MBBS Internship Programme

Phaneendra Yalavarthy

Department: Computational and Data Sciences

Email ID: Yalavarthy@iisc.ac.in

Lab website link: http://cds.iisc.ac.in/faculty/yalavarthy/MIG/

Title of the project:

Development of Artificial Intelligence Tool for Automated Tracking and Segmentation of Median Nerve in Ultrasound Images.

Brief Description of Project Goals and Objectives:

Tracking of median nerve in ultrasound images which will allow diagnosis and prognosis of carpel tunnel syndrome (CTS) in an expedited manner. This neuromuscular Ultrasound Imaging data collection from Wrist to Proximal and Distal part of the arm is typically collected as a one-minute video sequence. Manual segmentation of these video sequence is time consuming. Medical Imaging Group (MIG) in collaboration with Aster-CMI Hospital has been developing an AI tool to enable faster diagnosis (reducing characterization time from one hour to three minutes) and aids the clinicians like Anesthesiologist, Radiologist, Neurologist, Rheumatologists and various clinicians involved in musculoskeletal disorders in procedures such as ultrasound guided injections. This tool current accuracy is around 85% equivalent to expert neurosonologist. The project aims at improving the developed AI tool with more rigorous validation.

Keywords: Artificial Intelligence, Semantic Segmentation, Ultrasound Imaging, Neurology, Validation.

References:

Ming-Huwi Horng, Cheng-Wei Yang, Yung-Nien Sun, Tai-Hua Yang, “”Deep Nerve: A New Convolutional Neural Network for the Localization and Segmentation of the Median Nerve in Ultrasound Image Sequences”.

Ultrasound in Medicine & Biology, Volume 46, Issue 9, 2020, Pages 2439-2452. https://doi.org/10.1016/j.ultrasmedbio.2020.03.017.

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William R Surin

Department: Microbiology and Cell Biology

Email ID: wrsurin@iisc.ac.in

Lab website link: https://mcbl.iisc.ac.in/william-r-surin/

Title of the project:

Assessment of platelet function by Flow Cytometry

Brief Description of Project Goals and Objectives:

Platelets and plasma proteins play a crucial role in haemostasis and thrombosis which are essential physiological processes. However, any alteration in the normal physiological process leads to hyper-aggregability of platelets and plasma factors which in turn causes an increased incidence of thrombotic events. Increased thrombotic events and formation of intravascular thrombus cause various thrombotic events like myocardial infarction, cardiac ischemia, deep vein thrombosis, stroke, etc. There are various predisposing factors like aging, smoking, hyperlipidemia, etc.
We propose to study the platelets for their hyperaggregability and to assess whether they respond to antiplatelet therapies. We propose to study platelets from blood either obtained from human volunteers or from laboratory animals.

Keywords: Cardiovascular, Thrombosis, Platelets, Anti-platelets

References:

Michelson, A. Antiplatelet therapies for the treatment of cardiovascular disease. Nat Rev Drug Discov 9, 154–169 (2010). https://doi.org/10.1038/nrd2957
Anantha Krishna TH, Kamalraj S, Anikisetty M, Naidu KA, Surin WR, Jayabaskaran C. Inhibition of thrombin, an unexplored function of retinoic acid. Biochem Biophys Rep. 2019 Apr 25;18:100636. doi: 10.1016/j.bbrep.2019.100636. PMID: 31049420; PMCID: PMC6484212.
Kumar S, Saran RK, Puri A, Gupta N, Sethi R, Surin WR, Dikshit M, Dwivedi SK, Narain VS, Puri VK. Profile and prevalence of clopidogrel resistance in patients of acute coronary syndrome. Indian Heart J. 2007 Mar-Apr;59(2):152-6. PMID: 19122249.

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Sandeep M Eswarappa

Department: Biochemistry

Email ID: sandeep@iisc.ac.in

Lab website link: https://sites.google.com/view/dr-sandeep-m-eswarappa/home?authuser=0

Title of the project:

Therapeutic induction of readthrough across disease-causing nonsense mutations

Brief Description of Project Goals and Objectives:

We use antisense oligonucleotides and a CRISPR system to achieve therapeutic induction of readthrough across disease-causing nonsense mutations. At present, we target beta-thalassemia, muscular dystrophy, and hereditary spherocytosis.

Keywords: Genetic disease, stop codon, nonsense mutation, CRISPR, antisense oligonucleotides

References:

Manjunath LE, Singh A, Sahoo S, Mishra A, Padmarajan J, Basavaraju CG, Eswarappa SM (2020) Stop codon readthrough of mammalian MTCH2 leading to an unstable isoform regulates mitochondrial membrane potential. J Biol Chem 295:17009-17026.
Kar D, Sellamuthu K, Devi Kumar S, Eswarappa SM (2020) Induction of translational readthrough across the thalassemia-causing premature stop codon in β-globin-encoding mRNA. Biochemistry 59: 80-84.
Singh A, Manjunath LE, Kundu P, Sahoo S, Das A, Suma HR, Fox PL, Eswarappa SM (2019) Let-7a-regulated translational readthrough of mammalian AGO1 generates a microRNA pathway inhibitor. EMBO J 38: e100727.

