@article { ISI:000295617000024, title = {High throughput quantitative analysis of melamine and triazines by MALDI-TOF MS}, journal = {Analytical Methods}, volume = {3}, number = {10}, year = {2011}, month = {OCT}, pages = {2360-2366}, publisher = {ROYAL SOC CHEMISTRY}, address = {THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND}, abstract = {

Quantitative and high throughput MALDI MS analysis of symmetrical triazines (s-triazines), and milk contaminated with melamine has been demonstrated. s-Triazines from a multi component aqueous test mixture, and melamine, a known adulterant in milk, were quantified at low parts-per-million (ppm) level using 2,5-dihydroxybenzoic acid (2,5-DHB) as a matrix. Mass spectral peak intensity ratios of the analyte and a suitable internal standard were used for the quantitation. Limit of detection at 20 {\textquoteleft}parts-per- billion{\textquoteright} (nano molar concentration) has been achieved for the s-triazines from the aqueous mixture. Quantitation from MALDI MS peak intensities was validated using LC-PDA and LC-ESI-MS analysis using both spectral peak intensities and areas under the chromatographic curves. Excellent linearity in low ppm concentrations along with good precision and accuracy, all of which were comparable to LC-ESI-MS data, were obtained with the advantage of rapid analysis.

}, issn = {1759-9660}, doi = {10.1039/c1ay05262d}, author = {Singh, Ajeet and Panchagnula, Venkateswarlu} } @article { ISI:000307207300023, title = {Enhanced permeation, leaf retention, and plant protease inhibitor activity with bicontinuous microemulsions}, journal = {Journal of Colloid and Interface Science}, volume = {383}, year = {2012}, month = {OCT}, pages = {177-183}, publisher = {ACADEMIC PRESS INC ELSEVIER SCIENCE}, address = {525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA}, abstract = {

Bicontinuous microemulsions (BCMEs) have excellent solubulizing properties along with low interfacial tension and aqueous content that can be controlled. In this work, water soluble plant protease inhibitor (PI), well characterized for its activity against insect pests, was incorporated into a BCME system and explored for permeation on hydrophobic leaf surfaces and protease inhibition activity. The bicontinuous nature of the microemulsion containing water:2-propanol:1-butanol (55:35:10 w/w) was characterized using conductivity and self-diffusion coefficient measurements. The PI was soluble in the water-rich bicontinuous domains, stable in the microemulsions, and protease inhibition activity was retained for a prolonged duration. The microemulsions ensured greater wettability and a wider spread of the PI on hydrophobic leaf surfaces as revealed by contact angle measurements. Significantly, trypsin inhibition activity assays of the PI recovered from the leaves after delivery from the microemulsion indicated a significant increase in the PI retention on the leaf. This BCME enabled greater leaf permeation and retention of the PI can be attributed to a temporary disruption of the waxy leaf surface followed by self-repair without causing any long term damage to the plant. (C) 2012 Elsevier Inc. All rights reserved.

}, keywords = {Bicontinuous microemulsion, Biopesticide, Microemulsion pesticide, protease inhibitor, Protein encapsulation, Protein permeation}, issn = {0021-9797}, doi = {10.1016/j.jcis.2012.06.025}, author = {Tamhane, Vaijayanti A. and Dhaware, Deepika G. and Khandelwal, Neha and Giri, Ashok P. and Panchagnula, Venkateswarlu} } @article { ISI:000337763200018, title = {Matrix-assisted laser desorption/ionization mass spectrometry analysis of dimethyl arginine isomers from urine}, journal = {Analytical Methods}, volume = {6}, number = {13}, year = {2014}, month = {APR}, pages = {4602-4609}, publisher = {ROYAL SOC CHEMISTRY}, address = {THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND}, abstract = {

