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Item Quantitative analysis of fibrillar collagen organization in the immediate proximity of embedded fibroblasts in 3D collagen hydrogels(The Indian Academy of Sciences, 2024-06) KANADE, SHAUNAK; DESAI, MILIE; BHATAVADEKAR, NEEL; BALASUBRAMANIAN, NAGARAJFibroblasts embedded in a 3D matrix microenvironment can remodel the matrix to regulate cell adhesion and function. Collagen hydrogels are a useful in vitro system to study cell–matrix interactions in a 3D microenvironment. While major matrix reorganizations are easily recognizable, subtle changes in response to environmental or biochemical cues are challenging to discern in 3D hydrogels. Three-dimensional collagen gels at 1.0 mg/ml vs 1.5 mg/ml were labelled with DQ-collagen and imaged by confocal reflectance microscopy to evaluate these small changes. An image analysis pipeline was developed, hydrogel area and number of cross-sections analysed were optimized, and fibrillar collagen properties (number of branches, number of junctions, and average branch length) were quantified. While no significant changes were seen in fibrillar collagen organization between 1.0 mg/ml and 1.5 mg/ml collagen hydrogels, embedded mouse fibroblasts caused a significant increase in collagen branching and organization. Using the phalloidin-labelled cells, this change was quantitated in immediate proximity of the cell. A distinct increase in branch and junction numbers was observed, significantly altered by small changes in collagen concentration (1.0 mg/ml vs 1.5 mg/ml). Together, this analysis gives a quantitative evaluation of how cells respond to and modify their immediate microenvironment in a 3D collagen hydrogel.Item Harnessing the innate immune system by revolutionizing macrophage-mediated cancer immunotherapy(The Indian Academy of Sciences, 2024-06) REGHU, GAYATRI; VEMULA, PRAVEEN KUMAR; BHAT, SARITA GANAPATHY; NARAYANAN, SREEJAImmunotherapy is a promising and safer alternative to conventional cancer therapies. It involves adaptive T-cell therapy, cancer vaccines, monoclonal antibodies, immune checkpoint blockade (ICB), and chimeric antigen receptor (CAR) based therapies. However, most of these modalities encounter restrictions in solid tumours owing to a dense, highly hypoxic and immune-suppressive microenvironment as well as the heterogeneity of tumour antigens. The elevated intra-tumoural pressure and mutational rates within fast-growing solid tumours present challenges in efficient drug targeting and delivery. The tumour microenvironment is a dynamic niche infiltrated by a variety of immune cells, most of which are macrophages. Since they form a part of the innate immune system, targeting macrophages has become a plausible immunotherapeutic approach. In this review, we discuss several versatile approaches (both at pre-clinical and clinical stages) such as the direct killing of tumour-associated macrophages, reprogramming pro-tumour macrophages to anti-tumour phenotypes, inhibition of macrophage recruitment into the tumour microenvironment, novel CAR macrophages, and genetically engineered macrophages that have been devised thus far. These strategies comprise a strong and adaptable macrophage-toolkit in the ongoing fight against cancer and by understanding their significance, we may unlock the full potential of these immune cells in cancer therapy.Item Diagnosis and treatment of cystic fibrosis in India: What is at stake for developing countries?(The Indian Academy of Sciences, 2024-06) PURUSHOTHAMAN, ANAND KUMAR; NATARAJAN, SRIKANTH; PANIGRAHI, TRAILOKYANATH; NELSON, EVERETTE JACOB REMINGTONCystic fibrosis (CF) is a life-threatening monogenic disease affecting thousands of people worldwide. Cystic fibrosis transmembrane conductance regulator (CFTR) is an ion channel that facilitates transportation of water and salts across epithelial cell membranes through the conductance of Cl? and other anions. A dysfunctional CFTR due to abnormalities in the cftr gene causes CF, which is believed to be a rare disease in India mainly due to mis/underdiagnosis. Although numerous diagnostic methods and treatment options are available for CF globally, most of these are unaffordable for developing countries like India. Currently, CF symptoms are managed with mucolytics, antibiotics, anti-inflammatory drugs, and various CFTR modulators based on the type of defect. While a definitive cure for CF remains elusive, advancements in stem cell and gene therapies hold promise