Department of Bioengineering

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 | 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 | 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 | 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 | 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 | 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.

Special Seminar by Prof. Yamuna Krishnan titled Intracellular electrophysiology
2023-07-11 16:00 - 17:00 | Biological Sciences Auditorium
The Centre for BioSystems Science and Engineering (BSSE) cordially invites you to attend a special seminar:
Speaker: Prof. Yamuna Krishnan
Department of Chemistry,
Institute for Biophysical Dynamics,
Grossman Institute for Neuroscience
University of Chicago
Title: Intracellular electrophysiology
Abstract:
I have been interested in exploring how the ionic milieu within an organelle facilitates organelle function. To map these lumenal chemistries, my lab developed a DNA-based, fluorescent reporter technology to quantitatively map ions such as H+, Cl- and Ca2+ within organelles (1). It can be applied to organelles of cells in culture, in live organisms (2) and in human patient cells (3,4). Our most recent reporter for absolute membrane potential ended a previous misconception by showing that many organelles do in fact, have membrane potential (4). Today I will discuss two new reporters for organellar Na+ and K+ : the final pieces needed to build an electrochemical model for organelle membranes (5,6). The only existing electrochemical model of a biological membrane is that of the cell membrane, first developed by Hodgkin and Huxley in 1952 for neurons (7). To accomplish this for organelles we will need input from physicists, cell biologists and electrophysiologists.
References:

Krishnan, Y. et. al. “Quantitative imaging of biochemistry in situ and at the nanoscale.” ACS Cent. Sci., 2020, 6, 1938–1954.
Narayanaswamy, N. et. al. “A pH-correctable, DNA-based fluorescent reporter for organellar Calcium.” Nature Methods, 2019, 16, 95-102.
Leung, K., et. al. “A DNA Nanomachine chemically resolves lysosomes in live cells.” Nature Nanotechnology, 2019, 14, 176-183.
Saminathan, A., et. al. “A DNA-based voltmeter for organelles.” Nature Nanotechnology, 2021, 16, 96-103.
Anees, P. et al. “DNA nanodevices for measuring the organelle-specific activity of potassium channels.” 2023, in revision.
Zou, J. et al. “A DNA nanodevice maps sodium at single organelle resolution” 2023, in revision.
Hodgkin A.L., Huxley A.F. “A quantitative description of membrane current and its application to conduction and excitation in nerve”. J. Physiol. 1952, 117, 500–44.

Seminar by Dr. Sudin Bhattacharya titled Deep Generative Learning of Single Cell Gene Expression to predict Dose-Dependent Chemical Perturbations
2023-07-03 16:00 - 17:00 | CES Seminar Hall, CES Seminar Hall, 3rd Floor, Biological Science Building
The Centre for BioSystems Science and Engineering (BSSE) cordially invites you to attend a departmental seminar.
Speaker: Dr. Sudin Bhattacharya
Department of Biomedical Engineering, Department of Pharmacology and Toxicology
Institute for Quantitative Health Science & Engineering
Michigan State University
Abstract:
Single cell RNA-sequencing allows us to study cell-type specificity and heterogeneity of biological responses to chemical perturbations. However, experimentally testing all relevant combinations of cell types, chemicals, and doses is a near-impossible task. A deep learning formalism called variational autoencoders (VAEs) has been shown to be effective in computationally predicting single-cell gene expression perturbations. We have developed single cell Variational Inference of Dose-Response (scVIDR), a VAE-based tool to predict the trajectory of cellular dose-response, which achieves better dose-response predictions than existing models. We show that scVIDR can predict dose-dependent gene expression changes across cell types and interpret the latent space of the autoencoder model in terms of biological pathways.

