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Title:  Experimental and theoretical development for optical and photoacoustic tomography

Speaker: Dr. Samir Biswas

Bio –Data: Dr Samir Biswas from University of Twente.

Abstract : Laser light based diagnostic methodologies are  getting  more important at present century due to its  imaging potentiality  of  functional tissue  parameters  such as various  chromophores   in tissue.  As an example we  can point out diffuse optical tomography  where  the heterogeneity  image of  tissue  is obtained  based on  absorption and scattering of light,  another example is the hybrid  photoacoustic  tomography where we see the  conversion of light into ultrasound through  molecular level physical phenomena which has potential to provide high resolution high contrast images  of various diseased and normal tissues.In this talk, I shall talk about  the  theoretical developments  such as inverse problem for retrieving the interior  domain information from boundary data and  instrument development  in diffuse optical tomography/photoacoustic tomography for ex-vivo and in-vivo imaging  on healthy  human subjects.  In particular, the composite tissue imaging using  self developed optical/photoacoustic imaging   system   for bulky tissue  imaging and micro blood vessels imaging in human finger joints for monitoring rheumatoid arthritis disease using  photoacoustic  computed tomography will be discussed.

Date & Time: 13th August 2014 2:30 pm at Rm. 232

Title:  “Engineering “Pathogen Mimicking Particles” and “Immune Priming Microenvironment” for cancer immunotherapy”

Speaker:  Dr. Pallab Pradhan

Bio –Data: Dr Pallab Pradhan from Georgia Tech, Atlanta USA.

Abstract : Existing approaches ofcancer immunotherapy have been largely unsuccessfulto generate sufficient antitumor immunity primarily due to the inherent weak immunogenicity of tumor self-antigens and poor T helper type 1 (Th1) and Cytotoxic T Lymphocyte (CTL) responses. Several key immunological events, as they happen in infection, need to be controlled to boost antitumor immunity. These are: a) recruitment of a large number of antigen presenting cells (APCs), especially dendritic cells (DCs), at the site of immunization, b) efficient delivery of antigen and danger signals to the migrated DCs, c) strong activation and maturation of the DCs with appropriate cytokine profile for antigen presentation and d) effective immunomodulation to generate a strong Th1 and CTL responses. We have developed biomaterial based “Pathogen Mimicking Particles (PMPs)” platform wherein multiple Toll Like Receptor (TLRs) agonists, immunomodulatory siRNA and tumor antigen (protein/DNA) can be loaded on micro/nanoparticles and delivered efficiently to dendritic cells. I will show our recent results on how these PMPs can be used to precisely control DC activation; maturation and cytokine profile, Th1/Th2 balance and ultimately modulate antitumor immunity. Also, we have developed a degradable in situ cross-linking hydrogel, which upon injection with a DC attracting chemokine along with PMPs creates an “Immune Priming Microenvironment” at the site of injection and thus resulting into a strong antitumor immune response. I will show our recent results on PMPs and “Immune Priming Microenvironment” mediated antitumor immune response in murine Melanoma and B cell Lymphoma models. Towards the end of my talk, I will discuss the role of immunosuppressive tumor microenvironment in dampening anti-tumor immune response and my future goalson targeting the tumor microenvironment using “Immunomodulatory Nanoparticles (IMN)” and a two-pronged approach of combined peripheral vaccination and tumor microenvironment immunomodulation to maximize antitumor immune response. 

Date & Time: 30th July 2014 2:30 pm at Rm. 232

Title:  “Design, Implementation, and Imaging of Position-Encoded Microfluidic Microsphere-Trap Arrays”

Speaker:  Dr. Pinaki Sarder

Bio –Data: Pinaki Sarder is a Post-Doctoral Research Associate in Radiology at the Washington University in St. Louis (WUSTL) School of Medicine. His research is focused on Integrated Optical Imaging using statistical signal processing, multi-photon microscopy, and fluorescence molecular tomography methods. He obtained his B. Tech. degree in Electrical Engineering (EE) from the Indian Institute of Technology, Kanpur, in 2003, and the M.Sc. and Ph.D. in EE from WUSTL in 2010. Dr. Sarder received an NIH funded Imaging Sciences Pathway fellowship in 2007. His publications include 11 refereed first-authored journal articles and one refereed first-authored book chapter. Dr. Sarder's research contributions span multiple disciplines, including signal processing, optimization, microscopy, and biomedical optics.

Abstract : Microarray devices are useful for detecting and analyzing biological targets, such as DNAs, RNAs, proteins, etc. Applications of microarrays range from fundamental research to clinical diagnostics and drug discovery. In this presentation, we consider a microsphere array device with predetermined positions of the microspheres. We implement it by employing microfluidic technology and a hydrodynamic trapping mechanism, and call the device position-encoded microfluidic microsphere-trap array. We design a novel geometric structure for this device, and develop a comprehensive and robust nonlinear optimization framework to maximize the microsphere arrays’ packing density. We use finite element simulations to investigate the hydrodynamic trapping of the microspheres. We have shown that the optimized device greatly outperforms the un-optimized device using microsphere-trapping experiments. To optimize the imaging performance of this device, we conduct a statistical design analysis to select the optimal distance between the microspheres as well as the optimal temperature. Our design simplifies the imaging and ensures a desired statistical performance for a given sensor cost. We illustrate our statistical design concept using numerical examples. The resulting optimal microfluidic microsphere-trap array device has high sensitivity, efficient packing, and guaranteed imaging performance. We conclude our discussion on microsphere array by providing a brief overview of a recent study conducted by our collaborators from medicine using the first prototype device built using our optimal statistical design method. In this study, our collaborators have established the detection limit of our device for sensing epidermal growth factor receptor, which is a receptor known to be abundantly expressed in a variety of cancers. We will discuss next future work and our other works on microscopy image segmentation, microarray image denoising, and deep tissue imaging using fluorescence diffuse optical tomography, multiphoton microscopy, and optical projection.