Isomeric asymmetric and symmetric dimethyl arginine (ADMA and SDMA respectively) residues are excreted in urine and are putative markers of cardiovascular and chronic kidney diseases. In this work, we demonstrate simultaneous and quantitative detection of endogeneous ADMA and SDMA from urine samples of healthy subjects using MALDI-TOF MS without any chromatographic separation. The DMA isomers yielded [M + H](+) ions along with their product ions formed due to MALDI in-source fragmentation. The precursor ions were validated using MALDI-TOF MS/MS as well as direct injection ESI-Q-TOF MS/MS. ADMA and SDMA generated unique product ions at similar to m/z 46 and similar to m/z 172 respectively in the MS-mode itself. These were advantageously used for full scan-mode absolute quantification of the isomeric metabolites. The m/z observed for all the ions was within 10 ppm mass accuracy. The calibration method was established by generating internal standard normalized peak area-based concentration response curves using synthetic standards. Good linearities (R-2 \> 0.95) with acceptable intra-assay, inter-assay variation (within 15\% RSD) and excellent recoveries were observed for quality control samples. Finally, endogeneous concentrations of the metabolites were determined in urine from healthy subjects (n = 11). ADMA and SDMA were found to be in the range of 1.6-8 mu M and 2.9-9.1 mu M in urine and were in agreement with previously reported physiological levels.

}, issn = {1759-9660}, doi = {10.1039/c4ay00309h}, author = {Bhattacharya, Nivedita and Singh, Ajeet and Ghanate, Avinash and Phadke, Gayatri and Parmar, Dharmesh and Dhaware, Deepika G. and Basak, Trayambak and Sengupta, Shantanu and Panchagnula, Venkateswarlu} } @article {43952, title = {CHO Cells Adapted to Inorganic Phosphate Limitation Show Higher Growth and Higher Pyruvate Carboxylase Flux in Phosphate Replete Conditions}, journal = {Biotechnology progress}, volume = {33}, year = {2017}, month = {MAY}, pages = {749-758}, type = {Article}, abstract = {Inorganic phosphate (P-i) is an essential ion involved in diverse cellular processes including metabolism. Changes in cellular metabolism upon long term adaptation to P-i limitation have been reported in E. coli. Given the essential role of P-i, adaptation to P-i limitation may also result in metabolic changes in animal cells. In this study, we have adapted CHO cells producing recombinant IgG to limiting P-i conditions for 75 days. Not surprisingly, adapted cells showed better survival under P-i limitation. Here, we report the finding that such cells also showed better growth characteristics compared to control in batch culture replete with P-i ( higher peak density and integral viable cell density), accompanied by a lower specific oxygen uptake rate and cytochrome oxidase activity towards the end of exponential phase. Surprisingly, the adapted cells grew to a lower peak density under glucose limitation. This suggests long term P-i limitation may lead to selection for an altered metabolism with higher dependence on glucose availability for biomass assimilation compared to control. Steady state U-C-13 glucose labeling experiments suggest that adapted cells have a higher pyruvate carboxylase flux. Consistent with this observation, supplementation with aspartate abolished the peak density difference whereas supplementation with serine did not abolish the difference. This supports the hypothesis that cell growth in the adapted culture might be higher due to a higher pyruvate carboxylase flux. Decreased fitness under carbon limitation and mutations in the sucABCD operon has been previously reported in E. coli upon long term adaptation to P-i limitation, suggestive of a similarity in cellular response among such diverse species. (C) 2017 American Institute of Chemical Engineers}, doi = {10.1002/btpr.2450}, author = {Maralingannavar, Vishwanathgouda; and Parmar, Dharmeshkumar and Pant, Tejal and Gadgil, Chetan and Panchagnula, Venkateswarlu and Gadgil, Mugdha} } @article {43702, title = {Determination of triazines and triazoles in grapes using atmospheric pressure matrix-assisted laser desorption/ionization high-resolution mass spectrometry}, journal = {Journal of Aoac International}, volume = {100}, year = {2017}, month = {MAY}, pages = {640-646}, type = {Article}, abstract = {A chromatography-free atmospheric pressure matrix-assisted laser desorption/ionization high-resolution mass spectrometry (AP-MALDI HRMS) method is described for the simultaneous and quantitative detection of triazines and triazoles in grapes. The analytes were detected reproducibly with high mass accuracy (mass error within 5 ppm) and further confirmed by collision-induced dissociation fragmentation in tandem MS. The LODs and LOQs for all the analytes were found to be in the nanogram per gram level (15-20 ng/g LOQ). Internal standard normalized high-resolution accurate mass extracted (HR-AM) peak intensities of the detected ions were used to generate the concentration response curves. Linearity (with R-2 values around 0.99) was obtained for these curves within a concentration range of 20-200 ng/g of the individual analytes. The accuracy and precision of the method were further established using QC samples. Validation and performance comparison of the AP-MALDI HRMS method with an existing standard method using LC with :triple quadrupole MS was carried out (evaluating sensitivity, accuracy, precision, and analysis time) using 20 table-grape field samples after QuEChERS extraction.}, doi = {10.5740/jaoacint.17-0047}, author = {Mahale, Vishal and Singh, Ajeet and Phadke, Gayatri S. and Ghanate, Avinash D. and Oulkar, Dasharath P. and Banerjee, Kaushik and Panchagnula, Venkateswarlu} } @article {43934, title = {Scalable metabolite supplementation strategy against antibiotic resistant pathogen Chromobacterium violaceum induced by NAD(+)/NADH(+) imbalanceA scalable metabolite supplementation strategy against antibiotic resistant pathogen Chromobacterium violaceu}, journal = {BMC Syst Biol. }, volume = {11}, year = {2017}, month = {APR}, abstract = {

