elegans and modeling of signaling pathways to machine learning applications in biological research, to name a few.

Seminar by Dr. Lorena Escudero Sanchez on "AI applications in radiological image analysis for cancer research
2023-02-23 14:30 - 15:30 UTC | M Tech Classroom, BSSE Annex
Speaker: Dr. Lorena Escudero Sanchez, University of Cambridge
Title: AI applications in radiological image analysis for cancer research
Abstract:
Imaging is one of the main pillars of clinical protocols for cancer care that provides essential non-invasive biomarkers for detection, diagnosis and response assessment. The development of Artificial Intelligence (AI) tools have proven potential to transform the analysis of radiological images, by significantly reducing processing time, by increasing the reproducibility of measurements and by improving the sensitivity of tumour detection compared to the standard visual interpretation, leading to cancer early detection. In this talk I will highlight some of the work done in our Radiogenomics and Quantitative Image Analysis group, covering methods for automated tumour segmentation, in particular in ovarian cancer, a highly complex, heterogeneous and metastatic cancer. I will also present studies on Radiomic features, quantitative measurements extracted directly from images such as CT or MR, and examples of Machine Learning models based on these variables to predict response to chemotherapy treatment. Finally, we will briefly see some examples of clinical applications of such image analysis methods.
About the Speaker:
Dr Lorena Escudero Sánchez is a particle physicist, with a PhD in neutrino physics, who has worked in large international collaborations for the neutrino oscillation experiments T2K (Japan), MicroBooNE and DUNE (US). She now works on AI applications to radiological image analysis for cancer research, at the Department of Radiology of the University of Cambridge and CRUK Cambridge Centre. She is also part of the Repository team of the National Cancer Imaging Translational Award (NCITA) consortium across different UK institutions. As a Senior Research Associate at the Department of Radiology in Cambridge, she leads the Radiogenomics and Quantitative Image Analysis group. She is also a Turing Fellow of The Alan Turing Institute, the UK national centre for AI and Data Science, a Borysiewicz Interdisciplinary Fellow of the University of Cambridge, and a Rokos Postdoctoral Research Associate at Queens’ College Cambridge.

Seminar by Dr. Mirunalini Thirugnanasambandam on Image-based biomechanics
2023-02-22 11:00 - 12:00 UTC | CES Seminar Hall, CES Seminar Hall, 3rd Floor, Biological Science Building
Title of Talk: Image-based biomechanics in the era of personalized medicine
Speaker Name: Mirunalini Thirugnanasambandam
Speaker Affiliation: Eindhoven University of Technology, Netherlands
Abstract of Talk
In the age of digital twins, when clinical management is moving towards a more personalized approach, it is often desired to evaluate patient-specific geometry and mechanical behavior. While ex-vivo tests can estimate individualized tissue properties, they are usually not a viable solution due to either tissue unavailability, or due to the tests being destructive. In my talk, I will shed light on novel methods for evaluation of patient-specific vascular biomechanics using an innovative combination of in-vivo imaging modalities (ultrasound and MRI), and image-based biomechanical modeling. In particular, aortic wall motion takes the central stage since it inherently contains information on local mechanical behavior of the aorta. I will also demonstrate the value of building multi-scale circulation loops representing (patho-) physiological conditions – illustrating that they not only serve to validate new techniques, but also possess the ability to shed light on disease mechanisms which may otherwise go unnoticed. Finally, a futuristic outlook on ways to improve the translational potential of these sophisticated models will be discussed.
Brief Bio of Speaker
Dr. Mirunalini Thirugnanasambandam obtained her undergraduate degree in Mechanical Engineering from College of Engineering Guindy, Anna University, Chennai. She did her Masters’ degree in Mechanical Engineering at McGill University, Canada, where she worked on signal processing techniques in non-linear systems. Her curiosity about non-linear systems in nature led her to pursue a PhD in cardiovascular biomechanics at University of Texas at San Antonio, USA, with Prof. Ender Finol, while doing a research exchange at Ecole des Mines, St Etienne, France, with Prof. Stephane Avril. She began her postdoctoral research at University of Bern, Switzerland, where she worked with Prof Dominik Obrist, and later began her current postdoctoral position at Eindhoven University of Technology, Netherlands with Dr. Richard Lopata. Her research focuses on both experimental and computational sides of cardiovascular mechanics, with special emphasis on abdominal aortic aneurysms and coronary microvascular obstruction. She has developed and validated computationally inexpensive novel methods to estimate vascular biomechanics from medical images.

