03400nas a2200469 4500008004100000245021600041210006900257260000800326300002500334490000700359520181800366100002202184700001902206700002802225700002702253700001802280700002402298700002002322700001802342700001902360700002502379700001802404700001802422700001702440700001402457700001702471700002402488700002202512700002202534700003002556700002002586700002202606700002302628700002502651700001502676700001902691700002202710700002002732700003002752700002402782856012402806 2011 eng d00aComparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control0 aComparative genomics of the pathogenic ciliate Ichthyophthirius  cOCT aArticle Number: R1000 v123 aBackground: Ichthyophthirius multifiliis, commonly known as Ich, is a highly pathogenic ciliate responsible for 'white spot', a disease causing significant economic losses to the global aquaculture industry. Options for disease control are extremely limited, and Ich's obligate parasitic lifestyle makes experimental studies challenging. Unlike most well-studied protozoan parasites, Ich belongs to a phylum composed primarily of free-living members. Indeed, it is closely related to the model organism Tetrahymena thermophila. Genomic studies represent a promising strategy to reduce the impact of this disease and to understand the evolutionary transition to parasitism. Results: We report the sequencing, assembly and annotation of the Ich macronuclear genome. Compared with its free-living relative T. thermophila, the Ich genome is reduced approximately two-fold in length and gene density and three-fold in gene content. We analyzed in detail several gene classes with diverse functions in behavior, cellular function and host immunogenicity, including protein kinases, membrane transporters, proteases, surface antigens and cytoskeletal components and regulators. We also mapped by orthology Ich's metabolic pathways in comparison with other ciliates and a potential host organism, the zebrafish Danio rerio. Conclusions: Knowledge of the complete protein-coding and metabolic potential of Ich opens avenues for rational testing of therapeutic drugs that target functions essential to this parasite but not to its fish hosts. Also, a catalog of surface protein-encoding genes will facilitate development of more effective vaccines. The potential to use T. thermophila as a surrogate model offers promise toward controlling 'white spot' disease and understanding the adaptation to a parasitic lifestyle.1 aCoyne, Robert, S.1 aHannick, Linda1 aShanmugam, Dhanasekaran1 aHostetler, Jessica, B.1 aBrami, Daniel1 aJoardar, Vinita, S.1 aJohnson, Justin1 aRadune, Diana1 aSingh, Irtisha1 aBadger, Jonathan, H.1 aKumar, Ujjwal1 aSaier, Milton1 aWang, Yufeng1 aCai, Hong1 aGu, Jianying1 aMather, Michael, W.1 aVaidya, Akhil, B.1 aWilkes, David, E.1 aRajagopalan, Vidyalakshmi1 aAsai, David, J.1 aPearson, Chad, G.1 aFindly, Robert, C.1 aDickerson, Harry, W.1 aWu, Martin1 aMartens, Cindy1 aVan de Peer, Yves1 aRoos, David, S.1 aCassidy-Hanley, Donna, M.1 aClark, Theodore, G. uhttps://library.ncl.res.in/content/comparative-genomics-pathogenic-ciliate-ichthyophthirius-multifiliis-its-free-living03263nas a2200385 4500008004100000245015400041210006900195260000800264490000600272520195200278100002202230700002302252700002202275700001802297700003002315700003002345700002302375700002002398700002002418700002302438700001902461700002802480700002002508700002302528700001702551700002302568700002502591700002002616700002002636700002502656700002202681700001602703700002702719856013102746 2012 eng d00aComparative genomics of the apicomplexan parasites toxoplasma gondii and neospora caninum: coccidia differing in host range and transmission strategy0 aComparative genomics of the apicomplexan parasites toxoplasma go cMAR0 v83 aToxoplasma gondii is a zoonotic protozoan parasite which infects nearly one third of the human population and is found in an extraordinary range of vertebrate hosts. Its epidemiology depends heavily on horizontal transmission, especially between rodents and its definitive host, the cat. Neospora caninum is a recently discovered close relative of Toxoplasma, whose definitive host is the dog. Both species are tissue-dwelling Coccidia and members of the phylum Apicomplexa; they share many common features, but Neospora neither infects humans nor shares the same wide host range as Toxoplasma, rather it shows a striking preference for highly efficient vertical transmission in cattle. These species therefore provide a remarkable opportunity to investigate mechanisms of host restriction, transmission strategies, virulence and zoonotic potential. We sequenced the genome of N. caninum and transcriptomes of the invasive stage of both species, undertaking an extensive comparative genomics and transcriptomics analysis. We estimate that these organisms diverged from their common ancestor around 28 million years ago and find that both genomes and gene expression are remarkably conserved. However, in N. caninum we identified an unexpected expansion of surface antigen gene families and the divergence of secreted virulence factors, including rhoptry kinases. Specifically we show that the rhoptry kinase ROP18 is pseudogenised in N. caninum and that, as a possible consequence, Neospora is unable to phosphorylate host immunity-related GTPases, as Toxoplasma does. This defense strategy is thought to be key to virulence in Toxoplasma. We conclude that the ecological niches occupied by these species are influenced by a relatively small number of gene products which operate at the host-parasite interface and that the dominance of vertical transmission in N. caninum may be associated with the evolution of reduced virulence in this species.1 aReid, Adam, James1 aVermont, Sarah, J.1 aCotton, James, A.1 aHarris, David1 aHill-Cawthorne, Grant, A.1 aKoenen-Waisman, Stephanie1 aLatham, Sophia, M.1 aMourier, Tobias1 aNorton, Rebecca1 aQuail, Michael, A.1 aSanders, Mandy1 aShanmugam, Dhanasekaran1 aSohal, Amandeep1 aWasmuth, James, D.1 aBrunk, Brian1 aGrigg, Michael, E.1 aHoward, Jonathan, C.1 aParkinson, John1 aRoos, David, S.1 aTrees, Alexander, J.1 aBerriman, Matthew1 aPain, Arnab1 aWastling, Jonathan, M. uhttps://library.ncl.res.in/content/comparative-genomics-apicomplexan-parasites-toxoplasma-gondii-and-neospora-caninum-coccidia02014nas a2200205 4500008004100000245006500041210006400106260000800170300001600178490000700194520133900201100002501540700002601565700002601591700002201617700002001639700002801659700002801687856009301715 2012 eng d00aTDR Targets: a chemogenomics resource for neglected diseases0 aTDR Targets a chemogenomics resource for neglected diseases cJAN aD1118-D11270 v403 aThe TDR Targets Database (http://tdrtargets.org) has been designed and developed as an online resource to facilitate the rapid identification and prioritization of molecular targets for drug development, focusing on pathogens responsible for neglected human diseases. The database integrates pathogen specific genomic information with functional data (e.g. expression, phylogeny, essentiality) for genes collected from various sources, including literature curation. This information can be browsed and queried using an extensive web interface with functionalities for combining, saving, exporting and sharing the query results. Target genes can be ranked and prioritized using numerical weights assigned to the criteria used for querying. In this report we describe recent updates to the TDR Targets database, including the addition of new genomes (specifically helminths), and integration of chemical structure, property and bioactivity information for biological ligands, drugs and inhibitors and cheminformatic tools for querying and visualizing these chemical data. These changes greatly facilitate exploration of linkages (both known and predicted) between genes and small molecules, yielding insight into whether particular proteins may be druggable, effectively allowing the navigation of chemical space in a genomics context.1 aMagarinos, Maria, P.1 aCarmona, Santiago, J.1 aCrowther, Gregory, J.1 aRalph, Stuart, A.1 aRoos, David, S.1 aShanmugam, Dhanasekaran1 aVan Voorhis, Wesley, C. uhttps://library.ncl.res.in/content/tdr-targets-chemogenomics-resource-neglected-diseases03245nas a2200649 4500008004100000022001400041245011300055210006900168260009900237300002700336490000600363520119100369100001801560700001901578700002101597700002601618700002001644700001801664700001701682700002801699700002301727700002401750700001901774700001701793700002201810700002001832700002101852700002601873700002001899700001601919700002101935700002501956700001901981700002802000700002002028700001802048700001702066700002602083700002302109700002702132700002402159700001802183700001802201700001602219700002402235700002202259700001802281700002502299700002002324700002002344700002602364700002102390700001802411700002202429700001602451856012802467 2015 eng d a2050-084X00aChromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites0 aChromerid genomes reveal the evolutionary path from photosynthet aSHERATON HOUSE, CASTLE PARK, CAMBRIDGE, CB3 0AX, ENGLANDbELIFE SCIENCES PUBLICATIONS LTDcJUL aArticle Number: e069740 v43 a

The eukaryotic phylum Apicomplexa encompasses thousands of obligate intracellular parasites of humans and animals with immense socio-economic and health impacts. We sequenced nuclear genomes of Chromera velia and Vitrella brassicaformis, free-living non-parasitic photosynthetic algae closely related to apicomplexans. Proteins from key metabolic pathways and from the endomembrane trafficking systems associated with a free-living lifestyle have been progressively and non-randomly lost during adaptation to parasitism. The free-living ancestor contained a broad repertoire of genes many of which were repurposed for parasitic processes, such as extracellular proteins, components of a motility apparatus, and DNA-and RNA-binding protein families. Based on transcriptome analyses across 36 environmental conditions, Chromera orthologs of apicomplexan invasion-related motility genes were co-regulated with genes encoding the flagellar apparatus, supporting the functional contribution of flagella to the evolution of invasion machinery. This study provides insights into how obligate parasites with diverse life strategies arose from a once free-living phototrophic marine alga.

1 aWoo, Yong, H.1 aAnsari, Hifzur1 aOtto, Thomas, D.1 aKlinger, Christen, M.1 aKolisko, Martin1 aMichalek, Jan1 aSaxena, Alka1 aShanmugam, Dhanasekaran1 aTayyrov, Annageldi1 aVeluchamy, Alaguraj1 aAli, Shahjahan1 aBernal, Axel1 adel Campo, Javier1 aCihlar, Jaromir1 aFlegontov, Pavel1 aGornik, Sebastian, G.1 aHajduskova, Eva1 aHorak, Ales1 aJanouskovec, Jan1 aKatris, Nicholas, J.1 aMast, Fred, D.1 aMiranda-Saavedra, Diego1 aMourier, Tobias1 aNaeem, Raeece1 aNair, Mridul1 aPanigrahi, Aswini, K.1 aRawlings, Neil, D.1 aPadron-Regalado, Eriko1 aRamaprasad, Abhinay1 aSamad, Nadira1 aTomcala, Ales1 aWilkes, Jon1 aNeafsey, Daniel, E.1 aDoerig, Christian1 aBowler, Chris1 aKeeling, Patrick, J.1 aRoos, David, S.1 aDacks, Joel, B.1 aTempleton, Thomas, J.1 aWaller, Ross, F.1 aLukes, Julius1 aObornik, Miroslav1 aPain, Arnab uhttps://library.ncl.res.in/content/chromerid-genomes-reveal-evolutionary-path-photosynthetic-algae-obligate-intracellular-102643nas a2200301 4500008004100000022001400041245005500055210005500110260006700165300001200232490000700244520171800251653001701969653001201986653001401998653001102012653002002023653000902043100002502052700002302077700002102100700002402121700002102145700003602166700002802202700002502230856008602255 2015 eng d a1615-985300aInvestigation of phosphoproteome in RAGE signaling0 aInvestigation of phosphoproteome in RAGE signaling a111 RIVER ST, HOBOKEN 07030-5774, NJ USAbWILEY-BLACKWELLcJAN a245-2590 v153 a

The receptor for advanced glycation end products (RAGE) is one of the most important proteins implicated in diabetes, cardiovascular diseases, neurodegenerative diseases, and cancer. It is a pattern recognition receptor by virtue of its ability to interact with multiple ligands, RAGE activates several signal transduction pathways through involvement of various kinases that phosphorylate their respective substrates. Only few substrates have been known to be phosphorylated in response to activation by RAGE (e.g., nuclear factor kappa B); however, it is possible that these kinases can phosphorylate multiple substrates depending upon their expression and localization, leading to altered cellular responses in different cell types and conditions. One such example is, glycogen synthase kinase 3 beta which is known to phosphorylate glycogen synthase, acts downstream to RAGE, and hyperphosphorylates microtubule-associated protein tau causing neuronal damage. Thus, it is important to understand the role of various RAGE-activated kinases and their substrates. Therefore, we have reviewed here the details of RAGE-activated kinases in response to different ligands and their respective phosphoproteome. Furthermore, we discuss the analysis of the data mined for known substrates of these kinases from the PhosphoSitePlus (http://www.phosphosite.org) database, and the role of some of the important substrates involved in cancer, diabetes, cardiovascular diseases, and neurodegenerative diseases. In summary, this review provides information on RAGE-activated kinases and their phosphoproteome, which will be helpful in understanding the possible role of RAGE and its ligands in progression of diseases.

