@article {43255, title = {Comparative 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 control}, journal = {Genome Biology}, volume = {12}, year = {2011}, month = {OCT}, pages = {Article Number: R100}, abstract = {Background: Ichthyophthirius multifiliis, commonly known as Ich, is a highly pathogenic ciliate responsible for {\textquoteright}white spot{\textquoteright}, a disease causing significant economic losses to the global aquaculture industry. Options for disease control are extremely limited, and Ich{\textquoteright}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{\textquoteright}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 {\textquoteright}white spot{\textquoteright} disease and understanding the adaptation to a parasitic lifestyle.}, doi = {10.1186/gb-2011-12-10-r100}, author = {Coyne, Robert S. and Hannick, Linda and Shanmugam, Dhanasekaran and Hostetler, Jessica B. and Brami, Daniel and Joardar, Vinita S. and Johnson, Justin and Radune, Diana and Singh, Irtisha and Badger, Jonathan H. and Kumar, Ujjwal and Saier, Milton and Wang, Yufeng and Cai, Hong and Gu, Jianying and Mather, Michael W. and Vaidya, Akhil B. and Wilkes, David E. and Rajagopalan, Vidyalakshmi and Asai, David J. and Pearson, Chad G. and Findly, Robert C. and Dickerson, Harry W. and Wu, Martin and Martens, Cindy and Van de Peer, Yves and Roos, David S. and Cassidy-Hanley, Donna M. and Clark, Theodore G.} } @article {43249, title = {Comparative genomics of the apicomplexan parasites toxoplasma gondii and neospora caninum: coccidia differing in host range and transmission strategy}, journal = {Plos Pathogens}, volume = {8}, year = {2012}, month = {MAR}, abstract = {Toxoplasma 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.}, doi = {10.1371/journal.ppat.1002567}, author = {Reid, Adam James and Vermont, Sarah J. and Cotton, James A. and Harris, David and Hill-Cawthorne, Grant A. and Koenen-Waisman, Stephanie and Latham, Sophia M. and Mourier, Tobias and Norton, Rebecca and Quail, Michael A. and Sanders, Mandy and Shanmugam, Dhanasekaran and Sohal, Amandeep and Wasmuth, James D. and Brunk, Brian and Grigg, Michael E. and Howard, Jonathan C. and Parkinson, John and Roos, David S. and Trees, Alexander J. and Berriman, Matthew and Pain, Arnab and Wastling, Jonathan M.} } @article {43253, title = {TDR Targets: a chemogenomics resource for neglected diseases}, journal = {Nucleic Acids Research}, volume = {40}, year = {2012}, month = {JAN}, pages = {D1118-D1127}, abstract = {The 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.}, doi = {10.1093/nar/gkr1053}, author = {Magarinos, Maria P. and Carmona, Santiago J. and Crowther, Gregory J. and Ralph, Stuart A. and Roos, David S. and Shanmugam, Dhanasekaran and Van Voorhis, Wesley C.} } @article { ISI:000358250800001, title = {Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites}, journal = {Elife}, volume = {4}, year = {2015}, month = {JUL}, pages = {Article Number: e06974}, publisher = {ELIFE SCIENCES PUBLICATIONS LTD}, address = {SHERATON HOUSE, CASTLE PARK, CAMBRIDGE, CB3 0AX, ENGLAND}, abstract = {

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.