Date & Time: 29th July 2014 11:00 am at Rm. 232

Title:  “Wavefront aberrations, adaptive optics and examples from vision science”

Speaker:  Professor V. Lakshminarayanan

Bio –Data: Professor Vasudevan Lakshminarayanan is currently a Professor in departments of Optometry and Vision Science, Physics and   Electrical and Computer Engineering and center for Bioengineering and Biotechnology at University of Waterloo.  He completed his doctoral studies from University of California Berkeley in 1985 and served as Assistant Professor at University of california Irvine. From  1993 to 2006, Dr Lakshminarayanan served University of Missouri as Assistant and Associate Professor and then from 2006 onwards, as a Professor in departments of Optometry and Vision Science, Physics and   Electrical and Computer Engineering at University of Waterloo Optometry and Vision Science at University of Waterloo. He is also a member of the academic council at Nanyang Technological University, Singapore. He is a fellow of AAAS, APS, IOP, OSA and SPIE.Dr Lakshminarayanan is a  Technical Editor/Associate editor of a number of journals, including Optics Letters, Journal of Modern Optics, Clinical Optometry, American Journal of Biomedical Engineering, Optoelectronics and Photonics, Optics and Photonics News, Ophthalmology Research, etc.  He is also scientific reviewer for a number of journals, as well as NIH, A-STAR (Singapore funding agency), DFG(German funding agency), etc. He has   over 300 publications (papers, conference proceedings, chapters, etc.) in areas ranging from molecular spectroscopy, biomedical engineering, applied mathematics, cognitive science and perception, optical science and engineering, science education/policy as well as in physiological optics/vision science.

Abstract : The techniques of adaptive optics has revolutionized astronomy. Another major application of adaptive optics is in vision science. In this talk I will introduce the basic principles of adaptive optics and wavefront aberrations and then talk about their applications in vision science. More specifically I will describe a computational model that will predict human vision performance (as measured by visual acuity) based on wavefront aberration measurements. A second application is in the study of tear film break-up which is shown to be chaotic.

Date & Time: 28th July 2014 10:30 am at Rm. 232

Title:  “Factors Affecting the Cues for Concurrent Vowel Identification: Vowel Level, Age and Hearing Loss”

Speaker:  Dr. AnanthaKrishna C

Bio –Data: Post doctoral fellow from Medical University of South Carolina, USA. Dr Anantha Krishna completed his doctoral studies from Dept of Biomedical Engineering at Purdue University.  

Abstract : Younger adults with normal hearing have a remarkable ability to understand a single talker in the presence of multiple talkers (e.g., in a noisy environment). Differences in fundamental frequency (F0) and spectral characteristics are two important cues for talkers’ segregation. However, this ability to understand a single talker is reduced in older adults with normal hearing and older adults with hearing loss. The auditory mechanisms underlying these deficits due to increased age and hearing loss are still not known.Concurrent vowels (or two simultaneous vowels) is an experimental paradigm for understanding the effects of F0 and formant (or spectral) difference cues on their identification. The relative contributions of F0 and formant cues were investigated in younger adults with normal hearing by varying the vowel level and F0 difference conditions. Vowel identification scores were poorer at the lowest and highest levels for each F0 condition, and F0 benefit was reduced at the lowest level as compared to higher levels. To understand the neural correlates underlying level- dependent changes in vowel identification, a computational auditory-nerve model was used to estimate F0 and formant difference cues under the same listening conditions. At lower levels, poorer F0 benefit may be attributed to poorer phase locking to both F0s. At higher levels, poorer identification scores may relate to poorer phase locking to the second formant due to broader auditory filters. These findings suggest that concurrent vowel identification may be partly influenced by level-dependent changes in phase locking of auditory-nerve fibers to F0s and formants of both vowels. To understand the effects of age and hearing loss, older adults with normal hearing and older adults with hearing loss listened to concurrent vowels. The overall identification scores of simultaneous vowels across F0 difference were reduced with age and then further declined with hearing loss. Previous studies have shown that there are anatomical and physiological changes in the ear and auditory-nerve fibers due to increased age and hearing loss. We hypothesized that these changes could reduce phase locking of auditory-nerve fibers to formants and F0s and thus might affect the overall vowel identification scores. A computational auditory-nerve model was used to test this hypothesis. Our preliminary modeling predictions suggest that age-and hearing loss-related changes in the ear and auditory-nerve fibers could explain some of the reduced identification scores. The findings from these studies can be beneficial for proposing a better physiologically inspired signal processing algorithm for hearing aids, cochlear implants and automatic speech recognition systems.

Date & Time: 24th June 2014 10:00 am at Rm. 232

Title:  “Functionalization of Graphene Oxide Nanosheets for  Advancement in Anti-microbials and Electrochemical Biosensors”

Speaker:  Dr. Murugan Veerapandian

Bio –Data: Dr. Murugan V.  finished his Bachelor in Pharmaceutical Sciences (2007) from The Tamil Nadu Dr. M.G.R. Medical University, Chennai. He then moved South Korea where he did M.S.in Bionanotechnology (Biomedical Engineering major) under the guidance of Prof. Kyusik Yun (Gachon University) and continued doctoral thesis work with him. During his research stay in South Korea, Dr. Murugan synthesized different class of functionalized nanomaterials (metal, metal-metal oxide and graphene oxide). Currently Dr Murugan is a GRSTB postdoctoral scholar for  from Quebec government, Canada jointly work with Prof. Julian Zhu and Prof. Suzanne Giasson, Dept. of Chemistry, University of Montreal. 

