Department of Bioengineering

11th Annual Symposium, BE 2025
2025-01-09 14:30 - 2025-01-10 17:00 (Asia/Kolkata) | TCS Smart-X Hub Building, IISc
11th Annual Symposium, BE 2025

BE Symposium Schedule: Click here

BE Seminar: Mesoscale Epithelial Mechanobiology and Cellular Interfaces
2024-12-16 16:00 - 17:00 (Asia/Kolkata)
Speaker: Dr. Jacopo Di Russo
Group Leader
Institute of Molecular and Cellular Anatomy, RWTH Aachen University
& Leibniz-Institute for Interactive Materials, Aachen Germany.
Title: Mesoscale Epithelial Mechanobiology and Cellular Interfaces
Abstract: Mechanical properties regulate tissue functions at a multicellular length scale or mesoscale. These properties depend on the interaction of cells with their interfaces, hence on the balance between intercellular tension and the extracellular matrix (ECM) adhesion forces.
Dr. Jacopo Di Russo’s group aims to dissect the role of cell-ECM and cell-cell communication in epithelial mechanobiology, starting from the medically relevant retinal epithelium. In contrast to the experimental investigation of traditional biological sciences, his laboratory uses cross-disciplinary approaches combining synthetic hydrogels with stem cell-based models. They particularly develop and adapt biohybrid systems where cells interact with hydrogels that are designed to control cell-cell or cell-ECM adhesion. Synthetic material allows the unique reduction of the degree of freedom in the cellular/tissue system, thus helping us to reveal phenotypical tissue plasticity and molecular function.
The talk will first give an overview of published work1,2 on understanding how ECM physical (elasticity) and biochemical cues (receptor density) impact epithelial system properties, namely stress heterogeneity and intercellular force coordination. The talk will also show that these properties are not only in vitro observations but play pivotal roles in controlling the vision. A density gradient of ECM characterises the contractility of the retinal epithelium in vivo and modulates its efficiency in supporting photoreceptor cells’ homeostasis. Furthermore, Dr. Jacopo will show data from the ongoing work which addresses different aspects of the mechanobiology of tissue ageing. They optimised a phototunable hydrogel as substrates for epithelia to model ECM local remodelling on demand. Moreover, we developed microgels used as phototunable phantom cells to simulate age-related tissue mechanical anisotropy. Altogether, They can dissect the relationship between tissue mechanics and function by controlling the temporal and spatial properties of cellular interfaces.
About the Speaker: Dr. Jacopo Di Russo studied cell biology in Florence (Italy) for then joining the laboratory of Prof. Lydia Sorokin in Muenster (Germany) as Marie Curie Fellow. There he studied how extracellular matrix influences physiological responses. In 2015 he joined the laboratory of Prof. Joachim Spatz at the Max Planck Institute for Medical Research in Heidelberg (Germany) deepening his knowledge on cell adhesion at biophysical levels. Since 2019 he is an independent group leader at the Interdisciplinary Center for Clinical Research of the RWTH Aachen. Jacopo Di Russo’s research aims to understand the interplay of extracellular matrix biochemical and physical information in controlling epithelial mechanobiology.
Date: 16th December
Time: 4.00 PM
Venue: IDR Classroom – 05: G21

BE Seminar: Cell and Gene Therapy Manufacturing: Bridging the Skillset Gap by Training the Next Generation Workforce
2024-12-13 11:00 - 12:00 (Asia/Kolkata) | IDR Building – G12: Classroom 3
Speaker: Dr. Shalu Suri
Co-Director of Engineering Workforce Development (EWD) NSF Engineering Research Center for Cell Manufacturing Technologies (CMaT) Georgia Tech, USA.
Date: 13th December
Time: 11.00 AM
Venue: IDR Classroom – 3: G12
Title: Cell and Gene Therapy Manufacturing: Bridging the Skillset Gap by Training the Next Generation Workforce
Abstract: With the approval of the multiple cell and gene therapies by the FDA in the past few years and the tremendous promise of emerging biopharmaceutical drugs – biomanufacturing, especially the transformative areas of cell and gene-therapy manufacturing, has rapidly become one of the most dynamic and rapidly growing sectors of the biotech and pharma industry in the United States, and around the world. However, the growth of the field can only be realized by the successful development of a well-trained workforce. The lack of an adequately trained workforce has already been identified as a major barrier hindering the growth of biomanufacturing and biotherapies today and this situation will only worsen as the field continues to expand. Cell Manufacturing Technologies (CMaT), the NSF funded multi-institute Engineering Research Center in the Coulter Department of Biomedical Engineering at Georgia Tech, is the first and only comprehensive multi-institute center in the world focused on developing transformative tools, technologies, and processes for scalable, quality-driven biomanufacturing of cell therapies, and preparing adequately trained workforce. Dr. Suri was recruited as Associate Director of Engineering Workforce Development (EWD) pillar of NSF CMaT ERC by Georgia Tech and Emory Medicine in Jan 2020 from Cornell University to spearhead the creation of this well-trained and diverse biomanufacturing workforce that could nurture this nascent industry and thus reduce the skillset gap. In the last 4+ years, Dr. Suri has spearheaded multiple high-impact workforce development efforts. Of particular importance is the virtual professional training program entitled “Workforce Development in Biomanufacturing – Training in Cell and Gene Therapy” developed in collaboration with International Society for Cell and Gene Therapy (ISCT) which has trained 300+ professionals globally. In addition, she has also led the development of a week-long hands-on Cell manufacturing training program in partnership with ISCT. Dr. Suri has championed multiple efforts at K-12 and 2-year college levels towards workforce training. She collaborates with instructors from a number of 2-year technical colleges on cell manufacturing curriculum development and its integration into their curriculum to address the shortage of entry level trained workers. In her talk she will provide a broad overview of the field and highlight the work the center has done in the last 7 years to move this field forward.
About the Speaker: Dr. Shalu Suri is the Co-director of Engineering workforce Development (EWD) pillar of NSF Engineering Research Center for Cell Manufacturing Technologies (CMaT) at Georgia Tech. She joined CMaT in 2020 as the Associate Director and became the Co-director in 2022. Prior to joining GT, she was a lecturer in BME at Cornell University where she was instrumental in designing and teaching multiple UG and graduate classes for which she received Cornell’s Teaching Excellence Award. At CMaT, she spearheads multiple high-impact efforts across academic levels (K12-industry) towards curriculum development, professional education, and preparing future cell manufacturing workforce. She has received multiple honors including GT’s 2024 Outstanding Professional Education Award for her contributions to the field of professional education and GT’s 2023 Student Recognition of Excellence in Teaching CIOS Honor Roll. She serves on the National Advisory Council of NSF-InnovATEBIO biotechnology education center. She received her undergraduate degree from Kanpur University and her MS from Indian Institute of Technology Bombay (India), and her PhD in Biomedical Engineering from the University of Texas at Austin. She received her postdoctoral training from Georgia Tech.

BE Seminar: The influence of chemo-mechanical cues from the cell environment on the chromatin organization
2024-11-21 11:00 - 12:00 (Asia/Kolkata) | CES Seminar Hall, CES Seminar Hall, 3rd Floor, Biological Science Building
Speaker: Dr. Aayush Kant
Postdoctoral Researcher at the University of Pennsylvania, Philadelphia
Title: The influence of chemo-mechanical cues from the cell environment on the chromatin organization
Abstract: Cells continuously experience a range of physical and chemical stimuli from their environment shaping their behavior and identity, a process that is particularly evident in diseases such as cancer. As tumor cells interact with an evolving extracellular matrix or metastasizing cells squeeze through the blood vessels during intravasation, these stimuli trigger immediate cellular response and drive long-term phenotypic changes in the cell identity. A key mechanism underscoring these changes in cell behavior is the dynamic reorganization of chromatin – the macromolecular complex of DNA and associated proteins within the nucleus – regulating gene expression. In this talk, I will present our recent advancements in developing a mesoscale mathematical model that captures the spatiotemporal chromatin reorganization in response to environmental cues – both chemical, such as epigenetic dysregulation, and physical, in the form of osmotic shocks or mechanical deformation. This model demonstrates the experimentally observed emergent segregation of chromatin into euchromatin, with expressed genes, and tightly compacted silenced heterochromatin, which often associates with the nuclear lamina. I will discuss how environment-driven kinetics of histone modifications, such as methylation and acetylation, affect the spatial chromatin distribution and the overall nuclear stiffness. I will also demonstrate how physical forces can directly alter chromatin compaction, determining gene accessibility. Our theoretical predictions are validated by experimental observations obtained via high-resolution imaging and genomic sequencing techniques. The model, grounded on agnostic thermodynamic principles, offers insights into several disease progressions, including metastatic cancer, non-alcoholic fatty liver disease, and tendinosis. Our model establishes a novel framework for mechanistically understanding the evolution of cell phenotypic identity in the context of disease mechanisms, which is helpful in identifying therapeutic interventions.
About the Speaker: Dr. Aayush Kant is a Postdoctoral Researcher at the University of Pennsylvania (Philadelphia) specializing in the study of physical forces within cells and organelles and their impact on cellular function. His research interests lie in developing a mechanistic understanding of biological systems using fundamental continuum-scale physical principles along with analytical and numerical methods. He is currently investigating how physical and chemical signals from the cell and the cell surroundings help reorganize the genome. This work utilizes mathematical modeling techniques rooted in non-equilibrium thermodynamics, variational principles and phase-field modeling. Aayush received his Ph.D. in 2019 through a joint program between the Indian Institute of Technology Bombay (Mumbai) and Monash University (Clayton, Australia), where he explored the mechanistic principles underlying the long-term pathophysiology following a traumatic brain injury. This work exemplifies yet another chemical-degradation coupled force-transduction system, a theme that Aayush is quite keen to further explore.