}, issn = {2050-084X}, doi = {10.7554/eLife.06974}, author = {Woo, Yong H. and Ansari, Hifzur and Otto, Thomas D. and Klinger, Christen M. and Kolisko, Martin and Michalek, Jan and Saxena, Alka and Shanmugam, Dhanasekaran and Tayyrov, Annageldi and Veluchamy, Alaguraj and Ali, Shahjahan and Bernal, Axel and del Campo, Javier and Cihlar, Jaromir and Flegontov, Pavel and Gornik, Sebastian G. and Hajduskova, Eva and Horak, Ales and Janouskovec, Jan and Katris, Nicholas J. and Mast, Fred D. and Miranda-Saavedra, Diego and Mourier, Tobias and Naeem, Raeece and Nair, Mridul and Panigrahi, Aswini K. and Rawlings, Neil D. and Padron-Regalado, Eriko and Ramaprasad, Abhinay and Samad, Nadira and Tomcala, Ales and Wilkes, Jon and Neafsey, Daniel E. and Doerig, Christian and Bowler, Chris and Keeling, Patrick J. and Roos, David S. and Dacks, Joel B. and Templeton, Thomas J. and Waller, Ross F. and Lukes, Julius and Obornik, Miroslav and Pain, Arnab} } @article { ISI:000347895500008, title = {Investigation of phosphoproteome in RAGE signaling}, journal = {Proteomics}, volume = {15}, number = {2-3, SI}, year = {2015}, month = {JAN}, pages = {245-259}, publisher = {WILEY-BLACKWELL}, address = {111 RIVER ST, HOBOKEN 07030-5774, NJ USA}, abstract = {

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.

}, keywords = {Cell biology, Disease, Glycation, Kinase, Phosphoproteome, RAGE}, issn = {1615-9853}, doi = {10.1002/pmic.201400169}, author = {Batkulwar, Kedar B. and Bansode, Sneha B. and Patil, Gouri V. and Godbole, Rashmi K. and Kazi, Rubina S. and Chinnathambi, Subashchandrabose and Shanmugam, Dhanasekaran and Kulkarni, Mahesh J.} } @article { ISI:000354378200018, title = {Iron superoxide dismutases in eukaryotic pathogens: new insights from apicomplexa and trypanosoma structures}, journal = {Acta Crystallographica Section F-Structural Biology Communications}, volume = {71}, number = {5, SI}, year = {2015}, month = {MAY}, pages = {615-621}, publisher = {WILEY-BLACKWELL}, address = {111 RIVER ST, HOBOKEN 07030-5774, NJ USA}, abstract = {

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.

}, keywords = {Apicomplexa, iron superoxide dismutase, Trypanosoma}, issn = {1744-3091}, doi = {10.1107/S2053230X15004185}, author = {Phan, Isabelle Q. H. and Davies, Douglas R. and Moretti, Nilmar Silvio and Shanmugam, Dhanasekaran and Cestari, Igor and Anupama, Atashi and Fairman, James W. and Edwards, Thomas E. and Stuart, Kenneth and Schenkman, Sergio and Myler, Peter J.} } @article {42935, title = {Leucas mollissima, a source of bioactive compounds with antimalarial and antimycobacterium activities}, journal = {Planta Medica Letter}, volume = {2}, year = {2015}, month = {JAN}, pages = {e35-e38}, abstract = {

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 {\textpm} 0.25 {\textmu}M), promising antimycobacterium activity [IC50 4.50 {\textpm} 0.75 {\textmu}M (3.31 {\textmu}g/mL)] against M. tuberculosis H37Ra and at 100 {\textmu}g/mL, showed 55.6 \% inhibition of M. bovis. Compound 9 showed moderate inhibition of P. falciparum growth (35 \% inhibition at 10 {\textmu}M) with respect to the positive control atovaquone and 67.4 \% inhibition against M. bovis at 100 {\textmu}g/mL with respect to the positive control rifampicin.

}, author = {Chinchansure, Ashish A. and Arkile, Manisha A. and Shukla, Anurag and Shanmugam, Dhanasekaran and Sarkar, Dhiman and Joshi, Swati P.} } @article {45430, title = {CSGID solves structures and identifies phenotypes for five enzymes in toxoplasma gondii}, journal = {Frontiers in Cellular and Infection Microbiology}, volume = {8}, year = {2018}, month = {OCT}, type = {Article}, abstract = {

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.