Special talk by Mr. Sarath Kolli on "Automation of therapeutics design in the era of Artificial Intelligence"
2023-02-21 11:00 - 12:00 UTC | CES Classroom, CES Classroom, 3rd Floor, Biological Science Building
Speaker: Mr. Sarath Kolli, CEO of Boltzmann Labs
Title: Automation of therapeutics design in the era of Artificial Intelligence
Abstract:
Automation of the therapeutic design process through the integration of AI has drastically improved the efficiency and effectiveness of pharmaceutical research. With the power to assess large amounts of data within a short timeframe, AI algorithms can detect patterns, recognize target proteins and design potential treatments – all of which can be achieved much faster than human scientists can manage. This has resulted in the creation of groundbreaking drugs which have revolutionized the way that diseases are tackled. The speed of AI algorithms is one of the major benefits that has been gained from automating therapeutic design.
AI algorithms are capable of rapidly processing massive data sets and accurately pinpointing target proteins and designing potential medications. This allows scientists to save time and money. Furthermore, these AI tools can be used to refine the production process of these pharmaceuticals, making them more efficient. Additionally, AI algorithms can assess vast amounts of data and make predictive conclusions with a higher degree of accuracy compared to manual methods. This has significantly raised the success rate of clinical trials, which has been a long-standing difficulty in the pharmaceutical sector.
The emergence of AI in the pharmaceutical industry has meant a shift in the way treatments are discovered. By using AI algorithms to analyze data from various sources, such as genomics, proteomics, and pharmacology, new targets for drugs have been identified, which has resulted in new treatments for previously incurable diseases. As AI technology advances, even more, breakthroughs can be expected in the future, providing much-needed hope to those in need.

Seminar by Prof. Herbert Levine on "Cell – ECM interactions and their relevance for cancer progression
2023-02-20 16:00 - 17:00 UTC | CES Seminar Hall, CES Seminar Hall, 3rd Floor, Biological Science Building
Speaker: Prof. Herbert Levine (Satish Dhawan Visiting Chair Professor, IISc)
Title: Cell – ECM interactions and their relevance for cancer progression
Abstract:
During metastasis, tumor cells must traverse fibrous extracellular matrix (ECM) en route to the circulation. Conversely, immune cells must traverse the same medium en route to attacking a tumor. Thus, the study of the reciprocal feedbacks between cell motility and ECM is a crucial aspect of understanding cancer progression and its possible interdiction. This understanding is made more difficult by the highly nonlinear mechanics of ECM and by the multiple modes of cell motion in complex media. This talk will focus on recent progress as well as open issues in this rapidly advancing research topic.
About the Speaker:
Herbert Levine is a University Distinguished Professor of Physics and Bioengineering at Northeastern University. He is also the co-director of a National Science Foundation Physics Frontier Center devoted to theoretical biological physics. He earned his Ph.D. and an M.A. in physics from Princeton University and a B.S. in physics from Massachusetts Institute of Technology. For several decades, he has been an acknowledged leader in applying methods from physical science to diverse living systems – self-organization of bacterial colonies, directed motion of eukaryotic cells, biophysical modeling of cancer progression and metastasis, and tumor-immune interactions. He spent 25 years on the faculty of UCSD before moving to Rice University in 2012. He has served as an Associate Editor of Biophysical Journal and as the Editor-in-Chief of Physical Biology. He is a Fellow of American Physical Society (APS), and an elected member of the American Academy of Arts and Sciences (AAAS) & National Academy of Sciences (NAS).

LUMICKS (Amsterdam, The Netherlands) , "Tractor beams and single molecules: How to visualize and manipulate single biomolecules in real-time
2023-02-15 12:00 - 13:00 UTC | CES Seminar Hall, CES Seminar Hall, 3rd Floor, Biological Science Building
Title: Tractor beams and single molecules: How to visualize and manipulate single biomolecules in real-time
Abstract:
Imagine you could directly see the location and dynamics of individual proteins binding to a piece of single DNA. What if you could assemble your biological complex step by step and see it in action in real-time? What if you could manipulate the structure of your biomolecule and quickly change buffer conditions to test your experimental hypotheses? By using “molecular tractor beams”, the C-trap makes that a reality.
Essential biological processes performed by proteins interacting with DNA or cytoskeletal protofilaments are key to cell metabolism and life. In order to understand the molecular basis of life, as well as the pathological conditions that develop when processes go wrong, it is critical to get detailed insights into these processes at the molecular level. Not only at the highest resolution, but also in real time.
During this seminar, we will take you through an exciting journey of different research topics in which dynamic single molecule studies revealed remarkable insights. In each study, the C-Trap system was used; our easy-to-use platform that combines optical tweezers with fluorescence microscopy. We will explain how the ability to control, visualize and manipulate single molecules in real time, changes the way we answer tough scientific questions in the field of DNA processing, single-protein dynamics, liquid-liquid phase separation (LLPS) and beyond.