10aCell biology10aDisease10aGlycation10aKinase10aPhosphoproteome10aRAGE1 aBatkulwar, Kedar, B.1 aBansode, Sneha, B.1 aPatil, Gouri, V.1 aGodbole, Rashmi, K.1 aKazi, Rubina, S.1 aChinnathambi, Subashchandrabose1 aShanmugam, Dhanasekaran1 aKulkarni, Mahesh, J. uhttps://library.ncl.res.in/content/investigation-phosphoproteome-rage-signaling-001985nas a2200301 4500008004100000022001400041245011300055210006900168260006700237300001200304490000700316520091400323653001601237653003001253653001601283100002601299700002401325700002801349700002801377700001801405700002001423700002301443700002401466700002001490700002201510700002101532856013001553 2015 eng d a1744-309100aIron superoxide dismutases in eukaryotic pathogens: new insights from apicomplexa and trypanosoma structures0 aIron superoxide dismutases in eukaryotic pathogens new insights  a111 RIVER ST, HOBOKEN 07030-5774, NJ USAbWILEY-BLACKWELLcMAY a615-6210 v713 a

Prior studies have highlighted the potential of superoxide dismutases as drug targets in eukaryotic pathogens. This report presents the structures of three iron-dependent superoxide dismutases (FeSODs) from Trypanosoma cruzi, Leishmania major and Babesia bovis. Comparison with existing structures from Plasmodium and other trypanosome isoforms shows a very conserved overall fold with subtle differences. In particular, structural data suggest that B. bovis FeSOD may display similar resistance to peroxynitrite-mediated inactivation via an intramolecular electron-transfer pathway as previously described in T. cruzi FeSOD isoform B, thus providing valuable information for structure-based drug design. Furthermore, lysine-acetylation results in T. cruzi indicate that acetylation occurs at a position close to that responsible for the regulation of acetylation-mediated activity in the human enzyme.

10aApicomplexa10airon superoxide dismutase10aTrypanosoma1 aPhan, Isabelle, Q. H.1 aDavies, Douglas, R.1 aMoretti, Nilmar, Silvio1 aShanmugam, Dhanasekaran1 aCestari, Igor1 aAnupama, Atashi1 aFairman, James, W.1 aEdwards, Thomas, E.1 aStuart, Kenneth1 aSchenkman, Sergio1 aMyler, Peter, J. uhttps://library.ncl.res.in/content/iron-superoxide-dismutases-eukaryotic-pathogens-new-insights-apicomplexa-and-trypanosoma-002190nas a2200193 4500008004100000245010600041210006900147260000800216300001200224490000600236520148400242100002901726700002401755700001901779700002801798700001901826700002101845856013001866 2015 eng d00aLeucas mollissima, a source of bioactive compounds with antimalarial and antimycobacterium activities0 aLeucas mollissima a source of bioactive compounds with antimalar cJAN ae35-e380 v23 a

A phytochemical investigation of the acetone extract from the aerial parts of Leucas mollissima afforded one new (−)epi-marmelo lactone, (2 S, 4R, 6 S)-2,6-dimethyl-6 hydroxy-7-ene-4-olide (1), along with five known compounds, schensianol A (2), vanillin (3), β-hydroxy propiovanillone (4), lanost-9(11),25-diene-3β,24β-diol (5), and lanost-9(11),23E(24)-diene-3β,25-diol (6). Similarly, an investigation of the methanol extract of the aerial parts of L. mollissima resulted in the isolation of three known compounds, (+)-syringaresinol (7), anisofolin A (8), and apigenin 7-O-β-D(− 6′′-p-E-coumaroyl)-glucoside (9). Structure elucidation of the isolated compounds was carried out using detailed analysis of 1D and 2D nuclear magnetic resonance. All compounds were evaluated for antimalarial activity against Plasmodium falciparum (3D7) and for antimycobacterium activity against Mycobacterium tuberculosis H37Ra and Mycobacterium bovis. Compound 8 was found to have promising antimalarial activity (IC50 4.39 ± 0.25 µM), promising antimycobacterium activity [IC50 4.50 ± 0.75 µM (3.31 µg/mL)] against M. tuberculosis H37Ra and at 100 µg/mL, showed 55.6 % inhibition of M. bovis. Compound 9 showed moderate inhibition of P. falciparum growth (35 % inhibition at 10 µM) with respect to the positive control atovaquone and 67.4 % inhibition against M. bovis at 100 µg/mL with respect to the positive control rifampicin.

1 aChinchansure, Ashish, A.1 aArkile, Manisha, A.1 aShukla, Anurag1 aShanmugam, Dhanasekaran1 aSarkar, Dhiman1 aJoshi, Swati, P. uhttps://library.ncl.res.in/content/leucas-mollissima-source-bioactive-compounds-antimalarial-and-antimycobacterium-activities02827nas a2200409 4500008004100000022001500041245009200056210006900148260000800217490000600225520153200231100002301763700002801786700002501814700002001839700001501859700002501874700002401899700002801923700001801951700002301969700001801992700002302010700001802033700002102051700001802072700002602090700002402116700002702140700002302167700002802190700002002218700001702238700002402255700001802279856012002297 2018 eng d a 2235-298800aCSGID solves structures and identifies phenotypes for five enzymes in toxoplasma gondii0 aCSGID solves structures and identifies phenotypes for five enzym cOCT0 v83 a

Toxoplasma gondii, an Apicomplexan parasite, causes significant morbidity and mortality, including severe disease in immunocompromised hosts and devastating congenital disease, with no effective treatment for the bradyzoite stage. To address this, we used the Tropical Disease Research database, crystallography, molecular modeling, and antisense to identify and characterize a range of potential therapeutic targets for toxoplasmosis. Phosphoglycerate mutase II (PGMII), nucleoside diphosphate kinase (NDK), ribulose phosphate 3-epimerase (RPE), ribose-5-phosphate isomerase (RPI), and ornithine aminotransferase (OAT) were structurally characterized. Crystallography revealed insights into the overall structure, protein oligomeric states and molecular details of active sites important for ligand recognition. Literature and molecular modeling suggested potential inhibitors and druggability. The targets were further studied with vivoPMO to interrupt enzyme synthesis, identifying the targets as potentially important to parasitic replication and, therefore, of therapeutic interest. Targeted vivoPMO resulted in statistically significant perturbation of parasite replication without concomitant host cell toxicity, consistent with a previous CRISPR/Cas9 screen showing PGM, RPE, and RPI contribute to parasite fitness. PGM, RPE, and RPI have the greatest promise for affecting replication in tachyzoites. These targets are shared between other medically important parasites and may have wider therapeutic potential.

1 aLykins, Joseph, D.1 aFilippova, Ekaterina, V1 aHalavaty, Andrei, S.1 aMinasov, George1 aZhou, Ying1 aDubrovska, Ievgeniia1 aFlores, Kristin, J.1 aShuvalova, Ludmilla, A.1 aRuan, Jiapeng1 aBissati, Kamal, El1 aDovgin, Sarah1 aRoberts, Craig, W.1 aWoods, Stuart1 aMoulton, Jon, D.1 aMoulton, Hong1 aMcphillie, Martin, J.1 aMuench, Stephen, P.1 aFishwick, Colin, W. G.1 aSabini, Elisabetta1 aShanmugam, Dhanasekaran1 aRoos, David, S.1 aMcleod, Rima1 aAnderson, Wayne, F.1 aNgo, Huan, M. uhttps://library.ncl.res.in/content/csgid-solves-structures-and-identifies-phenotypes-five-enzymes-toxoplasma-gondii01008nas a2200157 4500008004100000245015600041210006900197260000800266520033300274100002500607700001900632700001900651700002800670700002100698856013100719 2018 eng d00aEfforts to access the potent antitrypanosomal marine natural product janadolide: synthesis of des- tert -butyl janadolide and its biological evaluation0 aEfforts to access the potent antitrypanosomal marine natural pro cFEB3 aTo identify novel antitrypanosomal agents based on Janadolide, a potent macrocyclic polyketide–peptide hybrid, a macrolactonization strategy was explored. We prepared des-tert-butyl Janadolide and evaluated its antitrypanosomal activity. Our findings suggest that the tert-butyl group is necessary for the desired bioactivity.1 aAthawale, Paresh, R.1 aJachak, Gorakh1 aShukla, Anurag1 aShanmugam, Dhanasekaran1 aReddy, Srinivasa uhttps://library.ncl.res.in/content/efforts-access-potent-antitrypanosomal-marine-natural-product-janadolide-synthesis-des-tert01802nas a2200193 4500008004100000022001400041245010800055210006900163260000800232490000700240520109100247100002401338700002401362700002501386700002401411700002101435700002801456856012401484 2018 eng d a2045-232200aEvaluating antimalarial efficacy by tracking glycolysis in Plasmodium falciparum using NMR spectroscopy0 aEvaluating antimalarial efficacy by tracking glycolysis in Plasm cDEC0 v 83 aGlucose is an essential nutrient for Plasmodium falciparum and robust glycolytic activity is indicative of viable parasites. Using NMR spectroscopy, we show that P. falciparum infected erythrocytes consume similar to 20 times more glucose, and trophozoites metabolize similar to 6 times more glucose than ring stage parasites. The glycolytic activity, and hence parasite viability, can be measured within a period of 2 h to 5 h, using this method. This facilitates antimalarial bioactivity screening on ring and trophozoite stage parasites, exclusively. We demonstrate this using potent and mechanistically distinct antimalarial compounds such as chloroquine, atovaquone, cladosporin, DDD107498 and artemisinin. Our findings indicate that ring stage parasites are inherently more tolerant to antimalarial inhibitors, a feature which may facilitate emergence of drug resistance. Thus, there is a need to discover novel antimalarial compounds, which are potent and fast acting against ring stage parasites. The NMR method reported here can facilitate the identification of such molecules.1 aShivapurkar, Rupali1 aHingamire, Tejashri1 aKulkarni, Akshay, S.1 aRajamohanan, P., R.1 aReddy, Srinivasa1 aShanmugam, Dhanasekaran uhttps://library.ncl.res.in/content/evaluating-antimalarial-efficacy-tracking-glycolysis-plasmodium-falciparum-using-nmr02706nas a2200265 4500008004100000022001500041245011400056210006900170260000800239300001200247490000700259520181200266100001902078700002602097700001902123700002402142700002102166700002002187700001402207700002302221700002002244700002002264700002802284856012802312 2018 eng d a 0020-751900a Glycolysis is important for optimal asexual growth and formation of mature tissue cysts by Toxoplasma gondii0 aGlycolysis is important for optimal asexual growth and formation cOCT a955-9680 v483 aToxoplasma gondii can grow and replicate using either glucose or glutamine as the major carbon source. Here, we have studied the essentiality of glycolysis in the tachyzoite and bradyzoite stages of T. gondii, using transgenic parasites that lack a functional hexokinase gene (Delta hk) in RH (Type-1) and Prugniaud (Type-II) strain parasites. Tachyzoite stage 411k parasites exhibit a fitness defect similar to that reported previously for the major glucose transporter mutant, and remain virulent in mice. However, although Prugniaud strain Delta hk tachyzoites were capable of transforming into bradyzoites in vitro, they were severely compromised in their ability to make mature bradyzoite cysts in the brain tissue of mice. Isotopic labelling studies reveal that glucose-deprived tacyzoites utilise glutamine to replenish glycolytic and pentose phosphate pathway intermediates via gluconeogenesis. Interestingly, while glutaminedeprived intracellular Delta hk tachyzoites continued to replicate, extracellular parasites were unable to efficiently invade host cells. Further, studies on mutant tachyzoites lacking a functional phosphoenolpyruvate carboxykinase (Delta pepck1) revealed that glutaminolysis is the sole source of gluconeogenic flux in glucose-deprived parasites. In addition, glutaminolysis is essential for sustaining oxidative phosphorylation in zihk parasites, while wild type (wt) and Delta pepck1 parasites can obtain ATP from either glycolysis or oxidative phosphorylation. This study provides insights into the role of nutrient metabolism during asexual propagation and development of T. gondii, and validates the versatile nature of central carbon and energy metabolism in this parasite. (C) 2018 Australian Society for Parasitology. Published by Elsevier Ltd. All rights reserved.1 aShukla, Anurag1 aOlszewski, Kellen, L.1 aLlinas, Manuel1 aRommereim, Leah, M.1 aFox, Barbara, A.1 aBzik, David, J.1 aXia, Dong1 aWastling, Jonathan1 aBeiting, Daniel1 aRoos, David, S.1 aShanmugam, Dhanasekaran uhttps://library.ncl.res.in/content/glycolysis-important-optimal-asexual-growth-and-formation-mature-tissue-cysts-toxoplasma01900nas a2200193 4500008004100000022001400041245011600055210006900171260000800240300001300248490000700261520120700268100001901475700002001494700002301514700001601537700002801553856012501581 2018 eng d a1545-788500aHighly diverged novel subunit composition of apicomplexan F-type ATP synthase identified from Toxoplasma gondii0 aHighly diverged novel subunit composition of apicomplexan Ftype  cJUL ae20061280 v163 a

