Publications of NIPGR Scientists
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Item Reimagining plant science training in the era of generative AI: A global perspective(Oxford University Press, 2026) Moghe, Gaurav; Zimic-Sheen, Alen; Chen, Dijun; Yadav, Gitanjali; Cao, Guangshuo; Tufan, Hale; Williams, Jason; Szymański, Jędrzej; Kim, Jeongwoon; Busta, Lucas; Mutwil, Marek; Verdu, Miguel; Zimic, Mirko; Provart, Nicholas J; Makunga, Nokwanda; Wilkins, Olivia; Sun, Qi; VanBuren, Robert; Marks, Rose A; Rhee, Seung Y; Jiang, Yu; Xie, YuyingIn recent years, a deluge of big and diverse datasets from hundreds of plant species coupled with spectacular innovations in artificial intelligence (AI) and generative AI (GenAI), has altered the landscape of plant science. These developments are increasingly democratizing the field, reducing the entry barriers to complex data analysis and enabling a new wave of innovative research while introducing new challenges. Therefore, in this era, it is critical that we train the next generation of plant scientists to be AI-literate, i.e., not only proficient in using AI but also vigilant about its pitfalls and biases. In this Perspective, we call for six strategic shifts necessary for training the next generation of plant scientists. We argue that while maintaining a core focus on subject expertise, educators should simultaneously emphasize development of new AI-forward pedagogical and evaluation frameworks that reward interdisciplinary and critical thinking, human-driven knowledge synthesis, self-directed learning, and conceptual understanding of workflows. For effective critique and sound interpretations based on biological reality, plant scientists must be explicitly trained in recognizing biases underlying GenAI models. Finally, we highlight the structural barriers hindering the equitable and ethical use of GenAI, where awareness and resolution is critical for sustainable growth of the field. Through the above conceptual framework and numerous plant-science focused illustrative activities, examples, and resources meant for students and educators alike, this Perspective defines high-level emphasis areas for GenAI-enabled scientific training, aimed at creating a more effective, engaged, and adaptive community of plant scientists.Item Global bibliometry on three decades of methyl jasmonate-induced plant defense research reveals growth of a specialty area in biology(Open Science Publishers LLP, 2025) Chugh, Vipul; Kumari, Kamlesh; Yamal, Gupta; Checker, Vibha Gulyani; Yadav, Gitanjali; Kathpalia, RenuMethyl jasmonate (MeJA), a naturally existing plant hormone, acts as a vital defense and signaling molecule. Although this hormone has been discovered recently, published reports spanning the last several decades have shown the pleiotropic effects of the hormone raising numerous questions about its regulation, biogenesis, and mode of action. In this work, we explore the complete scientific research on MeJa from its discovery in 1992, spanning research conducted over three decades, through a complex network analysis of 2,542 documents authored by about 9,000 individuals. Several indicators of research progress were evaluated, including co-authorship networks, keyword thematic maps, indices of national and international collaboration, annual scientific production, and most productive affiliations. These indices not only enabled us to evaluate the importance of a specialty discipline in literature but also the place of nations in determining research directionality and the significance of quality of work. Overall, this bibliometric analysis identifies current research trends in a specialty area in biology and we hope that our work would pave the way for greater international collaborations among researchers and a better understanding of research gaps and future scope of work in the actively expanding field of MeJA induced plant defense, stress, and developmental processes.Item Data for development and the role of CODATA of the International Science Council (ISC)(NATL INST SCIENCE COMMUNICATION-NISCAIR, 2024) Selematsela, Daisy; Mujoomunshi, Usha; Yadav, GitanjaliWhile the discussion on data for development gains traction in society especially with the focus on Sustainable Development Goals(SDGs), there is the need for more insight into the long-standing global perspectives on data and information for science. The International Science Council (ISC) established in 1932 as International Council for Scientific Unions (ICSU) aims to strengthen international science for the benefit of society. The key principle is the "Universality of Science"1which interprets science as a collective effort working for the common good, but a growing number of scientists, policy-makers, and social scientists argue that science is often too isolated from society to fulfil this promise. This brings in the concept of 'Open Science' to close the gap between science and society by democratizing scientific knowledge, for the benefit of everyone. The Committee on Data (CODATA), an interdisciplinary body of ISC is the focus of this paper, along with recent perspectives regarding its role and needs of science in the present information-driven society.Item The #semantic climate community: making open-source software for knowledge liberation(NATL INST