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Lakshminarayana Rao

Department: Centre For Sustainable Technologies

Email ID: narayana@iisc.ac.in

Lab website link: https://sites.google.com/site/narayanarao/

Title of the project:

Use of Plasma Activated Water for Medical Applications include, cancer treatment, diabetic wounds

Brief Description of Project Goals and Objectives:

Plasma activated water: PAW has many fundamental questions still not answered such as: what determines the chemistry of PAW? and how to selectively generate/control the desired water chemistry? The research direction is to understand the interactions/relations between the cold plasma operating parameters such as plasma volume, electrode configuration, operating current, and electron temperature with the plasma chemistry in the headspace. The approach to answer this is to carefully map all the 900+ chemical reactions involving 33 species and mathematical modelling of the system. The plan is to establish a relation between the species generated around the plasma to that of the PAW. To be specific, it is understood that ~ 50 ppm levels of H2O2 along with the ~ 20 ppb level of per-oxynitrate contributes to the antimicrobial nature of the PAW. However, how to achieve only these species in PAW by suppressing other chemistry is yet to be understood. Designing plasma systems to prepare PAW with high species selectivity and yield will revolutionize the application of PAW for specific applications such as cancer treatment, burn wounds and treatment of multidrug-resistant bacteria. For this work, the plan is to continue working with established collaborations both inside and outside IISc namely the Department of Microbiology and Cell Biology and M/s Sri Shankara Research Centre, Rangadore Memorial Hospital. This work will open a new field of plasma medicine.

Keywords:Plasma activated water, Reactive oxygen species, OH radical, Burn Wounds, Cancer Treatment

References:

P S Ganesh Subramanian, Aditi Jain, Anand M Shivapuji, Nagalingam R Sundaresan , S Dasappa, and Lakshminarayana Rao, Plasma activated water from a dielectric barrier discharge plasma source for the selective treatment of cancer cells, Plasma Processes and Polymers, https://doi.org/10.1002/ppap.201900260
Lakshminarayana Rao, Anand M Shivapuji and Dasappa S. Achieving anti-microbial property of plasma activated water on near neutral pH conditions. MS-CST-2018-082, PD033948IN-SC
Lakshminarayana Rao, Punith N, Ashish Singh, and Dipshikha C. A process and a setup to generate near neutral pH, highly potent plasma activated water for surface hygiene and wound healing applications

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Pradipta Biswas

Department: Centre for Product Design and Manufacturing & Robert Bosch Centre for Cyber Physical Systems

Email ID: pradipta@iisc.ac.in

Lab website link: https://cambum.net/I3D.htm

For more details: click here

Title of the project:

Cognitive load estimation for Astronauts

Brief Description of Project Goals and Objectives:

Designing experiments for estimating cognitive load of astronauts for India’s maiden Human Space Flight mission. The experiment will be designed for a Virtual Reality simulator developed at the I3D lab. Astronauts will undertake representative task and the intern will be responsible to record and analyse EEG and ocular parameters. Software and hardware support will be provided.

Keywords: Cognitive Load, Aerospace, EEG, Pupil Dilation, Fixation Rate

References:

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K V S Hari

Department: Electrical Communication Engineering

Email ID: hari@iisc.ac.in

Lab website link: https://ece.iisc.ac.in/~hari/wordpress/

Title of the project:

Enabling data-driven critical care: Integration of clinical environment and applications of machine
learning.

Brief Description of Project Goals and Objectives:

The management of the critically ill is a complex task with a continuous stream of data presented to the intensive care unit (ICU) team. With the increasing number of data points available for each decision, such data may be overlooked or under-valued. The risks of not recognizing an impending catastrophe, variations in practice, and widespread lack of consensus in evidence-based medicine, have real consequences in critical care. We propose an ecosystem of data-driven critical care that remembers every patient the ICU has taken care of, employs machine learning algorithms to answer the most vital clinical questions, reduces the burden on the intensivists and their teams, and overall improves the quality of care.
Aims:
(a) Integration of clinical environment: Create a comprehensive, machine-readable, digital picture of the patient’s stay and care in the intensive care unit. Create a continuously growing dataset and incorporate further ICU beds across partner hospitals.
(b) Applications of machine learning: Build models to detect, predict and recommend for common causes of mortality in the intensive care unit.
(c) Enable global contribution: Curated open-access dataset, code, and repository of clinical questions and technology needs. Serve as benchmark datasets available to the research community.

Keywords: ICU, Deep Learning, Signal Processing, Echocardiography

References:

Johnson, A. E. W. et al. MIMIC-III, a freely accessible critical care database. Scientific Data 3, 160035 (2016).
Komorowski, M., Celi, L. A., Badawi, O., Gordon, A. C. & Faisal, A. A. The Artificial Intelligence Clinician learns optimal treatment strategies for sepsis in intensive care. Nature Medicine 24, 1716–1720 (2018).
Fagerström, J., Bång, M., Wilhelms, D. & Chew, M. S. LiSep LSTM: A Machine Learning Algorithm for Early Detection of Septic Shock. Scientific Reports 9, 15132 (2019).
Tomašev, N. et al. A clinically applicable approach to continuous prediction of future acute kidney injury. Nature 572, 116–119 (2019).
Ouyang, D. et al. Video-based AI for beat-to-beat assessment of cardiac function. Nature 580, 252–256 (2020).

