Ashoka International Summer Research Programme (AISRP)

Optimising workflow for tissue specific knockdown of cytoskeletal genes in C. elegans

Faculty: Anup Padmanabhan, Assistant Professor of Biology, Co-ordinator (Ph.D. program in Biology) Ashoka University

Co-supervisor name: NONE

Department/Research Centre: Biology

Project Description: C. elegans is a widely used model organism to study various questions in cell biology. This project requires participant to (1) generate C.elegans strains that is capable of tissue specific RNAi mediated knockdown of target genes , (2) cloning of RNAi plasmid containing specific fragments of genes to be knocked down, (3) validation of the tissue specific knockdown of some of these genes

The participant will be trained to handle C. elegans, C. elegans genetics, PCR, cloning and basic microscopy for estimating knockdown efficiency. A prior experience in any of the techniques above will make it easier and faster to accomplish the goals.

Duration (in weeks): 10 weeks (15 June – 24 August)

Start date: 6/15/2025.

End date: 8/24/2025

Level of Interns: Senior Undergraduates or Master’s Students

Max Number of interns accepted on this project: 1

Project type: Lab project

Technical skill/knowledge requisites: Basic Cell Biology, experience in molecular biology is added advantage.

Quantitative and economic social choice behaviour in zebrafish

Faculty: Bittu K R, Associate Professor of Biology and Psychology

Co-supervisor name: NONE

Department/Research Centre: Biology and Psychology

Project Description: The overall goal of these projects is to examine the ways in which quantitative cognition functions in the zebrafish system. One set of projects looks at economic rationality in zebrafish social decision making relative to decoy effects, internal hunger states and social boldness. A second project works on movement perception and quantitative cognition by zebrafish larvae in the context of social decision making as well as foraging and predator evasion. A third project looks at stress and social choices, to explore the ways in which stress impacts various traits we are interested in zebrafish: learning, social decision making, and foraging behaviour. We use stressful dominance/submissive dyadic interactions, social isolation, neuroinflammation and chronic unpredictable early life stress protocols to look into the mechanisms behind stress-induced analgesia and resilience in zebrafish larvae as well. A fourth project quantifies optimism bias in an animal model and set up an assay for how various factors influence that bias. A fifth project quantifies the ecological dis/advantages and metabolic markers of depressive behaviour to quantify the ecological costs and benefits of different behavioural strategies in zebrafish.

Duration (in weeks): 8 weeks (between May – August)

Start date: 5/20/2025

End date: 8/12/2025

Level of Interns: Senior Undergraduates or Master’s Students

Max Number of interns accepted on this project: 3

Project type: Combination of field & lab project

Technical skill/knowledge requisites: Just enthusiasm is required – any additional skills or knowledge is a bonus but not a prerequisite.

Trustworthy AI

Faculty: Aalok Thakkar, Associate Professor of Computer Science

Co-supervisor name: NONE

Department/Research Centre: Computer Science

Project Description: Several concerns about large language models (LLMs) persist, particularly regarding their robustness against adversarial inputs, data privacy, and structured reasoning capabilities. This project aims to address these challenges through a comprehensive compositional verification framework. The primary objective is to decompose the correctness specification into distinct correctness criteria for each layer of the LLM architecture. By developing verification methods tailored to these individual layers, we can establish an assume-guarantee style verification process that ensures each component meets its specified requirements. This modular approach not only facilitates easier debugging and maintenance but also strengthens the overall security posture of LLMs by enabling targeted interventions in identified vulnerable areas. In particular, the project will focus on verifying the robustness of LLMs against adversarial attacks, ensuring that they can withstand unexpected inputs without compromising their functionality or integrity. Additionally, we will explore methods to safeguard data privacy, employing formal techniques to prevent leakage of sensitive information during model training and inference. The project offers opportunities for senior undergraduates and master’s students from diverse backgrounds to engage in literature reviews, algorithm development, implementation, and research. By participating in this initiative, students will gain practical skills in compositional verification and AI while contributing to the advancement of robust and privacy-preserving technologies.

Duration (in weeks): 10 weeks (between June – August)

Start date:5/15/2025

End date: 8/24/2025

Level of Interns: Senior Undergraduates or Master’s Students

Max Number of interns accepted on this project: 3

Project type: Online

Technical skill/knowledge requisites: Familiarity with LLM architecture and fundamentals of verification, strong programming skills

Access to Health Insurance and Health behavior

Faculty: Aparajita Dasgupta, Associate Professor of Economics

Co-supervisor name: NONE

Department/Research Centre: Economics

Project Description: In this project we aim to investigate how access to health insurance bears upon health investments in both curative as well as preventive healthcare and child health outcomes in the developing country setting.

