Department of Bioengineering

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

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

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

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

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

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

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

Seminar by Prof. Marty Pagel on "Molecular Imaging of the Tumor Microenvironment"
2023-03-20 16:00 - 17:00 UTC | 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.

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 UTC | 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.

Special Lecture by Prof. Carla Rothlin titled: Cracking the cell death code
2023-04-27 16:00 - 17:00 UTC | 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.

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 UTC | 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.

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 UTC | 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.

Special Seminar by Prof. Yamuna Krishnan titled Intracellular electrophysiology
2023-07-11 16:00 - 17:00 UTC | 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. 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.

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. 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. 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.

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.

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: 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: 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 : 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: 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, 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 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: 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: 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: 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: 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 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: 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 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.