Abstract : Physico-chemical and biological modification of nanomaterials have proven their synergistic utilities in advancement of biomedical applications. Since its discovery in 2004, graphene and its chemical derivatives has been the focus of intense biomedical research. Among the graphene-based materials, due to its large scale feasibility, economical precursor source and multiple oxygen functional groups, graphene oxide nanosheet is recognized as the suitable starting material for widespread biomedical application. This talk will highlight my previous research activities on chemical and physical functionalization of graphene oxide  nanosheets, especially focused on modification of metal-metal oxide/polymer nanoparticles for biosensor platform (clinical hyperglycemia and quercetin) and UV photoirradiation effect for efficient anti-bacterials. Finally, I will present my current research work on hybrid nanoparticles and functionalized graphene oxide nanosheet for cancer biomarker’s (sialic acid and kinase) detection.

Date & Time: 26th May 2014 10:00 am at Rm. 232

Title:  Using transformative coarse-graining methods to unravel sub-cellular and cellular processes in biological systems at multiple length and time scales

Speaker:  Dr Anand Srivastava

Bio –Data: Dr Anand Srivastava, who is a post doctoral fellow at Department of Chemistry, Institute for Biophys. Dynamics and Comp. Institute, University of Chicago.

Abstract : Cells communicate with each other by sending and receiving signals that are transmitted across the cell membrane using a large number of proteins, nucleotides and macromolecules. In this talk, I will focus on two membrane-signaling protein systems and one RNA-mediated protein clustering system. The first protein, Bin-Amphiphysin-Rvs (BAR) domain, belongs to the class of “curvature-sensing” proteins, whichcan cause dramatic deformations in cell membranes and is known to participate inprocesses such as cell fusion, fission and endocytosis. The second protein,Pleckstrin homology (PH) domain, is a “charge-sensing” protein, which originates in the cytoplasm and uses an intricate electrostatic search mechanismto steer towards very specific-areas of the cell surface.It then binds to a special class of rare lipid (PIPx) and regulates important cellular processes due to this specific binding. If time permits, I will also discuss my current work on HIV-1 systems, where I am developing ultra low-resolution coarse-grained models to understand the process of formation of virus-like particle (VLP) and the role of genomic-RNA as a scaffolding agent in the assembly of structural Gag poly-protein on the membrane surface of the immature virion.

Date & Time: 20th March 2014 2:30 pm at Rm. 232

Title:  “Solving the Puzzle of Blast Trauma: The Mechanics of Traumatic Brain Injury (TBI) in Warfare ”

Speaker:   Dr. Shailesh Ganpule

Bio –Data: Dr. Shailesh Ganpule obtained his bachelor's in mechanical engineering from Government College of Engineering, Karad, India and Ph.D. in mechanical engineering and applied mechanics from University of Nebraska-Lincoln, USA. His doctoral work was focused on understanding mechanics of blast induced traumatic brain injury. He is currently a postdoctoral research fellow at the Johns Hopkins University (JHU), USA. His work at JHU is focused on developing high-fidelity multi-scale models of the anatomy and physiology of the living human brain to study the onset and specific forms of traumatic brain injury. Dr. Ganpule’s broad research interests pertain to computational and experimental (solid) mechanics with emphasis on applications of these topics in biology and biomedical engineering. His current research interests are injury biomechanics and neurobiology.

Abstract :Though blast induced neurotrauma (BINT) is recognized as the “signature wound” in the recent military conflicts, the basic question of whether the primary blast waves alone can cause mild traumatic brain injury (mTBI) remains unanswered. This work is aimed to address this issue. Mechanics of primary blast loading on Realistic Explosive Dummy (RED) and post-mortem human specimen (PMHS) heads is studied using experiments and validated numerical models. During the experiments, response of heads is studied at various incident blast intensities (70 kPa, 140 kPa and 200 kPa) and Intracranial pressures (ICPs), surface pressures, and surface strains are measured. When the incident blast intensity is increased, statistically significant increase in the peak ICP and total impulse (p<0.05) is seen. The results from RED and PMHS heads are further correlated with animal experiments. Animal models show extensive neuronal damage with 100% survival and since the mechanical insult in PMHS and animal brains are comparable, it is suggested that primary blast waves alone can cause mTBI in humans. A thoroughly validated MRI based human head model is also employed to confirm and interpret experimental observations. Through the validated human head model, it is demonstrated that wave propagation through skin‐skull‐brain parenchyma plays an important role in governing ICP‐time histories. The effect of military helmets on the head response is also analyzed. It is found that the blast mitigation offered by the current military helmets is marginal, if at all.

Date & Time: 12th March 2014 10:00 am at Rm. 232

Title:  “ Probing Astrocytes with Carbon Nanotubes: Implications for Translational Medicine

Speaker:  Manoj K. Gottipati

Bio –Data: Manoj K. Gottipati from the University of Alabama, Brimingham, AL.

Abstract :Carbon nanotubes (CNTs) with their unique physical and chemical properties have emerged as a promising material for use in biomedical applications, especially neural prosthesis. We have varied the morpho-functional and proliferative features of astrocytes, the most abundant glial cells present in the brain, using diverse forms of CNTs, which were either applied to cells as colloidal aqueous solutes or served as strata for cellular growth. We have shown that chemically-functionalized water-soluble single-walled carbon nanotubes (ws-SWCNTs), when applied to the culture media, were biocompatible and made the astrocytes larger and stellate/mature, changes that were associated with an increase in glial fibrillary acidic protein immunoreactivity (GFAP-ir)(Gottipati et al., 2012). Thus, ws-SWCNTs could have more beneficial effects at the site of a traumatic brain injury or spinal cord injury than previously thought; by affecting astrocytes, they could provide for a more comprehensive re-establishment of the brain’s computational power. We have also used films of SWCNTs as retainable strata for the growth of astrocytes in culture (Gottipati et al., 2013). We have shown that SWCNT films of varying thicknesses (10, 30 and 60 nm) were also biocompatible for the growth of astroglial cells. The specific amount of coating appeared important as well, as they differentially affected astrocytic growth. Astrocytes plated onto SWCNT films of higher thickness (60 nm) grew bigger and rounder in culture, which was associated with a decrease in GFAP-ir. Additionally, there was a graded increase in the adhesion and proliferation of astrocytes with an increase in the thickness of the SWCNT films. Described changes in astrocytic morpho-functional properties are critical to understand because CNT-coated electrodes have been shown to be advantageous over standard metal electrodes for use as neural implants in brain recordings and stimulation in vivo. Our data can be used to make predictions/estimates on the amount of coating that might work best for coating the implants. Taken together these studies demonstrate that CNTs can be used as strata and colloidal aqueous solutes to affect astrocytic growth, thus showing the proof-of-principle for their use in neural prosthesis applications..