BE Seminar: Nanomedicine and Genome Editing Approaches for Disease Therapies
2024-11-19 11:30 - 12:30 (Asia/Kolkata) | IDR Building – G12: Classroom 3
Speaker: Dr. Gang Bao
Department of Bioengineering, Rice University
Title: Nanomedicine and Genome Editing Approaches for Disease Therapies
Abstract: The design and optimization of nanomedicine and genome editing – based tools and methods provide unprecedented opportunities for achieving better control of biological processes, and drastic improvements in disease diagnosis and treatments. Recent advances include the development of multi-functional nanoparticles and CRISPR/Cas systems for biological and medical applications.
In this talk, he will first present the recent work on magnetic nanoparticles in the lab, including the synthesis and functionalization of magnetic nanocluster for treating metastatic cancer. He will then present the design and optimization of CRISPR/Cas9-based genome editing for treating sickle cell disease. The challenges and opportunities in developing in vivo genome editing will also be discussed.
About The Speaker: Dr. Gang Bao is the Foyt Family Professor in the Department of Bioengineering at Rice University. He is also a CPRIT Senior Scholar in Cancer Research and the Director of the Cancer Bioengineering Collaborative at Rice University. Dr. Bao received his undergraduate and Master’s degrees from Shandong University in China, and his PhD degree from Lehigh University in the US. Dr. Bao is a Fellow of the American Association of Advancement in Science (AAAS), American Institute for Medical and Biological Engineering (AIMBE), Biomedical Engineering Society (BMES), American Society of Mechanical Engineers (ASME), American Physical Society (APS), and International Academy of Medical and Biological Engineers (IAMBE).
Dr. Bao’s current research is focused on the development of genome editing and nanomedicine tools and approaches for biological and disease studies, including magnetic nanoparticle-based diagnosis and treatment of chronic diseases such as cancer, viral and non-viral based in vivo delivery methods, design and optimization of CRISPR/Cas9 for gene editing, and the application of gene editing for treating sickle cell disease and cystic fibrosis.

BE Seminar: Mechanisms driving genome structure and regulating biological function by Dr. Sumitabha Brahmachari
2024-09-02 16:00 - 17:00 (Asia/Kolkata) | CES Seminar Hall, CES Seminar Hall, 3rd Floor, Biological Science Building
Title: Mechanisms driving genome structure and regulating biological function
Speaker: Dr. Sumitabha Brahmachari,
Center for Theoretical Biological Physics,
Rice University, USA.
Abstract: Quantitative understanding of the genomic structure and its relevance to biological function remains a significant challenge. With advancements in experimental techniques like Hi-C and various types of imaging, there is a need for an integrative modeling framework that extracts mechanistic insights from experimental data. In this talk, I will focus on building computational tools for the physical modeling of the genome that directly incorporates Hi-C data to construct ensembles of genomic structures. These ensembles are consistent with imaging studies providing independent validation. I will discuss how the modeling framework is helping us discover the evolutionarily conserved principles governing genome organization and elucidate the modus operandi of various molecular drivers. The mechanistic insights from the data-driven structures are explicating an intimate regulatory relationship between genome structure and cellular function. Notably, the framework will play a crucial role in examining the relevance of three-dimensional genome structure in various diseases caused by the aberrant functionality of architectural proteins.
About the Speaker: Sumitabha Brahmachari is a Postdoctoral Associate at the Center for Theoretical Biological Physics at Rice University, Houston, TX, working on topics related to the organization and mechanics of DNA. He is interested in developing quantitative models of chromosomes that incorporate techniques from statistical mechanics, machine learning, and molecular dynamics to understand how various proteins structure the genome and what information the structure might hold. He received his Ph.D. from the Department of Physics and Astronomy at Northwestern University, where he was a Molecular Biophysics Training Fellow. Dr. Brahmachari is an active member of the American Physical Society and has organized scientific sessions in APS meetings and led workshops and outreach initiatives, including mentoring summer students as a part of the NSF Frontiers in Science program.

Prof. Rinti Banerjee Memorial Lecture by Prof. Uma K Maheshwari
2024-08-14 16:00 - 17:30 (Asia/Kolkata) | Faculty Hall

BE Seminar: Quantifying Cell-State Densities in Single-Cell Phenotypic Landscapes by Dr. Manu Setty
2024-08-12 16:00 - 17:00 (Asia/Kolkata) | CES Seminar Hall, CES Seminar Hall, 3rd Floor, Biological Science Building
Speaker: Dr. Manu Setty
Assistant Professor
Fred Hutch Cancer Centre, Seattle, USA.

Title: Quantifying Cell-State Densities in Single-Cell Phenotypic Landscapes
Abstract: Single-cell studies have clearly established the continuous nature of cell-state transitions in trajectories of differentiation and disease. Moreover, fundamental processes such as proliferation and apoptosis generate a non-uniform distribution of states within these continuous landscapes. Thus, modeling of trajectories using single-cell data necessitates not only a continuous representation but one that accounts for variability in cell-state density. In addition to being reflective of the underlying biology, continuous representations also enable the utilization of well-developed frameworks in multivariate statistics and dynamical systems to model and interpret large-scale single-cell data. In this seminar, I will describe our recent algorithm, Mellon, that provides a fully continuous representation of high-dimensional single-cell landscapes. Mellon infers a continuous density function that can be employed to infer cell-state density at both observed cell-states represented by individual cells and potential unobserved cell-states. I will present how Mellon can help dissect the density landscape of differentiating systems, revealing a consistent pattern of high-density regions corresponding to major cell types intertwined with low-density, rare transitory states. Our work provides evidence implicating enhancer priming and the activation of master regulators in the emergence of these transitory states. Finally, I will describe our ongoing work in leveraging continuous representations for interpreting multi-condition, multi-modal single-cell data.
About The Speaker: Manu Setty is an Assistant Professor at Fred Hutch Cancer Center in the Basic Sciences Division. Manu received his PhD from the Weill Cornell Graduate School in the lab of Christina Leslie where he developed machine learning algorithms for regulatory network inference and received the Frank Lappin Horsfall Fellowship award for his thesis. He then undertook a post-doctoral fellowship in the lab of Dana Pe’er where he developed trajectory detection algorithms using single-cell data and demonstrated the continuous nature of cell-fate choices during differentiation. He was recognized with the Tri-I Breakout Prize for his work at MSK. He now heads a lab that develops computational methods using single-cell and spatial data to model and interpret biological trajectories.

BE & DBG Seminar titled "Loss of tissue structure in cancer: a mechanobiological perspective." by Prof. Tanmay Lele
2024-08-06 16:00 - 17:00 (Asia/Kolkata) | DBG Seminar Hall, 1st Floor, Biological Science Building
The Department of Bioengineering (BE) and Department of Developmental Biology and Genetics (DBG) cordially invites you to attend a Seminar
Speaker: Prof. Tanmay Lele
Department of Biomedical Engineering, Texas A&M University, USA
Title: Loss of tissue structure in cancer: a mechanobiological perspective
Abstract: In glandular epithelial cancers such as breast cancer, the usual orderly arrangement of cells that surround a central lumen becomes disrupted. This loss of tissue architecture can facilitate invasive migration of cells into the surrounding microenvironment and subsequent cancer metastasis. I will present our recent work which shows that an imbalance in cellular mechanical force causes tissue lumens to collapse due to mechanical instabilities. This collapse is followed by an extraordinary inside-out eversion that drives collective migration of clusters of cells through the 3D extracellular matrix (ECM). I will discuss how individual migrating cancer cells negotiate the confining spaces in tissue with a focus on the limiting role of the nucleus in confinement. I will conclude with an exploration of how alterations to the mechanical properties of the ECM in tumors might impose a selection pressure on genetically variable tumor cell populations resulting in more malignant cell phenotypes.
About the Speaker: Tanmay Lele is a Professor of Biomedical Engineering and Chemical Engineering at Texas A&M University. He obtained his Ph.D. in Chemical Engineering from Purdue University followed by postdoctoral research in Vascular Biology at Harvard Medical School/Children’s Hospital. He obtained his B. Chem. Eng. degree from UDCT, Mumbai.
His research focuses on understanding the mechanisms underlying the loss of cancer tissue structure and aberrant tumor mechanobiology. Over the years, his research group has made significant contributions to the field including a recent paper that reports the first dynamic observations of acinar eversion caused by a mechanical destabilization. His group combines molecular biology and cell biology techniques with computational modeling to investigate cancer mechanobiology comprehensively. He is a fellow of the Biomedical Engineering Society and the American Institute of Medical and Biological Engineering.