Seminar by Dr. Sooryanarayana Varambally titled Integrative Data Analysis Using UALCAN platform For Cancer Biomarker Discovery And Therapeutic Targeting
2023-06-26 14:30 - 17:00 | CES Seminar Hall, CES Seminar Hall, 3rd Floor, Biological Science Building
Speaker: Dr. Sooryanarayana Varambally (University of Alabama at Birmingham)
Title: Integrative Data Analysis Using UALCAN platform For Cancer Biomarker Discovery And Therapeutic Targeting
Abstract:
Cancer is a complex disease that exhibits diverse morphological, histological and molecular alterations during the initiation, progression and metastasis. Cancer is a leading cause of death both in India and the western countries. Lung, mouth, esophagus, stomach, and nasopharynx cancers are the most common cancers in men and cancer of the breast and cervix, uterine are the most common cancers in women in India. Lung, breast, prostate and colon cancer are common in the western countries. Advances in molecular profiling and sequencing technologies have resulted in generation of massive datasets for cancer genomics, transcriptomics, and proteomics. These have presented promising avenues for cancer research. Mining these data and utilizing them to their full potential requires the development of intuitive, innovative and user-friendly web-portals. Not all cancers are the same, and cancers of the same organ show molecular heterogeneity. Multiple “Omics” data and clinical parameters of patients help stratify cancers based on mutational status, gene expression, and survival patterns, all of which may have relevant associations with stage, race/ethnicity, histologic subtypes, genetic aberrations, or other clinicopathologic parameters. In addition, since the identification of DNA methylation and histone modification, it has become clear that epigenetic modifiers that regulate gene expression play a crucial role in cancer progression.
In this era of precision medicine, it is imperative that researchers and clinicians have the capability to identify candidate subclass-specific cancer biomarkers for the purposes of early diagnosis, prediction of disease recurrence, identification of molecular determinants for therapeutic targeting, and re-purposing drugs to inhibit cancer growth. The Cancer Genome Atlas (TCGA) Research Network has profiled more than 10,000 human tumors of 33 cancer types to discover genomic and epigenetic alterations. The Clinical Proteomic Tumor Analysis Consortium (CPTAC) provides data on protein expression in various cancers. Integrative informatics tools that harness these molecular modalities and allow intuitive analysis will allow researchers to uncover biological insights of specific tumors. The present talk focuses on our effort in the area of BIG cancer data dissemination through researcher-centric, distinctive, and continuously evolving web platform, UALCAN (https://ualcan.path.uab.edu, Yes! You All Can), for detailed data analyses and visualization. UALCAN, released in 2017, has been visited over 11,85,000 times by researchers from over 100 countries and has been cited about 4,000 times, creating a large global user base making cancer research a team effort and enabling numerous cancer target discoveries and biomarker development. Further, here, I will discuss about identification of viable targets, validation.
About the speaker:
Dr. Sooryanarayana Varambally did his undergraduate studies at Poornaprajna College, Udupi and M.Sc. in Biochemistry at Kasturba Medical College, Mangalore. Varambally earned his Ph.D. in Biochemistry from the Indian Institute of Science in Bangalore, India in 1997 under the mentorship of Late Prof. PR Adiga and Prof. Sandhya Visweswariah. He completed a research fellowship in immunology at INSERM unit at Hospital Broussias in Paris, France with Dr. Srinivas Kaveri, and a second research fellowship in cancer biology with Dr. Arul Chinnaiyan at the University of Michigan’s Department of Pathology. He later joined the Michigan Center for Translational Pathology in Ann Arbor as a faculty member. In 2015, he joined the UAB Heersink School of Medicine Department of Pathology where he now serves as a professor and Director of Translational Oncologic Pathology Research as well as Co-Director of Cancer Biology Graduate Program and scientist at O’Neal Comprehensive Cancer Center and Informatics Institute. In an effort to enhance precision targeting in the fight against cancer, Dr. Varambally initiated and led the development of a comprehensive proteogenomic cancer data analysis platform, UALCAN (ualcan.path.uab.edu, University of ALabama at Birmingham CANcer Portal, Yes! You All Can). This user friendly public cancer data analysis tool allows cancer researchers and clinicians to examine cancer data and identify biomarkers and precision targets, making cancer research a global team effort. UALCAN has received more than 1.2 million visits from over 100 countries and has been cited in more than 4,000 research articles in the last 6 years. Dr. Varambally has co-authored more than 150 manuscripts. Many of his work has been published in journal like Science, Nature, Cancer Cell, Cancer Discovery, Nature Medicine, NEJM, JAMA, Nature Biotechnology, PNAS and Cancer Research, among others. His work has been cited over 43,000 times. Varambally was a member of the team that won the inaugural American Association for Cancer Research (AACR) Team Science Award in 2007 and received the Research Faculty Recognition Award from the University of Michigan in 2009. In 2021 he received the Outstanding Achievement Award from the Society of American Asian Scientists in Cancer Research. He was the recipient of the 2023 Dean’s Excellence Award in Research at the University of Alabama at Birmingham.