Date & Time: 6th March 2014 11:30 am at Rm. 232

Title:  “Revealing neural mechanisms of information processing using a simple brain ”

Speaker:   Dr Nitin Gupta

Bio –Data: Dr Nitin Gupta completed his BTech in computer science from IIT Kanpur and then Moved to University of California San Diego, where he carried out his Doctoral studies in Bioinformatics and Systems Biology. His main research interests are in Neuro engineering and cognitive neuro sciences.  

Abstract :The remarkable capabilities organized by the brain—from seeing to singing, from remembering to running—originate in the electrical activities of neurons. Neurons interact with each other forming circuits, which process sensory information and drive appropriate behaviors. I am interested in understanding the fundamental mechanisms used by neural circuits for processing information. The insect olfactory system (sense of smell) provides an ideal testbed because of its simple organization, rich behavior, and amenability to in vivo experiments. I will describe our recent work using this system and the tools of electrophysiology, imaging, and computational simulations for studying circuit properties, such as inhibition and oscillatory synchronization. I will also describe new experiments testing whether the precise timing of neural activity, at the scale of tens of milliseconds, carries useable information in the responses of relatively quiet neurons. I will end by outlining new directions for my future work, in which I plan to explore how information from different senses is combined, how information from the two sides of the body is compared, and how behavioral preferences to sensory stimuli are encoded in the brain.

Date & Time: 14th February 2014 11:30 am at Rm. 232

Title:  “Particle Engineering of Stem Cells using Surface Modified Drug Delivery Systems for Phenotype Control & Targeted Cancer Therapy ”

Speaker:  Dr Sudhir Ranganath

Bio –Data: Dr. Sudhir Ranganath is an IUSSTF Postdoctoral Fellow at Brigham & Women’s Hospital, Harvard Medical School, USA.  He received his B.E in Chemical Engineering from Bangalore University, M.Sc and PhD in Chemical & Biomolecular Engineering from the National University of Singapore (NUS). His research is at the interface of biomaterials, drug delivery and stem cell bioengineering with applications in cancer treatment and regenerative medicine.

Abstract : Mesenchymal stem cells (MSCs) are attractive candidates to bring about repair and regeneration owing primarily to their immunomodulatory secretome. Each year, multiple MSC-based clinical trials are investigated, however the major unmet need is controlling the secretome post-transplantation. We demonstrate a novel, non-genetic, transient, particle engineering approach of MSCs to attenuate undesirable pro-inflammatory secretome. Under inflammatory stimulus (TNF-α) MSCs secrete significantly augmented levels of pro-inflammatory mediators. To sustainably reduce secretion of these mediators, we developed poly-L-lactide-co-glycolide (PLGA) based microparticles for controlled release of a small molecule inhibitor of NF-κB signalling. The microparticles were surface modified with poly-L-lysine (PLL) to facilitate increased internalization in MSCs. Preconditioning MSCs with the inhibitor followed by TNF-α activation failed to attenuate pro-inflammatory secretome. Conversely, intracellular release of the inhibitor from microparticles in TNF-α activated MSCs significantly attenuated pro-inflammatory secretome for at least six days in vitro. Secretome from particle engineered MSCs significantly reduced migration of human monocytes in vitro and relevant to diseases such as atherosclerosis and cardiac fibrosis. This microparticle engineering approach may have great implications in the development of MSC secretome as therapeutic in particular and for controlling stem cell phenotype post-transplantation in general. MSCs are also known to be tumor tropic and hence could be developed as targeted delivery vehicles to metastatic tumor sites. In particular, prostate cancer metastasis necessitates efficient targeting of anti-cancer drugs while reducing host systemic toxicity. Prostate specific antigen (PSA) is highly expressed in the extracellular space within prostate cancer and absent in blood and other tissues and thus is an important therapeutic candidate. In this study, we developed PLGA-based microparticles loaded with a PSA-cleavable prodrug. The microparticles were surface modified using chitosan or multiple lipid bi-layers. Surface modification altered the surface charge and in addition, prevented initial burst release of the highly potent prodrug and maximized internalization of microparticles in MSCs without affecting viability in vitro. Maintaining MSC viability is extremely critical to allow homing to tumors and releasing the prodrug at the target site. Hence this particle-in-cell engineering approach may be developed as a platform technology for targeted delivery of cancer therapeutics. 

Date & Time: 12th February 2014 2:30 pm at Rm. 232

Title:  “Regulation of Tau phosphorylation and toxicity : Insights from a Drosophila model of neurodegeneration” and “Insulin resistance as a risk factor for Alzheimer’s Disease”

Speaker:  Dr Shreyasi

Bio –Data: Dr Shreyasi from Dept of Neurology, Univ of Texas Medical Branch. 

