Institutional Publications

Permanent URI for this collectionhttps://ndkr-library.nipgr.ac.in/handle/123456789/11

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Start date: 2020Has files: No

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    AtFusionDB: A comprehensive database of fusion transcripts in model plant Arabidopsis thaliana
    (Springer Nature Publishing AG, 2026) Shree, Tanu; Kumar, Shailesh
    Fusion transcripts are chimeric RNAs, produced by the joining of two different RNAs at the RNA level or as a product of gene fusion at the DNA level. In this era of high-throughput sequencing technologies, it is easy to identify novel molecules like fusion transcripts in different systems. That's because, initially, supposed to be the well-known cancer biomarkers, fusion transcripts are also validated in normal human physiology. In Planta, discrete reports are available, indicating the presence of fusion transcripts but no dedicated web resource is available for the plant-specific fusion transcripts. This chapter describes the first plant-specific database of fusion transcripts, i.e., AtFusionDB ( http://www.nipgr.res.in/AtFusionDB ), which contains the information on fusion transcripts identified in the model plant Arabidopsis thaliana. This database can be exploited to get significant information about gene/transcript fusion in plants.
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    Validation of plant fusion peptides using proteomics data
    (Springer Nature Publishing AG, 2026) Hamid, Fiza; Aftab, Sahrish; Shree, Tanu; Kumar, Shailesh
    Fusion transcripts and their fused protein products are emerging as exciting entities in molecular biology, offering potential applications in diagnostics and therapeutics. These fusion proteins, derived from the translation of fusion transcripts, hold promise as unique biomarkers and targets for intervention. While numerous algorithms exist to identify fusion RNAs, the detection and validation of their protein counterparts through proteomics remains a growing area of research. This challenge is particularly intriguing in plant biology, where fusion events may affect stress responses, development, and adaptation. This chapter provides an accessible and practical workflow for validating plant fusion peptides using publicly available proteomics datasets.
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    Geminivirus-induced reprogramming of plant defense mechanisms: molecular insights and research frontiers
    (Annual Reviews, 2026) Sharma, Namisha; Sett, Susmita; Prasad, Manoj
    Geminiviruses employ multifunctional protein ammunition to evade robust plant defense pathways. Key viral proteins effectively manipulate host signaling mechanisms to create a permissive environment for viral replication. Rapid evolutionary adaptation of geminiviruses, synergized by the proliferation of insect vectors, creates a challenge for effective disease control. Current plant resistance against geminiviruses primarily relies on antiviral RNA silencing and the localized cell death mechanism as an outcome of the hypersensitive response. To win the escalating arms race between geminivirus manipulation and subsequent plant counteracting strategies and effectively restrict viral invasion, these defense strategies need to be updated or supplemented with novel engineering approaches. In this review, we provide a critical contemporary understanding of viral reprogramming pathways and host counter-defense responses that provide new avenues to improve plant immunity against geminiviruses.
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    The intersection of AI and genomics in health and disease: Advancements and applications
    (Elsevier B.V., 2026) Kaushik, Love; Vivek, A T; Arora, Simran; Hamid, Fiza; Mukherjee, Kanka; Bisht, Niyati; Chaudhary, Sakshi; Shukla, Jagriti; Nawani, Sakshi; Kumar, Shailesh
    AI and genomics are revolutionizing precision medicine by using machine learning (ML) to analyze large-scale next-generation sequencing (NGS) data, identifying genetic mutations and biomarkers for personalized therapies. In practice, this accelerates drug discovery and enhances variant detection, while in cancer genomics, AI enables early detection via liquid biopsies and refines treatment by integrating multi-omics data to improve therapeutic precision. However, challenges such as data biases in underrepresented populations, limited model interpretability, and ethical concerns regarding privacy and algorithmic inequity hinder clinical adoption and demand robust governance. Efforts to diversify datasets also face standardization hurdles, although explainable AI and federated learning provide promising solutions for improving transparency and privacy. In this chapter, we discuss the role of AI in advancing genomics from diagnostics to novel therapies and emphasize the need for equitable frameworks to ensure responsible implementation, thereby paving the way for breakthroughs in personalized medicine.
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    Quantification of jasmonic acid and salicylic acid in plant-insect interactions
    (Springer Nature Publishing AG, 2026) Meena, Mukesh Kumar
    Plants encounter a variety of insect herbivores and have developed complex defense mechanisms against different feeding strategies. Phytohormones jasmonic acid (JA) and salicylic acid (SA) play a central role in recognizing and mounting appropriate defense response against pathogens. Primarily, JA provides resistance against chewing insect herbivores, whereas SA bolster defense against biotrophs and phloem-feeding insects (aphids and whitefly). Complex interaction of JA and SA signaling creates a plant stress memory which helps to generate elevated defense response to future insect threats. Phytohormone quantification can provide significant insights about activated plant defense response and involved signaling pathways. Here, we describe a detailed and reproducible protocol for phytohormone quantification (SA, ABA, JA, and JA-Ile) in insect-fed Arabidopsis leaves tissues. JA and JA-Ile quantification results clearly indicate their contribution in plant adaptation and defense response.
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    Insect herbivory simulation and insect bioassays to study plant stress memory response
    (Springer Nature Publishing AG, 2026) Meena, Mukesh Kumar