BE Seminar: Self-Powered Devices Based on Triboelectrification by Prof. Zong-Hong Lin
2024-08-05 16:00 - 17:00 (Asia/Kolkata) | DBG Seminar Hall, 1st Floor, Biological Science Building
Title: Self-Powered Devices Based on Triboelectrification
Speaker: Prof. Zong-Hong Lin
National Taiwan University
Abstract: Designing devices with self-powered sensing function has become a popular research field since its emergence in recent decades. Triboelectrification occurs when two materials come into contact with each other, causing charge transfer that leads to oppositely charged surfaces; the amount of charge transfer varies depending on material composition. By combining triboelectrification with electrostatic induction, relevant devices can be designed. If used for energy collection purposes, scientists generally refer to them as Triboelectric Nanogenerators (TENGs); but if used for self-powered sensing purposes, scientists call them Triboelectric Nanosensors (TENSs). In our previous research on TENSs, we demonstrated the concept of selective detection of some targets by specific materials or their surface-modified probes. When the targets are adsorbing or binding to the surface, different electrical output signals will be generated compared to before, and these changes can be used for qualitative and quantitative analysis of the targets. In the past few years, we have further developed solid-liquid TENSs for measuring targets such as metal ions, small molecules, proteins, and microorganisms. Compared with our previously developed solid-solid TENSs, we have not only improved several shortcomings but also established sensing mechanism and working principle which are very important research achievements in this field. We also look forward to expanding the applications of the solid-liquid TENSs in the near future.
About the Speaker: Dr. Zong-Hong Lin received his PhD from the National Taiwan University (NTU) in 2009 and continued with his postdoctoral research at the NTU and Georgia Tech during the years of 2010-2014. Subsequently, Dr. Lin joined the Institute of Biomedical Engineering, National Tsing Hua University (NTHU) as an Assistant Professor in 2014 and was successfully promoted to Associate Professor and Full Professor in 2017 and 2021, respectively. At the same time, Dr. Lin was also an adjunct faculty at the Department of Power Mechanical Engineering and the Department of Chemistry. In 2023, he moved to the Department of Biomedical Engineering at NTU. He has published more than 160 SCI papers (sum of the times cited: 15990, h-index: 62), as well as received recognition for his research contribution, such as CHEN-YUNG Chair Professor (2023) of NTU, Academic Excellence Award, College of Engineering of NTU (2023), Fellow of the Royal Society of Chemistry (2022), Outstanding Research). Award of the Taiwan National Science and Technology Council (NSTC) (2024), Future Tech Award of the Taiwan NSTC (2021, 2022 and 2023), Ta-You Wu Memorial Award of the Taiwan NSTC (2021), Young Scholar Fellowship of the Taiwan NSTC (2020), IEEE-NANOMED New Innovator Award (2019) and Young Investigator Award of the NTHU (2018).

BE Seminar titled "Next-Generation Solutions in medicine: Overcoming Drug Resistance in Cancer" by Dr. Raghuraman Kannan
2024-08-01 15:00 - 16:00 (Asia/Kolkata) | CES Seminar Hall, CES Seminar Hall, 3rd Floor, Biological Science Building
Title: NEXT-GENERATION SOLUTIONS IN MEDICINE: OVERCOMING DRUG RESISTANCE IN CANCER.
Abstract: Research in my laboratories is focused on uncovering the underlying root causes of cancer’s resistance to drugs. Specifically, the work aims to identify and validate the mechanisms that drive this resistance. After elucidating the mechanism, we have designed new nano-delivery devices specific to the target to improve the effectiveness of FDA-approved treatments by restoring tumor sensitivity. We have made significant progress in recent years, including identifying a new “dual therapeutic pair” to overcome the resistance for the first time. We have also engineered stimuli-responsive nano-delivery devices to deliver more drugs to drug-resistant tumors and developed a novel class of material called Gelasomes for RNA therapy. In this seminar, I will present details about the successes, challenges, and prospects of the above-listed projects.
About the Speaker: Dr. Kannan is a faculty of Radiology and Bioengineering at the University of Missouri (MU) and has been a faculty member at MU since 2005. He leads the program on clinical translation of nanomaterials at MU. He received his M.S. degree in chemistry from the Indian Institute of Technology at Madras in 1993 and his Ph.D. degree in chemistry, from the Indian Institute of Science in 1999. Dr. Kannan’s current research focuses on the following areas: § Oncology and Immuno-Oncology: Developing drugs to overcome drug resistance in cancer. Dr. Kannan’s work includes the study of AXL inhibition, siRNA therapeutics, and the tumor immune microenvironment in lung and ovarian cancer. § Nanomedicine: Designing and developing novel supraparticle systems, including the Gold-Gelasomes and supraparticle self-assembly for targeted drug delivery and reduced toxicity in cancer treatment. § Medical Imaging and Diagnostics: Developing sensors for early detection of diabetic retinopathy and a near-infrared (NIR) imaging camera for cardiac imaging. Dr. Kannan is currently leading the NIH-supported “Clinical translational of nanomedicine” project with the aim of treating human cancer patients in the year 2027. As of now, Dr. Kannan holds 23 patents and patent applications published and licensed. His patent portfolio spans across gene delivery systems, CRISPR, nanotechnology, and medical imaging devices, contributing significantly to advancements in medical science and technology. Translational Research: Dr. Kannan has founded multiple companies that focus on translating his research into practical medical applications, bridging the gap between laboratory discoveries and clinical solutions. Dr. Kannan is a co-founder of four start-up companies based on his research. Two of his companies have raised several million-dollar investments from pharmaceutical companies. Education: Dr. Kannan is actively involved in developing new courses in Biomedical innovation and entrepreneurship; classroom teaching of basic principles of drug resistance in oncology; developing new laboratory experiments to provide hands-on experience to students; mentoring undergraduate, graduate, and post-doctoral fellows; and providing research opportunities to K-12 students in nanomedicine.

BE Seminar titled "Engineering bottom-up synthetic cells to mimic life-like functions" by Dr Taniya Chakraborty
2024-07-29 16:00 - 17:00 (Asia/Kolkata) | DBG Seminar Hall, 1st Floor, Biological Science Building
Title: Engineering bottom-up synthetic cells to mimic life-like functions
Abstract: How did life evolve from non-living matter on early Earth, and is it possible to recreate this transition artificially in a laboratory setting? Reconstructing well-defined functional molecular entities, components, and modules from the bottom-up to create a synthetic cell will provide new insights into the mechanisms of life. Optogenetic proteins, metalloenzymes, and RNA nanotechnology are powerful tools for engineering synthetic cells to mimic life-like functions such as communication, differentiation, or the central dogma. Synthetic cells engineered with photo-switchable proteins allowed control over adhesion and chemical communication between them, which strongly depended on their spatial proximity and can also be photo-regulated. While cells typically communicate through diffusible molecules, nonchemical communication remains elusive. Light-based signaling is possible in synthetic cell communities inspired by deep-sea bioluminescent-based predator-prey communities, where light signals triggered synthetic cell adhesion and facilitated predator-prey interactions, providing a blueprint for light-based intercellular communication.
Pluripotent cells can yield different cell types determined by the specific sequence of differentiation signals encountered, with pluripotency in synthetic cells achieved by incorporating three dormant apo-metalloenzymes, enabling differentiation toward distinct fates depending on the sequence of specific metal ions transported with ionophores.
The central dogma at the core of molecular biology states that information flows from DNA to RNA and then to protein. Conceptually, a novel approach is introduced towards synthetic life by leveraging RNA origami as an alternative to proteins, requiring only a single copying step between genetic information and function. For the first time, RNA origami tiles were designed, which fold co-transcriptionally from a DNA template and self-assemble into higher-order 3D RNA origami nanotubes similar to the cytoskeleton network inside synthetic cells, reaching several micrometers in length.
Synthetic cells not only serve to understand the fundamental question of the origin of life but also find therapeutic applications. Inspired by the phage display technique, synthetic cells were used for the first time to display genetically encoded RNA to bind with specific proteins of interest on the synthetic cell surface. This liposome display technique exhibits promising potential for a broad array of applications in detecting proteins of interest or antigens and may represent a step toward the evolution of synthetic cells. Bottom-up construction of synthetic cells offers not only insights into the origin of life but also promises significant advancements in therapeutic and biotechnological applications.
About The Speaker: Dr. Tanya began her PhD in 2018 under the MaxSynBio project, one of the pioneering scientific endeavours to explore the question, “What is life, and is it possible to completely recreate life synthetically based on a bottom-up approach?” She completed PhD in 2022 at the Max Planck Institute for Polymer Research and Gutenberg University, Mainz, Germany. During my doctoral studies, she also worked as a guest researcher at the Institute of Physiological Chemistry and Patho Biochemistry at the University of Muenster. Throughout my PhD, she designed her own projects focused on mimicking chemical and light-mediated communication in synthetic cells and published them as the first author in high-impact international journals. She worked independently and also designed projects for other PhD students in the group, supervising their work. Building upon my expertise in protein engineering and optogenetics, she transitioned to a post-doctoral role at the Max Planck Institute for Medical Research immediately upon completing her PhD in 2022, where she began exploring the potential of DNA/RNA nanotechnology.
In 2023, she secured an independent post-doctoral grant from the German Ministry of Research, enabling her to delve into the therapeutic applications of bottom-up synthetic cells and develop innovative techniques for liposome display. She is currently pursuing this research in collaboration with the Max Planck Institute for Medical Research and Heidelberg University. As part of her commitment to academic excellence, she introduced a new course titled “Biophysics and Synthetic Biology” for master’s students at Heidelberg University.
Throughout her academic journey, she has actively participated in numerous international conferences, presenting her research findings and fostering collaborations on a global scale. Additionally, she has contributed as a reviewer for several Nature Journals. Presently, she is deeply invested in the field of synthetic immunology, aiming to leverage synthetic cells for the development of therapeutic targets and vaccines, thereby advancing beyond traditional immunotherapy and drug delivery approaches.