Abstract : Hyperphosphorylation of tau at multiple sites has been implicated in the formation of neurofibrillary tangles in Alzheimer’s disease; however, the relationship between toxicity and phosphorylation of tau has not been clearly elucidated. Putative tau kinases that play a role in such phosphorylation events include the proline-directed kinases GSK-3β and Cdk5, as well as non proline-directed kinases such as MARK/PAR-1; however, whether the cascade of events linking tau phosphorylation and neurodegeneration involves sequential action of kinases as opposed to parallel pathways is still a matter of controversy. Here, we employed a well characterized Drosophila model of tauopathy to investigate the interdependence of tau kinases in regulating the phosphorylation and toxicity of tau in vivo. We found that tau mutants resistant to phosphorylation by MARK/PAR-1 were indeed less toxic than wild type tau; however, this was not due to their resistance to phosphorylation by GSK-3β/Shaggy. On the contrary, a tau mutant resistant to phosphorylation by GSK-3β/Shaggy retained substantial toxicity, and was found to have increased affinity for microtubules as compared to wild type tau. The fly homologues of Cdk5/p35 did not have major effects on tau toxicity or phosphorylation in this model.  These data suggest that, in addition to tau phosphorylation, microtubule binding plays a crucial role in regulation of tau toxicity when misexpressed. These data have important implications for the understanding and interpretation of animal models of tauopathy. Additionally, we have also deciphered a mechanistic linkage between defective insulin receptor pathway leading to tau hyperphosphorylation implying insulin resistance as a potential risk factor for Alzheimer’s Disease.

Date & Time: 22th January 2014 10:00 am at Rm. 232

Title:  “Integrative modelling of biological function: examples from the brain, circulation and lungs”

Speaker:  Dr. Vinod Suresh

Bio –Data: Dr. Vinod Suresh  completed his BTech from IIT Madras in Chemical Engineering and his PhD research from Stanford University. As a postdoctoral fellow at the University of Michigan, Dr Vinod developed fluid dynamics models of surfactant delivery and liquid ventilation gas exchange in the lungs. His later postdoctoral work at the University of California, Irvine focused on studying nitric oxide transport and metabolism in the lungs using cell culture systems and mathematical modelling. Currently he is a faculty at Auckland Bioengineering Institute, New Zealand.  Dr Vinod's research focuses on study of biotransport phenomena at scales ranging from cellular to empirical approaches to iteratively build, test and improve models. 

Abstract : Advances in biological knowledge, engineering technology and computational power have provided scientists with new tools to probe how the human body works. Increasingly, biological research fuses quantitative measurements with detailed mathematical descriptions of structure and function. In this talk I will present three examples to illustrate how empirical information from biomedical imaging and gene/protein expression studies can be combined with the principles of conservation of mass/momentum/energy to develop computational models of cell, tissue and organ function; and how insights from this amalgamation can be used to develop more effective research and clinical tools. The first example concerns the study of blood flow and oxygen consumption in the brain. Optical and magnetic resonance imaging studies have yielded a wealth of information about the changes in blood flow, vessel volume and oxygen tension that occur in the brain during neural activation. The interpretation of these data in terms of the underlying biophysical processes and reconciliation of apparently contradictory observations is a significant challenge. I will present a mathematical model that predicts that arteries are responsible for the majority of volume changes during brief activation, but that dilation in capillaries and veins becomes increasingly important during longer activation. When oxygen transport is include, the model indicates that an increase in the oxygen permeability of capillaries during neural activation is necessary to reconcile predictions with measurements and that a widely-used method of calculating dynamic oxygen consumption rates suffers from serious flaws. The second example concerns the development of a modular, open source computational description of blood flow in the human circulatory system. Medical imaging data has made it possible to create anatomically accurate structural models of organs and organ systems. The description of metabolite transport and hormonal regulation at the whole body level requires the organs to be coupled by a spatial model of circulatory system. I will present the development of an anatomically accurate model of the systemic circulation using data from the Visible Human Project (www.nlm.nih.gov/research/visible/). Average blood flow and pressure in the vessels was computed using a simplified form of the governing equations of fluid mechanics coupled with a lumped parameter description of the peripheral circulation. I will describe how the implementation of the model in the OpenCMISS and CellML modelling frameworks of the Physiome Project (physiomeproject.org/software/) facilitates model exchange, reuse and customisation. The third example concerns the use of cell culture models to study water, salt and drug transport across the epithelial barrier in lung alveoli. Hydration of the alveolar lining in the normal lung is maintained by absorption and secretion of water and salt across the epithelium. The alveolar epithelium is also attractive as a non-invasive delivery portal for inhaled drugs due to its large surface area and low enzymatic activity. Using data from electrical, permeability and gene/protein expression studies I will present evidence for the use of the NCI-H441 cell line as an appropriate in vitro system to model these processes.

Date & Time: 29th November 2013 11:00 am at Rm. 232

Title:  “Bio-engineering strategies for repair and regeneration of nervous system”

Speaker:  Dr. Srinivas Madduri

Bio –Data: Dr. Srinivas Madduri from the department of Chemistry and applied biology, ETH Zurich, Switzerland. 

Date & Time: 13th November 2013 4:00 pm at Rm. 232

Title:  “Nanopore Biophysics: From Gene Sequencing to Gene Silencing”