for permanent cure in the near future. In this review, we discuss the prevalence of CF cases in India, affordable diagnostic methods, and treatment options amenable for developing countries. We further emphasize the scope for the universal newborn screening programme.Item Milk supply chain as a reservoir of antimicrobial-resistant Staphylococcus species(The Indian Academy of Sciences, 2024-05) SUPRIYA, K; KARABASANAVAR, NAGAPPA; MADHAVAPRASAD, CB; SIVARAMAN, GK; GIRISH, PS; WAGHE, PRASHANTKUMAR; KOTRESH, AM; FAIROZE, MOHAMED NADEEMMilk is a source of essential nutrients, but food safety across the milk supply chain has emerged as an integral part of food trade. Of the several food safety hazards, antimicrobial-resistant Staphylococcus species have emerged as one of the major microbial hazards with significant public health concerns. The present cross-sectional study was undertaken with the objective to isolate Staphylococcus species from the milk supply chain, characterize isolates for antimicrobial resistance, and trace the origin of isolates using molecular techniques. Samples collected from the formal and informal milk supply chains showed prevalence of Staphylococcus species of 4.3% (n=720); isolates were identified as coagulase-positive (S. aureus 67.7% and S. intermedius 6.4%) and coagulase-negative (S. lentus 9.6%, S. sciuri 3.2%, S. xylosus 3.2%, S. schleiferi 3.2%, S. felis 3.2%, and S. gallinarum 3.2%) species. Staphylococcus isolates showed antimicrobial resistance to methicillin (32.2%), ?-lactam (41.9%), and macrolide-lincosamide-streptogramin B (3.2%). Staphylococcus isolates phenotypically resistant to methicillin also carried the mecA gene and displayed diverse pulsed field gel electrophoresis (PFGE) profiles, indicating their diverse origins in the milk supply chain. Based on the similarity of PFGE profile, the origin of one of the Staphylococcus isolates was traced to the soil in contact with milch cows. The findings of this study highlight the need for more comprehensive microbial risk analysis studies across the milk supply chain, capacity building, creation of awareness among stakeholders about the judicious use of antimicrobials, and protection of public health using a One-Health approach.Item NMR-based comparative metabolomics of quiescent muscle cells(The Indian Academy of Sciences, 2024-05) PUROHIT, GUNJAN; RAMESH, AKILA; PATEL, ANANT B; DHAWAN, JYOTSNAAdult muscle tissue largely comprised of differentiated myofibers also harbors quiescent muscle-resident stem cells (MuSCs) that are responsible for its maintenance, repair and regeneration. Emerging evidence suggests that quiescent MuSCs exhibit a specific metabolic state, which is regulated during physiological and pathological alterations. However, a detailed understanding of the metabolic state of quiescent MuSCs and its alteration during activation and repair is lacking. Direct profiling of MuSCs in vivo is challenging because the cells are rare and dispersed, while isolation and enrichment leads to their activation and loss of quiescence. In this study, we employed 1H-nuclear magnetic resonance (NMR) spectroscopy to profile metabolites in an established culture model of quiescent MuSC-derived myoblasts and compared with activated, proliferative and differentiated muscle cells to determine the state-specific metabolome. We report that the proliferating and differentiated cells are highly enriched in metabolites involved in energy generation, the quiescent state is enriched in metabolites related to phospholipid catabolism (glycerophosphocholine and choline) and depleted for phosphocholine which is enriched in proliferating cells. We propose that the ratio of these metabolites may be useful as a biomarker of MuSC quiescence.Item A study on expression of GRP78 and CHOP in neutrophil endoplasmic reticulum and their relationship with neutrophil apoptosis in the development of sepsis(The Indian Academy of Sciences, 2024-04) ZHAO, JINCHUAN; YANG, PING; LU, LI; YI, TAO; LI, YUNFENG; MAO, WEI; ZHOU, QIN; LIN, KEWe investigated the relationship between neutrophil apoptosis and endoplasmic reticulum stress (ERS) in sepsis and its mechanism. A prospective cohort study was conducted by recruiting a total of 58 patients with sepsis. Peripheral blood samples were collected on 1, 3, 5 and 7 days after admission to the ICU. The expressions of endoplasmic reticulum specific glucose regulatory protein 78 (GRP78), C/EBP homologous protein (CHOP), apoptosis signal-regulating kinase 