BACKGROUND: The leading edge of the global problem of antibiotic resistance necessitates novel therapeutic strategies. This study develops a novel systems biology driven approach for killing antibiotic resistant pathogens using benign metabolites. RESULTS: Controlled laboratory evolutions established chloramphenicol and streptomycin resistant pathogens of Chromobacterium. These resistant pathogens showed higher growth rates and required higher lethal doses of antibiotic. Growth and viability testing identified malate, maleate, succinate, pyruvate and oxoadipate as resensitising agents for antibiotic therapy. Resistant genes were catalogued through whole genome sequencing. Intracellular metabolomic profiling identified violacein as a potential biomarker for resistance. The temporal variance of metabolites captured the linearized dynamics around the steady state and correlated to growth rate. A constraints-based flux balance model of the core metabolism was used to predict the metabolic basis of antibiotic susceptibility and resistance. CONCLUSIONS: The model predicts electron imbalance and skewed NAD/NADH ratios as a result of antibiotics - chloramphenicol and streptomycin. The resistant pathogen rewired its metabolic networks to compensate for disruption of redox homeostasis. We foresee the utility of such scalable workflows in identifying metabolites for clinical isolates as inevitable solutions to mitigate antibiotic resistance.

}, keywords = {Antibiotic resistance; Flux balance analysis; Flux variability analysis; Metabolism; Metabolomic; NAD; NADH; Redox homeostasis}, doi = {10.1186/s12918-017-0427-z}, author = {Banerjee, Deepanwita and Parmar, Dharmeshkumar and Bhattacharya, Nivedita and Ghanate, Avinash D. and Panchagnula, Venkateswarlu and Raghunathan, Anu} } @conference {44600, title = {Differential responses of CHO cells adapted to limitation of inorganic phosphate, glucose or glutamine}, booktitle = {255th National Meeting and Exposition of the American-Chemical-Society (ACS) - Nexus of Food, Energy, and Water}, year = {2018}, month = {MAR }, publisher = {American-Chemical-Society, 1155 16TH ST, NW, Washington, DC 20036 USA}, organization = {American-Chemical-Society, 1155 16TH ST, NW, Washington, DC 20036 USA}, address = {New Orleans, LA}, author = {Maralingannavar, Vishwanathgouda and Parmar, Dharmeshkumar and Pant, Tejal and Gadgil, Chetan and Panchagnula, Venkateswarlu and Gadgil, Mugdha} } @article {44220, title = {Integrative analysis of rewired central metabolism in temozolomide resistant cells}, journal = {Biochemical and Biophysical Research Communications}, volume = {495}, year = {2018}, month = {JAN}, pages = {2010-2016}, type = {Article}, abstract = {