Speaker:  Dr. Gautam V. Soni

Bio –Data: Dr. Gautam Soni from Kavli Institute of Nanoscience, TuDelft

Abstract : Structure‐Function relationship is ubiquitous in almost all of the nature's self‐assembled systems. Specifically in biological systems, my main research interest is to study the dynamic heterogeneities in structural populations of proteins and DNA‐protein complexes that regulate cellular function as well as stress response. Both, the DNA sequence, as well as its protein‐driven & highly packaged form‐ the chromatin fiber, are examples of how nature regulates cellular functions by efficient organization and dynamic re‐organization of biological structures. Since mid‐90s, nanodevices, especially nanopore biosensing has shown astonishing resolution in single molecule detection and identification and have provided a unique framework to study heterogeneity between individual biocomplexes. This has lead to new and exciting applications in both biophysics and nanobiotechnology. In this three‐part talk, I will first present my work on design and development of a novel nanopore‐based technology for ultra‐fast and low‐cost DNA sequencing. To achieve signal contrast required for single nucleotide differentiation, I engineered a unique combination of state‐of‐the‐art solid‐state nanopore technology with high speed fluorescence imaging at single molecule resolution. This has led to the emergence of the first synthetic nanopore based single‐molecule DNA sequencing platform. In the second part of my talk, I will show first ever application of solid‐state nanopores in screening structural states of nucleosomes and chromatin. By measuring voltage driven changes in ionic current as a single nucleosome translocates through a nanopore, I can detect subtle changes in nucleosomal sub‐structural volume and charge state. This resolution of single molecule detection of DNA‐bound local protein structure in label‐free manner is unprecedented. Finally, I will talk about my future research work on studying epigenetic gene silencing by chromatin condensation using nanodevices. Molecular mechanisms that regulate condensation of chromatin structure, a key element in epigenetic gene control, is poorly understood. I will propose to develop a concerted biophysical, chemical and nanoscience based approach to study kinetics of architectural proteins‐driven chromatin compaction by coupling nanopore biosensing to optical tweezers based force spectroscopy. The outcome of my proposed research will shed light on primary mechanism of chromatin folding and the role of chromatin architecture based gene‐silencing in disease, DNA repair, aging and cancer.

Date & Time: 19th July 2013 2:00 pm at Rm. 232

Title:  “A Zebrafish Model to Characterize von-Hippel Lindau Disease”

Speaker:  Dr. Kiran Santhakumar


Bio –Data: Dr. Kiran Santhakumar from University of Sheffield.

Abstract : onHippel-Lindau (VHL) disease, a heritable disorder caused by mutations in the VHL gene, is characterized by development of a variety of tumors, most commonly malignant clear cell renal cell carcinoma (ccRCC).  A well-studied function of VHL protein is the oxygen-dependent regulation of hypoxia-inducible factor1-a (HIF1-a) but it also possesses other functions that are essential for tumor suppression.  Zebrafish has two VHL gene orthologues, vhl and vhl-like (vll).Our studies show that vhl gene to function primarily in the HIF signaling pathway and the vll to play a novel role in maintenance of genome stability.  To study VHL-HIF signaling during tumorigenesis and development in zebrafish, we developed a unique in vivo reporter for hypoxia, expressing EGFP driven byprolyl hydroxylase 3 (phd3) promoter/regulatory elements. Zebrafishvhl mutants displaya systemic hypoxia response, reflected by strong and ubiquitous transgene expression.Upon exposure todimethylbenzanthracene (DMBA), the vhl heterozygous fish showed an increase in the occurrence of hepatic andintestinal tumors, a subset of which exhibited strong transgene expression, suggesting loss of Vhl function in these tumor cells.Homozygous vll-/-null mutant zebrafish are observed to be viable and fertile.  A six month old Tg(phd3::EGFP)+/+; vhl+/- fish exhibited ~2-4 EGFP+ cells in the skin epithelia, due to spontaneous loss of heterozygosity (LOH) at the vhl locus.  Interestingly, under the vll-/- background, 6-month old Tg(phd3::EGFP)+/+; vhl+/- fish exhibited a sharp increase in the number of EGFP+ cells (~250-400 EGFP+ cells per fish), suggesting a potential role for Vll in genome integrity. To characterize this phenotype further, we developed powerful embryonic assays utilizing TALEN technology, and identified specificroles for Vll protein in HR and SSA double strand break pathways. Our studies have established a unique zebrafish model system to noninvasively study VHL signaling during tumorigenesis and development. 

Date & Time: 28th June 2013 10:30 Am at Rm. 232

Title:  “"Calcium phosphate based bioceramics for hard tissue engineering"

Speaker:  Dr. Prakash Parthiban

Bio –Data: Dr. Prakash Parthiban from tohoku University, Japan

Abstract :

Date & Time: 17th June 2013 11:30 Am at Rm. 232

Title:  “Translational Biomedical Engineering: Innovating at the Scale of Life”

Speaker:  Dr. Jonathan Pillai


Bio –Data:  Dr. Jonathan Pillai completed his Doctorate studies from Ohio State University in Biomedical Engineering and currently is a Stanford Biodesign fellow. 

Abstract: Biomedical Engineering has enormous potential to deliver innovative solutions to problems in healthcare and life sciences, particularly for developing countries like India. However, for technology to be truly effective and translational, solutions have to be scalable according to the biology being affected, from the molecular level to the whole body. This is particularly true in the field of drug delivery, where the efficacy of pharmacological agents is directly affected by our ability to deliver them at the appropriate location at an adequate dose. This talk will cover examples of innovative solutions in drug delivery at three different scales, viz. at the cellular, tissue and organ-system levels. At the cellular level, the PRINT™ process of applying nanotechnology for translational biomedical applications is discussed. This process utilizes the principles and processes of silicon microfabrication traditionally employed in the semi-conductor industry to generate highly customizable shapes, sizes and material-specific particulate systems. These systems were then applied to two clinical areas, viz. aerodynamic drug-delivery vehicles for pulmonary medicine, as well as particulate vaccines for evaluating and engineering immune responses.  At the tissue level,the process of soft lithography was scaled up to fabricate thin films. By incorporating an oxygen-sensitive pharmacological agent, these films were evaluated for applications in wound healing, using electron paramagnetic resonance imaging.Finally, the Biodesign process of med-tech innovation is briefly described. This is a process of “bottom-up” innovation for medical devices starting from unmet clinical needs. As an example, a recent invention of a medical device targeting intervention at the organ-system level in Gastro-intestinal disease is covered. 