SCIENCE COMMUNICATION-NISCAIR, 2024) Yadav, Gitanjali; Hegde, Shweata; Kumari, Renu; Kumari, Neeraj; Murray-Rust, Peter; Worthington, Simon#semantic Climate is an international open research community led by young Indian scientists who use Open Notebook Science to transform information into structured filtered and actionable knowledge. The key project mission is to liberate scientific climate data, making it equitable and freely accessible to everyone. The #semantic Climate community achieves this through two central activities, namely collaborative open notebook science, and citizen engagement. The first activity is research oriented and involves creation of a proof-of-concept software toolkit that uses AI over NLP to transform locked literature (such as PDF documents) into semantic, hypermedia form. This is a non-trivial task, that has haunted developers for over three decades, and the #semantic Toolkit makes complex climate reports not just easily accessible, but also processable by machines, embedded in the Global Knowledge Graph and thereby connected to multilingual resources. The second activity is where the #semantic Climate community engages citizens in climate action and awareness through interactive hackathons, open and transparent working practices, and using Git versioning. From a citizen science perspective, this includes designing community outreach activities (games), giving attribution to all participants, and engaging the wider public in the culture and practices of science (verifiable knowledge, review, data science, modern infrastructure use, etc). This article is an overview of the #semantic Climate community building efforts, and how the project employs strategies, techniques, and ideas from the fields of Open Notebook Science. The open-source software culture and projects follow UNESCO Open Science values, and knowledge justice for the Global South, towards addressing knowledge neo-colonisation.Item AI & ethics: charting a responsible future(NATL INST SCIENCE COMMUNICATION-NISCAIR, 2024) Yadav, Gitanjali; Munshi, Angad; Kumari, Renu; Singh, Dhananjay; Kumari, Neeraj; Munshi, Usha MujooArtificial intelligence (AI) is rapidly transforming the world, but its development and deployment raise critical ethical questions. This paper explores the key themes that emerged from a national conclave on AI and Ethics in India, bringing together industry and academic leaders. We examine the potential of AI for various sectors, with a thematic case study for the Genome Biology sector, alongside concerns about bias, privacy, and accountability. AI development and use, while underscoring the need for an ethical framework to guide its evolution, emphasizes the need for collaboration between academia and industry to develop ethical frameworks and translate principles into practical applications. In summary, ethical AI may serve as a moral framework of AI technologies to ensure that our technological capability aligns with fundamental societal values and human dignity on the road to progress. This framework by definition would not be a static set of commandments but a dynamic constantly evolving idea about the use of technologies like AI.Item Editorial: Plant transcription factors associated with abiotic stress tolerance in crops and wild-relatives(Frontiers Media S.A., 2024) Puglia, Giuseppe Diego; Frugis, Giovanna; Yadav, GitanjaliEditorial on the Research Topic Plant transcription factors associated with abiotic stress tolerance in crop and wild-relatives Global climate change (GCC), by altering the intensity and frequency of potentially damaging weather events such as droughts, waterlogging, heat waves, and cold spells, has altered seasonal weather patterns, causing severe problems for plant crops and wildlife species (Cramer et al., 2011; Asseng et al., 2015; Minoli et al., 2019). To cope with these challenges, plants have evolved complex regulatory mechanisms that enable them to respond and adapt to changing environmental conditions, while maintaining a balance between optimal growth and stress (Eckardt et al., 2023). This Research Topic brings together several contributions that highlight the role of transcriptional regulation in plant responses to abiotic stresses and hypothesise its role in stress tolerance. The studies published in this Research Topic deal with well-recognised groups of transcription factors (TFs), but also with new ones whose association with the response to abiotic stresses has been demonstrated by recent molecular advances. This evidence allows us to shed light on the mechanisms by which plants respond to different stresses, with a focus on abiotic stresses such as salt, drought, cold, and waterlogging.Item Role of transcriptional regulation in auxin-mediated response to abiotic stresses(Frontiers Media S.A., 2024) Marzi, Davide; Brunetti, Patrizia; Saini, Shashank Sagar; Yadav, Gitanjali; Puglia, Giuseppe Diego; Dello, Ioio RaffaeleGlobal climate change (GCC) is posing a serious threat to organisms, particularly plants, which are sessile. Drought, salinity, and the accumulation of heavy metals alter soil composition and have detrimental effects on crops and wild plants. The hormone auxin plays a pivotal role in the response to stress conditions through the fine regulation of plant growth. Hence, rapid, tight, and