1 (ASK1), Bcl-2-like 11 (BIM), death receptor 5 (DR5), c-Jun N-terminal kinases (JNK) and p38 were detected by Western blot and PCR. The subcellular location of CHOP and GRP78 was observed by immunofluorescence analysis. Spearman correlation was used to analyze the correlation between the expression of chop protein and the apoptosis rate of peripheral blood neutrophils. Healthy volunteers in the same period were selected as the healthy control group. The expression of GRP78 protein was significantly elevated on the first day of ICU admission and showed a decreasing trend on the third, fifth and seventh day, but was significantly higher than the corresponding healthy control group. The expression of CHOP protein reached the highest level on the third day. The expression of chop protein in each group was significantly higher than that in the corresponding healthy control group. Immunofluorescence staining clearly showed that the CHOP protein accumulated in the nucleus, with an elevation in the intensity of GRP78. The neutrophil apoptosis rate of sepsis patients on the 1st, 3rd, 5th and 7th day of ICU stay was significantly higher than that of the healthy control group, with the highest apoptosis rate on the 3rd day, and then decreased gradually. CHOP protein expression level was significantly positively correlated with neutrophil apoptosis rate in sepsis patients. Endoplasmic reticulum stress occurs in neutrophils during the development of sepsis. GRP78 protein and CHOP protein may be involved in the pathological process of neutrophil apoptosis in sepsis.Item Discovery of antibacterial biogenic magnetosome nanoparticles from Providencia sp. MTBPRB-1: Screening, purification and characterization(The Indian Academy of Sciences, 2024-05) RAJALAKSHMI, ARUMUGAM; RAMESH, MANICKAM; ABIRAMI, RENGARAJAN SAI THANGA; KAVITHA, KUPPUSWAMY; SURESH, GOPAL; PRABAKARAN, VADIVEL; PUVANAKRISHNAN, RENGARAJULU; RAMESH, BALASUBRAMANIANBacterial species referred to as magnetotactic bacteria (MTB) biomineralize iron oxides and iron sulphides inside the cell. Bacteria can arrange themselves passively along geomagnetic field lines with the aid of these iron components known as magnetosomes. In this study, magnetosome nanoparticles, which were obtained from the taxonomically identified MTB isolate Providencia sp. PRB-1, were characterized and their antibacterial activity was evaluated. An in vitro test showed that magnetosome nanoparticles significantly inhibited the growth of Staphylococcus sp., Pseudomonas aeruginosa, and Klebsiella pneumoniae. Magnetosomes were found to contain cuboidal iron crystals with an average size of 42 nm measured by particle size analysis and scanning electron microscope analysis. The energy dispersive X-ray examination revealed that Fe and O were present in the extracted magnetosomes. The extracted magnetosome nanoparticles displayed maximum absorption at 260 nm in the UV-Vis spectrum. The distinct magnetite peak in the Fourier transform infrared (FTIR) spectroscopy spectra was observed at 574.75 cm?1. More research is needed into the intriguing prospect of biogenic magnetosome nanoparticles for antibacterial applications.Item Abundance and age structure of critically endangered long-billed (Gyps indicus) and white-rumped (G. bengalensis) vultures at the breeding colonies of Kaghaznagar Forest Division and its adjoining areas in the Deccan Plateau, India(The Indian Academy of Sciences, 2024-05) RAVIKANTH, MANCHIRYALA; BASKARAN, NAGARAJANKaghaznagar and Sironcha Forest Divisions in the Deccan Plateau of India support large breeding colonies of critically endangered species of long-billed Gyps indicus (LBV) and white-rumped G. bengalensis (WRV) vultures. To assess their abundance and age-structure, that are important population parameters, they were surveyed every month at their breeding colonies; LBV at Palarapu cliff during 2010–2021 and Lakkameda cliff during 2015–2021, and WRV at Dechilpeta during 2014–2021. Breeding colonies of LBV supported a mean of 32 ± 1.3 individuals during 2015–2021. Although its number increased from 34 individuals in 2015 to 42 in 2017, it declined significantly to 10 in 2021. In contrast, WRV with a mean of 49 ± 3.35 individuals between 2014 and 2021 increased from 22 to 66. Data on the population structure show that adults constitute bulk of the population in both LBV (78 ± 1.2%) and WRV (80 ± 2.1%) with a low proportion of young age-classes of sub-adults, juveniles and chicks. With a declining trend and low