}, issn = { 2235-2988}, doi = {10.3389/fcimb.2018.00352}, author = {Lykins, Joseph D. and Filippova, Ekaterina V and Halavaty, Andrei S. and Minasov, George and Zhou, Ying and Dubrovska, Ievgeniia and Flores, Kristin J. and Shuvalova, Ludmilla A. and Ruan, Jiapeng and El Bissati, Kamal and Dovgin, Sarah and Roberts, Craig W. and Woods, Stuart and Moulton, Jon D. and Moulton, Hong and Mcphillie, Martin J. and Muench, Stephen P. and Fishwick, Colin W. G. and Sabini, Elisabetta and Shanmugam, Dhanasekaran and Roos, David S. and Mcleod, Rima and Anderson, Wayne F. and Ngo, Huan M.} } @article {44462, title = {Efforts to access the potent antitrypanosomal marine natural product janadolide: synthesis of des- tert -butyl janadolide and its biological evaluation}, journal = {ACS Omega}, year = {2018}, month = {FEB}, abstract = {To identify novel antitrypanosomal agents based on Janadolide, a potent macrocyclic polyketide{\textendash}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.}, doi = {10.1021/acsomega.7b01920}, author = {Athawale, Paresh R. and Jachak, Gorakh and Shukla, Anurag and Shanmugam, Dhanasekaran and Reddy, Srinivasa} } @article {45352, title = {Evaluating antimalarial efficacy by tracking glycolysis in Plasmodium falciparum using NMR spectroscopy}, journal = {Scientific Reports}, volume = { 8}, year = {2018}, month = {DEC}, type = {Article}, abstract = {Glucose 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.}, issn = {2045-2322}, doi = {10.1038/s41598-018-36197-3}, author = {Shivapurkar, Rupali and Hingamire, Tejashri and Kulkarni, Akshay S. and Rajamohanan, P. R. and Reddy, D. Srinivasa and Shanmugam, Dhanasekaran} } @article {45446, title = { Glycolysis is important for optimal asexual growth and formation of mature tissue cysts by Toxoplasma gondii}, journal = {International Journal for Parasitology }, volume = {48}, year = {2018}, month = {OCT}, pages = {955-968}, type = {Article}, abstract = {Toxoplasma 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.}, issn = { 0020-7519}, doi = {10.1016/j.ijpara.2018.05.013}, author = {Shukla, Anurag and Olszewski, Kellen L. and Llinas, Manuel and Rommereim, Leah M. and Fox, Barbara A. and Bzik, David J. and Xia, Dong and Wastling, Jonathan and Beiting, Daniel and Roos, David S. and Shanmugam, Dhanasekaran} } @article {44655, title = {Highly diverged novel subunit composition of apicomplexan F-type ATP synthase identified from Toxoplasma gondii}, journal = {Plos Biology}, volume = {16}, year = {2018}, month = {JUL}, pages = {e2006128}, type = {Article}, abstract = {

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.

}, issn = {1545-7885}, doi = {10.1371/journal.pbio.2006128}, author = {Salunke, Rahul and Mourier, Tobias and Banerjee, Manidipa and Pain, Arnab and Shanmugam, Dhanasekaran} } @article {44618, title = {Specific stereoisomeric conformations determine the drug potency of cladosporin scaffold against malarial parasite}, journal = {Journal of Medicinal Chemistry}, volume = {61}, year = {2018}, month = {JUL}, pages = {5664-5678}, abstract = {

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.

}, issn = {0022-2623}, doi = {10.1021/acs.jmedchem.8b00565}, author = {Das, Pronay and Babbar, Palak and Malhotra, Nipun and Sharma, Manmohan and Jachak, Goraknath R. and Gonnade, Rajesh G. and Shanmugam, Dhanasekaran and Harlos, Karl and Yogavel, Manickam and Sharma, Amit and Reddy, D. Srinivasa} } @article {44494, title = {Targeted phenotypic screening in plasmodium falciparum and toxoplasma gondii reveals novel modes of action of medicines for malaria venture malaria box molecules}, journal = {mSphere}, volume = {3}, year = {2018}, month = {JAN}, pages = { e00534-17}, type = {Journal Article}, abstract = {The 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 {\textmu}M 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.}, issn = {23795042}, doi = {10.1128/mSphere.00534-17}, author = {Subramanian, Gowtham}, editor = {Belekar, Meenakshi A.} } @article {46107, title = {Demystifying a hexuronic acid ligand that recognizes Toxoplasma gondii and blocks its invasion into host cells}, journal = {Organic \& Biomolecular Chemistry}, volume = {17}, year = {2019}, month = {MAY}, pages = {4535-4542}, type = {Article}, abstract = {

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.