coordinated regulation of its concentration is achieved by auxin modulation at multiple levels. Beyond the structural enzymes involved in auxin biosynthesis, transport, and signal transduction, transcription factors (TFs) can finely and rapidly drive auxin response in specific tissues. Auxin Response Factors (ARFs) such as the ARF4, 7, 8, 19 and many other TF families, such as WRKY and MADS, have been identified to play a role in modulating various auxin-mediated responses in recent times. Here, we review the most relevant and recent literature on TFs associated with the regulation of the biosynthetic, transport, and signalling auxin pathways and miRNA-related feedback loops in response to major abiotic stresses. Knowledge of the specific role of TFs may be of utmost importance in counteracting the effects of GCC on future agriculture and may pave the way for increased plant resilience.Item Cavity architecture based modulation of ligand binding tunnels in plant START domains(Elsevier B.V., 2023) Mahtha, Sanjeet Kumar; Kumari, Kamlesh; Gaur, Vineet; Yadav, GitanjaliThe Steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domain represents an evolutionarily conserved superfamily of lipid transfer proteins widely distributed across the tree of life. Despite significant expansion in plants, knowledge about this domain remains inadequate in plants. In this work, we explore the role of cavity architectural modulations in START protein evolution and functional diversity. We use deep-learning approaches to generate plant START domain models, followed by surface accessibility studies and a comprehensive structural investigation of the rice START family. We validate 28 rice START domain models, delineate binding cavities, measure pocket volumes, and compare these with mammalian counterparts to understand evolution of binding preferences. Overall, plant START domains retain the ancestral α/β helix-grip signature, but we find subtle variation in cavity architectures, resulting in significantly smaller ligand-binding tunnels in the plant kingdom. We identify cavity lining residues (CLRs) responsible for reduction in ancestral tunnel space, and these appear to be class specific, and unique to plants, providing a mechanism for the observed shift in domain function. For instance, mammalian cavity lining residues A135, G181 and A192 have evolved to larger CLRs across the plant kingdom, contributing to smaller sizes, minimal STARTs being the largest, while members of type-IV HD-Zip family show almost complete obliteration of lipid binding cavities, consistent with their present-day DNA binding functions. In summary, this work quantifies plant START structural & functional divergence, bridging current knowledge gaps.Item Quantification of pollen viability in Lantana camara by digital holographic microscopy(Cambridge University Press, 2023) Kumar, Vipin; Goyal, Nishant; Prasad, Abhishek; Babu, Suresh; Khare, Kedar; Yadav, GitanjaliPollen grains represent the male gametes of seed plants and their viability is critical for sexual reproduction in the plant life cycle. Palynology and viability studies have traditionally been used to address a range of botanical, ecological and geological questions, but recent work has revealed the importance of pollen viability in invasion biology as well. Here, we report an efficient visual method for assessing the viability of pollen using digital holographic microscopy (DHM). Imaging data reveal that quantitative phase information provided by the technique can be correlated with viability as indicated by the outcome of the colorimetric test. We successfully test this method on pollen grains of Lantana camara, a well-known alien invasive plant in the tropical world. Our results show that pollen viability may be assessed accurately without the usual staining procedure and suggest potential applications of the DHM methodology to a number of emerging areas in plant science.Item Metabolomics and molecular physiology perspective for drought and salinity stress tolerance(Taylor & Francis Group, 2022) Jadhav, Sagar Sudam; Kumari, Renu; Mahtha, Sanjeet Kumar; Purama, Ravi Kiran; Lamba, Vinita; Yadav, GitanjaliAmong abiotic stresses, drought and salinity are mainly affecting crop production. Reactive oxygen species are produced during most of abiotic stresses and can damage cellular components. Therefore, plants produce specific antioxidants (e.g. carotenoids, xanthophylls), metabolites (e.g. flavonoids, phenols), osmoregulatory solutes (e.g. proline, sucrose) and thylakoid stabilizing isoprenes. Plant metabolic networks are complex, and excessive demand for these stress-responsive metabolites during abiotic stress is met only by reconfiguring the metabolic network. This chapter mainly discusses drought and salt stress-specific plant metabolomic and molecular responses and gives insights into signaling network involved thereof. Metabolomics combined with conventional breeding approaches (using introgression lines) has proven to be able to map abiotic stress-responsive loci and key candidates. The role of kinases and argonautes and the prospecting of stress-responsive metabolic quantitative trait loci and alleles are also discussed. The importance of amino acid and hormone metabolism and its connection with epigenetics is reviewed.