@article {8740, title = {Neem leaf glycoprotein binding to Dectin-1 receptors on dendritic cell induces type-1 immunity through CARD9 mediated intracellular signal to NFκB. [Mass Spectrometry - Proteomics Facility]}, journal = {Cell Commun Signal}, volume = {22}, year = {2024}, month = {2024 Apr 23}, pages = {237}, abstract = {

BACKGROUND: A water-soluble ingredient of mature leaves of the tropical mahogany {\textquoteright}Neem{\textquoteright} (Azadirachta indica), was identified as glycoprotein, thus being named as {\textquoteright}Neem Leaf Glycoprotein{\textquoteright} (NLGP). This non-toxic leaf-component regressed cancerous murine tumors (melanoma, carcinoma, sarcoma) recurrently in different experimental circumstances by boosting prime antitumor immune attributes. Such antitumor immunomodulation, aid cytotoxic T cell (T)-based annihilation of tumor cells. This study focused on identifying and characterizing the signaling gateway that initiate this systemic immunomodulation. In search of this gateway, antigen-presenting cells (APCs) were explored, which activate and induce the cytotoxic thrust in T cells.

METHODS: Six glycoprotein-binding C-type lectins found on APCs, namely, MBR, Dectin-1, Dectin-2, DC-SIGN, DEC205 and DNGR-1 were screened on bone marrow-derived dendritic cells from C57BL/6\ J mice. Fluorescence microscopy, RT-PCR, flow cytometry and ELISA revealed Dectin-1 as the NLGP-binding receptor, followed by verifications through RNAi. Following detection of β-Glucans in NLGP, their interactions with Dectin-1 were explored in silico. Roles of second messengers and transcription factors in the downstream signal were studied by co-immunoprecipitation, western blotting, and chromatin-immunoprecipitation. Intracellularization of FITC-coupled NLGP was observed by processing confocal micrographs of DCs.

RESULTS: Considering extents of hindrance in NLGP-driven transcription rates of the cytokines IL-10 and IL-12p35 by receptor-neutralization, Dectin-1 receptors on dendritic cells were found to bind NLGP through the ligand{\textquoteright}s peripheral β-Glucan chains. The resulting signal phosphorylates PKCδ, forming a trimolecular complex of CARD9, Bcl10 and MALT1, which in turn activates the canonical NFκB-pathway of transcription-regulation. Consequently, the NFκB-heterodimer p65:p50 enhances Il12a transcription and the p50:p50 homodimer represses Il10 transcription, bringing about a cytokine-based systemic-bias towards type-1 immune environment. Further, NLGP gets engulfed within dendritic cells, possibly through endocytic activities of Dectin-1.

CONCLUSION: NLGP{\textquoteright}s binding to Dectin-1 receptors on murine dendritic cells, followed by the intracellular signal, lead to NFκB-mediated contrasting regulation of cytokine-transcriptions, initiating a pro-inflammatory immunopolarization, which amplifies further by the responding immune cells including T cells, alongside their enhanced cytotoxicity. These insights into the initiation of mammalian systemic immunomodulation by NLGP at cellular and molecular levels, may help uncovering its mode of action as a novel immunomodulator against human cancers, following clinical trials.

}, keywords = {Animals, Azadirachta, CARD Signaling Adaptor Proteins, Dendritic Cells, Lectins, C-Type, Mice, Mice, Inbred C57BL, NF-kappa B, Plant Leaves, Protein Binding, Signal Transduction}, issn = {1478-811X}, doi = {10.1186/s12964-024-01576-z}, author = {Ganguly, Nilanjan and Das, Tapasi and Bhuniya, Avishek and Guha, Ipsita and Chakravarti, Mohona and Dhar, Sukanya and Sarkar, Anirban and Bera, Saurav and Dhar, Jesmita and Dasgupta, Shayani and Saha, Akata and Ghosh, Tithi and Das, Juhina and Sk, Ugir Hossain and Banerjee, Saptak and Laskar, Subrata and Bose, Anamika and Baral, Rathindranath} } @article {8813, title = {A novel acidic pH-dependent metacaspase governs defense-response against pathogens in tomato [Mass Spectrometry - Proteomics Facility]}, journal = {Plant Physiology and Biochemistry}, volume = {213}, year = {2024}, pages = {108850}, abstract = {