Special Lecture by Prof. Carla Rothlin titled: Cracking the cell death code
2023-04-27 16:00 - 17:00 | Biological Sciences Auditorium
Title: Cracking the cell death code
Abstract:
Cell death is an invariant feature throughout our lifespan, starting with extensive scheduled cell death during morphogenesis and continuing under homeostasis in adult tissues. Additionally, cells become victims of accidental, unscheduled death following injury and infection. Cell death in each of these occasions triggers specific and specialized responses in the living cells that surround them or are attracted to the dying/dead cells. These responses sculpt tissues during morphogenesis, replenish lost cells in homeostasis to maintain tissue/system function, and repair damaged tissues after injury. Wherein lies the information that sets in motion the cascade of effector responses to cell death? I will present a framework for thinking about cell death in terms of the specific effector responses that accompanies various cell death modalities. I will propose a three-fold “cell death code” consisting of information intrinsic to the dying/dead cell, their surroundings and the identity of the responder.
About the speaker:
Prof. Carla Rothlin is currently the Dorys McConnell Duberg Professor of Immunobiology and Professor of Pharmacology, and Co-Leader, Cancer Immunology, Yale Cancer Center. She is the recipient of many prestigious awards including the senior research award from the Crohn’s and Colitis foundation of America, the early excellence award from the American Asthma Foundation and the HHMI faculty scholar from the Howards Hughes Medical Institute.

Special Lecture by Dr. Gaurav Das on "The food fly: neural circuits of feeding and emesis in Drosophila"
2023-03-24 14:00 - 15:00 | CES Seminar Hall, CES Seminar Hall, 3rd Floor, Biological Science Building
Title: The food fly: neural circuits of feeding and emesis in Drosophila
Abstract:
Our group is broadly interested in understanding how the brain communicates with the gut and other organ systems to regulate food/nutrient intake. Food intake is mainly influenced by innate sensory inputs and also by memories of past feeding experiences. We have developed and improved handy assays for quantifying feeding and memory in flies. Armed with these assay we are trying to understand the neural circuitry that control specific feeding phenotypes.
The ability to avoid, and reject toxic foods that cause malaise are of the greatest importance to animals. Incredibly, fruit flies show emesis or vomiting upon toxin ingestion. We show that the requirement of the neurotransmitters serotonin and dopamine in regulating emesis is conserved between flies and mammals. We also have evidencethat suggests that flies form a robust long-lasting aversive memory, reinforced by the internal sickness caused by toxin ingestion. We are now elucidating the circuitry that underlies innate and naive emesis in flies.
About the speaker:
Gaurav did his BSc in Chemistry with Microbiology from Ahmednagar College, Ahmednagar, Maharashtra, and then an MSc in Biotechnology from Jawaharlal Nehru University, New Delhi. For his Ph.D., he studied mouse retina development, in the lab of Dr. Edward Levine, at The University of Utah, Salt Lake City, Utah, USA. He then moved to the lab of Dr. Scott Waddell, at the UMASS Chan Medical School, to understand how aversive food memories are formed in the Drosophila brain and guide behavior. He moved with the lab to the University of Oxford, UK to continue his postdoctoral research. In December 2017, he joined NCCS to establish the Brain and Feeding Behavior Laboratory.

Seminar by Prof. Marty Pagel on "Molecular Imaging of the Tumor Microenvironment"
2023-03-20 16:00 - 17:00 | CES Seminar Hall, CES Seminar Hall, 3rd Floor, Biological Science Building
Speaker: Prof. Marty Pagel (The University of Texas MD Anderson Cancer Center, Houston, Teax )
Title: Molecular Imaging of the Tumor Microenvironment
Abstract:
Tumor acidosis, hypoxia and vascular perfusion are well-known characteristics of the tumor microenvironment. We have developed MRI, PET/MRI, multispectral optoacoustic tomography (MSOT) and electron paramagnetic resonance imaging (EPRI) to measure extracellular pH, oxygenation and pharmacokinetics transport rates in solid tumors. We apply these molecular imaging methods to preclinical tumor models, and we have translated some of our methods to evaluate patients who have cancer. We are especially focused on employing molecular imaging to predict treatment effect before starting therapy, and to evaluate the early response to treatment, during evaluations of chemotherapy, radiotherapy and immunotherapy. This presentation will discuss a variety of molecular imaging methods and research applications, and also discuss a value proposition for molecular imaging.
About the speaker:
Dr. Marty Pagel is a Professor in the Departments of Cancer Systems Imaging and Imaging Physics at the University of Texas MD Anderson Cancer Center. His research in academia and industry has evolved from physical chemistry to molecular imaging. His current research employs a variety of imaging modalities to interrogate biomarkers of the tumor microenvironment. He has developed these methods for pre-clinical and clinical imaging, especially to evaluate cancer therapies. Dr. Pagel has held many leadership positions in molecular imaging, including roles in scientific societies of WMIS, SNMMI and the ISMRM, and serves as the Associate Editor of Radiology. When away from the lab and imaging facilities, Marty enjoys coffee, jazz music, Green Bay Packers football games, and a variety of wilderness adventures.

MTech program in Bioengineering
2023-03-15 08:00 - 17:00
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 | 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
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 | 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 | 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 | 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 | 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 | 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 | 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 | 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
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 | 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 | 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

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 | 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 | 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 | 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 | 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.