The mitochondrial F-type ATP synthase, a multisubunit nanomotor, is critical for maintaining cellular ATP levels. In T. gondii and other apicomplexan parasites, many subunit components necessary for proper assembly and functioning of this enzyme appear to be missing. Here, we report the identification of 20 novel subunits of T. gondii F-type ATP synthase from mass spectrometry analysis of partially purified monomeric (approximately 600 kDa) and dimeric (> 1 MDa) forms of the enzyme. Despite extreme sequence diversification, key F-O subunits a, b, and d can be identified from conserved structural features. Orthologs for these proteins are restricted to apicomplexan, chromerid, and dinoflagellate species. Interestingly, their absence in ciliates indicates a major diversion, with respect to subunit composition of this enzyme, within the alveolate clade. Discovery of these highly diversified novel components of the apicomplexan F-type ATP synthase complex could facilitate the development of novel antiparasitic agents. Structural and functional characterization of this unusual enzyme complex will advance our fundamental understanding of energy metabolism in apicomplexan species.

1 aSalunke, Rahul1 aMourier, Tobias1 aBanerjee, Manidipa1 aPain, Arnab1 aShanmugam, Dhanasekaran uhttps://library.ncl.res.in/content/highly-diverged-novel-subunit-composition-apicomplexan-f-type-atp-synthase-identified01881nas a2200265 4500008004100000022001400041245011900055210006900174260000800243300001400251490000700265520098400272100001601256700001801272700002001290700002101310700002601331700002401357700002801381700001701409700002201426700001701448700002101465856012901486 2018 eng d a0022-262300aSpecific stereoisomeric conformations determine the drug potency of cladosporin scaffold against malarial parasite0 aSpecific stereoisomeric conformations determine the drug potency cJUL a5664-56780 v613 a

The dependence of drug potency on diastereomeric configurations is a key facet. Using a novel general divergent synthetic route for a three-chiral center antimalarial natural product cladosporin, we built its complete library of stereoisomers (cladologs) and assessed their inhibitory potential using parasite-, enzyme-, and structure-based assays. We show that potency is manifest via tetrahyropyran ring conformations that are housed in the ribose binding pocket of parasite lysyl tRNA synthetase (KRS). Strikingly, drug potency between top and worst enantiomers varied 500-fold, and structures of KRS-cladolog complexes reveal that alterations at C3 and C10 are detrimental to drug potency whereas changes at C3 are sensed by rotameric flipping of glutamate 332. Given that scores of antimalarial and anti-infective drugs contain chiral centers, this work provides a new foundation for focusing on inhibitor stereochemistry as a facet of antimicrobial drug development.

1 aDas, Pronay1 aBabbar, Palak1 aMalhotra, Nipun1 aSharma, Manmohan1 aJachak, Goraknath, R.1 aGonnade, Rajesh, G.1 aShanmugam, Dhanasekaran1 aHarlos, Karl1 aYogavel, Manickam1 aSharma, Amit1 aReddy, Srinivasa uhttps://library.ncl.res.in/content/specific-stereoisomeric-conformations-determine-drug-potency-cladosporin-scaffold-against02881nas a2200277 4500008004100000022001300041245016600054210006900220260000800289300001500297490000600312520188200318100002502200700002702225700001902252700001902271700001702290700002202307700002502329700002302354700002102377700002102398700002802419700002902447856012702476 2018 eng d a2379504200aTargeted phenotypic screening in plasmodium falciparum and toxoplasma gondii reveals novel modes of action of medicines for malaria venture malaria box molecules0 aTargeted phenotypic screening in plasmodium falciparum and toxop cJAN a e00534-170 v33 aThe Malaria Box collection includes 400 chemically diverse small molecules with documented potency against malaria parasite growth, but the underlying modes of action are largely unknown. Using complementary phenotypic screens against Plasmodium falciparum and Toxoplasma gondii, we report phenotype-specific hits based on inhibition of overall parasite growth, apicoplast segregation, and egress or host invasion, providing hitherto unavailable insights into the possible mechanisms affected. First, the Malaria Box library was screened against tachyzoite stage T. gondii and the half-maximal effective concentrations (EC50s) of molecules showing ≥80% growth inhibition at 10 µM were determined. Comparison of the EC50s for T. gondii and P. falciparum identified a subset of 24 molecules with nanomolar potency against both parasites. Thirty molecules that failed to induce acute growth inhibition in T. gondii tachyzoites in a 2-day assay caused delayed parasite death upon extended exposure, with at least three molecules interfering with apicoplast segregation during daughter cell formation. Using flow cytometry and microscopy-based examinations, we prioritized 26 molecules with the potential to inhibit host cell egress/invasion during asexual developmental stages of P. falciparum. None of the inhibitors affected digestive vacuole integrity, ruling out a mechanism mediated by broadly specific protease inhibitor activity. Interestingly, five of the plasmodial egress inhibitors inhibited ionophore-induced egress of T. gondii tachyzoites. These findings highlight the advantage of comparative and targeted phenotypic screens in related species as a means to identify lead molecules with a conserved mode of action. Further work on target identification and mechanism analysis will facilitate the development of antiparasitic compounds with cross-species efficacy.1 aSubramanian, Gowtham1 aBelekar, Meenakshi, A.1 aShukla, Anurag1 aTong, Jie, Xin1 aSinha, Ameya1 aChu, Trang, T. T.1 aKulkarni, Akshay, S.1 aPreiser, Peter, R.1 aReddy, Srinivasa1 aTan, Kevin, S. W1 aShanmugam, Dhanasekaran1 aChandramohanadas, Rajesh uhttps://library.ncl.res.in/content/targeted-phenotypic-screening-plasmodium-falciparum-and-toxoplasma-gondii-reveals-novel01559nas a2200217 4500008004100000022001400041245011500055210006900170260000800239300001400247490000700261520076500268100002701033700003001060700001601090700002701106700002301133700002801156700002501184856013201209 2019 eng d a1477-052000aDemystifying a hexuronic acid ligand that recognizes Toxoplasma gondii and blocks its invasion into host cells0 aDemystifying a hexuronic acid ligand that recognizes Toxoplasma  cMAY a4535-45420 v173 a

Toxoplasma gondii is a ubiquitous eukaryotic pathogen responsible for toxoplasmosis in humans and animals. This parasite is an obligate intracellular pathogen and actively invades susceptible host cells, a process which is mediated by specific receptor-ligand interactions. Here, we have identified an unnatural 2,4-disulfated D-glucuronic acid (Di-S-GlcA), a hexuronic acid composed of heparin/ heparan sulfate, as a potential carbohydrate ligand that can selectively bind to T. gondii parasites. More importantly, the gelatin conjugated Di-S-GlcA multivalent probe displayed strong inhibition of parasite entry into host cells. These results open perspective for the future use of Di-S-GlcA epitopes in biomedical applications against toxoplasmosis.

1 aSubramani, Balamurugan1 aShantamurthy, Chethan, D.1 aMaru, Parag1 aBelekar, Meenakshi, A.1 aMardhekar, Sandhya1 aShanmugam, Dhanasekaran1 aKikkeri, Raghavendra uhttps://library.ncl.res.in/content/demystifying-hexuronic-acid-ligand-recognizes-toxoplasma-gondii-and-blocks-its-invasion-host03253nas a2200301 4500008004100000022001400041245015900055210006900214260000800283300001100291490000800302520224400310653002002554653000902574653001402583653000802597653001702605653001402622100002702636700002302663700002102686700001902707700002502726700002402751700002802775700002202803856012602825 2019 eng d a0014-489400aMitochondrial cytochrome oxidase C subunit III (cox3) gene as a sensitive and specific target for molecular detection of Babesia gibsoni infection in dogs0 aMitochondrial cytochrome oxidase C subunit III cox3 gene as a se cNOV a1077710 v2063 a

A PCR targeting mitochondrial cytochrome oxidase subunit III (cox3) for molecular detection of Babesia gibsoni infection in dogs has been developed in this study. Fifty blood samples from suspected clinical cases from dogs, brought to the veterinary college clinics, were examined for presence of B. gibsoni using conventional diagnosis by microscopic examination of Giemsa stained thin blood smears. In addition, species specific PCRs targeting ITS-1 region (BgITS-1 PCR) and nested PCR targeting 18S ribosomal RNA gene (Bg18SnPCR) were carried out. A 634 bp PCR fragment of B. gibsoni cox3 gene was amplified in positive samples from three geographical locations of Satara, Wai and Pune in Maharashtra state of India. From analysis of the sequence of the B. gibsoni cox3 gene, we found that the Indian isolate had 96-98% similarity to the isolate from Japan and China. Post sequencing, de-novo diagnostic primer pair for species specific amplification of 164 bp fragment of B. gibsoni cox3 was designed and the PCR was standardized. The diagnostic results of de-novo Bgcox3 PCR were compared with BgITS-1 PCR and Bg18S nPCR. Thin blood smears detected 22% (11/50) samples positive for small form of Babesia species. The BgITS-1 PCR detected 25% samples (15/50) as positive and Bg18S nPCR detected 80% (40/50) B. gibsoni positive samples. The de-novo Bgcox3 PCR detected 66% (33/50) samples positive for B. gibsoni (at 95% CI). The analytical sensitivity of cox3 PCR was evaluated as 0.000003% parasitaemia or 09 parasites in 100 mu l of blood. The de-novo diagnostic cox3 PCR did not cross react with control positive DNA from other haemoprotozoa and rickettsia like B. vogeli, Hepatozoon canis, Trypanosoma evansi, Ehrlichia cants and Anaplasma platys. Statistically, cox3 PCR had better diagnostic efficiency than ITS-1 PCR in terms of sensitivity (p = 0.0006). No statistically significant difference between results of cox3 PCR and 18S nPCR was observed (p = 0.1760). Kappa values estimated for each test pair showed fair to moderate agreement between the observations. Specificity of Bgcox3 PCR was 100% when compared with microscopy or BgITS-1 PCR. Sensitivity of Bgcox3 PCR was 100% when compared with that of Bg18S nPCR.