The importance of metacaspases in programmed cell death and tissue differentiation is known, but their significance in disease stress response, particularly in a crop plant, remained enigmatic. We show the tomato metacaspase expression landscape undergoes differential reprogramming during biotrophic and necrotrophic modes of pathogenesis; also, the metacaspase activity dynamics correlate with the disease progression. These stresses have contrasting effects on the expression pattern of SlMC8, a Type II metacaspase, indicating that SlMC8 is crucial for stress response. In accordance, selected biotic stress-related transcription factors repress SlMC8 promoter activity. Interestingly, SlMC8 exhibits maximum proteolysis at an acidic pH range of 5{\textendash}6. Molecular dynamics simulation identified the low pH-driven protonation event of Glu246 as critical to stabilize the interaction of SlMC8 with its substrate. Mutagenesis of Glu246 to charge-neutral glutamine suppressed SlMC8{\textquoteright}s proteolytic activity, corroborating the importance of the amino acid in SlMC8 activation. The glutamic acid residue is found in an equivalent position in metacaspases having acidic pH dependence. SlMC8 overexpression leads to heightened ROS levels, cell death, and tolerance to PstDC3000, and SlMC8 repression reversed the phenomena. However, the overexpression of SlMC8 increases tomato susceptibility to necrotrophic Alternaria solani. We propose that SlMC8 activation due to concurrent changes in cellular pH during infection contributes to the basal resistance of the plant by promoting cell death at the site of infection, and the low pH dependence acts as a guard against unwarranted cell death. Our study confirms the essentiality of a low pH-driven Type II metacaspase in tomato biotic stress-response regulation.

}, keywords = {Cell death, host-pathogen interaction, Metacaspase, pH sensitivity, Tomato}, issn = {0981-9428}, doi = {https://doi.org/10.1016/j.plaphy.2024.108850}, url = {https://www.sciencedirect.com/science/article/pii/S0981942824005187}, author = {Shrabani Basak and Debarati Paul and Rohit Das and Shubhra Ghosh Dastidar and Pallob Kundu} } @article {8588, title = {A new species of Bufoides Pillai and Yazdani 1973 (Amphibia: Bufonidae) from Mizoram (India) and the delimitation of the distribution range of Bufoides meghalayanus (Yazdani \& Chanda 1971) to the Khasi hills, Meghalaya (India) [Next Gen Genomics Facility]}, journal = { Biodiversitas Journal of Biological Diversity}, volume = {Vol. 24 No. 9}, year = {2023}, month = {10/2023}, chapter = {4617}, abstract = {

Naveen RS, Tapley B, Chandramouli SR, Jervis PA, Babu S, Meetei AB, Karunakaran PV. 2023. A new species of\ Bufoides\ Pillai and Yazdani 1973 (Amphibia: Bufonidae) from Mizoram\ (India) and the delimitation of the distribution range of\ Bufoides meghalayanus\ (Yazdani \& Chanda 1971) to the Khasi hills, Meghalaya\ (India). Biodiversitas 24: 4617-4627.\ The Oriental toad genus\ Bufoides\ currently comprises two species:\ Bufoides meghalayanus\ and\ B. kempi. Populations of\ Bufoides\ from Mizoram were previously considered to be conspecific with\ Bufoides meghalayanus,\ although it has been hypothesized that these populations could represent an undescribed species. An uncorrected p-distance at the 16S rDNA gene between the Mizoram population and each of the two congeneric species was 2.74-3.0\% and 3.5\% for\ B. meghalayanus\ and\ B. kempi\ respectively. We describe the population from Dampa Tiger Reserve, Mizoram, as new based on molecular from two specimens and morphological data from two adult males and one adult female. We confirm that\ B. meghalayanus\ is endemic to the Khasi Hills in Meghalaya and it does not occur in Mizoram. The new species from Mizoram differs from congeneric species by differences in interdigital webbing, coloration, skin tuberculation and the presence of ovoid, tuberculated and depressed parotoid glands. Like other\ Bufoides\ species, it is a microhabitat specialist and utilizes streamside rock crevices as refugia, which might make it vulnerable to changes in habitat. The new species is currently only known to occur in Dampa Tiger Reserve and it is probably range-restricted and likely meets the International Union for Conservation of Nature{\textquoteright}s criteria for being assessed as Critically Endangered.