Date & Time Wednesday 20th March 2013 2:00 Am at Rm. 232

Title:  “Cytoplasmic acto-myosin network determine nuclear shape”

Speaker:  Dr.Anoop V. Cherian

Bio –Data: Dr.Anoop V. Cherian has completed his PhD from Max Planck Institute of Biochemistry, Germany. His areas of expertise includes cellular biophysics, study of cell dynamics and applications of  laser and optics in Biology. 

Abstract : Maintaining nuclear shape is essential for chromatin organization and gene regulation. Previous studies suggested the existence of cytosolic actin assemblies that transfer mechanical signals from the cell periphery to the nucleus. However, no such structures connecting plasma membrane and nucleus have so far been visually identified. Using combination of live cell fluorescence imaging and transmission electron microscopy, we now demonstrate the existence of an extensive cytoplasmic network of actin in mammalian epithelial cells. Cytoplasmic network is physically connected to both the nucleus and the plasma membrane. De-polymerization of actin or inhibition of myosin II leads to a collapse of nuclei, indicating that the identified acto-myosin structures exert forces on the nuclear envelope. Simultaneously de-polymerization of actin and microtubules using low concentration of Lat B and nocodazole lead to the imbalance of the nucleus and deformation of the nucleus shape. Taken together, our results suggest that a cytosolic acto-myosin network plays an essential role in the control of nuclear shape.

Date & Time: 5th February 2013 11:30 Am at Rm. 232

Title: “A synergy-based brain-machine interface for  dexterous control of prosthetic hands”

Speaker:  Dr. Ramana Vinjamuri

Bio –Data: Dr. Ramana Vinjamuri is currently a research faculty working on Brain Machine interfaces at the BME dept at John Hopkins University.

Abstract : Spinal cord injury (SCI) is a debilitating injury that disrupts the quality of life, level of independence and social participation of individuals. Recent surveys indicate that, for over 45% regaining arm and hand function would improve their quality of life significantly. While sophisticated Functional Electric Stimulation (FES) systems have been developed (e.g. Freehand), one of the main challenges is obtaining multiple independent control signals that allow stimulation of muscles in a coordinated fashion that generates continuous and natural hand movements.  Brain machine interface (BMI) provides a viable and powerful solution for this user-control problem by accessing and decoding the native motor control signals in the brain. One of the major challenges is extending this technology to control high-dimensional systems like controlling a human hand with above 27 degrees of freedom (DoF). Movement planning functions in the brain are hypothesized to happen in a low-dimensional subspace of movements called movement primitives often referred as synergies. Synergies enable control of multiple DoF of movement with fewer control signals. By combining the advantages of a synergy-based model for dimensionality reduction and good spatial and temporal resolution provided by an electrocorticography (ECoG) based BMI dexterous control of prosthetic hands can be achieved. Using the above method agile control of assistive devices including FES can be achieved.

Date & Time: 14th  December 2012 10:00 Am at Rm 132

Title:  “Molecular Imaging : Future Trends."

Speaker  Dr. Sikandar Shaikh

Bio -Data Dr. Sikandar Shaikh is Radiologist currently at Yashoda hospitals and he is specialized in PET-CT and molecular imaging. He has completed his MBBS in 1997 from B R Ambedkar university and specialized in Radiology with a diploma is Medical Radio Diagnosis and then a Diplomate National Board. He has also secured n diploma from European Board of Radiology Austria. His research interests include role of PET-CT in molecualr imaging, molecular and nanoimaging applications. 

Date & Time: 17th  August 2012 10:00 Am at Rm 202

Title: “ Detection of disorders in the spinal cord from MR images, and Segmentation of the liver from CT images.

Speaker:  Dr. Suryaprakash  Kompalli.

Bio -Data Dr. Suryaprakash Kompalli is currently working as a Research Scientist at HP Labs India where he is involved in video analytics research in the “Future School” project. Before joining HP Labs, he was a Research Associate at Wayne State University working on medical imaging and high performance computing. He received a Bachelors in Computer Science and Engineering (2001) from Mumbai University, India, MS (2003) and PhD (2007) in Computer Science from the University at Buffalo, SUNY. His research interests include Image Processing, Pattern Recognition, and computing on GPUs. He has contributed to research articles and patents in the domains of Document Image Processing, Human Computer Interaction, and Medical Image Analysis.

Abstract : We present a new method for automatic detection of the lumbar vertebrae and disk structure from MR images. In clinical settings, radiologists utilize several images of the lumbar structure for diagnosis of lumbar disorders. These images are co-registered by technicians and represent orthogonal features of the lumbar region. We combine information from T1W sagittal, T2W sagittal and T2W axial MR images to automatically label disks and vertebral columns. The method achieves 98.8% accuracy for the disk labeling task on a test set of 67 images containing 335 disks.Segmentation of the liver from images of the abdominal area is a critical first stage in several computer assisted diagnostic and surgical procedures. Physical properties of the abdominal organs present major challenges to the segmentation stage. The softness of liver tissue, for example, causes easy movements and deformations during image acquisition. The liver is adjacent to several organs such as stomach, kidney, and heart that have similar material characteristics. We present results on an algorithm that uses Markov Random Fields to obtain an initial contour of the liver. Gradient vector fields (GVF) and active contours are used to refine the initial estimate and segment the liver.

Date & Time: 13th  August 2012 10:00 Am at Rm 202

Title: “Raman Spectroscopy studies and its applications in early diagnosis of Cancer”

Speaker:  Dr Murali Krishna

Bio –Data:  Dr Murali Krishna from Cancer Research Institute, Advanced Center for Treatment, Research and Education  In  Cancer (ACTREC), Tata Memorial Center (TMC),  Mumbai Dr Murali Krishna is a  Scientific Officer F  and Principal investigator  at ACTREC, TMC Mumbai.