10aBabesia gibsoni10acox310aDiagnosis10aDog10amitochondria10amolecular1 aBetgiri, Aishwarya, A.1 aJadhav, Sameer, N.1 aPawde, Mrunalini1 aShukla, Anurag1 aMote, Chandrashekhar1 aPawar, Prashant, D.1 aShanmugam, Dhanasekaran1 aKundu, Krishnendu uhttps://library.ncl.res.in/content/mitochondrial-cytochrome-oxidase-c-subunit-iii-cox3-gene-sensitive-and-specific-target01833nas a2200241 4500008004100000022001400041245012600055210006900181260000800250300001400258490000700272520099600279653001301275653002201288653002001310653002901330653001201359100002201371700001901393700002801412700002601440856012501466 2019 eng d a0739-110200aStructural insights into the unique inhibitory mechanism of Kunitz type trypsin inhibitor from Cicer arietinum L. Vol. 370 aStructural insights into the unique inhibitory mechanism of Kuni cJUL a2669-26770 v373 a

Kunitz-type trypsin inhibitors bind to the active pocket of trypsin causing its inhibition. Plant Kunitz-type inhibitors are thought to be important in defense, especially against insect pests. From sequence analysis of various Kunitz-type inhibitors from plants, we identified CaTI2 from chickpea as a unique variant lacking the functionally important arginine residue corresponding to the soybean trypsin inhibitor (STI) and having a distinct and unique inhibitory loop organization. To further explore the implications of these sequence variations, we obtained the crystal structure of recombinant CaTI2 at 2.8 angstrom resolution. It is evident from the structure that the variations in the inhibitory loop facilitates non-substrate like binding of CaTI2 to trypsin, while the canonical inhibitor STI binds to trypsin in substrate like manner. Our results establish the unique mechanism of trypsin inhibition by CaTI2, which warrant further research into its substrate spectrum.

10aChickpea10acrystal structure10ainhibitory loop10aKunitz trypsin inhibitor10aTrypsin1 aBendre, Ameya, D.1 aSuresh, C., G.1 aShanmugam, Dhanasekaran1 aRamasamy, Sureshkumar uhttps://library.ncl.res.in/content/structural-insights-unique-inhibitory-mechanism-kunitz-type-trypsin-inhibitor-cicer-001015nas a2200265 4500008004100000022001400041245019100055210006900246260000800315300001400323490000600337100002500343700002700368700001900395700001900414700001700433700002200450700002500472700002300497700002100520700002200541700002800563700002900591856012900620 2019 eng d a2379-504200aTargeted phenotypic screening in plasmodium falciparum and toxoplasma gondii reveals novel modes of action of medicines for malaria venture malaria box molecules (vol 3, e00534-17, 2018)0 aTargeted phenotypic screening in plasmodium falciparum and toxop cAPR ae00159-190 v41 aSubramanian, Gowtham1 aBelekar, Meenakshi, A.1 aShukla, Anurag1 aTong, Jie, Xin1 aSinha, Ameya1 aChu, Trang, T. T.1 aKulkarni, Akshay, S.1 aPreiser, Peter, R.1 aReddy, Srinivasa1 aTan, Kevin, S. W.1 aShanmugam, Dhanasekaran1 aChandramohanadas, Rajesh uhttps://library.ncl.res.in/content/targeted-phenotypic-screening-plasmodium-falciparum-and-toxoplasma-gondii-reveals-novel-002270nas a2200241 4500008004100000245007000041210006900111260000900180300001600189490000700205520148900212100002201701700002301723700002401746700001601770700002001786700002801806700002501834700002301859700002101882700002301903856010201926 2020 eng d00aApproach to nigericin derivatives and their therapeutic potential0 aApproach to nigericin derivatives and their therapeutic potentia cNOV  a43085-430910 v103 a

A new nigericin analogue that has been chemically modified was synthesized through a fluorination process from the parent nigericin, produced from a novel Streptomyces strain DASNCL-29. Fermentation strategies were designed for the optimised production of nigericin molecule and subjected for purification and structural analysis. The fermentation process resulted in the highest yield of nigericin (33% (w/w)). Initially, nigericin produced from the strain DASNCL-29 demonstrated polymorphism in its crystal structure, i.e., monoclinic and orthorhombic crystal lattices when crystallised with methanol and hexane, respectively. Furthermore, nigericin produced has been subjected to chemical modification by fluorination to enhance its efficacy. Two fluorinated analogues revealed that they possess a very potent antibacterial activity against Gram positive and Gram negative bacteria. To date, the nigericin molecule has not been reported for any reaction against Gram-negative bacteria, which are increasingly becoming resistant to antibiotics. For the first time, fluorinated analogues of nigericin have shown promising activity. In vitro cytotoxicity analysis of fluorinated analogues demonstrated tenfold lesser toxicity than the parent nigericin. This is the first type of study where the fluorinated analogues of nigericin showed very encouraging activity against Gram-negative organisms; moreover, they can be used as a candidate for treating many serious infections.

1 aSahu, Amit, Kumar1 aSaid, Madhukar, S.1 aHingamire, Tejashri1 aGaur, Megha1 aKhan, Abujunaid1 aShanmugam, Dhanasekaran1 aBarvkar, Vitthal, T.1 aDharne, Mahesh, S.1 aBharde, Atul, A.1 aDastager, Syed, G. uhttps://library.ncl.res.in/content/approach-nigericin-derivatives-and-their-therapeutic-potential01926nas a2200253 4500008004100000022001400041245011500055210006900170260000800239300000900247490000700256520106700263100001801330700001901348700002301367700002201390700002301412700001901435700001801454700001901472700002801491700002401519856012901543 2020 eng d a2041-172300aDistinct metabolic states of a cell guide alternate fates of mutational buffering through altered proteostasis0 aDistinct metabolic states of a cell guide alternate fates of mut cJUN a29260 v113 a

Metabolic changes alter the cellular milieu; can this also change intracellular protein folding? Since proteostasis can modulate mutational buffering, if change in metabolism has the ability to change protein folding, arguably, it should also alter mutational buffering. Here we find that altered cellular metabolic states in E. coli buffer distinct mutations on model proteins. Buffered-mutants have folding problems in vivo and are differently chaperoned in different metabolic states. Notably, this assistance is dependent upon the metabolites and not on the increase in canonical chaperone machineries. Being able to reconstitute the folding assistance afforded by metabolites in vitro, we propose that changes in metabolite concentrations have the potential to alter protein folding capacity. Collectively, we unravel that the metabolite pools are bona fide members of proteostasis and aid in mutational buffering. Given the plasticity in cellular metabolism, we posit that metabolic alterations may play an important role in cellular proteostasis.

1 aVerma, Kanika1 aSaxena, Kanika1 aDonaka, Rajashekar1 aChaphalkar, Aseem1 aRai, Manish, Kumar1 aShukla, Anurag1 aZaidi, Zainab1 aDandage, Rohan1 aShanmugam, Dhanasekaran1 aChakraborty, Kausik uhttps://library.ncl.res.in/content/distinct-metabolic-states-cell-guide-alternate-fates-mutational-buffering-through-altered02262nas a2200217 4500008004100000022001400041245011000055210006900165260000900234300001500243490000700258520148900265100002801754700002601782700002101808700001601829700002801845700002401873700001901897856012801916 2020 eng d a0305-104800aTDR Targets 6: driving drug discovery for human pathogens through intensive chemogenomic data integration0 aTDR Targets 6 driving drug discovery for human pathogens through cJAN  aD992-D10050 v483 a

The volume of biological, chemical and functional data deposited in the public domain is growing rapidly, thanks to next generation sequencing and highly-automated screening technologies. These datasets represent invaluable resources for drug discovery, particularly for less studied neglected disease pathogens. To leverage these datasets, smart and intensive data integration is required to guide computational inferences across diverse organisms. The TDR Targets chemogenomics resource integrates genomic data from human pathogens and model organisms along with information on bioactive compounds and their annotated activities. This report highlights the latest updates on the available data and functionality in TDR Targets 6. Based on chemogenomic network models providing links between inhibitors and targets, the database now incorporates network-driven target prioritizations, and novel visualizations of network subgraphs displaying chemical- and target-similarity neighborhoods along with associated target-compound bioactivity links. Available data can be browsed and queried through a new user interface, that allow users to perform prioritizations of protein targets and chemical inhibitors. As such, TDR Targets now facilitates the investigation of drug repurposing against pathogen targets, which can potentially help in identifying candidate targets for bioactive compounds with previously unknown targets. TDR Targets is available at https://tdrtargets.org.

1 aLandaburu, Lionel, Uran1 aBerenstein, Ariel, J.1 aVidela, Santiago1 aMaru, Parag1 aShanmugam, Dhanasekaran1 aChernomoretz, Ariel1 aAguero, Fernan uhttps://library.ncl.res.in/content/tdr-targets-6-driving-drug-discovery-human-pathogens-through-intensive-chemogenomic-data02901nas a2200349 4500008004100000022001400041245017200055210006900227260000800296300001400304490000700318520169700325653002202022653001102044653003402055653000802089653001702097653002502114653002602139653001402165653003002179100002402209700002402233700002702257700001602284700002502300700002002325700001902345700002802364700002902392856013002421 2020 eng d a0066-480400aWhole-cell phenotypic screening of medicines for malaria venture pathogen box identifies specific inhibitors of plasmodium falciparum late-stage development and egress0 aWholecell phenotypic screening of medicines for malaria venture  cMAY ae01802-190 v643 a

We report a systematic, cellular phenotype-based antimalarial screening of the Medicines for Malaria Venture Pathogen Box collection, which facilitated the identification of specific blockers of late-stage intraerythrocytic development of Plasmodium falciparum. First, from standard growth inhibition assays, we identified 173 molecules with antimalarial activity (50% effective concentration [EC50] <= 10 mu M), which included 62 additional molecules over previously known antimalarial candidates from the Pathogen Box. We identified 90 molecules with EC50 of <= 1 mu M, which had significant effect on the ring-trophozoite transition, while 9 molecules inhibited the trophozoite-schizont transition and 21 molecules inhibited the schizontring transition (with >= 50% parasites failing to proceed to the next stage) at 1 mu M. We therefore rescreened all 173 molecules and validated hits in microscopy to prioritize 12 hits as selective blockers of the schizont-ring transition. Seven of these molecules inhibited the calcium ionophore-induced egress of Toxoplasma gondii, a related apicomplexan parasite, suggesting that the inhibitors may be acting via a conserved mechanism which could be further exploited for target identification studies. We demonstrate that two molecules, MMV020670 and MMV026356, identified as schizont inhibitors in our screens, induce the fragmentation of DNA in merozoites, thereby impairing their ability to egress and invade. Further mechanistic studies would facilitate the therapeutic exploitation of these molecules as broadly active inhibitors targeting late-stage development and egress of apicomplexan parasites relevant to human health.