BE Seminar: Physics of Nuclear Organization
2024-06-12 15:00 - 16:00 (Asia/Kolkata) | DBG Seminar Hall, 1st Floor, Biological Science Building
Speaker: Dr. Rakesh Das
Max-Planck-Institute for the Physics of Complex Systems, Germany
Title: Physics of Nuclear Organization
Abstract: Spatiotemporal organization of the subnuclear medium plays a crucial role in genome regulation [1]. However, the effect of active perturbation from various molecular actions in the medium on this organization remains unclear. In this seminar, I will mainly focus on our recent investigations into how such activities influence the coordination of subnuclear compartments (SNCs, such as transcription factories) with chromatin and the compartmentalization of chromatin into eu- and heterochromatic regions, and discuss their biological implications. We have developed a polymer physics-based computational framework where chromatin is perturbed by a non-localized active mechanism mimicking the action of Topoisomerase-II enzyme. Using a self-developed GPU-based parallelized computer code and a newly introduced theoretical model, we demonstrate that SNC dynamics in this complex system can be described by a combination of three modes, each linked to different physical aspects of the embedding medium. Notably, the activity enhances SNC dynamics through a slow mode associated with chromatin-mesh remodeling. This offers new insights into the role of global active perturbations in target-searching processes [2]. Additionally, we report the emergence of characteristic compartmentalization features, viz., wall-like organization of euchromatin with negative nematic ordering of the euchromatic segments due to activity. These features cannot be captured by an equilibrium physics-based theory. This highlights the critical role of such active perturbations in chromatin organization [3]. Given that activity correlates with factors like aging and cell cycle, our studies may shed light on cell state[1]specific genome regulation. I will conclude my seminar with a brief discussion of my future research plan on ‘Integrative Nuclear Architecture’, which investigates the spatiotemporal characteristics of the nucleus as collective features arising from interconnected cellular components.
About The Speaker: Dr. Rakesh Das is a theoretical and computational biophysicist who employs concepts from condensed matter physics and non-equilibrium physics to investigate biological systems. During his Ph.D. at S. N. Bose National Centre for Basic Sciences, he explored collective features in active matter and obtained his degree in 2019. Following that, he joined Mechanobiology Institute at National University of Singapore, Singapore for his first postdoctoral position. Since November 2023, he has held a Postdoctoral Guest Scientist position at Max-Planck-Institute for the physics of Complex Systems in Dresden, Germany. He is interested in the Physics of various cellular systems.

BE Seminar on "Harnessing immune system for the development of bio-therapeutics" by Dr. Anjali Barnwal
2024-05-21 16:00 - 17:00 UTC | CES Seminar Hall, CES Seminar Hall, 3rd Floor, Biological Science Building
Title: Harnessing immune system for the development of bio-therapeutics
Abstract: Leveraging the immune system for therapeutic advancement offers numerous advantages over standard treatments for inflammatory diseases. These advantages encompass precise targeting, enduring responses, minimal toxicity, and more. Diverse immunotherapies, such as antibody utilization, T-cell therapy, dendritic cell vaccination, among others, are actively under investigation. Given that vaccine strategies primarily operate via dendritic cell (DC) uptake and antigen presentation and recognizing the pivotal role of DCs in activating both innate and adaptive immunity, exploiting these attributes holds potential for developing effective therapeutics for inflammatory diseases like Cancer and COVID-19. These therapeutic modalities demonstrate enhanced antitumor efficacy across various tumor models. Furthermore, DC-based immunotherapy exhibits superior antiviral efficacy against Covid-19 compared to the commonly used free spike protein. While immunotherapies for inflammatory diseases are rapidly advancing in developed nations, India lags behind primarily due to cost and complexity barriers. Therefore, there is an unmet need for the development of cost-effective immunotherapeutic to enhance overall survival and quality of life for patients.
About the Speaker: Dr. Anjali Barnwal completed a bachelor’s degree in biotechnology from Patna University in 2013 and then obtained her master’s degree in biotechnology from the University of Hyderabad in 2015. After a year of dissertation work on the Dengue virus, her curiosity led her to delve into the development of therapeutics for Inflammatory disease. To pursue this interest further, she joined the Biomedical Engineering program at IIT Delhi for PhD in 2018. Throughout the doctoral research, she dedicated herself to developing immunotherapies for both COVID-19 and Cancer. Dr. Anjali’s PhD work resulted in many first-author publications in esteemed international journals. Notably, the cell-free vaccine developed for COVID-19 garnered attention in the Indian media for its superior efficacy. She was honored to receive the Amit Garg Memorial Research Award for the high-impact publication and the Dr. Sanjiv Bhatia Memorial Research Excellence Award for the best Ph.D. thesis (2023). During her PhD journey, she also took on the role of mentoring many master’s students and junior PhD candidates. As the first student in the lab, she played a pivotal role in its establishment, actively contributing to various aspects such as grant writing and management processes.
In July 2023, Dr. Anjali joined Duke University as a postdoctoral associate, where her research centers on understanding the intricate roles of various immune cells in the comprehensive response to immunotherapy. She is actively engaged in multiple projects aimed at enhancing antitumor efficacy and overall survival rates in murine Glioblastoma models.
In addition to her academic pursuits, she serves as a review editor at Frontiers in Immunology and Frontiers in Oncology, specializing in the Cancer Immunity and Immunotherapy section. Driven by her passion for advancing immunotherapy in India, she was drawn to join Flahybase as a visiting scientist which is a pioneering startup company specializing in computational biomedicine for precision oncology. She is passionate about continuing to contribute to the development of immunotherapeutics in India, with the goal of making them as widely accessible as they are in developed countries.

BE Seminar: All Wired Up: Harnessing Protein Polymers for Medicine and Nanotechnology
2024-04-29 11:00 - 12:30 UTC | CES Seminar Hall, CES Seminar Hall, 3rd Floor, Biological Science Building
Speaker: Dr. Aarat P. Kalra
IIT Delhi
Title: All Wired Up: Harnessing Protein Polymers for Medicine and Nanotechnology
Abstract: The successful interfacing of biochemistry with electronics is one of the grand challenges of nanotechnology. Biodegradable and biocompatible materials with structural integrity, that can perform mixed electronic and ionic roles are required for the development of the next generation of nanodevices. The interface of electronics and biochemistry is also crucial for medicine, with electric and magnetic field-based therapies being used for cancer treatment and wound healing.
Inside the eukaryotic cell, protein polymers such as microtubules and actin filaments play structural roles such as maintaining cell shape and orchestrating cell division. Short intermolecular distances between aromatic amino acids, the presence of a highly negative surface charge, and the structural regularity of the ordered protein ‘lattice’ allow the emergence of interesting properties in both protein polymers. Thus, microtubules and actin filaments are interesting candidates for use in biodegradable nanodevices, while also acting as the potential intracellular targets of electric field-based therapies.
The talk will focus on experiments revealing the nontrivial photophysical and electrostatic properties of microtubules. Our experiments reveal that energy can migrate by diffusive energy transfer over unexpectedly large distances (6.6 nm) in microtubules. We find that conventional Förster theory predicts a diffusion length of only ~2.3 nm; insufficient to explain our observations. Introducing the anesthetics etomidate and isoflurane decreases the observed energy diffusion length. We find significantly higher diffusion lengths when other mechanisms of energy transfer are considered. Collectively, our work shows that it is worth considering protein polymers for ultraviolet light-harvesting systems. Microtubules and actin filaments also have highly negatively charged surfaces, allowing them to store and possibly conduct ions. Our experiments on microtubules in solution show that they lowered their local pH value by as much as one unit on the pH scale and that they increased solution capacitance. This behavior indicates the potential of microtubules as charge storage devices both inside the cell and outside it, within protein-based electronic devices.
About the Speaker: Dr. Aarat Kalra is an Assistant Professor at the Centre for Biomedical Engineering at the Indian Institute of Technology, Delhi, and at the Department of Biomedical Engineering at the All India Institute of Medical Sciences, New Delhi.
He completed his Bachelor of Science (B.Sc. (Hons.) with distinction from Dayal Bagh Educational Institute (Agra, India) in chemistry, a Master of Science (M.Sc.) from McGill University in biology, and a Doctor of Philosophy (Ph.D.) with Prof. Jack Tuszynski at the University of Alberta in physics. Thereafter, he worked as a postdoctoral researcher at Princeton University with Prof. Gregory Scholes, publishing transformative work on microtubule electronics.
During his doctoral work, he was awarded the prestigious Alberta Innovates Graduate Student Scholarship and the micro-nano technology (MNT) Award (two times) over the course of his Ph.D. His work has shown that microtubules are unexpectedly effective light harvesters, changing their photophysical properties upon small-molecule binding. This work has been published by ACS Central Science, on the front cover of the March 2023 issue. He was invited to present a talk at Google in 2022, as part of a conference titled ‘Is Our Brain a Quantum Computer?’ At IIT Delhi, Dr. Kalra is a recipient of the Young Faculty Incentive Fellowship (YFIF).
Dr. Kalra’s work on microtubules has opened several new research directions and has been featured twice in the scientific magazine The New Scientist and recently in the Indian daily Hindustan Times.