Duration (in weeks): 10 weeks (between June – August)

Start date: 5/21/2025

End date: 8/21/2025

Level of Interns: Senior Undergraduates or Master’s Students

Max Number of interns accepted on this project: 3

Project type: Online

Technical skill/knowledge requisites: Knowledge pf Stata, Python, GIS Skills would be a bonus. Data analysis using stata/R and helping with manuscript preparation including reviewing literature, adding collated results on Latex, Copy editing of draft, finding new datasets relevant for the project Students should be proficient in data handling using stata or R and should have a working knowledge of latex. GIS skills would be greatly appreciated. Interested applicants should send their CV and a writing sample that has used data analysis. Applicants will be shortlisted based on a stata-based test. Experience with large scale household surveys will be good.

Impact of free-ranging dogs on a carnivore community in the Indian Himalaya

Faculty: Manvi Sharma, Assistant Professor, Environmental Studies,

Co-supervisor name: Pooja Chand

Department/Research Centre: Environmental Studies

Project Description: Land-use change is modifying wildlife habitats at unprecedented rates and studies predict that most of the wildlife is likely to be redistributed globally in this century. Changing land-use patterns has consequences for the behaviour, ecology, and abundance of wildlife populations, especially for large mammalian carnivores. A major anthropogenic stressor affecting carnivore populations is the threats posed by populations of free-ranging dogs in rapidly urbanising mountains. Current research suggests that free-ranging dogs not only compete indirectly with native carnivores over prey, but have direct effects, such as killing and attacking mesocarnivores, such as red fox. We lack in our understanding of overall community-wide impact of dogs on carnivore communities. This study aims to investigate the impact of free-ranging dog populations on the carnivore community in Himalaya. The study involves using camera-traps and playback speakers to quantify the nature of behavioural responses of carnivores to dog barks. The study will be conducted at our field site in Great Himalayan National Park (GHNP) in Himachal Pradesh. The GHNP region is home to a complex carnivore community including snow leopards, common leopard, brown bear, black bear, yellow-throated marten, red fox, civet, leopard card, and jungle. The student will deploy camera-traps paired with playback speakers which will play dog calls. The videos will be transcribed to quantify carnivore response of the species mentioned above. This study will help us in understanding how dogs might have a diverse range of consequences on the carnivore community in Himalaya. Through this study the student will gain experience in conducting camera-trapping surveys to study wild carnivore populations, such as snow leopards. The student will experience how a research question is framed and an ecological field study is designed to address the question. The student will learn how camera-trap data are analysed for making inferences using statistical models.

Duration (in weeks): 10 weeks (15 June – 24 August)

Start date: 6/15/2025

End date: 8/24/2025

Level of Interns: Senior Undergraduates or Master’s Students

Max Number of interns accepted on this project: 2

Project type: Field project

Technical skill/knowledge requisites: Motivation to travel to a remote mountain valley

Understanding elephant vocalizations

Faculty: Meghna Agarwala, Assistant Professor, Environmental Studies,

Co-supervisor name: Shikhar Srivastava

Department/Research Centre: Environmental Studies

Project Description: Human-elephant conflict (HEC) is a leading source of elephant mortality across the world and managers are increasingly focused on mitigating HEC. Because a large number of deaths are caused by sudden encounters between humans and elephants, the Forest Department is interested in working with us to develop an early warning signal to prevent sudden encounters. For this, we expect to collect acoustic recordings of elephant vocalizations at different elephant densities and in different habitats to develop a Convolution Neural Network (CNN) to detect elephant presence at a distance of ~3 km. Further, in order to deploy an early warning system that is effective in mitigating HEC, we need to understand how local residents negotiate HEC. We will conduct social surveys in villages adjoining our study areas to understand perceptions towards HEC and identify villages where conflict is only due to damages, as opposed to those where conflict is due to other under-lying and deep-rooted causes. We will work with villages to devise a deployment strategy for the early warning system. For villages where conflict has other deep-rooted causes, our surveys will inform us on best strategies to supplement our early warning system in mitigating HEC.

Duration (in weeks): 8 weeks (May – August)

Start date:07/01/2025

End date:8/31/2025

Level of Interns: Senior Undergraduates or Master’s Students

Max Number of interns accepted on this project: 2

Project type:Combination of field & lab project

Technical skill/knowledge requisites: Analyse data in lab.

Documentary on environmental history of India--as unearthed by paleo-sciences

Faculty: Meghna Agarwala, Assistant Professor, Environmental Studies,

Co-supervisor name: Jishnu Borgohain

Department/Research Centre: Environmental Studies

Project Description: Natural systems are dynamic and not static, and are influenced by historical legacies. Our work in Central India finds that forests have long been burned, and forests may have been co-created by humans. We would like a David Attenborough-style documentary made on the work, its findings and implications for understanding human-nature relations. Students can take fresh footage at our field station in Pachmarhi and interview traditional forest burners as well.