}, issn = {1477-0520}, doi = {10.1039/c9ob00744j}, author = {Subramani, Balamurugan and Shantamurthy, Chethan D. and Maru, Parag and Belekar, Meenakshi A. and Mardhekar, Sandhya and Shanmugam, Dhanasekaran and Kikkeri, Raghavendra} } @article {46313, title = {Mitochondrial cytochrome oxidase C subunit III (cox3) gene as a sensitive and specific target for molecular detection of Babesia gibsoni infection in dogs}, journal = {Experimental Parasitology}, volume = {206}, year = {2019}, month = {NOV}, pages = {107771}, type = {Article}, abstract = {

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.

}, keywords = {Babesia gibsoni, cox3, Diagnosis, Dog, mitochondria, molecular}, issn = {0014-4894}, doi = {10.1016/j.exppara.2019.107771}, author = {Betgiri, Aishwarya A. and Jadhav, Sameer N. and Pawde, Mrunalini and Shukla, Anurag and Mote, Chandrashekhar and Pawar, Prashant D. and Shanmugam, Dhanasekaran and Kundu, Krishnendu} } @article {46065, title = {Structural insights into the unique inhibitory mechanism of Kunitz type trypsin inhibitor from Cicer arietinum L. Vol. 37}, journal = {Journal of Biomolecular Structure \& Dynamics}, volume = {37}, year = {2019}, month = {JUL}, pages = {2669-2677}, type = {Article}, abstract = {

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.

}, keywords = {Chickpea, crystal structure, inhibitory loop, Kunitz trypsin inhibitor, Trypsin}, issn = {0739-1102}, doi = {10.1080/07391102.2018.1494633}, author = {Bendre, Ameya D. and Suresh, C. G. and Shanmugam, Dhanasekaran and Ramasamy, Sureshkumar} } @article {46175, title = {Targeted 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)}, journal = {MSphere}, volume = {4}, year = {2019}, month = {APR}, pages = {e00159-19}, type = {Correction}, issn = {2379-5042}, doi = {10.1128/mSphere.00159-19}, author = {Subramanian, Gowtham and Belekar, Meenakshi A. and Shukla, Anurag and Tong, Jie Xin and Sinha, Ameya and Chu, Trang T. T. and Kulkarni, Akshay S. and Preiser, Peter R. and Reddy, D. Srinivasa and Tan, Kevin S. W. and Shanmugam, Dhanasekaran and Chandramohanadas, Rajesh} } @article {46625, title = {Approach to nigericin derivatives and their therapeutic potential}, journal = {RSC Advances}, volume = {10}, year = {2020}, month = {NOV }, pages = {43085-43091}, type = {Article}, abstract = {

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.

}, doi = {10.1039/d0ra05137c}, author = {Sahu, Amit Kumar and Said, Madhukar S. and Hingamire, Tejashri and Gaur, Megha and Khan, Abujunaid and Shanmugam, Dhanasekaran and Barvkar, Vitthal T. and Dharne, Mahesh S. and Bharde, Atul A. and Dastager, Syed G.} } @article {46830, title = {Distinct metabolic states of a cell guide alternate fates of mutational buffering through altered proteostasis}, journal = {Nature Communications}, volume = {11}, year = {2020}, month = {JUN}, pages = {2926}, type = {Article}, abstract = {

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.

}, issn = {2041-1723}, doi = {10.1038/s41467-020-16804-6}, author = {Verma, Kanika and Saxena, Kanika and Donaka, Rajashekar and Chaphalkar, Aseem and Rai, Manish Kumar and Shukla, Anurag and Zaidi, Zainab and Dandage, Rohan and Shanmugam, Dhanasekaran and Chakraborty, Kausik} } @article {47004, title = {TDR Targets 6: driving drug discovery for human pathogens through intensive chemogenomic data integration}, journal = {Nucleic Acids Research}, volume = {48}, year = {2020}, month = {JAN }, pages = {D992-D1005}, type = {Article}, abstract = {

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.