proportion of young-age classes, the LBV breeding colonies are likely to decrease over time. Although WRV showed an increasing trend during the study period, the high adult proportion (80%) cannot guarantee its sustained growth.Item Predicting and reducing potential parasite infection between migratory livestock and resident Asiatic ibex of Pin valley, India(The Indian Academy of Sciences, 2024-04) KHANYARI, MUNIB; OYANEDEL, RODRIGO; KHARA, ABHIRUP; SHARMA, MANVI; MILNER-GULLAND, EJ; SURYAWANSHI, KULBHUSHANSINGH R; VINEER, HANNAH ROSE; MORGAN, ERIC RDisease cross-transmission between wild and domestic ungulates can negatively impact livelihoods and wildlife conservation. In Pin valley, migratory sheep and goats share pastures seasonally with the resident Asiatic ibex (Capra sibirica), leading to potential disease cross-transmission. Focussing on gastro-intestinal nematodes (GINs) as determinants of health in ungulates, we hypothesized that infection on pastures would increase over summer from contamination by migrating livestock. Consequently, interventions in livestock that are well-timed should reduce infection pressure for ibex. Using a parasite life-cycle model, that predicts infective larval availability, we investigated GIN transmission dynamics and evaluated potential interventions. Migratory livestock were predicted to contribute most infective larvae onto shared pastures due to higher density and parasite levels, driving infections in both livestock and ibex. The model predicted a c.30-day anti-parasitic intervention towards the end of the livestock’s time in Pin would be most effective at reducing GINs in both hosts. Albeit with the caveats of not being able to provide evidence of interspecific parasite transmission due to the inability to identify parasite species, this case demonstrates the usefulness of our predictive model for investigating parasite transmission in landscapes where domestic and wild ungulates share pastures. Additionally, it suggests management options for further investigation.Item SDF-1 promotes metastasis of NSCLC by enhancing chemoattraction of megakaryocytes through the PI3K/Akt signaling pathway(The Indian Academy of Sciences, 2024-05) AI, YIGUO; WAN, CHANGHONG; CHEN, ZIJIAN; WANG, YANSHENG; ZHAO, WEN; HUANG, WEIZHELung cancer (LC) is the leading cause of cancer-associated deaths worldwide, among which non-small-cell lung cancer (NSCLC) accounts for 80%. Stromal cell-derived factor-1 (SDF-1) inhibition results in a significant depletion of NSCLC metastasis. Additionally, SDF-1 is the only natural chemokine known to bind and activate the receptor CXCR4. Thus, we attempted to clarify the molecular mechanism of SDF-1 underlying NSCLC progression. Transwell migration, adhesion, and G-LISA assays were used to assess megakaryocytic chemotaxis in vitro and in vivo in terms of megakaryocytic migration, adherence, and RhoA activation, respectively. Western blotting was used to assess PI3K/Akt-associated protein abundances in MEG-01 cells and primary megakaryocytes under the indicated treatment. A hematology analyzer and flow cytometry were used to assess platelet counts in peripheral blood and newly formed platelet counts in Lewis LC mice under different treatments. Immunochemistry and flow cytometry were used to measure CD41+ megakaryocyte numbers in Lewis LC mouse tissue under different treatments. ELISA was used to measure serum TPO levels, and H&E staining was used to detect NSCLC metastasis. SDF-1 receptor knockdown suppressed megakaryocytic chemotaxis in Lewis LC mice. SDF-1 receptor inhibition suppressed megakaryocytic chemotaxis via the PI3K/Akt pathway. SDF-1 receptor knockdown suppressed CD41+ megakaryocyte numbers in vivo through PI3K/Akt signaling. SDF-1 receptor inhibition suppressed CD41+ megakaryocytes to hinder NSCLC metastasis. SDF-1 facilitates NSCLC metastasis by enhancing the chemoattraction of megakaryocytes via the PI3K/Akt signaling pathway, which may provide a potential new direction for seeking therapeutic plans for NSCLC.Item Intrinsic disorder in flaviviral capsid proteins and its role in pathogenesis(The Indian Academy of Sciences, 2024-05) SUNDAR, ANIRUDH; UMASHANKAR, PAVITHRA; SANKAR, PRIYANKA; RAMASAMY, KAVITHA; VENKATARAMAN, SANGITAA high level of disorder in many viral proteins is a direct consequence of their small genomes, which makes interaction with multiple binding partners a necessity for infection and pathogenicity. A segment of the flaviviral capsid protein (C), also known