An authenticated U87MG clonal glioblastoma cell line was investigated to identify a sub-population of neurospheroidal (NSP) cells within the main epithelial population (U87MG). The NSP cells sorted using Fluorescence Assisted Cell Sorting (FACS) showed varied morphology, 30\% lower growth rates, 40\% higher IC50 values for temozolomide drug and could differentiate into the glial cell type (NDx). Metabolite profiling using HR-LCMS identified glucose, glutamine and serine in both populations and tryptophan only in U87MG as growth limiting substrates. Glycine, alanine, glutamate and proline were secreted by U87MG, however proline and glycine were re-utilized in NSP. Exo-metabolite profiling and phenotypic microarrays identified differential metabolism of primary carbon sources glucose and derived pyruvate for U87MG; glutamine and derived glutamate metabolism in NSP. Differential mRNA abundance of AKT1, PTEN, PIK3CA controlling metabolism, drug efflux, nutrient transport and epigenetic control MDM2 are potentially critical in shaping DNA methylation effects of temozolomide. Our study provides a new insight into the combined effect of these factors leading to temozolomide resistance in NSP. (C) 2017 Elsevier Inc. All rights reserved.

}, keywords = {Glutamine, Metabolic rewiring, Metabolite profiling, mRNA abundances, Temozolomide resistance, U87MG}, issn = {0006-291X}, doi = {10.1016/j.bbrc.2017.12.073}, author = {Immanuel, Selva Rupa C. and Ghanate, Avinash D. and Parmar, Dharmeshkumar S. and Marriage, Fiona and Panchagnula, Venkateswarlu and Day, Nap J. and Raghunathan, Anu} } @article {46354, title = {Superfluous glutamine synthetase activity in Chinese Hamster Ovary cells selected under glutamine limitation is growth limiting in glutamine-replete conditions and can be inhibited by serine}, journal = {Biotechnology Progress}, volume = {35}, year = {2019}, month = {SEP-OCT}, pages = {UNSP e2856}, type = {Article}, abstract = {

Passaging and expansion of animal cells in lean maintenance medium could result in periods of limitation of some nutrients. Over time, such stresses could possibly result in selection of cells with metabolic changes and contribute to heterogeneity. Here, we investigate whether selection of Chinese Hamster Ovary (CHO) cells under glutamine limitation results in changes in growth under glutamine-replete conditions. In glutamine-limiting medium, compared to control cells passaged in glutamine-rich medium, the selected cells showed higher glutamine synthetase (GS) activity and attained a higher peak viable cell density (PVCD). Surprisingly, in glutamine-replete conditions, selected cells still showed a higher GS activity but a lower PVCD. We show that in glutamine-replete medium, PVCD of selected cells was restored on (a) inhibition of GS activity with methionine sulfoximine, (b) supplementation of aspartate-without affecting GS activity, and (c) supplementation of serine, which is reported to inhibit GS in vitro. Consistent with the reported effect of serine, inhibition of GS activity was observed upon serine supplementation along with reduced growth of cells under glutamine-limiting conditions. The latter observation is important for the design of glutamine-free culture medium and feed used for GS-CHO and GS-NS0. In summary, we show that CHO cells selected under glutamine limitation have superfluous GS activity in glutamine-replete medium, which negatively affects their PVCD. This may be due to its effect on availability of aspartate which was the limiting nutrient for the growth of selected cells in glutamine-replete conditions.

