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Thapar Institute of Engineering & Technology (TuDR)

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TuDR is the digital asset management system which integrates the intellectual output in the form of research articles, PhD theses, and M.Tech / M.E. theses. TuDR facilitates the sharing and exchange of intellectual output of the university.

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Recent Submissions

In Silico Approach for Identifying Small-Molecule Inhibitors of Cytochrome bd Oxidase in Mycobacterium tuberculosis
(2026-10-11) Virdi, Anshita; Qadri, Ovais Shafiq
Tuberculosis (TB), caused by Mycobacterium tuberculosis, is a major health concern all over the globe due to the presence of drug-resistant strains and the prolonged duration of existing treatment regimens. The bacterial electron transport chain (ETC) plays a pivotal role in energy generation and also the survival of M. tuberculosis, particularly under hostile host conditions. Cytochrome bd oxidase, a terminal oxidase of the ETC, is essential for bacterial persistence and has emerged as a promising therapeutic target. This study employs an in-silico drug discovery approach to identify potential small-molecule inhibitors of mycobacterial cytochrome bd oxidase. A comprehensive dataset of small molecules was gathered from publicly available databases including Keyorganics, Otava Chemicals, HTS Biochemie, ASINEX and an in-house library of CSIR-IIIM Jammu was also used. Preparation of the ligands was performed using the LigPrep module of the Schrödinger suite, while the crystal structure of cytochrome bd oxidase (PDB ID: 7NKZ) was prepared using the Protein Preparation Wizard. Potential binding pockets were recognized using the Sitemap module, followed by receptor grid generation by using glide module of the Schrödinger suite. Virtual screening was performed using Glide through a hierarchical docking protocol comprising HTVS, SP, and XP docking modes. The top 10% compounds were subsequently selected for molecular docking analysis. The most promising protein–ligand complexes were further examined by performing molecular dynamics simulations with the Desmond module to assess structural stability and interaction persistence. Binding free energy values were determined using the Prime MM-GBSA method based on simulation trajectories and after this ADMET analysis was executed by using webbased software like SwissADME and ProTox3.0. This integrated computational workflow identified several small molecules exhibiting strong binding affinity, stable interactions within the active site, favourable binding free energy profiles as well as favourable pharmacokinetic properties. These findings highlight newly identified lead compounds that can serve as potential inhibitors of cytochrome bd oxidase and provide a foundation for further experimental validation and anti-tuberculosis drug development.
Isolation, Screening, Optimization, and Scale-Up of Oleaginous Yeasts for Sustainable Single Cell Oil Production
(2026-10-11) Gupta, Harshita; Qadri , Ovais Shafiq
Fossil fuel reserves are rapidly diminishing and environmental issues are proliferating due to their massiveconsumption, thereby making the need to find alternative sustainable and renewable energy more of anurgentnecessity. Lipid-accumulating yeasts have been identified as useful oil-producing microorganismtoproducebiodiesel because they are renewable, grow at a very fast rate, and can utilize various substrates. Giventhesebenefits, the aim of the present study is to isolate, characterize and optimize an intracellular lipidproducingyeast for biofuel applications. Fourteen samples, each containing plant material, root soil andcurdwerecollected from various sources for isolation of yeast cultures. A stock culture from the laboratory(SS1) wasalso employed in the study. The isolates were first identified with wet mount preparation and examinationofthe samples under a microscope, and subsequently Sudan Black B were added to assess for lipid accumulation.SS1 was chosen for further study based on its lipid accumulation potential. The various nutritional parametersthat have an impact on the lipid production were then tested and optimized. The use of various carbonandnitrogen sources, including inexpensive substrates, were evaluated in order to produce an economical process. Based on the tested combinations, dextrose (20gL⁻¹) and corn steep liquor (20gL⁻¹) mediumresultedinthemaximum lipid production and hence it was chosen as the optimum medium. The optimized processwasfurther scaled up in an industrial scale fermenter (5-L) under controlled conditions to assess its scaleupforindustrial application. Intracellular lipids were extracted after cultivation and trans esterified to obtainfattyacid methyl esters (FAMEs). The composition and suitability of the extracted lipids and their derivativesforbiofuel production were determined by Thin Layer Chromatography (TLC), High PerformanceLiquidChromatography (HPLC) and Gas Chromatography-Mass Spectrometry (GC-MS) techniques. In this work 44 isolates of microorganisms were isolated of which 15 were yeast isolates and only oneof themwas oleaginous. A laboratory stock culture, however, grew better and was chosen for further study. Themaximum OD₆₀₀ of the culture reached 7 to 8 after 48 h, when the cells were grown in YPDmediumwitha1% inoculum, prior to optimization. Optimum inoculum size, nutritional parameters were determinedand3%inoculum, dextrose (20 g/L) and corn steep liquor (20 g/L) were obtained by which an increasedOD₆₀₀ ofabout 17 was obtained. These optimum conditions were then applied to the large scale biomass andlipidproduction. This study indicated that the strain of yeast used was capable of accumulating lipids effectivelywith inexpensive substrates. The success of process optimization, scale up, lipid extractionandcharacterization demonstrate potential for utilization of yeast oils as sustainable feedstocks for biodieselproduction, and they can be applied in renewable energy technologies in the future.
In vitro Regeneration of Elite Indian Soybean [Glycine max (L.) Merr.] Cultivars and a Comparative Transcriptomic Analysis of Regeneration Pathways