BE Seminar: The story of giant bacteriophage phiKZ and its potential usage as antimicrobials source
2024-04-25 16:00 - 17:00 UTC | CES Seminar Hall, CES Seminar Hall, 3rd Floor, Biological Science Building
Speaker: Maria Yakunina
Leader of research group,
Laboratory of molecular microbiology, Institute of Nanobiotechnologies, Peter the Great St.Petersburg Polytechnic University
Title: The story of giant bacteriophage phiKZ and its potential usage as antimicrobials source
Abstract: Bacteriophages are viruses that infect bacteria, serving as their natural enemies and our potential allies. Due to the constant arms race occurring in the microcosm, bacteriophages possess a vast array of tools to invade bacterial cells and utilize them for reproduction. In the seminar, I will discuss the giant bacteriophage phiKZ, which fundamentally alters the bacterial cell during infection. I will also talk about our current research focused on discovering the mechanisms through which the phage halts the life of a bacterial cell and how we can apply this knowledge.
About the speaker: Maria Yakunina is a leader of the laboratory of molecular microbiology at the Institute of Nanobiotechnologies, Peter the Great St. Petersburg Polytechnic University, Russia.

BE Seminar: Surgical Robotics: A Journey Across Scales
2024-04-25 14:30 - 15:30 UTC
Speaker: Prof. Sarthak Misra
Prof. Satish Dhawan Visiting Chair Professor
Date: 25th April 2024
Time: 2.30 pm – 3.30 pm
Venue: DBG Seminar Hall
Title: Surgical Robotics: A Journey Across Scales
Summary: This talk will provide an overview of ongoing work at the Surgical Robotics Laboratory. It covers topics ranging from the design of macro-scale flexible/continuum surgical instruments to the fabrication and control of futuristic medical micro-robots. Prof. Misra has been recently invited to IISc as a Prof. Satish Dhawan Visiting Chair Professor. This is his first lecture as part of his appointment at IISc.
About the Speaker: Prof. Sarthak Misra joined the University of Twente in 2009. He is currently a Full Professor in the Department of Biomechanical Engineering within the Faculty of Engineering Technology. He is also affiliated with the Department of Biomaterials and Biomedical Technology, University of Groningen, and University Medical Center Groningen. He leads the Surgical Robotics Laboratory. Prof. Sarthak obtained his doctoral degree in the Department of Mechanical Engineering at the Johns Hopkins University, Baltimore, USA. Prior to commencing his studies at Johns Hopkins, he worked for three years as a dynamics and controls analyst at MacDonald Dettwiler and Associates on the International Space Station Program. Prof. Sarthak received his Master of Engineering degree in Mechanical Engineering from McGill University, Montreal, Canada. He is the recipient of the European Research Council (ERC) Consolidator, Starting and Proof-of-Concept grants, Netherlands Organization for Scientific Research (NWO) VENI and VIDI awards, Link Foundation fellowship, McGill Major fellowship, and NASA Space Flight Awareness award. He is the co-chair of the IEEE Robotics and Automation Society Technical Committee on Surgical Robotics, and area co-chair of the IFAC Technical Committee on Biological and Medical Systems. Sarthak’s broad research interests are primarily in the area of applied mechanics at both macro and micro scales. He is interested in the modeling and control of electro-mechanical systems with applications to medical robotics.

BE Seminar: Machine Learning Approaches To The Interpretation Of the Tumor Microenvironment Using Spatial Immuno-profiling & Spatial Transcriptomics
2024-04-08 16:00 - 17:00 UTC | CES Seminar Hall, CES Seminar Hall, 3rd Floor, Biological Science Building
Speaker: Prof. Arvind Rao
Title: Machine Learning Approaches To The Interpretation Of the Tumor Microenvironment Using Spatial Immuno-profiling & Spatial Transcriptomics
Abstract: Spatial profiling technologies like hyper-plex immunostaining in tissue, spatial transcriptomics, etc. have the potential to enable a multi-factorial, multi-modal characterization of the tissue microenvironment. Scalable, quantitative methods to analyze and interpret spatial patterns of protein staining and gene expression are required to understand cell-cell relationships in the context of local variations in tissue structure. Objective scoring methods inspired by recent advances in statistics and machine learning can serve to aid the interpretation of these datasets, as well as their integration with other, companion data like genomics. In this talk, we will discuss elements of spatial profiling from multiple studies as well as paradigms from statistics and machine learning in the context of these problems. This talk will also discuss the use of AI/ML and spatial analytics of the tumor microenvironment to derive spatial biomarkers of immunotherapy.
About the Speaker: Dr. Arvind Rao is an Associate Professor in the Department of Computational Medicine and Bioinformatics at the University of Michigan. His group uses image analysis and machine learning methods to link image-derived phenotypes with genetic data, across biological scale (i.e. single cell, tissue, and radiology data). Such methods have found application in radiogenomics, drug repurposing based on phenotypic screens, and spatial profiling in tissue, as well as in spatial transcriptomics. Dr. Arvind received his Ph.D. in Electrical Engineering and Bioinformatics from the University of Michigan, specializing in transcriptional genomics, and was a Lane Postdoctoral Fellow at Carnegie Mellon University, specializing in bioimage informatics.

BE Seminar by Dr. Vanita Rahman titled The Role of Nutrition in the Prevention and Reversal of Type 2 Diabetes
2024-03-11 16:00 - 17:00 UTC | CES Seminar Hall, CES Seminar Hall, 3rd Floor, Biological Science Building
Speaker: Dr. Vanita Rahman
Title: The Role of Nutrition in the Prevention and Reversal of Type 2 Diabetes
Abstract: Non-communicable diseases, such as diabetes, obesity, and cardiovascular disease, are rising at an alarming rate in India due to the unique genetic risks of the Indian population and the westernization of the Indian diet and lifestyle. The current prevalence of obesity and diabetes in India is 40 and 16 percent, respectively. Diabetes is associated with significant morbidity and mortality, and heightened risk of cardiovascular disease, which is the leading cause of death in India. Although cardiometabolic conditions – diabetes, cardiovascular disease, dyslipidemia, obesity – are strongly influenced by dietary factors, the use of dietary interventions in often eclipsed by the use of medications in clinical practice.
In clinical trials, plant-based dietary interventions have led to lower cholesterol levels, improved glycemic control, sustainable weight loss, and, as part of a program including other lifestyle changes, reversal of coronary artery disease. Despite the benefits of plant-based diets, most physicians do not prescribe plant-based diets due to a lack of knowledge, time constraints, or concerns regarding patient interest or adherence.
Dr. Rahman will review the unique genetic vulnerability of the Indian population to diabetes and other cardiometabolic conditions, and the research evidence regarding the role of plant-based diets in the prevention and reversal of diabetes, obesity, and cardiovascular disease. She will also provide practical tips and resources to help the attendees make meaningful dietary changes.
About The Speaker: Dr. Vanita Rahman was born in New Delhi and spent her school-age years in Bangalore attending the New Horizon Public School. She completed her undergraduate and medical degrees at the University of Virginia. She is currently the clinic director at the Physicians Committee for Responsible Medicine, where she leads clinical research, facilitates nutrition education programs, and provides patient care with an emphasis on nutrition. Dr. Rahman is the principal investigator in two clinical trials exploring the role of Zoom-based nutrition education in obesity and diabetes management. She is also a clinical instructor in medicine at the George Washington University School of Medicine and frequently speaks at international conferences about the role of nutrition in chronic disease. Dr. Rahman is a board-certified internal medicine and lifestyle medicine physician, certified nutritionist, and personal trainer. She has authored several books on plant-based nutrition and published articles in peer-reviewed medical journals.
The Physicians Committee for Responsible Medicine is a nonprofit organization in Washington, D.C., that conducts clinical research and provides nutrition education. Physicians Committee experts have been principal investigators in dozens of clinical trials and published original research in peer-reviewed medical journals, including JAMA Network.