}, issn = {0305-1048}, doi = {10.1093/nar/gkz999}, author = {Landaburu, Lionel Uran and Berenstein, Ariel J. and Videla, Santiago and Maru, Parag and Shanmugam, Dhanasekaran and Chernomoretz, Ariel and Aguero, Fernan} } @article {46878, title = {Whole-cell phenotypic screening of medicines for malaria venture pathogen box identifies specific inhibitors of plasmodium falciparum late-stage development and egress}, journal = {Antimicrobial Agents and Chemotherapy}, volume = {64}, year = {2020}, month = {MAY}, pages = {e01802-19}, type = {Article}, abstract = {

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.

}, keywords = {DNA fragmentation, egress, Medicines for Malaria Venture, MMV, Pathogen Box, phenotypic screening, Plasmodium falciparum, schizonts, stage-specific inhibition}, issn = {0066-4804}, doi = {10.1128/AAC.01802-19}, author = {Patra, Alok Tanala and Hingamire, Tejashri and Belekar, Meenakshi A. and Xiong, Aoli and Subramanian, Gowtham and Bozdech, Zbynek and Preiser, Peter and Shanmugam, Dhanasekaran and Chandramohanadas, Rajesh} } @article {47790, title = {Antitumor effects of Ir(III)-2H-indazole complexes for triple negative breast cancer}, journal = {Inorganic Chemistry}, volume = {60}, year = {2021}, month = {NOV}, pages = {17593-17607}, type = {Article}, abstract = {In 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{\textendash}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{\textendash}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.}, doi = {10.1021/acs.inorgchem.1c02193}, url = {https://doi.org/10.1021/acs.inorgchem.1c02193}, author = {Panchangam, Rajeeva Lochana and Rao, Ramdas Nishanth and Balamurali, Musuvathi Motilal and Hingamire, Tejashri B. and Shanmugam, Dhanasekaran and Manickam, Venkatraman and Chanda, Kaushik} } @article {47373, title = {Chronic systemic exposure to IL6 leads to deregulation of glycolysis and fat accumulation in the zebrafish liver}, journal = {Biochimica ET Biophysica Acta-Molecular and Cell Biology of Lipids}, volume = {1866}, year = {2021}, month = {MAY}, pages = {158905}, type = {Article}, abstract = {

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.

}, keywords = {Aldolase b, DHAP, Inflammation, Interleukin 6, Lean NAFLD, Non-alcoholic fatty liver}, issn = {1388-1981}, doi = {10.1016/j.bbalip.2021.158905}, author = {Singh, Manoj K. and Jayarajan, Rijith and Varshney, Swati and Upadrasta, Sindhuri and Singh, Archana and Yadav, Rajni and Scaria, Vinod and Sengupta, Shantanu and Shanmugam, Dhanasekaran and Shalimar and Sivasubbu, Sridhar and Gandotra, Sheetal and Sachidanandan, Chetana} } @article {47500, title = {Conserved RNA binding activity of phosphatidyl inositol 5-phosphate 4-kinase (PIP4K2A)}, journal = {Frontiers in Molecular Biosciences}, volume = {8}, year = {2021}, month = {MAY}, pages = {631281}, type = {Article}, abstract = {Plasmodium 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 {\textquoteleft} 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.}, keywords = {malaria, posttranscriptional gene regulation, RNA-protein interaction, translation regulation}, doi = {10.3389/fmolb.2021.631281}, author = {Behari, Jatin and Borkar, Pranita and Vindu, Arya and Dandewad, Vishal and Upadrasta, Sindhuri and Shanmugam, Dhanasekaran and Seshadri, Vasudevan} } @article {47083, title = {Influence of domestication on specialized metabolic pathways in fruit crops}, journal = {Planta}, volume = {253}, year = {2021}, month = {FEB }, pages = {61}, type = {Review}, abstract = {

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.