Guest Lecture by Areejit Samal on Elucidating and leveraging the design principles towards realistic Boolean models of gene regulatory networks
2023-02-14 10:00 - 11:00 UTC
Title: Elucidating and leveraging the design principles towards realistic Boolean models of gene regulatory networks
Speaker: Areejit Samal (The Institute of Mathematical Sciences (IMSc), Chennai)
Venue: MRDG Conference Room
Abstract:
Boolean networks is a widely-used mathematical framework to model gene regulatory networks. Such Boolean models consist of a set of nodes, directed edges between the nodes, and Boolean functions representing the regulatory logic at each node in the network.
In the first part of my talk, I will discuss several biologically-meaningful types of BFs, and present our systematic study of their preponderance in a compilation of 2687 regulatory rules extracted from published Boolean models of diverse biological systems [1]. A surprising observation in the empirical dataset is that most Boolean functions have an odd ‘bias’. Thereafter, we are able to explain this observation along with the enrichment of read-once functions (RoFs) and its nested canalyzing functions (NCFs) subset, in terms of two complexity measures: Boolean complexity and average sensitivity. In particular, we show that the RoFs minimize Boolean complexity and the NCFs minimize the average sensitivity in addition to minimizing the Boolean complexity, and this highlights the importance of minimum complexity in the regulatory logic of biological networks [1].
In the second part of my talk, I will present our systematic framework leveraging biologically-meaningful regulatory logic and relative stability of cell fates or attractors for model selection of Boolean developmental gene regulatory networks [2]. In particular, I show the usefulness of mean first passage time (MFPT) as a measure to capture cell state transitions within the Boolean framework and construction of cellular lineage trees. Thereafter, I will show an application of these tools towards in-depth analysis and subsequent improvement of existing Boolean models of Arabidopsis root development [2].

A. Subbaroyan, O.C. Martin & A. Samal, Minimum complexity drives regulatory logic in Boolean models of living systems, PNAS Nexus, 1(1): pgac017 (2022).
A. Subbaroyan, P. Sil, O.C. Martin & A. Samal, Leveraging Developmental Landscapes for Model Selection in Boolean Gene Regulatory Networks, bioRxiv 2023.01.08.523151.

About the Speaker:
Areejit Samal is a faculty member in the computational biology group of The Institute of Mathematical Sciences, Chennai since April 2014. He obtained his Bachelors, Masters and PhD from University of Delhi. Subsequently, he did Postdoctoral research at the Max Planck Institute for Mathematics in the Sciences Leipzig, CNRS/LPTMS Orsay, Institute for Systems Biology Seattle, and ICTP Trieste. He has been a recipient of FEBS Short term Research Fellowship, Ramanujan Fellowship, Simons Associateship of ICTP and a Max Planck Partner Group. His research interests span the broad area of complex systems / networks, in particular, its applications to biological systems.

Seminar by Prof. Herbert Levine on The Tumor-Immune Interaction: Pieces of a Multiscale Story
2023-02-13 16:00 - 17:00 UTC | CES Seminar Hall, CES Seminar Hall, 3rd Floor, Biological Science Building
Title: The Tumor-Immune Interaction: Pieces of a Multiscale Story
Abstract:
One of the most important advances in cancer research over recent years has been the renewed excitement regarding using the immune system to attack malignant cells. Understanding and managing the battle between adaptive immunity and the tumor is a complex multiscale problem, involving the molecular biophysics of immune recognition, the cellular processes of direct checkpoint-dependent evasion, and the ecological dynamics of the microenvironmental milieu. This talk will highlight some of our recent attempts to analyze pieces of this problem and to begin to assemble these pieces into a coherent picture.
About the speaker:
Herbert Levine is a University Distinguished Professor of Physics and Bioengineering at Northeastern University. He is also the co-director of a National Science Foundation Physics Frontier Center devoted to theoretical biological physics. He earned his Ph.D. and an M.A. in physics from Princeton University and a B.S. in physics from Massachusetts Institute of Technology. For several decades, he has been an acknowledged leader in applying methods from physical science to diverse living systems – self-organization of bacterial colonies, directed motion of eukaryotic cells, biophysical modeling of cancer progression and metastasis, and tumor-immune interactions. He spent 25 years on the faculty of UCSD before moving to Rice University in 2012. He has served as an Associate Editor of Biophysical Journal and as the Editor-in-Chief of Physical Biology. He is a Fellow of American Physical Society (APS), and an elected member of the American Academy of Arts and Sciences (AAAS) & National Academy of Sciences (NAS).

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)