as the molecular recognition feature (MoRF), undergoes a disorder-to-order transition upon binding to several protein partners. To understand their role in pathogenesis, MoRFs were identified and their occurrence across different flaviviral capsids were studied. Despite lack of sequence similarities, docking studies of Cs with the host proteins indicate conserved interactions involving MoRFs across members of phylogenetic subclades. Additionally, it was observed from the protein–protein networks that some MoRFs preferentially bind proteins that are involved in specialized functions such as ribosome biogenesis. The findings point to the importance of MoRFs in the flaviviral life cycle, with important consequences for disease progression and suppression of the host immune system. Potentially, they might have impacted the way flaviviruses evolved to infect varied hosts using multiple vectors.Item Roles of mitochondrial alternative oxidase in photosynthetic electron transport in illuminated leaves of Arabidopsis thaliana at low temperature(The Indian Academy of Sciences, 2024-05) YAMADA, YUSUKE; SUZUKI, KUNIAKI; YANAGISHITA, HANA; NOGUCHI, KOATP-uncoupling alternative oxidase (AOX) in the plant respiratory chain is often induced under stress conditions such as low temperature (LT). The importance of AOX in photosynthesis has been examined, and leaves having larger amounts of AOX tended to show larger decrease in photosynthetic electron transport rate (ETR) by AOX inhibition. However, the details were not clarified. Here, we used three ecotypes of Arabidopsis thaliana which differed in AOX amounts and their responses to LT, and examined whether AOX amount was related to the degree of decrease in ETR by AOX inhibition. In Tiv-0, which originates from a warmer site, grown at high temperature (HT), AOX inhibition decreased ETR, but not in the other ecotypes. LT treatment significantly increased ETR and AOX, especially in Bur-0, but AOX inhibition did not decrease ETR in LT plants of any ecotype. AOX inhibition significantly increased the non-regulated energy dissipation in photosystem II (PSII), Y(NO), and decreased the maximal quantum yield of PSII, Fv/Fm, especially in LT plants. Since AOX inhibition did not affect the parameters of PSI, AOX inhibition may directly affect the reaction center of PSII in LT plants.Item The first embryo, the origin of cancer and animal phylogeny. III. The totipotency as revealed by morphogenesis and the neoplasia controlled by cellular differentiation(The Indian Academy of Sciences, 2024-06) COFRE, JAIMEWe have extensively described that the neoplastic process (NP) has deep evolutionary roots and we have made specific predictions about the connection between cancer and the formation of the first embryo, which allowed for the evolutionary radiation of metazoans. My main hypothesis is that the NP is at the heart of cellular mechanisms responsible for animal morphogenesis, and given its embryological basis, also at the center of cell differentiation—one of the most interesting and relevant aspects of embryogenesis. In this article, I take forward the idea of the role of physics in the modeling of the neoplastic functional module (NFM) and its contribution to morphogenesis to reveal the totipotency of the zygote. In my consideration of these arguments, I examine mechanical and biophysical clues and their intimate connection with cellular differentiation. I expound on how cancer biology is perfectly intertwined with embryonic differentiation and why it is considered a disease of cell differentiation. The neoplasia is controlled by textural gradients that lead to cell differentiation within the embryo. Thus, the embryo would be a benign tumor. Finally, inspired by evolutionary history and by what the nervous system represents for current biology and based on the impressive nervous system of ctenophores as seen in fossil records, I propose a hypothesis with physical foundations (mechanical morphogenesis) for the formation of a preneural pattern of the nervous system of the first animal embryo.Item Effect of spontaneous arbuscular mycorrhizal colonization in bread wheat varieties on the incidence of foliar diseases and grain yield(The Indian Academy of Sciences, 2023-04) Abarca, C; Simón, M R; Esquisabel, E; Velázquez, M SThis study aimed to determine the ability of different wheat genotypes to form a symbiosis with arbuscular mycorrhizal fungi (AMF) present in the field and the effect of such a symbiosis on disease