BE: Seminar, Mechanonucleargenomics
2024-03-06 16:00 - 17:00 UTC | CES Seminar Hall, CES Seminar Hall, 3rd Floor, Biological Science Building
Speaker: Kundan Sengupta
Title: Mechanonucleargenomics
Abstract: It is well established that chromosomes occupy a unique sub-volume in the interphase nucleus referred to as Chromosome Territories. Remarkably, chromosome territories are organized in a non-random manner with gene rich chromosome territories toward the center and gene poor chromosome territories proximal to the nuclear border. What are the molecular mechanisms that organize chromosome territories in a non-random manner in the nucleus? To address this question, we subjected cells to softer hydrogels with stiffness ranging from ~2 to ~55 kPa, while collagen coated glass coverslips (~1 GPa) served as reference. Cells exposed to softer substrates, showed an increase in surface area, over time.
Furthermore, transcriptomic analyses involving RNA-Seq revealed a strikingly altered transcriptome. Interestingly, cells on softer matrices also showed a significantly altered configuration in the otherwise highly invariant locations of chromosome territories. Remarkably, nuclear envelope proteins – lamins and LINC (linker of nucleoskeleton and cytoskeleton) complex, mislocalized into the nuclear interior. Interestingly, the nuclear organization of active and inactive histone marks was also altered along with the activation of Emerin phosphorylation – the inhibition of which attenuated the relay of mechanochemical signals into the nucleus, abrogating the movement of chromosome territories in cells exposed to softer matrices. Taken together, our studies highlight a remarkable plasticity, adaptability and resilience of the nucleus to counter and protect genome organization and function from external mechanical forces.
About the Speaker: Kundan Sengupta completed BSc, MSc from Bangalore University. PhD from TIFR, Mumbai. Postdoc from NCI/NIH. Currently, Dr. Kundan is a faculty at IISER-Pune.

BE Seminar: A Mathematical Odyssey: From Brain Biomechanics to Cancer Therapeutics
2024-03-04 16:00 - 17:00 UTC | CES Seminar Hall, CES Seminar Hall, 3rd Floor, Biological Science Building
Speaker: Dr Siv Sivaloganathan
Title: A Mathematical Odyssey: From Brain Biomechanics to Cancer Therapeutics
Abstract: In this talk, I will touch on some of the successes and obstacles encountered in the application of mathematics to the biomedical sciences. I hope to illustrate this with examples from hydrocephalus, tumorigenesis, and the utilization of High-Intensity Focused Ultrasound (HIFU) for cancer treatment. Mathematical models have proven instrumental in optimizing hydrocephalus treatments, and helped unveil some of the intricacies of tumor development and treatment response. Moreover, they continue to play a major role in the evolution of non-invasive HIFU as a strategy for cancer therapeutics. These examples underscore the profound impact of mathematical modeling in understanding physiological dysfunction and shaping effective interventions in clinical medicine.
About The Speaker: Dr. Siv Sivaloganathan is a Professor at the Department of Applied Mathematics, University of Waterloo, and heads the Biomedical Research Group there. Since 2004, he is also the Director of the Centre for Mathematical Medicine at Fields Institute in Toronto. He obtained his PhD from Oxford University, and has extensively trained multiple PhD students and postdoctoral fellows in mathematical biology in past 25 years. His expertise is in the field of biomechanics and the development of mathematical models of clinical conditions and diseases using continuum mechanics. He has been Principal Investigator on a number of grants including NSERC Collaborative Health and Hospital for Sick Children Foundation.

BE Seminar : Extracellular Matrix- A Transport Barrier for Drug Delivery
2024-02-12 16:00 - 17:00 UTC | CES Seminar Hall, CES Seminar Hall, 3rd Floor, Biological Science Building
Speaker: Dr. Rashmi Mohanty
Title: Extracellular Matrix- A Transport Barrier for Drug Delivery
Abstract: Extracellular Matrix (ECM) determines crucial cellular responses through cell-matrix interactions. Specific qualitative and quantitative changes occur in the ECM during disease and, in part, regulate critical events that determine pathological tissue phenotype. For example, in solid cancers, the extraordinarily dense fibrotic ECM is primarily responsible for the increased interstitial tissue pressure and stiff mechanical properties. The resulting dense stroma impedes the transport of therapeutic anticancer drugs, limiting effective drug delivery and, therefore, the therapeutic potential of drug candidates. To overcome the tumor ECM drug delivery barrier, during my PhD, I leveraged favorable surface physicochemical interactions between the tumor ECM and drug carriers to enhance the delivery and, hence, the therapeutic outcomes of antitumor drugs. I used genetically engineered peptide-presenting phage libraries as a high-throughput approach to screen and identify peptide coatings that would facilitate improved transport through the tumor microenvironment. Interestingly, in contrast to most studies, I found that a positively charged peptide “surface” enhanced penetration, uptake, and retention of particles in tumor tissue when compared to neutrally charged peptides. Next, I conjugated the peptide to immune checkpoint inhibitor antibodies, which, in a murine melanoma tumor environment, recruited a higher number of activated tumor-infiltrating T-cells, resulting in delayed tumor growth.
Having worked with cell culture, ex vivo tissue culture, and animal model development during my Ph.D., I realized there is an unmet gap in developing models that can more easily recapitulate the dynamic and transport features of disease. Believing that the emerging, complex multicellular 3D organoid systems would more accurately reflect the human physiological environment, I joined the Weiss lab for my postdoctoral study to implement synthetic biology tools for organoid design. Currently, I am working on recapitulating the native-like organ architecture in liver organoids by mimicking the honeycomb-like patterns in human livers. Combining synthetic biology, micro-robotics, and machine learning, we deliver biological cues at precise locations to control the differentiation of human-induced pluripotent stem cells (hiPSCs) in a spatiotemporal fashion.
Although organoids have emerged as the next-generation tool for disease modeling and drug screening, the formation of matured organoids remains a challenge, partly because the current models lack the natural context of endogenous cell-governing ECM secretion and assembly formation. In my future research program, I will employ synthetic biology principles to genetically engineer hiPSCs to secrete relevant ECM (as occurs in vivo) for designing tailor-made disease-specific organoids to investigate drug transport and drug delivery with an aim to accelerate the drug development pipeline.
About the speaker: Dr. Rashmi Mohanty is am a postdoctoral associate in the Department of Biological Engineering at the Massachusetts Institute of Technology. My current work focuses on employing synthetic biology tools to control cell fate decisions for the formation of programmable organoids. She has completed Ph.D. in the College of Pharmacy at the University of Texas at Austin (UT). During Ph.D., she worked on developing therapeutic moieties that can overcome the transport barrier of the tumor microenvironment for improved drug delivery. Prior to matriculating at UT, she received my Bachelor of Technology in Chemical Engineering from the National Institute of Technology (NIT) Rourkela and my Master of Technology in Chemical Engineering from the Indian Institute of Technology (IIT) Kanpur. Building from my knowledge and gained experiences with the limitations of current models used to recapitulate stroma-rich disease environments, in the long run, she is interested in designing 3D models that better reflect various disease environments to accelerate the progress of disease diagnostics and drug discovery.