}, keywords = {C-13 tracer analysis, CHO cells, glutamine limitation, Glutamine synthetase, GS-CHO, GS-NS0, selection under nutrient limitation, serine}, issn = {8756-7938}, doi = {10.1002/btpr.2856}, author = {Maralingannavar, Vishwanathgouda and Parmar, Dharmeshkumar and Panchagnula, Venkateswarlu and Gadgil, Mugdha} } @article {46955, title = {Plausible diagnostic value of urinary isomeric dimethylarginine ratio for diabetic nephropathy}, journal = {Scientific Reports}, volume = {10}, year = {2020}, month = {FEB}, pages = {2970}, type = {Article}, abstract = {

Altered circulatory asymmetric and symmetric dimethylarginines have been independently reported in patients with end-stage renal failure suggesting their potential role as mediators and early biomarkers of nephropathy. These alterations can also be reflected in urine. Herein, we aimed to evaluate urinary asymmetric to symmetric dimethylarginine ratio (ASR) for early prediction of diabetic nephropathy (DN). In this cross-sectional study, individuals with impaired glucose tolerance (IGT), newly diagnosed diabetes (NDD), diabetic microalbuminuria (MIC), macroalbuminuria (MAC), and normal glucose tolerance (NGT) were recruited from Dr. Mohans{\textquoteright} Diabetes Specialties centre, India. Urinary ASR was measured using a validated high-throughput MALDI-MS/MS method. Significantly lower ASR was observed in MIC (0.909) and MAC (0.741) in comparison to the NGT and NDD groups. On regression models, ASR was associated with MIC [OR: 0.256; 95\% CI: 0.158-0.491] and MAC [OR 0.146; 95\% CI: 0.071-0.292] controlled for all the available confounding factors. ROC analysis revealed ASR cut-point of 0.95 had C-statistic of 0.691 (95\% CI: 0.627-0.755) to discriminate MIC from NDD with 72\% sensitivity. Whereas, an ASR cut-point of 0.82 had C-statistic of 0.846 (95\% CI: 0.800 - 0.893) had 91\% sensitivity for identifying MAC. Our results suggest ASR as a potential early diagnostic biomarker for DN among the Asian Indians.

}, issn = {2045-2322}, doi = {10.1038/s41598-020-59897-1}, author = {Parmar, Dharmeshkumar and Bhattacharya, Nivedita and Kannan, Shanthini and Vadivel, Sangeetha and Pandey, Gautam Kumar and Ghanate, Avinash and Ragi, Nagarjuna Chary and Prabu, Paramasivam and Pramodkumar, Thyparambil Aravindakshan and Manickam, Nagaraj and Mohan, Viswanathan and Sripadi, Prabhakar and Kuppan, Gokulakrishnan and Panchagnula, Venkateswarlu} } @article {47113, title = {Integrated genetic and metabolic landscapes predict vulnerabilities of temozolomide resistant glioblastoma cells}, journal = {npj Systems Biology and Applications}, volume = {7}, year = {2021}, month = {JAN }, pages = {2}, type = {Article}, abstract = {

Metabolic reprogramming and its molecular underpinnings are critical to unravel the duality of cancer cell function and chemo-resistance. Here, we use a constraints-based integrated approach to delineate the interplay between metabolism and epigenetics, hardwired in the genome, to shape temozolomide (TMZ) resistance. Differential metabolism was identified in response to TMZ at varying concentrations in both the resistant neurospheroidal (NSP) and the susceptible (U87MG) glioblastoma cell-lines. The genetic basis of this metabolic adaptation was characterized by whole exome sequencing that identified mutations in signaling pathway regulators of growth and energy metabolism. Remarkably, our integrated approach identified rewiring in glycolysis, TCA cycle, malate aspartate shunt, and oxidative phosphorylation pathways. The differential killing of TMZ resistant NSP by Rotenone at low concentrations with an IC50 value of 5 nM, three orders of magnitude lower than for U87MG that exhibited an IC50 value of 1.8 mM was thus identified using our integrated systems-based approach.