severity and grain yield. A bioassay was performed during an agricultural cycle under field conditions in a randomized block factorial design. The factors used were application of fungicide (two levels: with and without fungicide) and wheat genotypes (six levels). Arbuscular mycorrhizal colonization, green leaf area index, and severity of foliar diseases were evaluated in the tillering and early dough stages. At maturity, the number of spikes per square metre the number of grains per spike, and the thousand-kernel weight were determined to estimate grain yield. In addition, the spores of Glomeromycota present in the soil were identified by morphological techniques. Spores belonging to 12 fungal species were recovered. Genotypic variability was found for arbuscular mycorrhization, with the cultivars Klein Liebre and Opata exhibiting the highest colonization values. The results obtained show a beneficial effect of mycorrhizal symbiosis on foliar disease resistance and grain yield in the controls, but the results varied in the case of fungicide treatment. A greater understanding of the ecological role of these microorganisms in agricultural systems can lead to more sustainable agronomic practices.Item Systems biology of plant metabolic interactions(The Indian Academy of Sciences, 2024-05) SARKAR, DEVLINA; KUNDU, SUDIPMetabolism is the key cellular process of plant physiology. Understanding metabolism and its dynamical behavior under different conditions may help plant biotechnologists to design new cultivars with desired goals. Computational systems biochemistry and incorporation of different omics data unravelled active metabolism and its variations in plants. In this review, we mainly focus on the basics of flux balance analysis (FBA), elementary flux mode analysis (EFMA), and some advanced computational tools. We describe some important results that were obtained using these tools. Limitations and challenges are also discussed.Item Role of mitochondria and chloroplasts during stomatal closure: Subcellular location of superoxide and H2O2 production in guard cells of Arabidopsis thaliana(The Indian Academy of Sciences, 2024-03) GAHIR, SHASHIBHUSHAN; BHARATH, PULIMAMIDI; SAINI, DEEPAK; PADMAJA, GUDIPALLI; RAGHAVENDRA, AGEPATI SStomatal guard cells are unique in that they have more mitochondria than chloroplasts. Several reports emphasized the importance of mitochondria as the major energy source during stomatal opening. We re-examined their role during stomatal closure. The marked sensitivity of stomata to both menadione (MD) and methyl viologen (MV) demonstrated that both mitochondria and chloroplasts helped to promote stomatal closure in Arabidopsis. As in the case of abscisic acid (ABA), a plant stress hormone, MD and MV induced stomatal closure at micromolar concentration. All three compounds generated superoxide and H2O2, as indicated by fluorescence probes, BES-So-AM and CM-H2DCFDA, respectively. Results from tiron (a superoxide scavenger) and catalase (an H2O2 scavenger) confirmed that both the superoxide and H2O2 were requisites for stomatal closure. Co-localization of the superoxide and H2O2 in mitochondria and chloroplasts using fluorescent probes revealed that exposure to MV initially triggered higher superoxide and H2O2 generation in mitochondria. In contrast, MD elevated superoxide/H2O2 levels in chloroplasts. However, with prolonged exposure, MD and MV induced ROS production in other organelles. We conclude that ROS production in mitochondria and chloroplasts leads to stomatal closure. We propose that stomatal guard cells can be good models for examining inter-organellar interactions.Item From sequence to consequence: Deciphering the complex cis-regulatory landscape(The Indian Academy of Sciences, 2024-03) DSILVA, GREG JUDE; GALANDE, SANJEEVCell type-specific expression of genes plays a pivotal role in the development and evolution of multicellular organisms over millions of years. The majority of regulatory control resides within the non-coding regions of the genome, referred to as ‘dark matter’, which contains cis-regulatory modules. These cis-regulatory modules function collectively and can impact gene expression even when located far from the target gene, exhibiting context-specific behaviour. Consequently, the cis-regulatory code governing gene expression patterns is intricate, in contrast to the universally understood genetic code. This overview centres on the current knowledge regarding cis-regulatory elements, primarily