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Nikhil Gandasi

Department: Molecular Development Reproduction and Genetics

Email ID: grnikhil@iisc.ac.in

Lab website link: https://nikhilgandasi.com

Title of the project:

Human pancreatic tissue to test hormone secretion defects during type-2 diabetes

Brief Description of Project Goals and Objectives:

The pancreatic functions are extensively studies using mouse models, but organization of pancreas varies a lot between mouse and human. Therefore, there is a large need to understand the cyto-architecture of pancreatic cells. This in turn will help in understanding the pancreatic exocrine disorders, pancreatitis, pancreatic cancer, and diabetes. A large proportion of our population is affected by these disorders and our work will focus on bringing in novel treatment targets, diagnostic tools to help people suffering from these ailments.
This project is a collaboration with Dr. Harshavardhan at Ramiah Hospital who will be providing the human pancreatic tissue. So we encourage medical students from Ramiah for this initiative.

Keywords:Pancreatic-islets, human-tissue, diabetes, hormone-secretion

References:

NR Gandasi, V Arapi, P Belekar, M Mickael, L Granlund, L Kothegala, R Fredriksson, S Bagchi. Glutamine uptake via SNAT6 and Caveolin regulates glutamine-glutamate (2021) International Journal of Molecular Sciences 22(3):1167
 

V Petrenko, NR Gandasi, D Sage, A Tengholm, S Barg, C Dibner. In pancreatic islets from type 2 diabetes patients the dampened circadian oscillators lead to reduced insulin and glucagon exocytosis (2020) Proceedings of National Academy of Sciences (PNAS) 117 (5):2484-2495.

NR Gandasi, P Yin, M Omar-Hmeadi, EO Laakso, P Vikman, S Barg. Glucose dependent granule docking limits insulin secretion and is decreased in human type-2 diabetes (2018) Cell Metabolism 27(2): 470-4785.

NR Gandasi, P Yin, M Riz, G Cortese, M Chibalina, P Rorsman, A Sherman, MG Pedersen and S Barg. Ca2+ channel clustering with insulincontaining granules is disturbed in type 2 diabetes (2017) Journal of Clinical Investigation 127(6):2353-2364

NR Gandasi and S Barg. Contact-induced clustering of syntaxin and munc18 docks secretory granules at the exocytosis site (2014) Nature Communications 5:3914

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Manish Arora

Department: Centre for Product Design and Manufacturing

Email ID: marora@iisc.ac.in

Lab website link: https://cpdm.iisc.ac.in/utsaah/

Title of the project:

SecureUltrasound

Brief Description of Project Goals and Objectives:

Teleultrsound system for improving reach of ultrasound technology to rural areas without risk of gender disclourse. System intergates sensors to construct 3D MRI like volume from 2D ultrasound images by integrating addtional sensors into the probe. System also incorprates GPS module to track physical location of the device.

Keywords:Ultrasound, PCPNDT, Freehand 3d

References:

Mozaffari MH, Lee WS. Freehand 3-D ultrasound imaging: a systematic review. Ultrasound in medicine & biology. 2017 Oct 1;43(10):2099-124.
Satvika Bharadwaj, Komal N. Shah, Yifan Zhao, Aparna Harindranath, Arun George, Kajoli B. Krishnan, Manish Arora, Semi-blinded freehand 3D ultrasound with novice users
Proceedings Volume 12035, Medical Imaging 2022: Image Perception, Observer Performance, and Technology Assessment; (2022) https://doi.org/10.1117/12.2610969

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Namrata Gundiah

Department: Mechanical Engineering

Email ID: namrata@iisc.ac.in

Lab website link: https://mecheng.iisc.ac.in/namrata/

Title of the project:

Mechano-diagnostics in cancer cell adhesions to substrates

Brief Description of Project Goals and Objectives:

The adhesion of cells to substrates occurs via integrin clustering and binding to the actin cytoskeleton. Oncogenes modify anchorage-dependent mechanisms in cells during cancer progression. Fluid shear devices provide a label-free way to quantify cell-substrate interactions, heterogeneities in the cell populations, and visualize the dynamic changes in signalling during adhesions to substrates. The goals of this work are to use interdisciplinary methods in mechanobiology to quantify cell adhesions in cancer cells. Students will learn to label cancer cells for specific markers, and subject them to a range of shear stresses using a custom fabricated and patented device on a microscope stage. Tractions exerted by cells on substrates will be measured and used to assess the role of contractility in adhesions. Such methods may be useful in developing mechano-diagnostic methods in cancers and to test the role of various pharmacological treatments that influence cell adhesions to substrates.

Keywords: Mechanobiology, cell adhesions, cancer metastasis

References:

Paddillaya, N, …,Gundiah, N.*, ‘Cell adhesion strength and tractions are mechano-diagnostic features of cellular invasiveness’, biorxiv (2022). https://www.biorxiv.org/content/10.1101/2021.12.30.474608v1
Paddillaya, N, …,Gundiah, N.*, ‘Biophysics of cell-substrate interactions under shear’, Frontiers : Cell Adhesion and Migration, 2019. https://doi.org/10.3389/fcell.2019.00251

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Praveen C Ramamurthy

Department: Materials Engineering

Email ID: praveen@iisc.ac.in

Lab website link: https://materials.iisc.ac.in/~praveen/

Title of the project:

Sensors for various ion detection in human blood

Brief Description of Project Goals and Objectives:

In our lab, we are designing, synthesizing and fabricating various sensors that specifically detect various metal ions and inorganic complexes and biological organisms. Would like to explore the suitability of these point of care detection systems for analyzing blood and studying its dynamics and interference effects.