    Plant stress memory response is an emerging field in plant–insect interaction. Recent reports indicate phytohormone jasmonic acid (JA) triggers long-term effects on the defense phenotype, transcriptome, and DNA methylome of Arabidopsis. Long-term JA-mediated induced resistance required MYC2/3/4 transcription factors and epigenetic regulatory components that prepare plants for future insect herbivore threats. Three weeks after transient JA signaling, 5-week-old plants retained induced resistance against herbivory but showed increased susceptibility to pathogens. This mechanism is linked with long-term priming and/or upregulation of JA-dependent defense genes but repression of ethylene- and salicylic acid-dependent genes. Still more research is required to fully understand plant stress memory response in plant–insect interaction. Here, a detailed and reproducible protocol for simulated herbivory and sample collection for transcriptomic and metabolomic studies is described to investigate involved defense signaling pathways. Furthermore, the insect bioassay protocol is described to study insect performance on various plant genotypes. Both protocols are robust and could be useful to study plant stress memory response in plant defense mechanisms through simulated herbivory and direct insect performance and feeding behavior by insect bioassays.
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    Novel method for rapid screening of chickpea for combined dry root rot disease and osmotic stress
    (Springer Nature Publishing AG, 2026) Ranjan, Shubhashish; Chavan, Chaitali Narendra; Senthil-Kumar, Muthappa
    Chickpea (Cicer arietinum L.), confronts substantial challenges from the emerging pathogenic fungus Macrophomina phaseolina (Tassi) Goid, causing dry root rot (DRR) disease. Chickpea plants severely affected by combined DRR and drought stress. Currently sick plot and sick pot method are utilized for germplasm screening to identify tolerant genotypes. These methods are time-consuming; therefore, we propose a novel methodology for the rapid screening of chickpea under combined DRR and osmotic stress conditions. This chapter introduces an adept high-throughput phenotyping methodology, conducted within controlled laboratory conditions, aiming to investigate the interaction between osmotic stress and DRR disease in chickpea crops. The methodology employs an innovative pouch technique for screening combined stress, providing a streamlined temporal investigation process and precise control over stress parameters. The incorporation of polyethylene glycol (PEG) enables the simultaneous imposition of osmotic stress alongside pathogen infection, making the methodology versatile for studying combined stress scenarios. This approach fills a gap in concurrent stress imposition techniques, enhancing germplasm screening by identifying genotypes with varying susceptibility and resistance levels. Thus, we suggest use of high-throughput phenotyping in combination genome-wide association study (GWAS) can take combined stress resistance breeding in chickpea at next level to combat food security and climate change.
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    A guide to culturing, maintenance, and leaf inoculation methods for rapid screening and quantification of sclerotinia sclerotiorum infection in mustard
    (Springer Nature Publishing AG, 2026) Malhotra, Bhanu; Tiwari, Ruchi; Varghese, Mohan; Bisht, Naveen C.
    Sclerotinia rot poses a significant challenge to the cultivation of oilseed Brassica crops, causing the reduction of seed number, weight, and quality leading to >95% yield losses globally. Due to its substantial economic impact on agriculture, Sclerotinia sclerotiorum has been extensively studied at the molecular level and has now been adopted as a model to investigate the host-pathogen interactions. Despite various procedures and strategies described in different reports, there exists a considerable disparity in how the pathogen is cultured, maintained, and manipulated across studies.This chapter provides a comprehensive guide to the fundamental procedures of working with S. sclerotiorum. It describes step-by-step methods for its routine culturing and maintenance over artificial media, replenishing and storing laboratory stocks, and conducting detached leaf assays-a robust method used for screening the mustard cultivars. Additionally, we outline the quantification of pathogen load in planta through qRT-PCR analysis. The methods presented in the current chapter are reproducible and can be suitably applied when working with different isolates of the pathogen.Through the present compilation, we aim to address the research gaps in methods involving the pathogen that would not only benefit the new researchers entering the field but also future research endeavors on white mold.
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    Interspecific hybridization using cicer microphyllum royle ex benth. for the genomic reconstruction of cultivated chickpea (Cicer arietinum L.)
    (Springer Nature Publishing AG, 2026) Kumari, Pummi; Singh, Mohar; Gayacharan; Shivam; Parida, Swarup K.
    Cicer microphyllum, native to cold and arid regions, offers a reservoir of beneficial alleles, including tolerance to biotic and abiotic stresses. It is a wild Cicer species from the tertiary gene pool of the cultivated chickpea. It has the potential to enhance the genetic base of cultivated species and provide useful genetic variability for crop improvement. Despite significant reproductive barriers, advancements in hybridization techniques and genomic tools have facilitated the development of viable hybrids between C. arietinum and C. microphyllum. The genomic reconstruction of the cultivated chickpea through the transfer of wild relative's genomic segments using backcrossing and molecular marker-assisted selection will help sustainable crop improvement and genetic gains.
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    Isolation of cytoskeleton and cytoskeleton-bound polysome, and identification of cytoskeletal proteins from a grain legume
    (Springer Nature Publishing AG, 2026) Kumar, Sunil; Chakraborty, Sohela; Chakraborty, Subhra; Chakraborty, Niranjan
    The plant cytoskeleton is an essential component of cellular architecture, enabling various critical metabolic processes, including cell division, differentiation, expansion and intracellular transport. It consists primarily of three distinct filamentous structures: microtubules, microfilaments and intermediate filaments. These structures are not static; they undergo continuous remodeling in response to environmental signals and developmental cues, which allow plants to adapt to changing conditions. The microtubules and actin filaments have previously been successfully isolated from various plant tissues, contributing to our understanding of their functions. Among the diverse plant families, legumes (Fabaceae) stand out as the third largest, encompassing approximately 20,000 species. They hold significant agricultural importance, ranking second to cereals in global crop production. To fully grasp the developmental and adaptive processes in legumes, it is essential to identify and understand their regulatory components. This chapter focuses on the isolation of cytoskeletal proteins from chickpea, a prominent grain legume, facilitating biochemical and proteomic analyses that may uncover new insights into the functioning of the cytoskeleton in legumes.