(2026-10-11) Kaur, Harmanpreet; Lohani , Neeta
Soybean [Glycine max (L.) Merr.] is among the most important oilseed and protein crops worldwide, yet its genetic improvement through biotechnology is constrained by a low and strongly genotype-dependent in vitro regeneration capacity. This study had two complementary objectives. To establish an efficient in vitro shoot-regeneration protocol for elite Indian soybean cultivars using cotyledonary-node explants, and to characterise the transcriptional programme underlying regeneration by a comparative analysis of the two principal regeneration routes, callus-mediated organogenesis and somatic embryogenesis. In the wet-laboratory component, four genotypes were evaluated on Gamborg's B5-based media supplemented with 6-benzylaminopurine. Shoot induction was genotype-dependent, and the best-performing cultivar achieved a shoot-induction frequency of up to 84%, establishing a reproducible regeneration system for the germplasm of interest. In the comparative transcriptomic component, two publicly available RNA-Seq datasets, a soybean callus time-series (PRJNA949161; Park et al., 2023) and a somatic-embryogenesis series (PRJNA369414; Ji et al., 2019), were quantified against the Wm82.a6.v1 reference assembly and analysed with DESeq2. Up-regulated genes from the two routes were partitioned by set logic into a shared core (3,906 genes), a callus-organogenesis-specific sector (10,658 genes), and a somatic-embryogenesis-specific sector (6,663 genes). Functional enrichment revealed distinct, biologically coherent signatures. The callus-specific sector was dominated by cell-division and cell-wall processes (phenylpropanoid biosynthesis, DNA replication, starch and sucrose metabolism), the embryogenesis-specific sector by chromatin reprogramming and storage-reserve metabolism (autophagy, ubiquitin-mediated proteolysis, Polycomb components), and the shared core by DNA methylation and genome-maintenance machinery. A curated panel of canonical regeneration regulators partitioned as the biology predicts, with shoot-organogenesis regulators (STM/KNOX, LBD, CUC) to the callus sector and embryo-identity regulators (BBM, AGL15, FUS3/ABI3) to the embryogenesis sector, and 372 callus-organogenesis-specific candidate regulators were prioritised for functional follow-up. The re-analysis 2 reproduced the published callus response pattern and independently recovered the DNA-methylation-reinforcement signature of the source embryogenesis study, confirming the fidelity of the comparative design. Together, the wet-laboratory protocol and the transcriptomic analysis convert an optimised regeneration system into a set of testable molecular hypotheses for improving regeneration efficiency in elite Indian soybean.
Fe₃O₄@MOF-808-Based Photocatalyst for the Biodegradation of Antibiotics
(2026-10-11) .Chahat; Lohani, Neeta; Nayak, Manoj Kumar
The widespread use of antibiotics in healthcare, agriculture, and animal husbandry has led to their continuous release into aquatic environments, posing significant risks to ecosystems and human health. Conventional wastewater treatment technologies are often inadequate to completely remove these persistent contaminants. In the present study, a Fe₃O₄@MOF-808 composite photocatalyst was synthesized via a green, sustainable approach that used neem leaf extract to prepare Fe₃O₄ nanoparticles. The synthesized Fe₃O₄ nanoparticles were subsequently incorporated into the MOF-808 framework to enhance photocatalytic performance and facilitate magnetic recovery. The structural, morphological, and optical properties of the synthesized materials were characterized using X-ray Diffraction (XRD), Fourier Transform Infrared Spectroscopy (FTIR), Raman spectroscopy, and Dynamic Light Scattering (DLS). The characterization results confirmed the successful formation of the Fe₃O₄@MOF-808 composite with good crystallinity, stability, and particle dispersion. Photocatalytic degradation studies demonstrated efficient removal of antibiotic pollutants under visible-light irradiation. The enhanced performance was attributed to improved charge separation, reduced electron–hole recombination, and increased generation of reactive oxygen species (ROS), including hydroxyl and superoxide radicals. The findings indicate that Fe₃O₄@MOF-808 is a promising, environmentally friendly, and reusable photocatalyst for wastewater treatment, offering an effective strategy for degrading antibiotic contaminants and protecting aquatic ecosystems.
Development of Biosensor for Detection of H₂O₂ through PB-MXene Composite Modified Screen-Printed Carbon Electrodes
(2026-10-11) Malhotra, Vanshika; Lohani, Neeta; Singh, Suman
Hydrogen peroxide is the most important reactive oxygen species and a key biomarker of oxidative stress linked to several physiological conditions, including cardiovascular and neurodegenerative disorders. The increased level of hydrogen peroxide may cause oxidative imbalance and DNA damage. The development of rapid, sensitive, and cost-effective methods for detecting hydrogen peroxide is highly important for biomedical diagnostics and healthcare applications. The present work focuses on a PB-MXene-modified screen-printed electrode for electrochemical detection of hydrogen peroxide. In this work, carbon and MXene inks were used for printing the electrodes. The developed platform targeted hydrogen peroxide over a concentration range of 0.01-100μM to obtain enhanced electrochemical response. Prussian blue and Ni-MOF/Ti3C2Tx composite were synthesized and characterized by UV-Vis spectroscopy, Fourier Transform Infrared Spectroscopy (FTIR), and X-ray Diffraction (XRD) and electrochemical techniques. The sensing studies were performed using electrochemical techniques (cyclic voltammetry and amperometry) to ensure sensitive detection of analytes. The proposed sensing platform provides a simple, low-cost, flexible, and efficient sensing for hydrogen peroxide detection. The biosensor provides high potential applications for point-of-care diagnostics, oxidative stress monitoring, and wearable biosensing technology