10aDNA fragmentation10aegress10aMedicines for Malaria Venture10aMMV10aPathogen Box10aphenotypic screening10aPlasmodium falciparum10aschizonts10astage-specific inhibition1 aPatra, Alok, Tanala1 aHingamire, Tejashri1 aBelekar, Meenakshi, A.1 aXiong, Aoli1 aSubramanian, Gowtham1 aBozdech, Zbynek1 aPreiser, Peter1 aShanmugam, Dhanasekaran1 aChandramohanadas, Rajesh uhttps://library.ncl.res.in/content/whole-cell-phenotypic-screening-medicines-malaria-venture-pathogen-box-identifies-specific02698nas a2200205 4500008004100000245008900041210006900130260000800199300001600207490000700223520201600230100003302246700002602279700003502305700002802340700002802368700002602396700002002422856005002442 2021 eng d00aAntitumor effects of Ir(III)-2H-indazole complexes for triple negative breast cancer0 aAntitumor effects of IrIII2Hindazole complexes for triple negati cNOV a17593-176070 v603 aIn this work, we have synthesized a series of novel C,N-cyclometalated 2H-indazole-ruthenium(II) and -iridium(III) complexes with varying substituents (H, CH3, isopropyl, and CF3) in the R4 position of the phenyl ring of the 2H-indazole chelating ligand. All of the complexes were characterized by 1H, 13C, high-resolution mass spectrometry, and elemental analysis. The methyl-substituted 2H-indazole-Ir(III) complex was further characterized by single-crystal X-ray analysis. The cytotoxic activity of new ruthenium(II) and iridium(III) compounds has been evaluated in a panel of triple negative breast cancer (TNBC) cell lines (MDA-MB-231 and MDA-MB-468) and colon cancer cell line HCT-116 to investigate their structure–activity relationships. Most of these new complexes have shown appreciable activity, comparable to or significantly better than that of cisplatin in TNBC cell lines. R4 substitution of the phenyl ring of the 2H-indazole ligand with methyl and isopropyl substituents showed increased potency in ruthenium(II) and iridium(III) complexes compared to that of their parent compounds in all cell lines. These novel transition metal-based complexes exhibited high specificity toward cancer cells by inducing alterations in the metabolism and proliferation of cancer cells. In general, iridium complexes are more active than the corresponding ruthenium complexes. The new Ir(III)-2H-indazole complex with an isopropyl substituent induced mitochondrial damage by generating large amounts of reactive oxygen species (ROS), which triggered mitochondrion-mediated apoptosis in TNBC cell line MDA-MB-468. Moreover, this complex also induced G2/M phase cell cycle arrest and inhibited cellular migration of TNBC cells. Our findings reveal the key roles of the novel C–N-cyclometalated 2H-indazole-Ir(III) complex to specifically induce toxicity in cancer cell lines through contributing effects of ROS-induced mitochondrial disruption along with chromosomal and mitochondrial DNA target inhibition.1 aPanchangam, Rajeeva, Lochana1 aRao, Ramdas, Nishanth1 aBalamurali, Musuvathi, Motilal1 aHingamire, Tejashri, B.1 aShanmugam, Dhanasekaran1 aManickam, Venkatraman1 aChanda, Kaushik uhttps://doi.org/10.1021/acs.inorgchem.1c0219302082nas a2200361 4500008004100000022001400041245011700055210006900172260000800241300001100249490000900260520094000269653001501209653000901224653001701233653001801250653001501268653003001283100002101313700002201334700002001356700002401376700001901400700001701419700001801436700002301454700002801477700001301505700002301518700002201541700002701563856013001590 2021 eng d a1388-198100aChronic systemic exposure to IL6 leads to deregulation of glycolysis and fat accumulation in the zebrafish liver0 aChronic systemic exposure to IL6 leads to deregulation of glycol cMAY a1589050 v18663 a

Inflammation is a constant in Non-Alcoholic Fatty Liver Disease (NAFLD), although their relationship is unclear. In a transgenic zebrafish system with chronic systemic overexpression of human IL6 (IL6-OE) we show that inflammation can cause intra-hepatic accumulation of triglycerides. Transcriptomics and proteomics analysis of the IL6-OE liver revealed a deregulation of glycolysis/gluconeogenesis pathway, especially a striking down regulation of the glycolytic enzyme aldolase b. Metabolomics analysis by mass spectrometry showed accumulation of hexose monophosphates and their derivatives, which can act as precursors for triglyceride synthesis. Our results suggest that IL6-driven repression of glycolysis/gluconeogenesis, specifically aldolase b, may be a novel mechanism for fatty liver. This mechanism may be relevant for NAFLD in lean individuals, an emerging class of NAFLD prevalent more in Asian Indian populations.

10aAldolase b10aDHAP10aInflammation10aInterleukin 610aLean NAFLD10aNon-alcoholic fatty liver1 aSingh, Manoj, K.1 aJayarajan, Rijith1 aVarshney, Swati1 aUpadrasta, Sindhuri1 aSingh, Archana1 aYadav, Rajni1 aScaria, Vinod1 aSengupta, Shantanu1 aShanmugam, Dhanasekaran1 aShalimar1 aSivasubbu, Sridhar1 aGandotra, Sheetal1 aSachidanandan, Chetana uhttps://library.ncl.res.in/content/chronic-systemic-exposure-il6-leads-deregulation-glycolysis-and-fat-accumulation-zebrafish02394nas a2200253 4500008004100000245009100041210006900132260000800201300001100209490000600220520153500226653001201761653004001773653002801813653002701841100001801868700002001886700001601906700002101922700002401943700002801967700002401995856012102019 2021 eng d00aConserved RNA binding activity of phosphatidyl inositol 5-phosphate 4-kinase (PIP4K2A)0 aConserved RNA binding activity of phosphatidyl inositol 5phospha cMAY a6312810 v83 aPlasmodium falciparum is a causative agent for malaria and has a complex life cycle in human and mosquito hosts. During its life cycle, the malarial parasite Plasmodium goes through different asexual and sexual stages, in humans and mosquitoes. Expression of stage-specific proteins is important for successful completion of its life cycle and requires tight gene regulation. In the case of Plasmodium, due to relative paucity of the transcription factors, it is postulated that posttranscriptional regulation plays an important role in stage-specific gene expression. Translation repression of specific set of mRNA has been reported in gametocyte stages of the parasite. A conserved element present in the 3 ` UTR of some of these transcripts was identified. Phosphatidylinositol 5-phosphate 4-kinase (PIP4K2A) was identified as the protein that associates with these RNA. We now show that the RNA binding activity of PIP4K2A is independent of its kinase activity. We also observe that PIP4K2A is imported into the parasite from the host on Plasmodium berghei and Toxoplasma gondii. The RNA binding activity of PIP4K2A seems to be conserved across species from Drosophila and C. elegans to humans, suggesting that the RNA binding activity of PIP4K may be important, and there may be host transcripts that may be regulated by PIP4K2A. These results identify a novel RNA binding role for PIP4K2A that may not only play a role in Plasmodium propagation but may also function in regulating gene expression in multicellular organisms.10amalaria10aposttranscriptional gene regulation10aRNA-protein interaction10atranslation regulation1 aBehari, Jatin1 aBorkar, Pranita1 aVindu, Arya1 aDandewad, Vishal1 aUpadrasta, Sindhuri1 aShanmugam, Dhanasekaran1 aSeshadri, Vasudevan uhttps://library.ncl.res.in/content/conserved-rna-binding-activity-phosphatidyl-inositol-5-phosphate-4-kinase-pip4k2a02984nas a2200301 4500008004100000022001400041245008000055210006900135260000900204300000700213490000800220520207700228653001002305653001802315653001202333653001602345653001702361653002802378653001002406100001602416700002602432700002702458700002202485700002802507700002102535700002002556856010602576 2021 eng d a0032-093500aInfluence of domestication on specialized metabolic pathways in fruit crops0 aInfluence of domestication on specialized metabolic pathways in  cFEB  a610 v2533 a

Main conclusionDuring the process of plant domestication, the selection and traditional breeding for desired characters such as flavor, juiciness and nutritional value of fruits, probably have resulted in gain or loss of specialized metabolites contributing to these traits. Their appearance in fruits is likely due to the acquisition of novel and specialized metabolic pathways and their regulation, driven by systematic molecular evolutionary events facilitated by traditional breeding.AbstractPlants change their armory of specialized metabolism to adapt and survive in diverse ecosystems. This may occur through molecular evolutionary events, such as single nucleotide polymorphism, gene duplication and transposition, leading to convergent or divergent evolution of biosynthetic pathways producing such specialized metabolites. Breeding and selection for improved specific and desired traits (fruit size, color, taste, flavor, etc.) in fruit crops through conventional breeding approaches may further alter content and profile of specialized metabolites. Biosynthetic routes of these metabolites have been studied in various plants. Here, we explore the influence of plant domestication and breeding processes on the selection of biosynthetic pathways of favorable specialized metabolites in fruit crops. An orderly clustered arrangement of genes associated with their production is observed in many fruit crops. We further analyzed selection-based acquisition of specialized metabolic pathways comparing first the metabolic profiles and genes involved in their biosynthesis, followed by the genomic organization of such genes between wild and domesticated horticultural crops. Domestication of crop plants favored the acquisition and retention of metabolic pathways that enhanced the fruit value while eliminated those which produced toxic or unfavorable metabolites. Interestingly, unintentional reorganization of complex metabolic pathways by selection and traditional breeding processes has endowed us with flavorful, juicy and nutritionally rich fruits.

10aAroma10aDomestication10aFlavour10aFruit crops10aGene cluster10aSpecialized metabolites10aTaste1 aDar, Saleem1 aDholakia, Bhushan, B.1 aKulkarni, Abhijeet, P.1 aOak, Pranjali, S.1 aShanmugam, Dhanasekaran1 aGupta, Vidya, S.1 aGiri, Ashok, P. uhttps://library.ncl.res.in/content/influence-domestication-specialized-metabolic-pathways-fruit-crops01129nas a2200241 4500008004100000022001400041245007400055210006900129260000900198300001400207490000900221520036100230653001800591653001500609653002300624653001600647100002700663700002300690700001900713700002800732700002100760856010600781 2021 eng d a1434-193X00aSynthesis and biological evaluation of hoshionolactam-based compounds0 aSynthesis and biological evaluation of hoshionolactambased compo cAPR  a2212-22180 v20213 aIn search of novel antitrypanosomal agents based on hoshinolactam (IC50=3.9 nM), we disclose the synthesis and biological evaluations of 14 different analogues of the natural product using combinations of different acids and lactams. Antitrypanosomal activity assays revealed that the synthesized analogues were less potent than the parent natural product.10aHoshinolactam10aOzonolysis10aParasitic diseases10aTrypanosoma1 aJachak, Gorakhnath, R.1 aElizebath, Drishya1 aShukla, Anurag1 aShanmugam, Dhanasekaran1 aReddy, Srinivasa uhttps://library.ncl.res.in/content/synthesis-and-biological-evaluation-hoshionolactam-based-compounds02085nas a2200253 4500008004100000022001400041245009600055210006900151260000800220300001400228490000800242520125000250100001801500700001901518700002001537700002001557700002101577700002101598700002101619700002801640700002601668700002201694856011501716 2022 eng d a0002-963700aCase report: a fatal case of babesiosis in a splenectomized male patient from Western India0 aCase report a fatal case of babesiosis in a splenectomized male  cMAY a1421-14250 v1063 a

Human babesiosis is a rare disease, caused by Babesia species and commonly transmitted by tick bite. Although human babesiosis is known to be asymptomatic in immunocompetent hosts, clinical cases of severe babesiosis have been reported from splenectomized or immunocompromised individuals. To our knowledge, only one case of human babesiosis in India has been previously reported. Here, we report a case of severe babesiosis with high parasitemia (similar to 70%) in a 30-year-old asplenic farmer. The patient presented with fever, yellowish discoloration of skin, oliguria, and anemia; he eventually developed multiorgan failure syndrome and died. Peripheral blood films were prepared and used to confirm the presence of piroplasms by microscopy. Total DNA isolated from blood was used for 18S ribosomal RNA gene fragment amplification by polymerase chain reaction, which was subjected to Sanger sequencing. Although 18S sequence indicated that the Babesia species infecting the patient was similar to that of other Babesia species originating from wild mammals, species identification could not be done. Phylogenetic analysis revealed that the patientderived pathogen is distinct because it forms a separate clade in the cladogram.