}, keywords = {Aroma, Domestication, Flavour, Fruit crops, Gene cluster, Specialized metabolites, Taste}, issn = {0032-0935}, doi = {10.1007/s00425-020-03554-4}, author = {Dar, M. Saleem and Dholakia, Bhushan B. and Kulkarni, Abhijeet P. and Oak, Pranjali S. and Shanmugam, Dhanasekaran and Gupta, Vidya S. and Giri, Ashok P.} } @article {47699, title = {Synthesis and biological evaluation of hoshionolactam-based compounds}, journal = {European Journal of Organic Chemistry}, volume = {2021}, year = {2021}, month = {APR }, pages = {2212-2218}, type = {Article}, abstract = {In 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.}, keywords = {Hoshinolactam, Ozonolysis, Parasitic diseases, Trypanosoma}, issn = {1434-193X}, doi = {10.1002/ejoc.202001588}, author = {Jachak, Gorakhnath R. and Elizebath, Drishya and Shukla, Anurag and Shanmugam, Dhanasekaran and Reddy, D. Srinivasa} } @article {48192, title = {Case report: a fatal case of babesiosis in a splenectomized male patient from Western India}, journal = {American Journal of Tropical Medicine and Hygiene}, volume = {106}, year = {2022}, month = {MAY}, pages = {1421-1425}, type = {Article}, abstract = {

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.

}, issn = {0002-9637}, doi = {10.4269/ajtmh.20-1118}, author = {Godbole, Ravi and Gaur, Avantika and Nayar, Priyanka and Kiruthiga, Kala and D{\textquoteright}Costa, Pradeep and Manchanda, Rumma and Khilari, Ajinkya and Shanmugam, Dhanasekaran and Muglikar, Kalpana D. and Kundu, Krishnendu} } @article {48348, title = {Engineering nucleotide sugar synthesis pathways for independent and simultaneous modulation of N-glycan galactosylation and fucosylation in CHO cells}, journal = {Metabolic Engineering}, volume = {74}, year = {2022}, month = {NOV}, pages = {61-71}, type = {Article}, abstract = {

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 {\textquoteleft}-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.

}, keywords = {Antibody, Cell engineering, Fucosylation, Fx, Galactosylation, Gale, glycosylation, Nucleotide sugar synthesis, Recombinant therapeutics}, issn = {1096-7176}, doi = {10.1016/j.ymben.2022.09.003}, author = {Prabhu, Anuja and Shanmugam, Dhanasekaran and Gadgil, Mugdha} } @article {48375, title = {Profiling of metabolic alterations in mice infected with malaria parasites via high-resolution metabolomics}, journal = {Molecular and Biochemical Parasitology}, volume = {252}, year = {2022}, month = {NOV}, pages = {111525}, type = {Article}, abstract = {

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.

}, keywords = {Host response, Infectious diseases, malaria, metabolite, Plasmodium}, issn = {0166-6851}, doi = {10.1016/j.molbiopara.2022.111525}, author = {Chhibber-Goel, Jyoti and Shukla, Anurag and Shanmugam, Dhanasekaran and Sharma, Amit} } @article {48993, title = {Antimalarial activity of anacardium occidentale leaf extracts against plasmodium falciparum transketolase (PfTK)}, journal = {Acta Parasitologica}, volume = {68}, year = {2023}, month = {DEC}, pages = {832-841}, type = {Article}, abstract = {

BackgroundAs per estimates by WHO in 2021 almost half of the world{\textquoteright}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.

}, keywords = {Anacardium occidentale L, Antimalarial activity, malaria, Plasmodium falciparum, Transketolase}, issn = {1230-2821}, doi = {10.1007/s11686-023-00718-6}, author = {Kaushik, Meenakshi and Hoti, Sugeerappa L. and Saxena, Jitendra Kumar and Hingamire, Tejashri and Shanmugam, Dhanasekaran and Joshi, Rajesh K. and Metgud, Sharada C. and Ungar, Banappa and Singh, Ishwar and Hegde, Harsha V.} } @article {48323, title = {Histidinal-based potent antimalarial agents}, journal = {ChemMedChem}, volume = {18}, year = {2023}, month = {MAY }, type = {Article}, abstract = {

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.

}, keywords = {artemisinin, chloroquine, digestive vacuole, docking, falcipains, falciparum, P}, issn = {1860-7179}, doi = {10.1002/cmdc.202200709}, author = {Meena, Chhuttan L. and Hingamire, Tejashri and Gupta, Tanya and Deshmukh, Bhagyashree and Karmodiya, Krishanpal and Joshi, Rakesh and Shanmugam, Dhanasekaran and Sanjayan, Gangadhar J.} } @article {48781, title = {Nanopore sequencing of RAGE gene polymorphisms and their association with type 2 diabetes}, journal = {ACS Omega}, volume = {8}, year = {2023}, month = {JUL}, pages = {25727-25738}, type = {Article}, abstract = {

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.