}, keywords = {Amphibian, conservation, cryptic diversity, Indo-Burma region, systematics, taxonomy}, issn = {1412-033X}, doi = {0.13057/biodiv/d240901}, url = {https://smujo.id/biodiv/article/view/14616}, author = {R.S. NAVEEN and BENJAMIN TAPLEY and S.R. CHANDRAMOULI and PHILLIP A. JERVIS and S. BABU and A.B. MEETEI and P.V. KARUNAKARAN} } @article {2589, title = {Novel studies of characterization, antioxidant, anticoagulant and anticancer activity of purified polysaccharide from Hypsizygus ulmarius mushroom [Mass Spectrometry - Glycomics]}, journal = {Bioactive Carbohydrates and Dietary Fibre}, volume = {27}, year = {2022}, pages = {100308}, abstract = {

A water-soluble polysaccharide (HUP-2) was isolated from H. ulmarius using hot water extraction and purified using ion exchange chromatography (DEAE cellulose-52) and gel filtration (Sepharose-6B). The structure characteristics of HUP-2 were investigated using high performance liquid chromatography (HPLC), Fourier transform infrared (FT-IR), nuclear magnetic resonance (NMR) spectrum, and gas chromatography-mass spectrometry (GC-MS), and XRD analysis revealed that it formed a semi-crystalline structure. HUP-2 is a monosaccharide with a molecular weight of 25.296\ kDa. The HUP-2 is assemble with 1.96\% rhamnose, 16.51\% mannose, 22.76\% galactose, and 19.43\% glucose. It could be found that the main backbone chain of HUP-2 consisted N-acetylglycosidic. The polysaccharide{\textquoteright}s DPPH radical scavenging activity ranged from 17.08 to 56.90\%. The radical scavenging activity of ABTS varied from 8.02 to 71.44\% at 0.5{\textendash}2.5\ mg/ml, whereas superoxide radical scavenging activity was 8.02{\textendash}63.03\%. The results of HUP-2 demonstrated an extension (p\ \<\ 0.01) of APTT relative to the saline sample at concentrations more than 5\ mg/mL. It exhibited a high antioxidant capacity as well. HUP-2 had significant inhibitory and cytotoxic effects in PC3 cells. HUP-2 arrested the cell cycle in the G0/G1 phase over all cells except PC3 cells. HUP-2 appears to have a wide range of biological applications, making it a good candidate for usage in functional foods, according to these studies.

}, keywords = {Anticancer, Anticoagulant, Antioxidant, HUP-2}, issn = {2212-6198}, doi = {https://doi.org/10.1016/j.bcdf.2022.100308}, url = {https://www.sciencedirect.com/science/article/pii/S2212619822000031}, author = {Alamelu Thimmaraju and Sudha Govindan} } @article {1638, title = {A Novel N4-Like Bacteriophage Isolated from a Wastewater Source in South India with Activity against Several Multidrug-Resistant Clinical Pseudomonas aeruginosa Isolates [Next Gen Genomics \& National Electron Cryo-Microscopy Facilities]}, journal = {mSphere}, volume = {6}, year = {2021}, month = {2021 Jan 13}, abstract = {