1 aGodbole, Ravi1 aGaur, Avantika1 aNayar, Priyanka1 aKiruthiga, Kala1 aD'Costa, Pradeep1 aManchanda, Rumma1 aKhilari, Ajinkya1 aShanmugam, Dhanasekaran1 aMuglikar, Kalpana, D.1 aKundu, Krishnendu uhttps://library.ncl.res.in/content/case-report-fatal-case-babesiosis-splenectomized-male-patient-western-india03197nas a2200277 4500008004100000022001400041245015400055210006900209260000800278300001000286490000700296520225700303653001302560653002102573653001702594653000702611653002002618653000902638653001802647653003102665653002902696100001802725700002802743700001902771856012902790 2022 eng d a1096-717600aEngineering nucleotide sugar synthesis pathways for independent and simultaneous modulation of N-glycan galactosylation and fucosylation in CHO cells0 aEngineering nucleotide sugar synthesis pathways for independent  cNOV a61-710 v743 a

Glycosylation of recombinant therapeutics like monoclonal antibodies (mAbs) is a critical quality attribute. N-glycans in mAbs are known to affect various effector functions, and thereby therapeutic use of such glycoproteins can depend on a particular glycoform profile to achieve desired efficacy. However, there are currently limited options for modulating the glycoform profile, which depend mainly on over-expression or knock-out of glyco-syltransferase enzymes that can introduce or eliminate specific glycans but do not allow predictable glycoform modulation over a range of values. In this study, we demonstrate the ability to predictably modulate the gly-coform profile of recombinant IgG. Using CRISPR/Cas9, we have engineered nucleotide sugar synthesis pathways in CHO cells expressing recombinant IgG for combinatorial modulation of galactosylation and fucosylation. Knocking out the enzymes UDP-galactose 4 `-epimerase (Gale) and GDP-L-fucose synthase (Fx) resulted in ablation of de novo synthesis of UDP-Gal and GDP-Fuc. With Gale knock-out, the array of N-glycans on recom-binantly expressed IgG is narrowed to agalactosylated glycans, mainly A2F glycan (89%). In the Gale and Fx double knock-out cell line, agalactosylated and afucosylated A2 glycan is predominant (88%). In the double knock-out cell line, galactosylation and fucosylation was entirely dependent on the salvage pathway, which allowed for modulation of UDP-Gal and GDP-Fuc synthesis and intracellular nucleotide sugar availability by controlling the availability of extracellular galactose and fucose. We demonstrate that the glycoform profile of recombinant IgG can be modulated from containing predominantly agalactosylated and afucosylated glycans to up to 42% and 96% galactosylation and fucosylation, respectively, by extracellular feeding of sugars in a dose-dependent manner. By simply varying the availability of extracellular galactose and/or fucose, galactosylation and fucosylation levels can be simultaneously and independently modulated. In addition to achieving the pro-duction of tailored glycoforms, this engineered CHO host platform can cater to the rapid synthesis of variably glycoengineered proteins for evaluation of biological activity.

10aAntibody10aCell engineering10aFucosylation10aFx10aGalactosylation10aGale10aglycosylation10aNucleotide sugar synthesis10aRecombinant therapeutics1 aPrabhu, Anuja1 aShanmugam, Dhanasekaran1 aGadgil, Mugdha uhttps://library.ncl.res.in/content/engineering-nucleotide-sugar-synthesis-pathways-independent-and-simultaneous-modulation-n02296nas a2200241 4500008004100000022001400041245011200055210006900167260000800236300001100244490000800255520148600263653001801749653002401767653001201791653001501803653001501818100002501833700001901858700002801877700001701905856013201922 2022 eng d a0166-685100aProfiling of metabolic alterations in mice infected with malaria parasites via high-resolution metabolomics0 aProfiling of metabolic alterations in mice infected with malaria cNOV a1115250 v2523 a

Background: Malaria infection can result in distinct clinical outcomes from asymptomatic to severe. The association between patho-physiological changes and molecular changes in the host, and their correlation with severity of malaria progression is not fully understood. Methods: In this study, we addressed mass spectrometry-based temporal profiling of serum metabolite levels from mice infected with Plasmodium berhgei (strain ANKA). Results: We show global perturbations and identify changes in specific metabolites in correlation with disease progression. While metabolome-wide changes were apparent in late-stage malaria, a subset of metabolites exhibited highly correlated changes with disease progression. These metabolites changed early on following infection and either continued or maintained the change as mice developed severe disease. Some of these have the potential to be sentinel metabolites for severe malaria. Moreover, glycolytic metabolites, purine nucleotide precursors, tryptophan and its bioactive derivatives were many fold decreased in late-stage disease. Interestingly, uric acid, a metabolic waste reported to be elevated in severe human malaria, increased with disease progression, and subsequently appears to be detoxified into allantoin. This detoxification mechanism is absent in humans as they lack the enzyme uricase. Conclusions: We have identified candidate marker metabolites that may be of relevance in the context of human malaria.

10aHost response10aInfectious diseases10amalaria10ametabolite10aPlasmodium1 aChhibber-Goel, Jyoti1 aShukla, Anurag1 aShanmugam, Dhanasekaran1 aSharma, Amit uhttps://library.ncl.res.in/content/profiling-metabolic-alterations-mice-infected-malaria-parasites-high-resolution-metabolomics03191nas a2200313 4500008004100000022001400041245011700055210006900172260000800241300001200249490000700261520213700268653002902405653002602434653001202460653002602472653001802498100002302516700002502539700002802564700002402592700002802616700002202644700002402666700001902690700001802709700002202727856012802749 2023 eng d a1230-282100aAntimalarial activity of anacardium occidentale leaf extracts against plasmodium falciparum transketolase (PfTK)0 aAntimalarial activity of anacardium occidentale leaf extracts ag cDEC a832-8410 v683 a

BackgroundAs per estimates by WHO in 2021 almost half of the world's population was at risk of malaria and > 0.6 million deaths were attributed to malaria. Therefore, the present study was aimed to explore the antimalarial activity of extracts derived from the leaves of the plant Anacardium occidentale L., which has been used traditionally for the treatment of malaria. Different extracts of A.occidentale leaves were prepared and tested for their inhibitory activity against recombinant P. falciparum transketolase (rPfTK) enzyme, in vitro. Further, growth inhibitory activity against cultivated blood stage P. falciparum parasites (3D7 strain), was studied using SYBR Green fluorescence-based in vitro assays. Acute toxicity of the hydro alcoholic extracts of leaves of A. occidentale (HELA) at different concentrations was evaluated on mice and Zebra fish embryos. HELA showed 75.45 +/- 0.35% inhibitory activity against the recombinant PfTk and 99.31 +/- 0.08% growth inhibition against intra-erythrocytic stages of P. falciparum at the maximum concentration (50 mu g/ml) with IC50 of 4.17 +/- 0.22 mu g/ml. The toxicity test results showed that the heartbeat, somite formation, tail detachment and hatching of embryos were not affected when Zebra fish embryos were treated with 0.1 to 10 mu g/ml of the extract. However, at higher concentrations of the extract, at 48 h (1000 mu g/ml) and 96 h (100 mu g/ml and 1000 mu g/ml, respectively) there was no heartbeat in the fish embryos. In the acute oral toxicity tests performed on mice, the extract showed no toxicity up to 300 mg/kg body weight in mice.ConclusionThe hydro-alcoholic extract of leaves of A. occidentale L. showed potent antimalarial activity against blood stage P. falciparum. Based on the observed inhibitory activity on the transketolase enzyme of P. falciparum it is likely that this enzyme is the target for the development of bioactive molecules present in the plant extracts. The promising anti-malarial activity of purified compounds from leaves of A. occidentale needs to be further explored for development of new anti-malarial therapy.

10aAnacardium occidentale L10aAntimalarial activity10amalaria10aPlasmodium falciparum10aTransketolase1 aKaushik, Meenakshi1 aHoti, Sugeerappa, L.1 aSaxena, Jitendra, Kumar1 aHingamire, Tejashri1 aShanmugam, Dhanasekaran1 aJoshi, Rajesh, K.1 aMetgud, Sharada, C.1 aUngar, Banappa1 aSingh, Ishwar1 aHegde, Harsha, V. uhttps://library.ncl.res.in/content/antimalarial-activity-anacardium-occidentale-leaf-extracts-against-plasmodium-falciparum01960nas a2200301 4500008004100000022001400041245004800055210004700103260000900150490000700159520111600166653001601282653001601298653002201314653001201336653001501348653001501363653000601378100002401384700002401408700001701432700002601449700002601475700001801501700002801519700002801547856008301575 2023 eng d a1860-717900aHistidinal-based potent antimalarial agents0 aHistidinalbased potent antimalarial agents cMAY 0 v183 a

Herein we report the synthesis and evaluation of peptide-histidinal conjugated drug scaffolds, which have the potential to target the hemoglobin-degrading proteases falcipain-2/3 from the human malaria parasite. Scaffolds with various substitutions were tested for antimalarial activity, and compounds 8 g, 8 h, and 15 exhibited EC50 values of similar to 0.018 mu M, similar to 0.069 mu M, and similar to 0.02 mu M, respectively. Structure-based docking studies on falcipain-2/3 proteases (PDB:2GHU and PDB:3BWK) revealed that compounds 8 g, 8 h, and 15 interact strongly with binding sites of falcipain-2/3 in a substrate-like manner. In silico ADME studies revealed that the molecules of interest showed no or minimal violations of drug-likeness parameters. Further, phenotypic assays revealed that compound 8 g and its biotinylated version inhibit hemoglobin degradation in the parasite food vacuole. The identification of falcipain-2/3 targeting potent inhibitors of the malaria parasite can serve as a starting point for the development of lead compounds as future antimalarial drug candidates.

10aartemisinin10achloroquine10adigestive vacuole10adocking10afalcipains10afalciparum10aP1 aMeena, Chhuttan, L.1 aHingamire, Tejashri1 aGupta, Tanya1 aDeshmukh, Bhagyashree1 aKarmodiya, Krishanpal1 aJoshi, Rakesh1 aShanmugam, Dhanasekaran1 aSanjayan, Gangadhar, J. uhttps://library.ncl.res.in/content/histidinal-based-potent-antimalarial-agents02193nas a2200241 4500008004100000022001400041245009400055210006900149260000800218300001600226490000600242520135800248100003201606700002501638700001701663700002301680700002201703700002401725700002801749700002801777700002501805856012101830 2023 eng d a2470-134300aNanopore sequencing of RAGE gene polymorphisms and their association with type 2 diabetes0 aNanopore sequencing of RAGE gene polymorphisms and their associa cJUL a25727-257380 v83 a

The receptor foradvanced glycation end products (RAGE)is a transmembraneprotein that interacts with its ligands, advanced glycation end products(AGEs). AGEs are elevated in diabetes and diabetic complications,leading to increased oxidative stress and activation of pro-inflammatorypathways facilitated by AGE-RAGE signaling. Polymorphisms inthe RAGE gene can potentially affect AGE-RAGEinteraction and its downstream signaling, which plays a crucial rolein the progression of diabetes and its complications. In this study,we used nanopore sequencing for genotyping of RAGE polymorphism and identified a maximum number of 33 polymorphisms,including two previously unreported novel mutations in a cohort ofhealthy, type 2 diabetics without nephropathy and type 2 diabeticswith nephropathy in order to identify associations. Two novel RAGE polymorphisms in the intron 8 and 3 & PRIME;UTR regionat genomic locations 32181834 and 32181132, respectively, were detectedwith a low frequency. For four previously reported polymorphisms,cross-validation by PCR-RFLP showed 99.75% concordance with nanoporesequencing. Analysis of genotype distribution and allele frequenciesrevealed that five single nucleotide polymorphisms, i.e., rs1800625,rs3131300, rs3134940, rs2070600, and rs9391855, were associated withan increased risk for type 2 diabetes.