BE Seminar: Drug Delivery across Biological Barriers for combatting and preventing infectious diseases
2024-02-05 16:00 - 17:00 UTC | CES Seminar Hall, CES Seminar Hall, 3rd Floor, Biological Science Building
Title: Drug Delivery across Biological Barriers for combatting and preventing infectious diseases.
Prof. Dr. Claus-Michael Lehr
Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research (HZI) Dept of Drug Delivery. and
Saarland University, Dept of Pharmacy,
Saarbrücken, Germany.
Abstract: Urgently needed anti-infective drugs and vaccines must reach their targets safely and efficiently. Not only the body’s outer epithelia, like e.g., gut, skin and lung, but also the bacterial cell envelope as well as the polymer matrix of bacterial biofilms represent important biological barriers which may delimit the transport of anti-infectives to their site of action (“bacterial bioavailability”).
To model the air-blood barrier of the peripheral human lung, our group was the first who published a protocol for growing monolayers of human alveolar epithelial cells in primary culture (hAEpC) to develop functional tight junctions and high transepithelial electrical resistance (TEER). Later we introduced a first polyclonal human alveolar epithelial (hAELVi) and just recently a monoclonal cell line (Arlo) with similar properties. These epithelial cells may be implemented in various micro-physiological systems, also to study the effect of breathing and co-cultivated with other cells types, like e.g., macrophages or endothelial cells. A particular challenge is the mixed culture with bacterial biofilms to model chronic lung infections, which can meanwhile be realized most elegantly by 3D bioprinting.
Such complex in-vitro models aim to reflect the (patho)physiology of specific organs or tissues either in healthy or reduce diseased state and to generate clinically meaningful readouts. They have been used for developing novel anti-infectives, like e.g., quorum sensing inhibitors, aiming to eradicate pathogens without inducing antimicrobial resistance. Aerosolizable nano-antibiotics are also being investigated to combat intracellular infections, such as e.g., tuberculosis or viral infections by Crispr/CAS-like approaches.
About The Speaker: Claus-Michael Lehr is Professor at Saarland University as well as cofounder and head of the department “Drug Delivery and Biological Barriers” at the Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), which was established as a branch of the Helmholtz Centre for Infection Research (HZI) Braunschweig in 2009. Prof. Lehr has also been cofounder of Across Barriers GmbH and of PharmBioTec GmbH, a non-for-profit contract research organization.
The research theme of Professor Lehr’s team is (preferentially: non-invasive) drug delivery across biological barriers, in particular the epithelia of the gastrointestinal tract, the skin, and the lungs. Recently, this has been expanded to microbial barriers, such as the bacterial cellular envelope, biofilms and host cell membranes. A substantial part of the lab’s activities is dedicated to innovative carrier’s systems, often based on nanotechnology, capable of safely and efficiently delivering drugs and vaccines across these barriers. In this context, the lab systematically investigates predictive cells and tissue models, preferentially human-based, to evaluate the safety and efficacy of novel therapeutic concepts and to facilitate their translation into the clinic.

BE Seminar: Living Therapeutic Materials – Hydrogel encapsulated bacteria for smart drug delivery
2024-01-31 16:00 - 17:00 UTC | CES Seminar Hall, CES Seminar Hall, 3rd Floor, Biological Science Building
Speaker: Dr. Shrikrishnan Sankaran
Title: Living Therapeutic Materials – Hydrogel encapsulated bacteria for smart drug delivery
Abstract: Living therapeutics is a rapidly growing field in which live microorganisms are engineered to produce and deliver drugs right within the body. A unique advantage of this approach is that the organisms can be programmed with smart functions to sense and process disease-associated stimuli from the patient and regulate the drugs they produce. Probiotic or host-friendly bacteria engineered to sense patients’ needs and deliver drugs in response are showing early promise in treating chronic diseases but two major challenges are slowing progress of this approach – (i) scarcity of genetic tools to program sensing functions in most medically relevant probiotics like lactobacilli & (ii) unpredictability of drug doses due to variable bacterial survival in the body. In this presentation, I will share my group’s multi-disciplinary approach to overcome these challenges by (i) expanding the poorly equipped genetic toolbox of probiotic lactobacilli with new gene regulatory and plasmid retention modules[1]. and (ii) encapsulating the bacteria in mechanically tunable hydrogels that can controllably sustain bacterial activity[2,3]. The engineered bacteria combined with hydrogels form living therapeutic materials, in which control over bacterial functions can be exerted through both genetic and mechanical means. Novel fundamental insights and application-oriented advances from our published and ongoing work will be presented.
About the Speaker: Dr. Shrikrishnan Sankaran is the head of the Bio programmable Materials research group, he combines bacterial engineering with biomaterials to develop engineered living materials for therapeutic and environmental applications. His group genetically programs beneficial bacteria with sensing, catalytic and therapeutic functions. These bacteria are encapsulated in soft materials like hydrogels to create living devices that perform these advanced functions long-term at low-costs and in an eco-friendly manner. Currently, a major focus of the group is expanding the genetic toolkit of non-model probiotic and commensal bacteria to achieve in situ controllable drug delivery.

BE Seminar on A dual-fluorescent reporter to identify mechanisms regulating the epithelial-to-mesenchymal transition in breast cancer
2024-01-23 11:00 - 12:00 UTC | CES Seminar Hall, CES Seminar Hall, 3rd Floor, Biological Science Building
Speaker: Prof. Michael Toneff, PhD, Departments of Biology and Biochemistry, Widener University.
Title: A dual-fluorescent reporter to identify mechanisms regulating the epithelial-to-mesenchymal transition in breast cancer.
Abstract: The epithelial-mesenchymal transition (EMT) is a developmental and wound-healing process whereby stationary epithelial cells undergo a reversible phenotypic change to a motile, mesenchymal-like state. EMT can aberrantly occur in carcinoma cells and is strongly linked to therapeutic resistance. Moreover, the ability of carcinoma cells to exhibit plasticity between epithelial and mesenchymal states may be critical for carcinoma cells to adapt to the different stages of metastatic progression. E-cadherin is an effector of the epithelial phenotype, and its expression is lost during EMT. ZEB1 is a transcription factor that promotes EMT via repression of E-cadherin and other epithelial genes. We developed a lentivirus-based, dual-fluorescent reporter that reflects the state of E-cadherin transcription and ZEB1 post-transcriptional regulation by the microRNA 200 family. This dual reporter enables the real-time identification of live cells in an epithelial, mesenchymal, or hybrid state, thus facilitating the study of the dynamic EMT phenomenon. Using this reporter, we identified several compounds that can reverse the mesenchymal phenotypes associated with poor breast cancer outcomes. Furthermore, we have identified epigenetic mechanisms, including DNA methylation and histone acetylation, as potentially critical determinants of complete vs. partial EMT states. In this talk, I will discuss how we have used our reporter to better understand how breast cancer cells achieve aggressive mesenchymal properties and to identify potential therapeutic targets to better treat this deadly disease.
Biography: Dr. Michael Toneff received his BS in Biology at Ohio State University in Columbus, Ohio where he became interested in someday teaching biology to undergraduates and performing cancer research. He moved to Houston, Texas and received his PhD at Baylor College of Medicine (BCM) in the laboratory of Dr. Yi Li, where he studied the hormone dependency of breast cancer initiation. Dr. Toneff was then awarded the NIH-funded IRACDA Postdoctoral Fellowship that combined post-doctoral research with teaching at minority-serving undergraduate institutions. Dr. Toneff joined the laboratory of Dr. Jeffrey Rosen at BCM as an IRACDA fellow. In the Rosen laboratory, he studied the epithelial-mesenchymal transition (EMT) in breast cancer where he developed the Z-cad dual fluorescent reporter to identify the EMT state of live cells. It was during this time that he first identified epigenetic mechanisms as a determinant of EMT states in breast cancer. During this time, he also taught several cell and molecular biology courses at the University of Houston-Downtown. Dr. Toneff is currently an Associate Professor of Biology at Widener University, a primarily undergraduate teaching institution just outside of Philadelphia, Pennsylvania. At Widener, he teaches both introductory and upper division cell and molecular biology courses. Moreover, he has continued to study EMT regulatory mechanisms in collaboration with others, including Dr. Mohit Jolly at IISc, while training undergraduate students in his research laboratory.

BE Seminar titled Employing Common Ions And Molecules For Sustainable Clean Water by Dr. Swathy J. R.
2024-01-18 14:00 - 15:00 UTC | CES Seminar Hall, CES Seminar Hall, 3rd Floor, Biological Science Building
Title: EMPLOYING COMMON IONS AND MOLECULES FOR SUSTAINABLE CLEAN WATER
Speaker: Dr. Swathy J. R.
Abstract: Despite the existence of several innovative solutions in the field of water purification, successful technologies continue to encounter significant challenges. Many of these technologies lack sustainability and durability due to frequent manual interventions and associated expenses. While various global entities, both governmental and non-governmental, are striving to provide clean water to those in need and are evaluating the water demand in the context of climate change, industries are struggling to find alternative options that are stable, cost-effective, uninterrupted, and reliable to address this critical issue. For these technologies to achieve sustainability and widespread adoption, they must not only be energy-efficient, rapid, and affordable, but also environmentally benign.
The objective of the presentation is to emphasize the synergistic effects of ions on biological systems and discuss the design of materials that can sustainably release both anions and cations. The talk will present the use of carbonates as one of the dimension to counteract cytotoxicity induced by arsenic. Additionally, insights into the application of ambient mass spectrometry as a tool for detecting biofouling on water purification materials will be shared during this session.
Biography: Dr. Swathy is a proactive researcher with an industrial exposure and holds her interdisciplinary doctoral degree from IIT MADRAS under the guidance of Padmashri. Prof. T. Pradeep (Chemistry), Prof. Ligy Philip (Civil Engr.) on the topic, “Employing Common Ions and Molecules for Sustainable Clean Water”. Further, she is now heading the Validation wing at R&D, Eureka Forbes Limited, monitoring technology development, institutional collaborations, bench-marking and field trial data processing. She drives open innovation and is a part of cross functional ratification team to develop robust strategies to support product applications.
She has a demonstrated history of technology transfer and application oriented research related to drinking water purification. Swathy’s research interests are in water chemistry & microbiology interface focusing on commercially viable and environmentally benign advanced materials, their Ionic interaction in water, and its analytical perspectives. Her work experience includes design, development, optimization, scale-up and ratification of commercial water purification technologies to address water pollution around the world. Analytical expertise to understand the performance of technologies and designing digital water monitoring systems are some of her highlighted deliveries.
She has 16+ Indian, US and WIPO patents and 10 high impact research publications in peer reviewed journals (Total impact factor of 81.6), in the area of sustainable solutions for drinking water purification. Her recent work on reducing the water wastage from Reverse osmosis technology has been incorporated into the Aquaguard® products under the names Aquaguard® Crystal NXT HR RO+UV+MTDS and Aquaguard® Aura HR RO+UV+MTDS, and are successful in the Indian market with diverse water conditions for the past 2 years.
She has also been elected as a talent to represent SDG – 6 (water), by the UNLEASH global community. She is a part of sustainability development team at Eureka Forbes Limited, for handling the corporate’s sustainability projects. She is presently serving as a subject matter expert in industry’s pollution control committee.
Her patented work titled ‘Anion effect on disinfection of silver’ was sold to a “US based Nanoholding Inc., a Delaware corporation” for its commercialization. Her work titled “Rollpure”, a rolling water purifier won the prestigious Gandhian Young Technological Innovation (GYTI) Award from the honorable President of India.