Multidrug-resistant community-acquired infections caused by the opportunistic human pathogen are increasingly reported in India and other locations globally. Since this organism is ubiquitous in the environment, samples such as sewage and wastewater are rich reservoirs of bacteriophages. In this study, we report the isolation and characterization of a novel N4-like lytic bacteriophage, vB_Pae_AM.P2 (AM.P2), from wastewater in Kerala, India. AM.P2 is a double-stranded DNA podovirus that efficiently lyses the model strain, PAO1, at a multiplicity of infection as low as 0.1 phage per bacterium and resistance frequency of 6.59 {\texttimes} 10 Synergy in bactericidal activity was observed between AM.P2 and subinhibitory concentrations of the antibiotic ciprofloxacin. Genome sequencing of AM.P2 revealed features similar to those of the N4-like phages LUZ7 and KPP21. As judged by two independent assay methods, spot tests and growth inhibition, AM.P2 successfully inhibited the growth of almost 30\% of strains from a contemporary collection of multidrug-resistant clinical isolates from South India. Thus, AM.P2 may represent an intriguing candidate for inclusion in bacteriophage cocktails developed for various applications, including water decontamination and clinical bacteriophage therapy. In India, multidrug resistance determinants are much more abundant in community-associated bacterial pathogens due to the improper treatment of domestic and industrial effluents. In particular, a high bacterial load of the opportunistic pathogen in sewage and water bodies in India is well documented. The isolation and characterization of bacteriophages that could target emerging strains, representing possible epicenters for community-acquired infections, could serve as a useful alternative tool for various applications, such as phage therapy and environmental treatment. Continuing to supplement the repertoire of broad-spectrum bacteriophages is an essential tool in confronting this problem.

}, issn = {2379-5042}, doi = {10.1128/mSphere.01215-20}, author = {Menon, Nitasha D and Kumar, Megha S and Satheesh Babu, T G and Bose, Sucharita and Vijayakumar, Gayathri and Baswe, Manasi and Chatterjee, Meghna and D{\textquoteright}Silva, Jovita Rowena and Shetty, Kavya and Haripriyan, Jayalekshmi and Kumar, Anil and Nair, Samitha and Somanath, Priyanka and Nair, Bipin G and Nizet, Victor and Kumar, Geetha B} } @article {1917, title = {Novel non intrusive continuous use ZeBox technology to trap and kill airborne microbes [Biomoneta Research Pvt. Ltd., a C-CAMP Startup / Electron Microscopy Facility]}, journal = {Scientific Reports}, volume = {11}, year = {2021}, month = {11/2021}, pages = {Article number: 22779 }, abstract = {

Preventing nosocomial infection is a major unmet need of our times. Existing air decontamination technologies suffer from demerits such as toxicity of exposure, species specificity, noxious gas emission, environment-dependent performance and high power consumption. Here, we present a novel technology called {\textquotedblleft}ZeBox{\textquotedblright} that transcends the conventional limitations and achieves high microbicidal efficiency. In ZeBox, a non-ionizing electric field extracts naturally charged microbes from flowing air and deposits them on engineered microbicidal surfaces. The surface{\textquoteright}s three dimensional topography traps the microbes long enough for them to be inactivated. The electric field and chemical surfaces synergistically achieve rapid inactivation of a broad spectrum of microbes. ZeBox achieved near complete kill of airborne microbes in challenge tests (5{\textendash}9 log reduction) and\ \>90\%\ efficiency in a fully functional stem cell research facility in the presence of humans. Thus, ZeBox fulfills the dire need for a real-time, continuous, safe, trap-and-kill air decontamination technology.

}, doi = {doi.org/10.1038/s41598-021-02184-4}, author = {Kruttika S. Phadke and Deepak G. Madival and Janani Venkataraman and Debosmita Kundu and K. S. Ramanujan and Nisha Holla and Jaywant Arakeri and Gaurav Tomar and Santanu Datta and Arindam Ghatak} } @book {1188, title = {The Neem Genome [Next Gen Genomics Facility]}, year = {2019}, publisher = {Springer Nature Switzerland AG}, organization = {Springer Nature Switzerland AG}, abstract = { }, keywords = {C-CAMP Genomics Facility, Illumina HiSeq 1000, Next Generation Sequencing, paired-end (PE) (2 {\texttimes} 100 nts) sequencing chemistry}, author = {Gowda, Malali and Sheetal, Ambardar and Kole, Chittaranjan} } @article {1012, title = {A Naturally Occurring Flavone (Chrysin): Chemistry, Occurrence, Pharmacokinetic, Toxicity, Molecular Targets and Medicinal Properties [High Throughput Screening Facility].}, journal = {Journal of Biologically Active Products from Nature}, volume = {8}, year = {2018}, pages = {208-227}, doi = {10.1080/22311866.2018.1498750}, url = {https://doi.org/10.1080/22311866.2018.1498750}, author = {Amir Siddiqui and . Badruddeen and Juber Akhtar and Shahab Uddin M.S. and Mohammad Irfan Khan and Mohammad Khalid and Mohammad Ahmad} } @article {764, title = {Nitrothiophene carboxamides, a novel narrow spectrum antibacterial series: Mechanism of action and Efficacy [Bugworks Res. Pvt. Ltd., a C-CAMP Startup]}, journal = {Sci Rep}, volume = {8}, year = {2018}, month = {2018 May 08}, pages = {7263}, abstract = {