Keywords:Point-of-care-device, portable solid-state sensor

References:

https://www.sciencedirect.com/science/article/pii/S0254058421010701

https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/full/10.1002/elan.201800052

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Anu Rangarajan

Department: Molecular Development Reproduction and Genetics

Email ID: anu@iisc.ac.in

Lab website link: https://mrdg.iisc.ac.in/anu-rangarajan/

Title of the project:

Interplay between diabetes and drug resistance in breast cancer progression

Brief Description of Project Goals and Objectives:

Breast cancer is the most common cancer among women the world over. Disease prognosis is adversely affected by comorbidities such as Type 2 Diabetes. In this study, we aim to study the molecular mechanisms of T2D-associated hyperglycemia in breast cancer progression. Abnormal glucose metabolism and effects on drug resistance would be studied in cell culture models mimicking physiological versus diabetic hyperglycemia using cell biology and molecular biology approaches.

Keywords: Breast cancer, Type 2 diabetes, hyperglycemia, glucose, drug resistance

References: 

Boyle P, et al. Diabetes and breast cancer risk: a meta-analysis. Br J Cancer. 2012 Oct 23;107(9):1608-17.
Schrauder MG, Fasching PA, Häberle L, Lux MP, Rauh C, Hein A, Bayer CM, Heusinger K, Hartmann A, Strehl JD, Wachter DL. Diabetes and prognosis in a breast cancer cohort. Journal of cancer research and clinical oncology. 2011 Jun;137(6):975-83.

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Deepak Kumar Saini

Department: Molecular Development Reproduction and Genetics

Email ID: deepaksaini@iisc.ac.in

Lab website link: https://sites.google.com/site/sainislab/home

Title of the project:

Developing a liver hepatocyte aging model system for studying the altered pharmacokinetic and pharmacodynamics of drugs and effects on fibrosis of the liver.

Brief Description of Project Goals and Objectives:

It is known that impairment of metabolic pathways in the aging liver may be related to hepatocyte senescence[1,2]. Senescent hepatocytes have altered expression of the Glut2 and Glut4 as well as other genes involved in hepatic metabolism of glucose, lipids and proteins such as PI3K/Akt, MAPK, Jak/S, NF-κB, TGFβ, IGF1 and Ca/cAMP[3]. Aging hepatocytes have reduced mitochondrial enzymes and senescent hepatocytes release interleukin 6 (IL-6), tumor necrosis factor1-α (TNFα) and (IL-8) that contribute to age-related inflammation (referred to as the senescence associated secretory phenotype)[4] The age-related changes in pharmacokinetics and pharmacodynamics, as well as the increased inter-individual variation mean optimal dose selection are a challenge for prescribing in older adults. Poor understanding of how hepatic clearance and toxicity are different with age results in suboptimal dose selection, poor efficacy, and/or increased toxicity. Of particular concern is the analgesic acetaminophen which has been in use for more than 50 years and is consumed by a large proportion of older adults. It is considered to be a relatively safe drug; however, caution must be taken because of its potential for toxicity. Better understanding of how age affects the hepatic clearance and toxicity of drugs will contribute to evidence-based prescribing for older people, leading to fewer adverse drug reactions without loss of benefit[5,6]
Objectives:
1.Establishing a model aging system of liver hepatocytes.
2.Use of liver hepatocyte model to compare clinical samples from alcoholic and non-alcoholic liver disease patients.
3.To assess the pharmacokinetic and pharmacodynamic of acetaminophen on the model hepatocyte system.

Keywords:Aging, liver, fibrosis, drug metabolism

References: 

Nicholas J. Hunt, Sun Woo (Sophie) Kang, Glen P. Lockwood, David G. Le Couteur, Victoria C. Cogger, Hallmarks of Aging in the Liver, Computational and Structural Biotechnology Journal, Volume 17, (2019) Pg 1151-1161,
A. Aravinthan, B. Challis, N. Shannon, M. Hoare, J. Heaney, G.J.M. Alexander
Selective insulin resistance in hepatocyte senescence. Exp Cell Res, 331 (1) (2015), pp. 38-45
A. Aravinthan, N. Shannon, J. Heaney, M. Hoare, A. Marshall, G.J.M. Alexander
The senescent hepatocyte gene signature in chronic liver disease. Exp Gerontol, 60 (2014), pp. 37-45
A. Navarro, A. Boveris
Rat brain and liver mitochondria develop oxidative stress and lose enzymatic activities on aging Am J Physiol Regul Integr Comp Physiol, 287 (5) (2004)
Mitchell SJ, Kane AE, Hilmer SN. Age-related changes in the hepatic pharmacology and toxicology of paracetamol. Curr Gerontol Geriatr Res. 2011;2011:624156.
Mitchell SJ, Hilmer SN, McLachlan AJ. Clinical pharmacology of analgesics in old age and frailty. Reviews in Clinical Gerontology. 2009;19(2):103–118.

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Kavita Babu

Department: Centre for neuroscience

Email ID: kavitababu@iisc.ac.in

Lab website link: http://www.cns.iisc.ac.in/home/people/kavita-babu/

Title of the project:

Understanding the behavioural changes in C.elegans by modulating the genes encoding neuropepties and assessing its influence on other associated genes

Brief Description of Project Goals and Objectives:

1. To assess the genes encoding the neuropeptides(NP) by RNA interference mehcanism to understand their behavioural effects in C.elegans
2.To look at the influence of silencing any one NP gene on the expression of other NP by qRT-PCR .
Over the past decades, Caenorhabditis elegans has increasingly been used as a model system to study the underlying molecular mechanisms that give rise to neurodegeneration and neurodegenerative disorders(ND)(1). Strong parallels have been observed in the genotype-to-phenotype correlations between the human NDs and the phenotypes of transgenic C. elegans ND models. This supports the approach as expression of mutant human proteins in C. elegans can closely model a fundamental property of these mutations in humans(2).
Neuropeptides(NP) have been established as modulators of behavior in a wide range of animals as they play a pivotal role in relaying information between the neurons during execution of behaviours.
Neuropeptides once released are not reuptaken until they’re degraded or inhibited and can exert direct effects on neuronal physiology within seconds to minutes, and can also modulate the gene expression over the course of hours to days(3);
Understanding this mechanism will therefore aid in the development of strategies for treatment of disorders associated with neuropeptide signaling defects.
Keywords: Molecular neurobiology, neuropeptides, neurogenetics

References: 

Umer S. Bhat, Navneet Shahi, Siju Surendran and Kavita Babu , (2021), Neuropeptides and Behaviours: How Small Peptides Regulate Nervous System Function and Behavioural output, Frontiers in Molecular Neuroscience, 14, 786471
Chen et al. Chemistry Central Journal (2015)
Anthony N. van den Pol, Neuropeptide Transmission in Brain Circuits, Neuron, Volume 76, Issue 1, 2012, Pages 98-115,

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Kumar Somasundaram

Department: Microbiology & Cell Biology (MCB)

Email ID: skumar1@iisc.ac.in

Lab website link: https://mcbl.iisc.ac.in/kumaravel-somasundaram/

Title of the project:

Genetics of brain tumors

Brief Description of Project Goals and Objectives:

The project’s primary emphasis is to understand the genetic and epigenetic alterations in cancer. The project will focus on glioma, the tumor of glial cells, which is the most common primary adult brain tumor. Despite advances in biology and therapeutic modalities, the prognosis of glioblastoma (GBM), the grade IV glioma, remains poor. Genetic and epigenetic changes are characteristic of all cancers.
The project will employ a comprehensive approach that integrates the changes in the genome and the epigenome of cancer. Training will involve the analysis of the whole-exome sequencing data to unravel the genomic changes and the changes at DNA methylation, chromatin modifications, noncoding RNA, mRNA modifications, and transcriptome changes to identify the epigenetic alterations. Integrating the genetic and epigenetic changes will lead to identifying signaling pathways and processes that are altered and unique to cancer cells. This exercise will identify novel targets for therapy. The proof of principle testing of the targets will be carried out using patient-derived cancer stem lines in vitro and intra-cranial orthotopic mouse glioma model using both human and murine glioma stem lines
Keywords: Cancer, brain tumors, glioma, genetics, mouse model

References: 

Pal J, Patil V, Kumar A, Kaur K, Sarkar C, Somasundaram K. Loss-of-Function Mutations in Calcitonin Receptor (CALCR) Identify Highly Aggressive Glioblastoma with Poor Outcome Clin Cancer Res. 2018, 24:1448-1458
Visvanathan A, Patil V, Arora A, Hegde AS, Arivazhagan A, Santosh V, Somasundaram K. Essential role of METTL3-mediated m6A modification in glioma stem-like cells maintenance and radioresistance. Oncogene 2018, 37, 522-533
Mondal B, Patil V, Shwetha SD, Sravani K, Hegde AS, Arivazhagan A, Santosh V, Kanduri M, Somasundaram K. Integrative functional genomic analysis identifies epigenetically regulated fibromodulin as an essential gene for glioma cell migration. Oncogene 2017, 36, 71-83
Kumar S, Verma T, Mukherjee R, Ariese F, Somasundaram K, Umapathy S Raman and infra-red microspectroscopy: towards quantitative evaluation for clinical research by ratiometric analysis Chem Soc Rev. 2016, 45:1879-900

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Jaya Prakash

Department: Instrumentation and Applied Physics

Email ID: jayap@iisc.ac.in

Lab website link: https://pnjayaprakash88.wixsite.com/fist-lab

Title of the project:

Predicting cardiovascular risk using artificial intelligence from computed tomography images

Brief Description of Project Goals and Objectives:

Coronary artery calcium is often used as a predictor of cardiovascular events. The aim here is to develop a robust and time-efficient artificial intelligence method to automatically quantify coronary calcium using computed tomography. Compare the performance of machine learning approaches with manual quantification, and robust test-retest reliability. Further ask question on whether this artificial intelligence approach can provide clinical value to enable automated prediction of cardiovascular events.
Keywords: Computed Tomography, Artificial Intelligence, Cardiovascular Risk Prediction, Calcium Sensing, Image Segmentation

References: 

Roman Zeleznik, et. al., “Deep convolutional neural networks to predict cardiovascular risk from computed tomography,” Nature Comm., 12, 715 (2021). https://www.nature.com/articles/s41467-021-20966-2#additional-information

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Purusharth I Rajyaguru

Department: Biochemistry

Email ID: rajyaguru@iisc.ac.in

Lab website link: https://rajgodhuli.wixsite.com/rajyaguru-lab

Title of the project:

Role of RNA granules in determining cytoplasmic mRNA fate

Brief Description of Project Goals and Objectives:

We are interested in understanding the role of low complexity sequence containing proteins in determining mRNA fate. We focus on conserved proteins with RGG-motifs to understand the role of low complexity sequences in regulating mRNA translation and decay.
Keywords: RNA granules, mRNA translation, RGG-motif proteins, mRNA fate

References: 