enhancers and their role in governing the spatiotemporal gene expression patterns, and how they have evolved and adapted across different species.Item Cobra (Naja naja) venom L-amino acid oxidase (NNLAAO70) induces apoptosis and secondary necrosis in human lung epithelial cancer cells(The Indian Academy of Sciences, 2024-03) RAYAPATI, ANANDA MURALI; VEMULAPATI, BHADRAMURTHY; CHANDA, CHANDRASEKHARSnake venom L-amino acid oxidases (LAAOs) are flavoenzymes with diverse physiological and pharmacological effects. These enzymes are found to showcase anticoagulant, antiplatelet, cytotoxicity and other biological effects in bite victims. However, the exact mechanism through which they exhibit several biological properties is not yet fully understood. The current study focussed on the purification of cobra venom LAAO and the functional characterization of purified LAAO. A novel L-amino acid oxidase NNLAAO70 with a molecular weight ~70 kDa was purified from the venom of an Indian spectacled cobra (Naja naja). NNLAAO70 showed high substrate specificity for L-His, L-Leu, and L-Arg during its LAAO activity. It inhibited adenosine di-phosphate (ADP) and collagen-induced platelet aggregation process in a dose-dependent manner. About 60% inhibition of collagen-induced and 40% inhibition of ADP-induced platelet aggregation was observed with a 40 ?g/ml dose of NNLAAO70. NNLAAO70 exhibited bactericidal activity on Bacillus subtilis, Escherichia coli, Bacillus megaterium, and Pseudomonas fluorescens. NNLAAO70 also showed cytotoxicity on A549 cells in vitro. It showed severe bactericidal activity on P. fluorescens and lysed 55% of cells. NNLAAO70 also exhibited drastic cytotoxicity on A549 cells. At 1 ?g/ml dosage, it demonstrated a 60% reduction in A549 viability and induced apoptosis upon 24-h incubation. H2O2 released during oxidative deamination reactions played a major role in NNLAAO70-induced cytotoxicity. NNLAAO70 significantly increased intracellular reactive oxygen species (ROS) levels in A549 cells by six fold when compared to untreated cells. Oxidative stress-mediated cell injury is the primary cause of NNLAAO70-induced apoptosis in A549 cells and prolonged oxidative stress caused DNA fragmentation and activated cellular secondary necrosis.Item Finding identical sequence repeats in multiple protein sequences: An algorithm(The Indian Academy of Sciences, 2024-02) MAURYA, VIKAS KUMAR; SANJEEVI, MADHUMATHI; RAHUL, CHANDRASEKAR NARAYANAN; MOHAN, AJITHA; RAMACHANDRAN, DHANALAKSHMI; SIDDALINGAPPA, RASHMI; RAUNIYAR, ROSHAN; KANAGARAJ, SEKARIn recent years, several experimental evidences suggest that amino acid repeats are closely linked to many disease conditions, as they have a significant role in evolution of disordered regions of the polypeptide segments. Even though many algorithms and databases were developed for such analysis, each algorithm has some caveats, like limitation on the number of amino acids within the repeat patterns and number of query protein sequences. To this end, in the present work, a new method called the internal sequence repeats across multiple protein sequences (ISRMPS) is proposed for the first time to identify identical repeats across multiple protein sequences. It also identifies distantly located repeat patterns in various protein sequences. Our method can be applied to study evolutionary relationships, epitope mapping, CRISPR-Cas sequencing methods, and other comparative analytical assessments of protein sequences.Item Crosstalk between photosynthesis and respiration in microbes(The Indian Academy of Sciences, 2024-03) SHIMAKAWA, GINGA; MATSUDA, YUSUKE; BURLACOT, ADRIENPhototrophic organisms harbor two main bioenergetic hubs, photosynthesis and respiration, and these processes dynamically exchange and share metabolites to balance the energy of the cell. In microalgae and cyanobacteria, the crosstalk between the light-triggered reactions of photosynthesis and respiration is particularly prominent with respiratory O2 uptake which can be stimulated upon illumination. Since its discovery, this light-enhanced respiration has been proposed to be critical in dissipating the excess reducing power generated by photosynthesis. Importantly, the physiological role and putative molecular mechanism involved have just recently started to be understood. Here, we revisit the physiological functions and discuss possible molecular mechanisms of interactions between the photosynthetic and respiratory electron flows in microalgae and cyanobacteria.