}, issn = {2470-1343}, doi = {10.1021/acsomega.3c00297}, author = {Chaurasiya, Arvindkumar H. and Khilari, Ajinkya A. and Kazi, Rubina and Jaiswal, Meera R. and Bhoite, Gouri M. and Padwal, Meghana K. and Momin, Abdulrahaman A. and Shanmugam, Dhanasekaran and Kulkarni, Mahesh J.} } @article {48819, title = {Tale of two waves: Delineating diverse genomic and transmission landscapes driving the COVID-19 pandemic in Pune, India}, journal = {Journal of Infection and Public Health}, volume = {16}, year = {2023}, month = {AUG}, pages = {1290-1300}, type = {Article}, abstract = {

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 {\textquoteleft}{\textquoteleft}band of five{\textquoteright}{\textquoteright} 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/).

}, keywords = {COVID-19, Delta, Omicron, SARS-CoV-2 genomic surveillance, Variant of concern, Whole Genome Sequencing (WGS)}, issn = {1876-0341}, doi = {10.1016/j.jiph.2023.06.004}, author = {Niveditha, Divya and Khan, Soumen and Khilari, Ajinkya and Nadkarni, Sanica and Bhalerao, Unnati and Kadam, Pradnya and Yadav, Ritu and Kanekar, Jugal B. and Shah, Nikita and Likhitkar, Bhagyashree and Sawant, Rutuja and Thakur, Shikha and Tupekar, Manisha and Nagar, Dhriti and Rao, Anjani G. and Jagtap, Rutuja and Jogi, Shraddha and Belekar, Madhuri and Pathak, Maitreyee and Shah, Priyanki and Ranade, Shatakshi and Phadke, Nikhil and Das, Rashmita and Joshi, Suvarna and Karyakarte, Rajesh and Ghose, Aurnab and Kadoo, Narendra and Shashidhara, L. S. and Monteiro, Joy Merwin and Shanmugam, Dhanasekaran and Raghunathan, Anu and Karmodiya, Krishanpal} } @article {49612, title = {Dietary supplementation of lactococcus lactis subsp. lactis BIONCL17752 on growth performance, and gut microbiota of broiler chickens}, journal = {Probiotics and Antimicrobial Proteins}, year = {2024}, month = {JUN}, type = {Article}, abstract = {

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{\textquoteright}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{\textquoteright}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{\textquoteright} health by positively affecting intestinal microbiota, achieving optimal growth, and lowering mortality, demonstrating the economic benefits of probiotic treatment in organic poultry farming.

}, keywords = {Antibiotic growth promotor, Broiler chickens, Functional genome analysis, Growth performance, Gut microbiota, Lactococcus lactis subsp. lactis}, issn = {1867-1306}, doi = {10.1007/s12602-024-10313-4}, author = {Navale, Vishwambar D. and Yadav, Rakeshkumar and Khilari, Ajinkya and Dharne, Mahesh and Shanmugam, Dhanasekaran and Vamkudoth, Koteswara Rao} } @article {49538, title = {32nd National Congress of Parasitology, Pune: bringing together India{\textquoteright}s parasitologists}, journal = {Trends in Parasitology}, volume = {41}, year = {2025}, month = {JAN}, pages = {1-7}, type = {Article}, abstract = {

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{\textquoteright}s vast and diverse parasitology community.

}, issn = {1471-4922}, doi = {10.1016/j.pt.2024.10.022}, author = {Purkayastha, Devatrisha and Pandit, Kushankur and Upadrasta, Sindhuri and Khilari, Ajinkya and Shanmugam, Dhanasekaran and Karmodiya, Krishanpal} } @article {49860, title = {Detection and variant characterization of lumpy skin disease virus from dairy cattle in India}, journal = {Virus Evolution}, volume = {11}, year = {2025}, month = {DEC}, pages = {veaf090}, type = {Article}, abstract = {

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.