The mechanism of efflux is a tour-de-force in the bacterial armoury that has thwarted the development of novel antibiotics. We report the discovery of a novel chemical series with potent antibacterial properties that was engineered to overcome efflux liability. Compounds liable to efflux specifically via the Resistance Nodulation and cell Division (RND) pump, AcrAB-TolC were chosen for a hit to lead progression. Using structure-based design, the compounds were optimised to lose their binding to the efflux pump, thereby making them potent on wild-type bacteria. We discovered these compounds to be pro-drugs that require activation in E. coli by specific bacterial nitroreductases NfsA and NfsB. Hit to lead chemistry led to the generation of compounds that were potent on wild-type and multi-drug resistant clinical isolates of E. coli, Shigella spp., and Salmonella spp. These compounds are bactericidal and efficacious in a mouse thigh infection model.

}, issn = {2045-2322}, doi = {10.1038/s41598-018-25407-7}, author = {Hameed P, Shahul and Bharatham, Nagakumar and Katagihallimath, Nainesh and Sharma, Sreevalli and Nandishaiah, Radha and Shanbhag, Anirudh P and Thomas, Teby and Narjari, Riya and Sarma, Maitrayee and Bhowmik, Purnendu and Amar, Prakruthi and Ravishankar, Rajani and Jayaraman, Ramesh and Muthan, Kubendran and Subbiah, Ramesh and Ramachandran, Vasanthi and Balasubramanian, V and Datta, Santanu} } @article {500, title = {Nickel azamacrocyclic complex activated persulphate based oxidative degradation of methyl orange: recovery and reuse of complex using adsorbents [Mass spectrometry - Metabolomics]}, journal = {RSC Adv.}, volume = {5}, year = {2015}, pages = {31716-31724}, abstract = {

Adsorbents are useful for the removal of metal complex based catalysts from the reaction medium. Moreover{,} effective catalysts may be recycled with the use of adsorbents. These facts inspired us to investigate the use of adsorbents for the recovery and reuse of a metal complex that could activate persulphate to effectively degrade an organic pollutant in water. Herein{,} we report the nickel complex (C1) activated persulphate based degradation of methyl orange (MO) in water and the removal of C1 using activated carbon (AC) and Amberlite (Am) as adsorbents. C1 adsorbed onto AC (C1-AC) was reused in the solid form to activate persulphate and degrade MO without leaching C1 into water. Additionally{,} solid C1-Am recovered from the degraded MO solution was ion exchanged using sodium chloride to obtain C1{,} which was reused for MO degradation. The study demonstrates the application of adsorbents such as AC and Am for the adsorptive recovery and reuse of a metal complex based persulphate activator.

}, doi = {10.1039/C5RA03350K}, url = {http://dx.doi.org/10.1039/C5RA03350K}, author = {Subramanian, Gokulakrishnan and Nalawade, Pranav and Hinder, Steven J. and Pillai, Suresh C. and Prakash, Halan} } @article {516, title = {A new C-type lectin (RVsnaclec) purified from venom of Daboia russelii russelii shows anticoagulant activity via inhibition of FXa and concentration-dependent differential response to platelets in a Ca{\texttwosuperior}$^{+}$-independent manner. (Mass spectrometry)}, journal = {Thromb Res}, volume = {134}, year = {2014}, month = {2014 Nov}, pages = {1150-6}, abstract = {