Roy R, Das G, Kuttanda I, Bhatter N and Rajyaguru PI (2022) Low complexity RGG-motif sequence is required for Processing body (P-body) disassembly. Nature Communications In press
Mohanan G*, Das A* and Rajyaguru PI (2021) Genotoxic stress response: What is the role of cytoplasmic mRNA fate? BioEssays 2021 Aug;43(8):e2000311.
Parbin S*, Damodharan S*, Rajyaguru PI (2021) Arginine methylation and cytoplasmic mRNA fate: An exciting new partnership. Yeast 10.1002/yea.3653.
Roy D and Rajyaguru PI (2018) Suppressor of clathrin deficiency (Scd6) – An emerging RGG-motif translation repressor. Wiley Interdiscip Rev RNA:e1479

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Dipankar Nandi

Department: Biochemistry

Email ID: nandi@iisc.ac.in

Lab website link: https://biochem.iisc.ac.in/dipankar-nandi.php

Title of the project:

Studying inhibitors of T cell activation

Brief Description of Project Goals and Objectives:

T lymphocytes play critical roles in the cellular immune response. T cells via their T cell receptors (TCR) recognize antigenic peptides in complex with the MHC proteins. However, this interaction alone is insufficient to trigger their activation and proliferation. Proper context is required and this, in addition to the TCR is provided by the binding of costimulatory receptors to their ligands, e.g. CD28 binding to CD80/CD86. Over the years, our laboratory has standardized in vitro systems of triggering T cells: he combination of PMA and Ionomycin, anti-CD3 and anti-CD28 etc. In addition, we can vary the strength of the signal etc. In the current project, we would like to screen and evaluate the potential of compounds that can inhibit T cell activation. Several assays will be used to study the efficacy of these compounds in inhibiting T cell activation. A better idea of how these compounds in inhibiting T cells will be determined by studying various readouts. Finally, the in vivo efficacy of these compounds in different model systems will be determined.
Keywords: Immunity, Lymphocytes, T cells, Signaling, Inhibitors

References: 

7-Hydroxy Frullanolide, a sesquiterpene lactone, increases intracellular calcium amounts, lowers CD4(+) T cell and macrophage responses, and ameliorates DSS-induced colitis.
Pathak S, Gokhroo A, Kumar Dubey A, Majumdar S, Gupta S, Almeida A, Mahajan GB, Kate A, Mishra P, Sharma R, Kumar S, Vishwakarma R, Balakrishnan A, Atreya H, Nandi D.
T cell costimulation, checkpoint inhibitors and anti-tumor therapy.
Nandi D, Pathak S, Verma T, Singh M, Chattopadhyay A, Thakur S, Raghavan A, Gokhroo A, Vijayamahantesh.
J Biosci. 2020;45:50.
Comparative analysis of thymic subpopulations during different modes of atrophy identifies the reactive oxygen species scavenger, N-acetyl cysteine, to increase the survival of thymocytes during infection-induced and lipopolysaccharide-induced thymic atrophy.
Majumdar S, Adiga V, Raghavan A, Rananaware SR, Nandi D.
Immunology. 2019 May;157(1):21-36. doi: 10.1111/imm.13043. Epub 2019 Feb 11
Differential susceptibility and maturation of thymocyte subsets during Salmonella Typhimurium infection: insights on the roles of glucocorticoids and Interferon-gamma.
Majumdar S, Deobagkar-Lele M, Adiga V, Raghavan A, Wadhwa N, Ahmed SM, Rananaware SR, Chakraborty S, Joy O, Nandi D.
Sci Rep. 2017 Jan 16;7:40793. doi: 10.1038/srep40793.

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Rahul Roy

Department: Chemical Engineering and BioSystems Science and Engineering

Email ID: rahulroy@iisc.ac.in

Lab website link: https://nanobiology.nanobiophotonics.org/

Title of the project:

Long-term immune protection generated by COVID-19 vaccines

Brief Description of Project Goals and Objectives:

COVID-19 vaccination is the first line of defence against the pandemic. However, most of the vaccines administered in India have a poor record of offering long-term immune protection. We are investigating why some vaccinated individuals are protected well from COVID-19 infection while others are not. This will allow us to design and develop the next generation of personalised vaccines. Apart from learning the intricacies of the immune response to vaccines, the internship will involve lot’s of hands-on experience in working with PBMCs, FACS, single cell analysis and immuno-profiling.
Keywords: COVID-19, vaccines, single cell immuno-profiling, FACS, immune memory

References: 

Moss, P. The T cell immune response against SARS-CoV-2. Nat Immunol 23, 186–193 (2022). https://doi.org/10.1038/s41590-021-01122-w
Miriam Merad,Catherine A. Blish,Federica Sallusto,Akiko Iwasaki,The immunology and immunopathology of COVID-19, Science, 375, 6585, (1122-1127), (2022). /doi/10.1126/science.abm8108

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Prasanta Kumar Ghosh

Department: Electrical Engineering

Email ID: prasantg@iisc.ac.in

Lab website link: https://spire.ee.iisc.ac.in/spire/

Title of the project:

Detection of Abnormal Heart Sounds / Murmurs using Signal Processing & Machine Learning Techniques

Brief Description of Project Goals and Objectives:

Auscultation of Heart Sounds requires excellent clinical examination skills and needs years of experience. Murmurs or abnormal heart sounds may be systolic, diastolic, or continuous & are produced by blood flow turbulence & are more prolonged than heart sounds. Automated identification of abnormal heart sounds or murmurs using signal processing techniques will aid in screening and early diagnosis of Valvular Heart Disorders in low-resource settings. Prof Prasanta Kumar Ghosh (Dept of Electrical Engineering) IISC in collaboration with Ai Health Highway are working on automated detection of abnormal heart sounds/ murmurs using AiSteth (Digital Stethoscope) We propose to develop a robust algorithm that will enable screening and early detection of Valvular Heart Disorders and aid newly graduated medical doctors, nurses and allied healthcare staff in primary healthcare clinic settings with no imaging facilities. The project will help the MBBS interns to work on real-world healthcare data and understand the fundamentals of machine learning and artificial intelligence and its application in healthcare.
Keywords: Machine Learning, Signal Processing, Artificial Intelligence, Data Analytics

References: 

A. Rao M V, S. BG, D. R. Megalmani, S. S. Jeevannavar and P. K. Ghosh, “Noise Robust Detection of Fundamental Heart Sound using Parametric Mixture Gaussian and Dynamic Programming,” 2021 43rd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), 2021
D. R. Megalmani, S. B. G, A. Rao M V, S. S. Jeevannavar and P. K. Ghosh, “Unsegmented Heart Sound Classification Using Hybrid CNN-LSTM Neural Networks,” 2021 43rd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), 2021

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Monto Mani

Department: Centre for Sustainable Technologies

Email ID: monto@iisc.ac.in

Lab website link: https://cst.iisc.ac.in/sudesi/

Title of the project:

Well-being achieved from earthen residences
(Funded by the British Academy, in collaboration with the University of Bath)

Brief Description of Project Goals and Objectives:

Occupant wellbeing involves an expression of mental satisfaction to the indoor environment, and is determined by various factors attributed to the occupant and the built-environment. Occupant related parameters include their sensory responses to various stimuli in the living environment, physiological functioning (thermo-regulation), attitude, social alignment, etc. Built-environment factors include intended and unintended sensory stimuli (dermal, visual, odour, etc.) effected by various building features, indoor environment quality, etc. Investigations into indoor environment quality, particular exposure to indoor toxicity, VOC’s, endocrine disrupting chemicals (EDCs), etc. is emerging and taking precedence. The current study examines the ability of diverse building typologies to regulate indoor moisture (moisture buffering) and the consequent impact on occupant health and comfort. The aim is to also examine the impact of varying moisture on indoor toxicity and the physiological/metabolic functioning (heart-rate, sweating and skin wettedness in this instance).
Keywords: Indoor environment quality, thermal comfort, moisture buffering, respiratory comfort, heart-rate, skin wettedness

References: 

P. Wolkoff and S. K. Kjærgaard, “The dichotomy of relative humidity on indoor air quality,” Environ. Int., vol. 33, no. 6, pp. 850–857, 2007, doi: 10.1016/j.envint.2007.04.004.
P. Wolkoff, “International Journal of Hygiene and Indoor air humidity , air quality , and health – An overview,” vol. 221, no. December 2017, pp. 376–390, 2018, doi: 10.1016/j.ijheh.2018.01.015.
J. Sundell, “On the history of indoor air quality and health,” Indoor Air, vol. 14, no. Suppl 7, pp. 51–58, 2004.
P. Höppe and I. Martinac, “Indoor climate and air quality. Review of current and future topics in the field of ISB study group 10,” Int. J. Biometeorol., vol. 42, no. 1, pp. 1–7, 1998, doi:10.1007/s004840050075

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Balaji Jayaprakash

Department: Center for Neuroscience

Email ID: jbalaji@iisc.ac.in

Lab website link: http://www.cns.iisc.ac.in/balaji/

Title of the project:

Developing VR Based Device for Administering Memory Tests to Measure Cognition as Function of Aging

Brief Description of Project Goals and Objectives:

Mammalian brain acquires, encodes, and consolidates memories for events and facts. Hippocampal formation is initially required for storing this information but over time these memories can be retrieved independent of hippocampus. Simultaneously hippocampus has been shown to be playing a critical role in spatial navigation. Thus, providing an opportunity to measure hippocampal function through measuring navigational ability. In this project we will be developing / administer VR based tasks to determine the ego centric and allocentric strategic components adopted by the humans during navigation. During a regular spatial navigation our brain utilizes both strategies however, the degree of preference for ego/allocentric behavior is strongly correlated with hippocampal function. In this project using vector analysis (as developed in our recent study Meenakshi et al, Hippocampus 2022) to measure this preference in a single task as a function of age in a population.
Keywords: Memory, Cognition, Egocentricity, Allocentricity, VR Task

References: 

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Saumitra Das

Department: Microbiology and Cell Biology

Email ID: sdas@iisc.ac.in

Lab website link: https://mcbl.iisc.ac.in/saumitra-das/

Title of the project:

Understanding the molecular mechanism of hepatitis C virus induced Hepato Cellular Carcinoma

Brief Description of Project Goals and Objectives:

Hepatocellular carcinoma (HCC) is one the most common type of cancers in the world causing around 83 lakh deaths world-wide per annum. One of the leading causes of HCC is cirrhosis, induced by viruses such as (Hepatitis B virus (HBV) and Hepatitis C virus (HCV). HBV being a DNA virus has been widely studied and also an effective vaccine against HBV is available. However, for HCV a complete cure still remains a challenge. Although it is possible to reduce the HCV viral load with administration of several direct acting antivirals (DAA), such as Sofosbuvir, Telaprevir etc., preventing the disease progression is a major clinical challenge in some patients. Therefore, to inhibit the disease progression, it is important to study the molecular basis of pathogenesis due to chronic infection with HCV, which often leads to HCC. Moreover, since both HBV and HCC have different modes of lifecycle, a comparative analysis of their pathogenesis would be necessary to investigate the distinctive features and different molecular players.
To investigate the same, we are planning to overexpress two major cancer-causing proteins from HCV (Core protein) and HBV (HBx protein) genomes respectively, in different liver cancer cell lines such as Huh 7, huh 7.5 and HepG2. We will further check the levels of targeted mRNAs, miRNAs and lncRNAs in these different cell lines post data compilation from TCGA database to understand how these molecules may help in cancer progression. Results can be validated in a liver organoid culture system for better understanding of the molecular mechanism of disease progression.
Keywords: Hepatitis C virus, Hepatocellular carcinoma

References: 

Sharma G, Tripathi SK, Das S*(2019) lncRNA HULC facilitates efficient loading of HCV-core protein onto lipid droplets and subsequent virus-particle release. Cellular Microbiology. 21(10):e13086. doi: 10.1111/cmi.13086. COVER PAGE Illustration

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Bikramjit Basu

Department: Materials Research Centre

Email ID: bikram@iisc.ac.in

Lab website link: https://bikramjitbasu.in/

Title of the project:

Manufacturing and clinical study of indigenously developed dental implants

Brief Description of Project Goals and Objectives:

Dental implants are used for the purpose of replacing lost teeth. Titanium alloy (Ti6Al4V) is a well-documented implant material with higher stiffness combined with equivalent biological characteristics. Along with other factors, implant design and surface topography can be factors to influence osseointegration, and hence it is necessary to evaluate the indigenously designed and surface-modified implants in a clinically controlled study with a long term follow up with an emphasis on clinical outcomes. High precision CNC machines will be used for manufacturing the IISC design dental implants followed by surface modifications, to match the commercially available control implants. The purpose of this study is to compare the clinical outcomes of indigenously designed implants with a commercially available Ti6Al4V implant. This will be a prospective, randomized and multi-centred study, in which patients in need of dental implants in the posterior maxilla and mandible will be treated with either the indigenous implant (test device) or the Straumann implant (control device). Only patients meeting the inclusion/exclusion criteria and providing informed consent forms will be enrolled in the study. The duration of the study will be approximately 1-2 years from initiation to completion of data analysis and reporting.
Keywords: Dental, biomaterial, osseointegration, clinical study

References: 

Thomé, G., Pires, S., Sallati, R.C., Cartelli, C.A., Moura, M.B., Trojan, L.C., 2019.Insertion torque of hybrid tapered implants with different types of instrumentation: An in vitro analysis and report of two cases. Journal of Osseointegration 11, 98–106.https://doi.org/10.23805/JO.2019.11.02.04
Maló, P., Lopes, A., de Araújo Nobre, M., Ferro, A., 2018. Immediate function dental implants inserted with less than 30 N·cm of torque in full-arch maxillary rehabilitations using the All-on-4 concept: retrospective study. International Journalof Oral and Maxillofacial Surgery 47, 1079–1085. https://doi.org/10.1016/j.ijom.2018.04.008
Lozano-Carrascal, N., Salomo-Coll, O., Gilabert-Cerda, M., Farre-Pages, N.,Gargallo-Albiol, J., Hernandez-Alfaro, F., 2016. Effect of implant macro-design on primary stability: A prospective clinical study. Medicina Oral Patología Oral yCirugia Bucal 21, e214–e221. https://doi.org/10.4317/medoral.21024
L. Bohner, M. Hanisch, J. Kleinheinz, S. Jung,Dental implants in growing patients: a systematic review, British Journal of Oral and Maxillofacial Surgery,Vol. 57, Issue 5,2019, pp 397-406, https://doi:10.1016/j.bjoms.2019.04.011.

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M S BOBJI

Department: Mechanical Engineering

Email ID: bobji@iisc.ac.in

Lab website link: https://mecheng.iisc.ac.in/people/m-s-bobji/

Title of the project:

Minimizing biopsy needle induced damage in soft tissues

Brief Description of Project Goals and Objectives:

Needle insertion into biological tissue is a common medical intervention technique used for drug delivery, neurosurgery, biopsy, minimally invasive surgery and robotic-assisted surgery. It is primarily a tissue cutting process and causes damage to the surrounding biological tissues. Recently, we have shown that the spikes in force encountered during hypodermic needle insertion is accompanied by periodic cone cracks. The damages due to cone cracks depend on needle geometry, insertion speed and tissue properties. In this work, we will study the tissue damages induced due to the insertion of various biopsy needles. Needle insertion experiments will be primarily carried out in tissue-mimicking transparent hydrogels. Based on the understanding from these experiments, the work will be extended to animal tissues. The overall aim of this work is to understand the needle tissue interaction during various biopsy procedures and to minimize the tissue damages.
Keywords: Soft Tissues, Tissue-mimicking hydrogels, Fracture, Biopsy needle insertion

References: 

Muthukumar M*, M S Bobji, K R Y Simha, ‘Cone cracks in tissue-mimicking hydrogels during hypodermic needle insertion: the role of water content’, Soft Matter (2022). https://doi.org/10.1039/D2SM00257D
Muthukumar M*, M S Bobji, K R Y Simha, ‘Needle insertion-induced quasiperiodic cone cracks in hydrogel’, Soft Matter (2021). https://doi.org/10.1039/D0SM02145H

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