Seminar by Dr. Mahipal Ganji on "Decoding the Stabilizing Energetics of DNA and Their Applications in DNA Nanotechnology and Super-resolution Imaging"
2023-10-09 16:00 - 17:00 UTC | CES Seminar Hall, CES Seminar Hall, 3rd Floor, Biological Science Building
The Department of Bioengineering (BE) cordially invites you to attend a Departmental Seminar.
Speaker: Dr. Mahipal Ganji
Department name: Dept. of Biochemistry, IISc.
Title: Decoding the Stabilizing Energetics of DNA and Their Applications in DNA Nanotechnology and Super-resolution Imaging
About the Speaker: Mahipal studied Physics at Nizam College Hyderabad, India, and Nanobiophysics at TU Dresden, Germany, followed by a PhD from Bionanoscience department at TU Delft, the Netherlands. After short stint as postdoc at the same institute, did a postdoctoral work at the Max-Planck Institute of Biochemistry, Martinsried Germany. His research is interested in understanding how genome is organized in a small compartment. We develop tools to understand factors that alter genome organization using single-molecule imaging and super-resolution microscopy approaches.
Abstract:
In the realm of biology, DNA within our cells constantly undergoes deformations, unwinding and rewinding, yet remarkably, genetic information is efficiently passed down through generations. In my talk, I will delve into our recent endeavors aimed at unraveling the world of stabilizing energetics within DNA. Specifically, we have developed an innovative multiplexed single-molecule assay, harnessing the power of DNA-PAINT super-resolution imaging and DNA nanotechnology. This advanced imaging technology enables us to conduct unbiased kinetic analyses of multiple stacking interactions in a single experiment. Our data reveals that the stability of individual dinucleotide interactions varies dramatically, allowing us to implicate them in diverse applications. During my presentation, I will explore their implications in understanding the mechanical properties of single-stranded DNA. Furthermore, I will discuss how these discoveries are paving the way for the development of efficient imaging probes and their relevance to the field of DNA nanotechnology.

Seminar by Dr. Praveen Kumar Vemula on "Biometerials and Chemical Biology Approaches for Solving Unmet Clinical Needs"
2023-09-04 16:00 - 17:00 UTC | CES Seminar Hall, CES Seminar Hall, 3rd Floor, Biological Science Building
Title: Biomaterials and Chemical Biology Approaches for Solving Unmet Clinical Needs
Speaker: Dr. Praveen Kumar Vemula
Faculty In Stem,
Bangalore.
About the Speaker: Dr. Praveen Kumar Vemula is an Associate Professor at the Institute for Stem Cell Science and Regenerative Medicine (in-Stem), Bangalore. He has completed Masters in Chemistry from Osmania University, and obtained PhD from Indian Institute of Science, Bangalore. His expertise is developing chemical technologies for medical applications. His work spans the fields of biomaterials, drug discovery, drug delivery, medical devices, and chemical biology. He has published >85 peer-reviewed papers, has given >200 national and international invited lectures including two TEDx talks, and has >30 issued or pending national/international patents, which have been licensed to multiple biotech companies. Several technologies developed in his lab have formed the foundation for multiple products on the market, and currently under development. His technologies have led to the launch of seven startup companies. Thus far, >20 products that are developed based on his technologies are in the market worldwide.
Abstract: Our lab is focusing on clinical translational research through biomaterials and chemical biology programs. By using chemical design tools, we have been developing therapeutic and prophylactic biomaterials for medical applications. For example, in this talk two specific examples will be discussed in detail. In one example, we will discuss development of potential drugs for the treatment of inflammatory bowel diseases using biomimicry-based drug discovery. In another example, we will discuss developing a novel blood bag technology to enhance the quality and shelf-life of stored blood that will have enormous clinical implication. Overall, we will see a snapshot of various technologies that could be developed in the lab and translated into the clinic/market.

Seminar by Dr. Sunil Laxman on “Economic principles of metabolic restoration in cells”
2023-08-14 16:00 - 17:00 UTC | CES Seminar Hall, CES Seminar Hall, 3rd Floor, Biological Science Building
Speaker: Dr. Sunil Laxman, Associate Investigator, DBT-in Stem, Bangalore
Title: Economic principles of metabolic restoration in cells
About the Speaker: Sunil Laxman is an associate investigator at DBT-in Stem, Bangalore. An old Bangalorean, Sunil completed his BTech at CBT, AU in Chennai, and a Ph.D. at the University of Washington, Seattle (with Prof. Joseph Beavo), where he developed an interest in principles of cell signaling. He went on to postdoctoral studies at UT Southwestern Medical Centre, with Profs. Steven McKnight and Benjamin Tu, which initiated interest in metabolism. The current goals of research in the Laxman lab are to identify the rules, chemical logic, and organizational principles of metabolic networks. Ongoing directions of research include understanding the formation and sensing of metabolites, and systems-level principles of metabolic network organization.
Abstract: Cell metabolism should be thought of as an economy, which is organized into supply and demand blocks (of precursors and products). But to build frameworks for metabolic exchange between cells, and how the evolution of metabolic/signalling pathways determines resource allocation strategies in cells. Findings from these studies are being integrated synthetic systems approaches for regenerative biology, food, and environmental biotechnology. The lab is supported by a DBT-Wellcome India Alliance Senior Fellowship, and other support from DST, DBT, and the EMBO YIP/Global Investigator network. what can supply-demand analysis teach us? Quantitative considerations of supply and demand should reveal multiple organizations of cellular responses. I will explore this central concept in this seminar, through two ongoing studies. In the first, we address how cells differentially prioritize the restoration of distinct amino acids, upon disrupting their supply, and construct a logic based on individual amino acid costs as well as composite demand. We find that cells employ a conserved strategy guided by the law of demand, to prioritize amino acid restorations upon transient limitation. In the second part of this seminar, we uncover how cells differentially treat amino acids that are internally available, vs those that accumulate externally. Quantitatively, these internal and external amounts can differ by orders of magnitude, and do not universally function as ‘public goods’. Distinct amino acids, based on ease of availability as well as functional requirements, can function either as contextually utilized public goods, or carefully protected, privatized resources that are banked for anticipated future requirements. I will end with speculation on how quantitative analyses of demand and supply can explain cellular resource allocation strategies in different environments.

Seminar by Dr. Bala (Balasubramanian) Venkatakrishnan, titled "Be On Top Of Your Cells: Flow Cytometry In The Cell Manufacturing Suite"
2023-08-07 16:00 - 17:00 UTC | CES Seminar Hall, CES Seminar Hall, 3rd Floor, Biological Science Building
Title: Be On Top Of Your Cells: Flow Cytometry In The Cell Manufacturing Suite
About the Speaker:
Bala Venkatakrishnan is a protein biochemist with a background in structural virology. He has spent about 10 years in academia followed by a little over 6 in the biotech industry (contract-research, pharma and a product based companies). He has a passion for science communication and people management as he seek to answer life’s important scientific and healthcare questions. He is been with Beckman Coulter for close to 2 years as part of their flow cytometry reagent R&D team. Outside the lab, he passionately drive Beckman’s DE+I and sustainability efforts.
Abstract: The large variety in flow cytometry applications (ranging from cell manufacturing to diagnostics) requires customized solutions to meet specific user needs. At Beckman Coulter Life Sciences, we emphasize customer-centric design with a focus on addressing key pain points. This talk will be a walkthrough on a range of Beckman products (hardware, software and reagents) that address flow cytometry needs in cell manufacturing and clinical research spaces.