}, keywords = {genotyping by sequencing, lumpy skin disease, multiplexed nested PCR, Oxford Nanopore technology, virus surveillance}, doi = {10.1093/ve/veaf090}, author = {Bajpai, Manali and Khilari, Ajinkya and Likhitkar, Bhagyashree and Musale, Pankaj and Jadhav, Santoshkumar and Dhanikachalam, Velu and Kakramkar, Payal and Bhave, Kaustubh and Swaminathan, Marimuthu and Joshi, Sachin and Shanmugam, Dhanasekaran} } @article {49893, title = {Expanding the Egbenema horizon: Novel species discovery in India and first complete genome assembly of the genus}, journal = {Algal Research-Biomass Biofuels and Bioproducts}, volume = {90}, year = {2025}, month = {AUG}, pages = {104256}, type = {Article}, abstract = {

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.

}, keywords = {16S rRNA, Biodiversity hotspots, Cyanobacteria, Egbenema bharatensis, ITS secondary structure, Northern Western Ghats, whole-genome sequencing}, issn = {2211-9264}, doi = {10.1016/j.algal.2025.104256}, author = {Bhagat, Jayesh M. and Khilari, Ajinkya A. and Shanmugam, Dhanasekaran and Patankar, Meena} } @article {49940, title = {Identification of genetic variations linked to buparvaquone resistance in Theileria annulata infecting dairy cattle in India}, journal = {Plos One}, volume = {20}, year = {2025}, month = {JUL}, pages = {e0326243}, type = {Article}, abstract = {

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.

}, doi = {10.1371/journal.pone.0326243}, author = {Musale, Pankaj and Khilari, Ajinkya and Gade, Rohini and Dhanikachalam, Velu and Jadhav, Santoshkumar and Bajpai, Manali and Turakani, Bhagya and Joshi, Akshay and Prajapati, Amar and Srivastava, Anand and Swaminathan, Marimuthu and Joshi, Sachin and Shanmugam, Dhanasekaran} } @article {49593, title = {Recommendations for sample selection, collection and preparation for NMR-based metabolomics studies of blood}, journal = {Metabolomics}, volume = {21}, year = {2025}, month = {MAY}, pages = {66}, type = {Review}, abstract = {

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.

}, keywords = {Blood, Metabolites, Metabolomics, NMR, Plasma, Serum, Standardization}, issn = {1573-3882}, doi = {10.1007/s11306-025-02259-7}, author = {Emwas, Abdul-Hamid and Zacharias, Helena U. and Alborghetti, Marcos Rodrigo and Gowda, G. A. Nagana and Raftery, Daniel and Mckay, Ryan T. and Chang, Chung-ke and Saccenti, Edoardo and Gronwald, Wolfram and Schuchardt, Sven and Leiminger, Roland and Merzaban, Jasmeen and Madhoun, Nour Y. and Iqbal, Mazhar and Alsiary, Rawiah A. and Shivapurkar, Rupali and Pain, Arnab and Shanmugam, Dhanasekaran and Ryan, Danielle and Roy, Raja and Schirra, Horst Joachim and Morris, Vanessa and Zeri, Ana Carolina and Alahmari, Fatimah and Kaddurah-Daouk, Rima and Salek, Reza M. and LeVatte, Marcia and Berjanskii, Mark and Lee, Brian and Wishart, David S.} } @article {50081, title = {Targeted genomic surveillance unveils genetic variations linked to regional malaria drug resistance dynamics in India}, journal = {Open Forum Infectious Diseases}, volume = {13}, year = {2026}, month = {MAR}, pages = {ofag106}, type = {Article}, abstract = {

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{\textquoteright}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{\textquoteright}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.

}, keywords = {drug resistance, malaria, Oxford nanopore, P. falciparum, pfMDR15}, issn = {2328-8957}, doi = {10.1093/ofid/ofag106}, author = {Khilari, Ajinkya and Sharma, Shweta and Bajpai, Manali and Viswan, K. Anju and Chaturvedi, Rini and Mirdha, Bijay R. and Rahi, Manju and Sharma, Amit and Shanmugam, Dhanasekaran} }