Duration (in weeks): 8 weeks (May – August)

Start date: 5/15/2025

End date: 7/15/2025

Level of Interns: Senior Undergraduates or Master’s Students

Max Number of interns accepted on this project: 2

Project type:Combination of field & lab project

Technical skill/knowledge requisites: Media, documentary film-making/long-form journalism.

Measure the magnetic hysteresis loop of a magnetic hetero structure using MOKE magnetometry

Faculty: Susmita Saha, Assistant Professor of Physics

Co-supervisor name: NONE

Department/Research Centre: Physics

Project Description: Studying the magnetization reversal of the magnetic hetero structures provides insights into their magnetic behavior, allowing for the optimization and tailoring of their magnetic properties. This knowledge aids in the design of improved high performance high-performance spintronic devices . The student need to use the magneto optical Kerr microscope set up present in the Complex magnetic characterization lab at Ashoka University to measure the hysteresis loop of a ferromagnetic hetero structure. The student also need to simulate the observations with the help of micromagentic simulator to explain the results.

Duration (in weeks): 8 weeks (between May – August)

Start date: 6/15/2024

End date: 8/10/2024

Level of Interns: Senior Undergraduates or Master’s Students

Max Number of interns accepted on this project: 1

Project type: Lab project

Technical skill/knowledge requisites: basic knowledge of Condensed matter Physics, and programming

Understanding domestic violence using the lens of complex trauma

Faculty: Simantani Ghosh, Assistant Professor of Psychology

Department/Research Centre: Psychology

Project Description: Violence against women, particularly in the form of Intimate Partner Violence (IPV), remains a grave concern worldwide. IPV not only inflicts physical harm but also leaves enduring psychological repercussions. The World Health Organization reported that, as of 2018, approximately one in three women globally experienced physical and/or sexual violence from an intimate or non-intimate partner. In India, Intimate Partner Violence takes on a broader dimension and has to be defined in terms of domestic violence (DV). DV in the South Asian context is deeply entrenched in cultural norms that subordinate women to men, reflecting prevalence rates similar to global figures. However, the nature of abuse extends beyond the conventional understanding of IPV, as Indian women often cohabit with not just their spouses but also marital relatives who can be perpetrators. Emergent data suggests that domestic violence among married women reportedly doubled between 2014-15 and 2019, despite NFHS surveys more or less replicating the WHO statistics (1 in 3 women, approximately) with respect to DV exposure. Episodic framing of issues pertaining to domestic violence, as is common in the literature, fails to capture the nuanced psychological consequences of sustained, and repetitive domestic violence. Researchers argue for a continuous trauma framework to better map the pervasive and chronic nature of domestic violence in India. The complex trauma theory, initially developed for childhood sexual abuse survivors, emerges as a relevant lens for understanding the multilayered trauma experienced by Indian women. Complex trauma theory posits that prolonged, inescapable trauma results in psychological disturbances beyond those defined by the clinical construct of PTSD. For Indian women, the pervasive environment of control, oppression, and abuse throughout childhood, adolescence, and adulthood aligns with the criteria of complex trauma. Our preliminary data (unpublished) also suggests that ever partnered Indian women trapped in abusive relationships often display psychological disturbances that are well aligned with the disorders of self organization (DSO) cluster of symptoms that complex trauma theory accommodates, that include interpersonal disturbances, negative self concept and extensive somatic symptoms. In this study we ask the overarching question whether Complex Trauma theory can be utilized to investigate consequences of domestic violence in ever partnered adult Indian women.

Duration (in weeks): 10 weeks

Start date: 6/15/2025

End date: 8/24/2025

Level of Interns: Senior Undergraduates or Master’s Students

Max Number of interns accepted on this project: 3

Project type: Online

Technical skill/knowledge requisites: Psychometric theory, null hypothesis testing, multiple regression, mediation and moderation

Impact of habitat degradation on small mammal microbiome

Faculty: Balaji Chattopadhyay,  Assistant Professor, Trivedi School of Biosciences

Co-supervisor name: NONE

Department/Research Centre: Trivedi School of Biosciences

Project Description: One of the unintended consequences of human mediated habitat destruction is the potential threat to humans and livestock from emerging zoonotic diseases. With the frequency of zoonotic diseases increasing significantly in the past two decades, understanding the potential causes of spillovers and anticipating hotspots for future outbreaks can collectively help in disease prevention thereby saving thousands of lives as well as financial resources. Among mammals, bats and rodents arguably harbor most diverse array of viruses with the potential for transmission into humans and other wildlife. They form a unique study system to investigate mechanisms of infection avoidance and to identify factors that facilitates spill-over of pathogens.