Abstract : Cancer is one of the serious health problems in developed as well developing countries. Cancer is a multi step process and usually passes through hyperplasia/metaplasia, dysplasia, carcinoma in situ, and eventually to invasive cancers. During this process several biomolecules are expressed which can be exploited to diagnose the pathological conditions. Prognosis depends on stage of diagnosis and, earlier the detection better the prognosis.Conventional approach of diagnosis and screening of cancers is based on morphological changes which are often rather late signs of an advanced disease. Hence, there is a need to develop new methods that are sensitive to molecular level variations, rapid and more objective. Optical spectroscopy methods, Raman, LIF and FTIR are being pursued as potential adjuncts/alternatives. Motivation, applicability of these technologies in cancer management will be discussed in this talk.

Date & Time:  2nd July 2012 11:00 Am at Rm 132

Title: "Anharmonic acoustic technique for detection of surface-bound particles"

Speaker: Dr. Sourav Ghosh

Bio -Data Dr. Sourav  Ghosh works as a Postdoctoral Research Associate in the Dept. of Chemistry, University of Cambridge, in an EU consortium project on the development of a rapid POC platform for infectious disease. In  his PhD from the Dept. of Engineering, University of Cambridge, he worked on the development of the presented nonlinear acoustic detection technique, which has been selected as one of 4 main approaches in the 14.5 million EUR project, jointly funded by  European  Commission and  European  pharmaceutical companies.  He has  got  his basic degree in Mechanical Engineering from Bengal Engineering and Science University and  a postgraduate degree in Biomedical Engineering from the Dept. of Engineering Science, University of Oxford.

Abstract: Receptor-based bio-detection techniques often suffer from non-specific interactions between the receptor and the analyte that are not easily dissociated in practice. Most existing detection techniques are unable to differentiate between specific and non-specific interactions, often leading to false positive responses. The presented work investigates, through modeling and experiments, the mechanical interactions of an in-plane resonator with surface-bound microparticles. It is found that the interactions of attached streptavidin-coated polystyrene microbeads with biotinylated thickness-shear-mode quartz resonators (sensor) cause a nonlinear modulation of the acoustic response of the sensor. In particular, the deviation in the magnitude of the electrical signal, measured at the third Fourier harmonic (3f) or three times the driving frequency f, is significant and approximately proportional to the number of bound beads, showing potential for single  microparticle detection. Interestingly, the deviation, as a function of the sensor oscillation amplitude, is found to hold a distinct relationship with the type of particle-surface interaction. This technique offers a new paradigm for detection of pathogens and biomolecules with a unique quality to differentiate between strengths of interaction of binding partners. Being an entirely electronic method requiring minimal sample processing, this is also suitable for implementation in rapid point-of-care (POC) detection platforms. Furthermore, the capability to quantify interaction strength shows promise in rapid force-spectroscopy and affinity-based screening, with important applications in in-vitro drug trials and individualized therapy.

Date & Time: 21st June 2012 11:30 Am at Rm 132

Title: “Insight into DNA intercalation using combined optical tweezers and line scanning fluorescence microscopy”

Speaker Dr. ChandraSekhar U. Murade  

Bio –Data: Dr ChandraSekhar U. Murade    carried out his Ph D in "DNA intercalation using combined optical tweezers and fluorescence microscopy" at University of Twente and is currently continuing at UTWENTE as a post-doctoral scientist specializing in Electrowetting, Optofluidics and Soft Matter.

Abstract : The functioning of a single cell, and indirectly that of a complete organism, is due to a large number of interlocking biological processes.  One of the most important interactions within the cell is the interaction of protein molecules with DNA. Protein molecules interact with DNA via either groove binding or intercalation. Within this talk I will focus on development of hybrid single molecule instrument “combined optical tweezers and line scanning fluorescence microscopy”. The instrument is capable of probing the change in the mechanical properties of a single double-stranded DNA (dsDNA) molecule as it is interacting with protein/ligand molecules, having the capability to detect the number and location of the protein/ligand molecules on the DNA simultaneously. This allows us to directly correlate the effect of protein/ligand binding with the mechanical properties of the DNA on a single molecule level. Our experiments revealed that the interaction of the intercalating ligands with the DNA is force dependent. Furthermore I will discuss about the structure of the DNA as function of applied force. 

Date & Time: 10st May 2012 2:00 Am at Rm 134

Title:  “Novel Applications of Cornea Biomechanics in Clinical Diagnosis

Speaker: Dr. Abhijit Sinha Roy 

Bio –Data: Dr. Abhijit Sinha Roy has completed his doctoral studies from Biomedical engineering dept. at Univ of Cincinnati, USA. Dr Sinha Roy is a PhD- scientist with active interest in studying the bio mechanical response of the cornea to surgical perturbations and collagen cross-linking. Currently he is a senior research associate at Cole Eye Institute, Cleveland

Abstract: The quality of vision determines our ability to perform adequately in our daily lives. Hence, it is absolutely paramount that perfect vision be obtained so as to achieve maximum success. The cornea is an avascular tissue which contributes 80% of the optical power of the eye. By surgical alterations, e.g., LASIK, we can achieve improvements in vision. However, the cornea is not a piece of plastic and it has an active biomechanical response to intervention. The goal of my research is to quantify this change in corneal tissue properties so as to provide an accurate prognosis of the improvement in vision quality and also to assist surgeons in designing better treatment plans for individual patients. In this talk, I will present novel finite element models that have been developed to model different surgical interventions e.g. LASIK, photorefractive keratectomy, collagen-crosslinking for treatment of both normal and degenerated corneas. The talk will demonstrate how these models have been adapted as inverse models to obtain patient-specific results in real-time using clinical data.

Date & Time: 17th March 2012 10:00 am at conference room1

Department of Biomedical Engineering, Indian Institute of Technology Hyderabad, Ordnance Factory Estate, Yeddumailaram - 502 205,
Andhra Pradesh, INDIA. Tel : +91 (40) 2301 6097