This is the first report on the characterization of a snaclec (RVsnaclec) purified from Daboia russelii russelii venom. The RVsnaclec is a heterodimer of two subunits, α (15.1 kDa) and β (9 kDa). These subunits are covalently linked to form multimeric (αβ)$_{2}$ and (αβ)$_{4}$ structures. Peptide mass fingerprinting analysis of RVsnaclec via LC-MS/MS demonstrated its similarity to snaclecs purified from other viperid snake venoms. Two tryptic peptide sequences of RVsnaclec revealed the putative conserved domains of C-type lectin (CTL). RVsnaclec dose-dependently increased the Ca-clotting time and prothrombin time of platelet-poor plasma (PPP); however, it did not affect the partial thromboplastin time (APTT) or thrombin time of PPP. The in vitro and in vivo anticoagulant activity of RVsnaclec is correlated to its binding and subsequent uncompetitive inhibition of FXa (Ki = 0.52 μmole) in a Ca(2+)-independent manner; however, supplementation with 0.25 mM Ca(2+) enhanced the Xa binding potency of RVsnaclec. Monovalent or polyvalent antivenom failed to neutralize its anticoagulant potency, and RVsnaclec did not inhibit trypsin, chymotrypsin, thrombin or plasmin. RVsnaclec was devoid of hemolytic activity or cytotoxicity against several human cancer cell lines, demonstrated concentration-dependent aggregation and deaggregation of human platelets, and inhibited the ADP-induced aggregation of platelet. RVsnaclec (5.0 mg/kg body weight) was non-lethal to mice and showed no adverse pharmacological effects, suggesting that it has potential as a lead compound for future therapeutic applications in cardiovascular disorders.

}, keywords = {Animals, Anticoagulants, Blood Coagulation, Blood Platelets, Calcium, Factor Xa, Factor Xa Inhibitors, Goats, Humans, Lectins, C-Type, Mice, Platelet Aggregation, Russell{\textquoteright}s Viper, Viper Venoms}, issn = {1879-2472}, doi = {10.1016/j.thromres.2014.09.009}, author = {Mukherjee, Ashis K and Dutta, Sumita and Mackessy, Stephen P} } @article {724, title = {Neutrophil extracellular traps contain mitochondrial as well as nuclear DNA and exhibit inflammatory potential.}, journal = {Cytometry A}, volume = {81}, year = {2012}, month = {2012 Mar}, pages = {238-47}, abstract = {

Neutrophils expel extracellular traps (NETs) to entrap and exterminate the invaded micro-organisms. Acute/chronic inflammatory disorders are often observed with aberrantly enhanced NETs formation and high nitric oxide (NO) availability. Recent study from this laboratory demonstrated release of NETs from human neutrophils following treatment with SNP or SNAP. This study is an extension of our previous finding to explore the extracellular bacterial killing, source of DNA in the expelled NETs, their ability to induce proinflammatory cytokines release from platelets/THP-1 cells, and assessment of NO-mediated free radical formation by using a consistent NO donor, DETA-NONOate. NO-mediated NETs exhibited extracellular bacterial killing as determined by colony forming units. NO-mediated NETs formation was due to the activation of NADPH oxidase and myeloperoxidase. NO- or PMA-mediated NETs were positive for both nuclear and mitochondrial DNA as well as proteolytic enzymes. Incubation of NETs with human platelets enhanced the release of IL-1β and IL-8, while with THP-1 cells, release of IL-1β, IL-8, and TNFα was observed. This study demonstrates that NO by augmenting enzymatic free radical generation release NETs to promote extracellular bacterial killing. These NETs were made up of mitochondrial and nuclear DNA and potentiated release of proinflammatory cytokines.

}, keywords = {Adult, Blood Platelets, DNA, DNA, Mitochondrial, Free Radicals, Humans, Inflammation, Interleukin-1beta, Interleukin-8, Mitochondria, NADPH Oxidases, Neutrophil Activation, Neutrophils, Nitric Oxide, Peroxidase, Tumor Necrosis Factor-alpha}, issn = {1552-4930}, doi = {10.1002/cyto.a.21178}, author = {Keshari, Ravi S and Jyoti, Anupam and Kumar, Sachin and Dubey, Megha and Verma, Anupam and Srinag, Bangalore S and Krishnamurthy, Hanumanthappa and Barthwal, Manoj K and Dikshit, Madhu} }