1 aChaurasiya, Arvindkumar, H.1 aKhilari, Ajinkya, A.1 aKazi, Rubina1 aJaiswal, Meera, R.1 aBhoite, Gouri, M.1 aPadwal, Meghana, K.1 aMomin, Abdulrahaman, A.1 aShanmugam, Dhanasekaran1 aKulkarni, Mahesh, J. uhttps://library.ncl.res.in/content/nanopore-sequencing-rage-gene-polymorphisms-and-their-association-type-2-diabetes04148nas a2200589 4500008004100000022001400041245012400055210006900179260000800248300001400256490000700270520236200277653001302639653001002652653001202662653003602674653002302710653003402733100002102767700001702788700002102805700002102826700002102847700001902868700001602887700002302903700001702926700002702943700001902970700001902989700002103008700001803029700002003047700001903067700001903086700002103105700002203126700001903148700002203167700001903189700001803208700001903226700002303245700001803268700002003286700002403306700002603330700002803356700002103384700002603405856012703431 2023 eng d a1876-034100aTale of two waves: Delineating diverse genomic and transmission landscapes driving the COVID-19 pandemic in Pune, India0 aTale of two waves Delineating diverse genomic and transmission l cAUG a1290-13000 v163 a

Background: Modern response to pandemics, critical for effective public health measures, is shaped by the availability and integration of diverse epidemiological outbreak data. Tracking variants of concern (VOC) is integral to understanding the evolution of SARS-CoV-2 in space and time, both at the local level and global context. This potentially generates actionable information when integrated with epidemiological outbreak data.Methods: A city-wide network of researchers, clinicians, and pathology diagnostic laboratories was formed for genome surveillance of COVID-19 in Pune, India. The genomic landscapes of 10,496 sequenced samples of SARS-CoV-2 driving peaks of infection in Pune between December-2020 to March-2022, were determined. As a modern response to the pandemic, a ``band of five'' outbreak data analytics approach was used. This integrated the genomic data (Band 1) of the virus through molecular phylogenetics with key outbreak data including sample collection dates and case numbers (Band 2), demographics like age and gender (Band 3-4), and geospatial mapping (Band 5).Results: The transmission dynamics of VOCs in 10,496 sequenced samples identified B.1.617.2 (Delta) and BA(x) (Omicron formerly known as B.1.1.529) variants as drivers of the second and third peaks of infection in Pune. Spike Protein mutational profiling during pre and post-Omicron VOCs indicated differential rank ordering of high-frequency mutations in specific domains that increased the charge and binding properties of the protein. Time-resolved phylogenetic analysis of Omicron sub-lineages identified a highly divergent BA.1 from Pune in addition to recombinant X lineages, XZ, XQ, and XM. Conclusions: The band of five outbreak data analytics approach, which integrates five different types of data, highlights the importance of a strong surveillance system with high-quality meta-data for understanding the spatiotemporal evolution of the SARS-CoV-2 genome in Pune. These findings have important implica-tions for pandemic preparedness and could be critical tools for understanding and responding to future outbreaks.& COPY; 2023 Published by Elsevier Ltd on behalf of King Saud Bin Abdulaziz University for Health Sciences. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

10aCOVID-1910aDelta10aOmicron10aSARS-CoV-2 genomic surveillance10aVariant of concern10aWhole Genome Sequencing (WGS)1 aNiveditha, Divya1 aKhan, Soumen1 aKhilari, Ajinkya1 aNadkarni, Sanica1 aBhalerao, Unnati1 aKadam, Pradnya1 aYadav, Ritu1 aKanekar, Jugal, B.1 aShah, Nikita1 aLikhitkar, Bhagyashree1 aSawant, Rutuja1 aThakur, Shikha1 aTupekar, Manisha1 aNagar, Dhriti1 aRao, Anjani, G.1 aJagtap, Rutuja1 aJogi, Shraddha1 aBelekar, Madhuri1 aPathak, Maitreyee1 aShah, Priyanki1 aRanade, Shatakshi1 aPhadke, Nikhil1 aDas, Rashmita1 aJoshi, Suvarna1 aKaryakarte, Rajesh1 aGhose, Aurnab1 aKadoo, Narendra1 aShashidhara, L., S.1 aMonteiro, Joy, Merwin1 aShanmugam, Dhanasekaran1 aRaghunathan, Anu1 aKarmodiya, Krishanpal uhttps://library.ncl.res.in/content/tale-two-waves-delineating-diverse-genomic-and-transmission-landscapes-driving-covid-1903345nas a2200253 4500008004100000022001400041245013800055210006900193260000800262520238100270653003102651653002102682653003102703653002302734653001902757653003702776100002702813700002302840700002102863700001902884700002802903700003002931856013002961 2024 eng d a1867-130600aDietary supplementation of lactococcus lactis subsp. lactis BIONCL17752 on growth performance, and gut microbiota of broiler chickens0 aDietary supplementation of lactococcus lactis subsp lactis BIONC cJUN3 a

The rapid rise of antimicrobial resistance (AMR) is a global concern, being triggered by the overuse or misuse of antibiotics in poultry farming sector. We evaluated Lactococcus lactis subsp. lactis BIONCL17752 strain, and characterized its probiotic potential to endure hostile gastrointestinal conditions. Genome sequencing analysis revealed probiotics traits, and gene clusters involved in bacteriocins, lactococcin A, and sactipeptides production. The absence of genes for antibiotic resistance, virulence, and biogenic amine production indicates the potential of probiotic strain. The BIONCL17752 strain was explored for antibiotic-free feed supplement for growth promotor in broiler chicken. The feed supplemented with 4 x 109 CFU/kg of probiotic strain, in combination with various concentrations of fructooligosaccharides (FOS) 1.0, 2.5, and 5.0 kg/tonne in starter, grower, and finisher diets, respectively. A significant improvement of body weight 152 to 171 g/bird (p < 0.05), and a low feed conversion ratio (FCR) of 1.62, was achieved without using synthetic antibiotics for growth promotion. The results of biochemical, hematological, and histological examinations showed normal features, indicating that the treatment had no harmful effects on the bird's health. Reduced levels of cholesterol, triglycerides, high-density lipoprotein (HDL), and low-density lipoprotein (LDL) in serum are an indication of the health benefits for the treated birds. Microbial community analysis of fecal samples of poultry birds exhibited a higher abundance of Bacteroidetes, Firmicutes, Proteobacteria, Actinobacteria, and Fusobacteria. Probiotic treatment resulted in reduced Firmicutes and increased Bacteroidetes (F/B ratio) in the broiler's gut which highlights the benefits of probiotic dietary supplements. Importantly, the probiotic-fed group exhibited a high abundance of carbohydrate-active enzymes (CAZyme) such as glycoside hydrolases (GH), glycoside transferases (GT), and carbohydrate-binding module (CBM) hydrolases which are essential for the degradation of complex sugar molecules. The probiotic potential of the BIONCL17752 strain contributes to broilers' health by positively affecting intestinal microbiota, achieving optimal growth, and lowering mortality, demonstrating the economic benefits of probiotic treatment in organic poultry farming.

10aAntibiotic growth promotor10aBroiler chickens10aFunctional genome analysis10aGrowth performance10aGut microbiota10aLactococcus lactis subsp. lactis1 aNavale, Vishwambar, D.1 aYadav, Rakeshkumar1 aKhilari, Ajinkya1 aDharne, Mahesh1 aShanmugam, Dhanasekaran1 aVamkudoth, Koteswara, Rao uhttps://library.ncl.res.in/content/dietary-supplementation-lactococcus-lactis-subsp-lactis-bioncl17752-growth-performance-and01763nas a2200205 4500008004100000022001400041245009200055210006900147260000800216300000800224490000700232520104800239100002801287700002201315700002401337700002101361700002801382700002601410856012101436 2025 eng d a1471-492200a32nd National Congress of Parasitology, Pune: bringing together India's parasitologists0 a32nd National Congress of Parasitology Pune bringing together In cJAN a1-70 v413 a

The 32nd National Congress of Parasitology (NCP) was held in person, 3-5 October 2024, at the Indian Institute of Science Education and Research Pune (IISER Pune), jointly organized by IISER Pune; the Council of Scientific and Industrial Research - National Chemical Laboratory, Pune; and Savitribai Phule Pune University (formerly University of Pune) in association with the Indian Society for Parasitology. The conference brought together around 250 attendees from across the country and abroad, including a diverse group of researchers, clinicians, industry experts, and students. The event provided a collaborative environment for exchanging research ideas relevant to the field of parasitology. The congress emphasized the concept of One Health, a holistic approach to address parasitic infections affecting humans and animals to promote overall health and well-being. In this TrendsTalk, the organizers provide an overview of the conference proceedings, which brought together India's vast and diverse parasitology community.

1 aPurkayastha, Devatrisha1 aPandit, Kushankur1 aUpadrasta, Sindhuri1 aKhilari, Ajinkya1 aShanmugam, Dhanasekaran1 aKarmodiya, Krishanpal uhttps://library.ncl.res.in/content/32nd-national-congress-parasitology-pune-bringing-together-indias-parasitologists02305nas a2200313 4500008004100000245009800041210006900139260000800208300001200216490000700228520125200235653002901487653002301516653002701539653003101566653002301597100001901620700002101639700002701660700001901687700002501706700002401731700002101755700002001776700002701796700001801823700002801841856012201869 2025 eng d00aDetection and variant characterization of lumpy skin disease virus from dairy cattle in India0 aDetection and variant characterization of lumpy skin disease vir cDEC aveaf0900 v113 a

The spread of a severe and often fatal form of lumpy skin disease (LSD) in cattle and water buffaloes has caused widespread mortality and morbidity of these animals in India. To track and understand the genetic changes occurring in the virus and to enable routine surveillance of the virus, multiplexed polymerase chain reaction (PCR) and sequencing methods were developed and validated in this study. Multiplexed nested PCR for LSD virus (LSDV) detection was optimized using skin lesion swabs and nasal samples collected from symptomatic and asymptomatic animals. For genotyping, overlapping PCRs to amplify the entire LSDV genome were developed and tested on field samples collected from the Maharashtra and Odisha states of India. Analysis of LSDV genomes from 41 field samples collected in 2022 and 2023 revealed the presence of highly conserved novel mutations. Phylogenetic analysis shows that a distinct genotype of LSDV has spread across India, which warrants genomic surveillance of the virus in the coming years to track the evolution and transmission of the virus. The non-invasive sample collection, detection, and genotyping methods described in this study can facilitate large-scale surveillance of LSDV in dairy animals.

10agenotyping by sequencing10alumpy skin disease10amultiplexed nested PCR10aOxford Nanopore technology10avirus surveillance1 aBajpai, Manali1 aKhilari, Ajinkya1 aLikhitkar, Bhagyashree1 aMusale, Pankaj1 aJadhav, Santoshkumar1 aDhanikachalam, Velu1 aKakramkar, Payal1 aBhave, Kaustubh1 aSwaminathan, Marimuthu1 aJoshi, Sachin1 aShanmugam, Dhanasekaran uhttps://library.ncl.res.in/content/detection-and-variant-characterization-lumpy-skin-disease-virus-dairy-cattle-india02432nas a2200265 4500008004100000022001400041245011700055210006900172260000800241300001100249490000700260520150700267653001301774653002601787653001801813653002501831653002801856653002701884653002801911100002301939700002501962700002801987700002002015856013102035 2025 eng d a2211-926400aExpanding the Egbenema horizon: Novel species discovery in India and first complete genome assembly of the genus0 aExpanding the Egbenema horizon Novel species discovery in India  cAUG a1042560 v903 a

The recognition of Egbenema bharatensis, a novel species of cyanobacteria from the Northern Western Ghats, extends the ecological and phylogenetic understanding of the genus Egbenema and highlights terrestrial microbial diversity of the region. Morphological characterization revealed resemblance with other Egbenema species but was inconclusive for definitive taxonomic classification. Preliminary phylogenetic analysis based on 16S rRNA gene sequences indicated affiliation with the genus but showed less than 98 % similarity to known species, pointing toward taxonomic distinctiveness. Analysis of the 16S-ITS region further supported this differentiation, revealing unique secondary structural features. Based on these findings, we propose the isolate as a novel species within Egbenema. Whole-genome sequencing provided full resolution and functional genome annotation revealed nitrogen fixation, cobalamin biosynthesis, and stress tolerance pathways, suggesting its metabolic versatility and potential biotechnological applications. The presence of multiple toxin-antitoxin systems also reflects its adaptability to environmental fluctuation. This study also presents the first complete genome of the genus Egbenema, filling a significant gap in cyanobacterial genomic resources. These findings encourage integrative taxonomic practices and affirm the significance of exploring biodiversity hotspots for uncovering cryptic microbial diversity with ecological and industrial potential.