}, doi = {10.1038/s41540-020-00161-7}, author = {Immanuel, Selva Rupa Christinal and Ghanate, Avinash D. and Parmar, Dharmeshkumar S. and Yadav, Ritu and Uthup, Riya and Panchagnula, Venkateswarlu and Raghunathan, Anu} } @article {49215, title = {Circulatory levels of lysophosphatidylcholine species in obese adolescents: Findings from cross-sectional and prospective lipidomics analyses}, journal = {NUTRITION METABOLISM AND CARDIOVASCULAR DISEASES}, volume = {34}, year = {2024}, month = {JUL}, pages = {1807-1816}, type = {Journal Article}, keywords = {Adolescent obesity, Asian Indians, biomarker, Lipidomics, Lysophosphatidyl- choline}, issn = {0939-4753}, doi = {10.1016/j.numecd.2024.02.009}, author = {Sharma, Sapna and Subrahmanyam, Yalamanchili Venkata and Ranjani, Harish and Sidra, Sidra and Parmar, Dharmeshkumar and Vadivel, Sangeetha and Kannan, Shanthini and Grallert, Harald and Usharani, Dandamudi and Anjana, Ranjit Mohan and Balasubramanyam, Muthuswamy and Mohan, Viswanathan and Jerzy, Adamski and Panchagnula, Venkateswarlu and Gokulakrishnan, Kuppan} } @article {49971, title = {Precision integrated identification of predictive first-trimester metabolomics signatures for early detection of gestational diabetes mellitus}, journal = {Cardiovascular Diabetology}, volume = {24}, year = {2025}, month = {NOV }, pages = {434}, type = {Article}, abstract = {

Background and aimGestational diabetes mellitus (GDM), a common pregnancy-related metabolic disorder, often goes undiagnosed until the second trimester, limiting early intervention opportunities. Given the higher prevalence of GDM in India, there is a critical need to investigate metabolomic biomarkers among Asian Indians, who exhibit greater insulin resistance and are predisposed to developing type 2 diabetes at an earlier age. This study aimed to identify early pregnancy metabolomic signatures predictive of GDM. MethodsAmong 2115 pregnant women from the STratification of Risk of Diabetes in Early pregnancy (STRiDE) study, we performed untargeted metabolomic profiling using UPLC-MS/MS at early pregnancy (\< 16 weeks) plasma samples from 100 women-comprising 50 with GDM and 50 normal (without GDM) based on oral glucose tolerance test (OGTT) at 24-28 weeks. Statistical and machine learning approaches, including logistic regression and random forest (RF), were applied to identify GDM-associated metabolites and construct predictive models. Pathway enrichment analysis was conducted using KEGG database annotations. ResultsA total of 49 metabolites were significantly associated with GDM, primarily involving lipid classes such as phosphatidylcholines, sphingomyelins, and triacylglycerols. RF analysis identified a panel of eight metabolites that achieved best predictive performance (AUC 0.880; 95\% CI: 0.809-0.951) for GDM. When combined with conventional clinical risk factors, the integrated model showed comparable prediction of GDM with AUC 0.88;: 95\% CI: 0.810-0.952). Enrichment analysis highlighted dysregulated pathways including glycerophospholipid and sphingolipid metabolism, autophagy, and insulin resistance. ConclusionThis study demonstrates the utility of early-pregnancy metabolomic profiling for predicting GDM in Indian women. The eight-metabolite panel offers a promising tool for early risk stratification of GDM, warranting validation in diverse populations.

}, keywords = {First trimester, Gestational diabetes mellitus, Indian women, Mass spectrometry, Metabolomics, Prediction}, doi = {10.1186/s12933-025-02978-0}, author = {Sharma, Sapna and Subrahmanyam, Yalamanchili Venkata and Gupta, Payal and Vadivel, Sangeetha and Deepa, Mohan and Tandon, Ansh and Sreedevi, Sreekumar and Ram, Uma and Narad, Priyanka and Parmar, Dharmeshkumar and Anjana, Ranjit Mohan and Raghunathan, Anu and Balasubramanyam, Muthuswamy and Mohan, Viswanathan and Sengupta, Abhishek and Adamski, Jerzy and Saravanan, Ponnusamy and Panchagnula, Venkateswarlu and Usharani, Dandamudi and Gokulakrishnan, Kuppan} }