To accurately predict future zoonotic outbreaks, one needs to first understand the causes and mechanisms of spillover, particularly the association between climate change (including habitat alterations), biodiversity and pathogen movement. While our knowledge in this regard is improving, identifying the exact variables and their interactions has proven difficult. Both climate change and habitat degradation have been implicated to interact with species biology in aiding spillover through intermediate hosts such as livestock. The main research aim is to understand the impact of habitat degradation and climate change on small mammal microbiome community and transmission of pathogens between hosts.

Duration (in weeks): 10 weeks (15 June – 24 August)

Start date: 6/15/2025

End date: 6/15/2025

Level of Interns: Senior Undergraduates or Master’s Students

Max Number of interns accepted on this project: 2

Project type: Combination of field & lab project

Technical skill/knowledge requisites: Knowledge of R and command line is helpful

Mapping diversity in viral epitopes recognised by human CD8 T cells

Faculty: Rama Akondy,  Assistant Professor of Biology

Co-supervisor name: NONE

Department/Research Centre: Trivedi School of Biosciences

Project Description: CD8+ T cells are crucial for detecting and eliminating infected or abnormal cells by recognizing viral epitopes presented on MHC class I molecules. The diversity of Human Leukocyte Antigen (HLA) alleles across populations significantly shapes the range of viral epitopes recognized by CD8+ T cells. India, with its considerable genetic diversity, has a unique distribution of HLA alleles that may influence immune responses to various viral infections. This project aims to identify widely expressed HLA alleles in Indian populations and map the diversity of viral epitopes recognized by CD8+ T cells. The study will involve mining immunological databases such as the Immune Epitope Database (IEDB) to extract viral epitopes that bind to the most prevalent HLA alleles in India. Special focus will be given to understanding how these differences in HLA alleles influence immune responses to viral infections. Viruses such as Respiratory Syncytial Virus (RSV), Influenza, SARS-CoV-2, and Dengue are of particular interest, but the student may choose to explore others that are relevant to the Indian context. The project will begin by identifying the most widely expressed HLA alleles in Indian populations through analysis of genetic studies and databases. Following this, viral epitopes from the selected viruses will be retrieved, and their binding affinities to the identified HLA alleles will be analyzed using computational tools. This will help determine which viral peptides are likely recognized by CD8+ T cells in India and highlight differences in immune recognition based on HLA diversity. The study will also differentiate between conserved epitopes, which are recognized across various populations, and those that vary based on HLA allele types, providing insights into population-specific immune responses.

Duration (in weeks): 6 weeks (15 June – 24 August)

Start date:07/01/2025

End date: 8/23/2025

Level of Interns: Senior Undergraduates or Master’s Students

Max Number of interns accepted on this project: 1

Project type: Online

Technical skill/knowledge requisites:Basic understanding of the immune system, MHC and ability to use computational tools such as IEDB is preferred.

Functional RNA in the phase-separated environment

Faculty: Sandeep Ameta, Assistant Professor of Biology Assistant Professor of Biology ,  

Co-supervisor name: NONE

Department/Research Centre: Biology

Project Description: Liquid-liquid phase separation (LLPS) is a notable feature of biological systems and plays a crucial role in spatiotemporal regulation. Furthermore, by acting as reaction crucibles, phase-separated droplets have also been assumed to play a major role in the emergence of life on early Earth. LLPS involves various non-covalent interactions, such as π- π, dipole-dipole, and hydrogen bonding, between biomolecules, resulting in a condensed internal microenvironment inside these phase-separated droplets. In vitro, such a complex environment can be mimicked by the phase separation of different polymers, including RNA and peptides, resulting in ‘liquid-like’ droplets. Even though these droplets support various biomolecular functions, we lack a comprehensive and quantitative understanding of how the internal heterogeneous and crowded environment influences the dynamics of biomolecules.
Employing various biochemical and biophysical approaches, our lab is interested in a quantitative understanding of parameters governing the dynamics of structured and functional RNAs in the complex environment of liquid-liquid phase separation. Furthermore, we also exploit these phase-separated droplets as a protocell model to address some pertaining questions regarding the emergence of evolvable systems in the context of the origins of life.

Duration (in weeks): 8-10 weeks (June -August with flexible dates )

Start date: 6/1/2025

End date: 8/16/2025

Level of Interns: Senior Undergraduates or Master’s Students

Max Number of interns accepted on this project: 1

Project type: Lab project

Technical skill/knowledge requisites: Biochemistry or Molecular Biology or Biophysics