10a16S rRNA10aBiodiversity hotspots10aCyanobacteria10aEgbenema bharatensis10aITS secondary structure10aNorthern Western Ghats10awhole-genome sequencing1 aBhagat, Jayesh, M.1 aKhilari, Ajinkya, A.1 aShanmugam, Dhanasekaran1 aPatankar, Meena uhttps://library.ncl.res.in/content/expanding-egbenema-horizon-novel-species-discovery-india-and-first-complete-genome-assembly02435nas a2200277 4500008004100000245012900041210006900170260000800239300001300247490000700260520148800267100001901755700002101774700001701795700002401812700002501836700001901861700002101880700001801901700002001919700002201939700002701961700001801988700002802006856012302034 2025 eng d00aIdentification of genetic variations linked to buparvaquone resistance in Theileria annulata infecting dairy cattle in India0 aIdentification of genetic variations linked to buparvaquone resi cJUL ae03262430 v203 a

Buparvaquone (BPQ) is used for the treatment of bovine theileriosis, a tickborne disease caused by parasites of the Theileria genus. Studies on T. annulata have linked the mechanism of BPQ resistance predominantly to genetic variations in the parasite cytochrome b (cytb) gene. In addition, cryptic mechanisms of resistance involving the parasite peptidyl-prolyl isomerase (pin1) and dihydroorotate dehydrogenase (dhodh) genes require assessment. In India, where bovine theileriosis is endemic, and BPQ is widely used for treatment, it is necessary to establish the prevalence of genetic variations linked to BPQ resistance. In this study, multiplexed PCR amplification and nanopore sequencing method was used for genotyping the complete gene loci of the three target genes. Analysis of 454 T. annulata field samples collected from seven different states of India revealed the presence of previously reported BPQ resistance associated variations S129G, A146T and P253S in cytb gene and A53P in pin1 gene. The A146T and I203V variations in cytb were found to be prevalent and mostly co-occurring, and their role in BPQ resistance needs further evaluation. This study has revealed the presence of previously reported BPQ resistance-linked mutations in cytb and pin1 genes in T. annulata infecting dairy cattle in India and establishes an Oxford nanopore sequencing method suitable for large-scale surveillance of genetic variation in Theileria parasites from field samples.

1 aMusale, Pankaj1 aKhilari, Ajinkya1 aGade, Rohini1 aDhanikachalam, Velu1 aJadhav, Santoshkumar1 aBajpai, Manali1 aTurakani, Bhagya1 aJoshi, Akshay1 aPrajapati, Amar1 aSrivastava, Anand1 aSwaminathan, Marimuthu1 aJoshi, Sachin1 aShanmugam, Dhanasekaran uhttps://library.ncl.res.in/content/identification-genetic-variations-linked-buparvaquone-resistance-theileria-annulata03085nas a2200577 4500008004100000022001400041245011300055210006900168260000800237300000700245490000700252520136700259653001001626653001601636653001701652653000801669653001101677653001001688653002001698100002301718700002601741700003301767700002501800700002001825700002001845700002001865700002201885700002201907700002101929700002201950700002201972700002201994700001802016700002402034700002402058700001602082700002802098700001902126700001402145700002802159700002002187700002402207700002202231700002502253700002002278700002002298700002102318700001502339700002302354856013002377 2025 eng d a1573-388200aRecommendations for sample selection, collection and preparation for NMR-based metabolomics studies of blood0 aRecommendations for sample selection collection and preparation  cMAY a660 v213 a

BackgroundMetabolic profiling of blood metabolites, particularly in plasma and serum, is vital for studying human diseases, human conditions, drug interventions and toxicology. The clinical significance of blood arises from its close ties to all human cells and facile accessibility. However, patient-specific variables such as age, sex, diet, lifestyle and health status, along with pre-analytical conditions (sample handling, storage, etc.), can significantly affect metabolomic measurements in whole blood, plasma, or serum studies. These factors, referred to as confounders, must be mitigated to reveal genuine metabolic changes due to illness or intervention onset.Review objectiveThis review aims to aid metabolomics researchers in collecting reliable, standardized datasets for NMR-based blood (whole/serum/plasma) metabolomics. The goal is to reduce the impact of confounding factors and enhance inter-laboratory comparability, enabling more meaningful outcomes in metabolomics studies.Key conceptsThis review outlines the main factors affecting blood metabolite levels and offers practical suggestions for what to measure and expect, how to mitigate confounding factors, how to properly prepare, handle and store blood, plasma and serum biosamples and how to report data in targeted NMR-based metabolomics studies of blood, plasma and serum.

10aBlood10aMetabolites10aMetabolomics10aNMR10aPlasma10aSerum10aStandardization1 aEmwas, Abdul-Hamid1 aZacharias, Helena, U.1 aAlborghetti, Marcos, Rodrigo1 aGowda, G., A. Nagana1 aRaftery, Daniel1 aMckay, Ryan, T.1 aChang, Chung-ke1 aSaccenti, Edoardo1 aGronwald, Wolfram1 aSchuchardt, Sven1 aLeiminger, Roland1 aMerzaban, Jasmeen1 aMadhoun, Nour, Y.1 aIqbal, Mazhar1 aAlsiary, Rawiah, A.1 aShivapurkar, Rupali1 aPain, Arnab1 aShanmugam, Dhanasekaran1 aRyan, Danielle1 aRoy, Raja1 aSchirra, Horst, Joachim1 aMorris, Vanessa1 aZeri, Ana, Carolina1 aAlahmari, Fatimah1 aKaddurah-Daouk, Rima1 aSalek, Reza, M.1 aLeVatte, Marcia1 aBerjanskii, Mark1 aLee, Brian1 aWishart, David, S. uhttps://library.ncl.res.in/content/recommendations-sample-selection-collection-and-preparation-nmr-based-metabolomics-studies03461nas a2200301 4500008004100000022001400041245012200055210006900177260000800246300001200254490000700266520249900273653002002772653001202792653002002804653001802824653001202842100002102854700001902875700001902894700001702913700002102930700002202951700001602973700001702989700002803006856012503034 2026 eng d a2328-895700aTargeted genomic surveillance unveils genetic variations linked to regional malaria drug resistance dynamics in India0 aTargeted genomic surveillance unveils genetic variations linked  cMAR aofag1060 v133 a

Background India has made substantial progress in reducing Plasmodium falciparum malaria cases and has set a target to eliminate malaria by 2030. Although artemisinin-based combination therapy (ACT) treatment remains effective, tracking regional differences in genetic variants associated with antimalarial resistance is required for effective drug policy implementation.Methods We analyzed 238 P. falciparum clinical samples from 6 Indian states by sequencing 15 parasite genes associated with reduced drug effectiveness. The method involved nanopore sequencing of target gene amplicons derived from dried blood spots using a highly-sensitive PfMDR15 surveillance panel.Results India's historical policy of artesunate-sulfadoxine-pyrimethamine in central India and artemether-lumefantrine in the Northeast has shaped contrasting resistance profiles. In the Northeast, chloroquine resistance persisted at high frequency (Pfcrt K76T and CVIET haplotype; Pfaat1 S258L), alongside quintuple and sextuple Pfdhfr-Pfdhps haplotypes conferring complete sulfadoxine-pyrimethamine resistance. Central India showed variable chloroquine resistance (parasites largely retained wild-type Pfcrt) and emerging lumefantrine tolerance (Pfmdr1 Y184F, Pfaat1 S258L). Interestingly, Delhi (Central India) parasites resembled profiles from the distant Northeast, which borders South East Asia. The detection of Pfaat1 S258L, previously reported only from Africa and associated with reduced lumefantrine susceptibility, suggests convergent evolution under ACT partner-drug pressure. No WHO-validated Pfk13 artemisinin resistance mutations were detected, supporting continued efficacy of ACT.Conclusions India's resistance landscape is fragmented, with signals of expanding lumefantrine tolerance and importation or evolution of globally relevant mutations. These findings highlight the importance of integrating molecular genomic surveillance into malaria control policy to monitor and protect ACT effectiveness and advance malaria elimination. Monitoring of drug resistance associated mutations in P. falciparum parasites is critical for effective drug treatment. We have demonstrated the use of a scalable genomic surveillance protocol for tracking drug resistance linked mutations in parasite genes from clinical isolates in India. The study suggests extensive regional diversity in antimalarial resistance profiles and provides the first hint of possible emergence of lumefantrine tolerance in India.

10adrug resistance10amalaria10aOxford nanopore10aP. falciparum10apfMDR151 aKhilari, Ajinkya1 aSharma, Shweta1 aBajpai, Manali1 aViswan, Anju1 aChaturvedi, Rini1 aMirdha, Bijay, R.1 aRahi, Manju1 aSharma, Amit1 aShanmugam, Dhanasekaran uhttps://library.ncl.res.in/content/targeted-genomic-surveillance-unveils-genetic-variations-linked-regional-malaria-drug03345nas a2200313 4500008004100000022001400041245018000055210007000235260000900305300000800314490000700322520226900329100002002598700001602618700002402634700001602658700002202674700001902696700001902715700001802734700001902752700002802771700001802799700001902817700001702836700002802853700002102881856012902902 2026 eng d a2041-488900aβ-catenin-driven innate and metabolic reprograming in macrophages fuel T-cell-dependent inflammation in Toxoplasma gondii infection: implications for therapeutic intervention0 aβcatenindriven innate and metabolic reprograming in macrophages  cJUN  a5680 v173 a

Toxoplasma gondii activates innate immunity via TLR11/12 in mice, but the lack of functional human counterparts leaves a gap in understanding parasite sensing in humans. Here, we bridge this gap by uncovering a host-intrinsic sensing mechanism, wherein beta-catenin signaling mediates immune recognition of T. gondii. Notably, this parasite hijacks the PI3K-AKT-beta-catenin pathway in macrophages to promote its replication. While beta-catenin ablation, either genetically or pharmacologically (XAV939), disavows this process, thereby inhibiting replication. Phospho-beta-catenin-TCF4 drives IRF4 transcription, followed by phosphorylation of IRF4, which regulates CYBB transcription. Augmented CYBB enhances mitochondrial-ROS and triggers mitophagy via PINK1/PARKIN, whereas ablation of beta-catenin preserves mitochondrial fitness, thereby impeding parasite growth. Enhanced ROS can oxidize host mitochondrial DNA, which then functions as a host-associated molecular pattern (HAMP). This activates the cytosolic pathogen recognition receptor (PRR) AIM2, triggering the AIM2-NLRP3-ASC-caspase-1-IL-1 beta inflammasome cascade. This cascade leads to gasdermin-D-mediated pyroptosis, a process that critically depends on the phosphorylation of beta-catenin. T. gondii's ASP5 protease plays an essential role in the phosphorylation of beta-catenin-mediated inflammasome activation. Metabolically, beta-catenin-dependent enhanced ROS stabilized HIF-1 alpha, which stimulates the HKII-LDH-A axis, promoting the Warburg effect, histone acetylation and pro-inflammatory M1-macrophage polarization (IL-12/IL-6/IL-23/TNF-alpha). beta-catenin ablation shifts metabolism to oxidative-phosphorylation, fostering M2-phenotype (IL-2/IL-10/TGF-beta) that abrogates parasites survival. beta-catenin also strengthens MHC-TCR avidity, driving Th1/Tc1, Th9/Tc9, and Th17/Tc17 paradigm, whereas beta-catenin inhibition promotes anti-inflammatory Th2/Tc2/Threg/Tcreg differentiation. Additionally, macrophage intrinsic beta-catenin dictates metabolic divergence in both CD4(+) and CD8(+)T-cells. Notably, beta-catenin-deletion in macrophages protects mice (beta-cat Delta M Phi) against infection, highlighting that XAV939 has therapeutic potential against toxoplasmosis.

1 aKumari, Geetika1 aKumar, Amit1 aMuduli, Rasmiranjan1 aDas, Mayami1 aBhowmik, Prithwik1 aSingha, Biplab1 aNamdeo, Ankita1 aDcosta, Criss1 aWadhwa, Neerja1 aMaras, Jaswinder, Singh1 aKundu, Rakesh1 aGupta, Nishith1 aAnand, Ruchi1 aShanmugam, Dhanasekaran1 aMajumdar, Tanmay uhttps://library.ncl.res.in/content/%CE%B2-catenin-driven-innate-and-metabolic-reprograming-macrophages-fuel-t-cell-dependent