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172 results on '"Glaros, Trevor"'

1. Feature-agnostic metabolomics for determining effective subcytotoxic doses of common pesticides in human cells.

Author

Rivera, Emilio S, LeBrun, Erick S, Breidenbach, Joshua D, Solomon, Emilia, Sanders, Claire K, Harvey, Tara, Tseng, Chi Yen, Thornhill, M Grace, Blackwell, Brett R, McBride, Ethan M, Luchini, Kes A, Alvarez, Marc, Williams, Robert F, Norris, Jeremy L, Mach, Phillip M, and Glaros, Trevor G

Subjects
PHENOMENOLOGICAL biology, MOLECULAR biology, CARBARYL, PESTICIDES, RESEARCH personnel, METABOLOMICS
Abstract

Although classical molecular biology assays can provide a measure of cellular response to chemical challenges, they rely on a single biological phenomenon to infer a broader measure of cellular metabolic response. These methods do not always afford the necessary sensitivity to answer questions of subcytotoxic effects, nor do they work for all cell types. Likewise, boutique assays such as cardiomyocyte beat rate may indirectly measure cellular metabolic response, but they too, are limited to measuring a specific biological phenomenon and are often limited to a single cell type. For these reasons, toxicological researchers need new approaches to determine metabolic changes across various doses in differing cell types, especially within the low-dose regime. The data collected herein demonstrate that LC-MS/MS-based untargeted metabolomics with a feature-agnostic view of the data, combined with a suite of statistical methods including an adapted environmental threshold analysis, provides a versatile, robust, and holistic approach to directly monitoring the overall cellular metabolomic response to pesticides. When employing this method in investigating two different cell types, human cardiomyocytes and neurons, this approach revealed separate subcytotoxic metabolomic responses at doses of 0.1 and 1 µM of chlorpyrifos and carbaryl. These findings suggest that this agnostic approach to untargeted metabolomics can provide a new tool for determining effective dose by metabolomics of chemical challenges, such as pesticides, in a direct measurement of metabolomic response that is not cell type-specific or observable using traditional assays. [ABSTRACT FROM AUTHOR]

Published
2024
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3. Multidimensional mass profiles increase confidence in bacterial identification when using low-resolution mass spectrometers.

Author

Sasiene, Zachary J., LeBrun, Erick S., Velappan, Nileena, Anderson, Austin R., Patterson, Nathan H., Dufresne, Martin, Farrow, Melissa A., Norris, Jeremy L., Caprioli, Richard M., Mach, Phillip M., McBride, Ethan M., and Glaros, Trevor G.

Subjects
MATRIX-assisted laser desorption-ionization, TANDEM mass spectrometry, MASS spectrometers, YERSINIA pestis, TECHNOLOGICAL innovations, MASS spectrometry, DAUGHTER ions
Abstract

Field-forward analytical technologies, such as portable mass spectrometry (MS), enable essential capabilities for real-time monitoring and point-of-care diagnostic applications. Significant and recent investments improving the features of miniaturized mass spectrometers enable various new applications outside of small molecule detection. Most notably, the addition of tandem mass spectrometry scans (MS/MS) allows the instrument to isolate and fragment ions and increase the analytical specificity by measuring unique chemical signatures for ions of interest. Notwithstanding these technological advancements, low-cost, portable systems still struggle to confidently identify clinically significant organisms of interest, such as bacteria, viruses, and proteinaceous toxins, due to the limitations in resolving power. To overcome these limitations, we developed a novel multidimensional mass fingerprinting technique that uses tandem mass spectrometry to increase the chemical specificity for low-resolution mass spectral profiles. We demonstrated the method's capabilities for differentiating four different bacteria, including attentuated strains of Yersinia pestis. This approach allowed for the accurate (>92%) identification of each organism at the strain level using de-resolved matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) data to mimic the performance characteristics of miniaturized mass spectrometers. This work demonstrates that low-resolution mass spectrometers, equipped with tandem MS acquisition modes, can accurately identify clinically relevant bacteria. These findings support the future application of these technologies for field-forward and point-of-care applications where high-performance mass spectrometers would be cost-prohibitive or otherwise impractical. [ABSTRACT FROM AUTHOR]

Published
2024
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8. Network Topologies and Dynamics Leading to Endotoxin Tolerance and Priming in Innate Immune Cells

Author

Fu, Yan, Glaros, Trevor, Zhu, Meng, Wang, Ping, Wu, Zhanghan, Tyson, John J, Li, Liwu, and Xing, Jianhua

Subjects
Quantitative Biology - Molecular Networks, Quantitative Biology - Quantitative Methods
Abstract

The innate immune system, acting as the first line of host defense, senses and adapts to foreign challenges through complex intracellular and intercellular signaling networks. Endotoxin tolerance and priming elicited by macrophages are classic examples of the complex adaptation of innate immune cells. Upon repetitive exposures to different doses of bacterial endotoxin (lipopolysaccharide) or other stimulants, macrophages show either suppressed or augmented inflammatory responses compared to a single exposure to the stimulant. Endotoxin tolerance and priming are critically involved in both immune homeostasis and the pathogenesis of diverse inflammatory diseases. However, the underlying molecular mechanisms are not well understood. By means of a computational search through the parameter space of a coarse-grained three-node network with a two-stage Metropolis sampling approach, we enumerated all the network topologies that can generate priming or tolerance. We discovered three major mechanisms for priming (pathway synergy, suppressor deactivation, activator induction) and one for tolerance (inhibitor persistence). These results not only explain existing experimental observations, but also reveal intriguing test scenarios for future experimental studies to clarify mechanisms of endotoxin priming and tolerance., Comment: 15 pages, 8 figures, submitted

Published
2012
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16. Reinspection of a Clinical Proteomics Tumor Analysis Consortium (CPTAC) Dataset with Cloud Computing Reveals Abundant Post-Translational Modifications and Protein Sequence Variants

Author

Prakash, Amol, primary, Taylor, Lorne, additional, Varkey, Manu, additional, Hoxie, Nate, additional, Mohammed, Yassene, additional, Goo, Young Ah, additional, Peterman, Scott, additional, Moghekar, Abhay, additional, Yuan, Yuting, additional, Glaros, Trevor, additional, Steele, Joel R., additional, Faridi, Pouya, additional, Parihari, Shashwati, additional, Srivastava, Sanjeeva, additional, Otto, Joseph J., additional, Nyalwidhe, Julius O., additional, Semmes, O. John, additional, Moran, Michael F., additional, Madugundu, Anil, additional, Mun, Dong Gi, additional, Pandey, Akhilesh, additional, Mahoney, Keira E., additional, Shabanowitz, Jeffrey, additional, Saxena, Satya, additional, and Orsburn, Benjamin C., additional

Published
2021
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25. Paper spray ionization: Applications and perspectives

Author

McBride, Ethan M., primary, Mach, Phillip M., additional, Dhummakupt, Elizabeth S., additional, Dowling, Sarah, additional, Carmany, Daniel O., additional, Demond, Paul S., additional, Rizzo, Gabrielle, additional, Manicke, Nicholas E., additional, and Glaros, Trevor, additional

Published
2019
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30. Cover Image

Author

Mach, Phillip M., primary, Dhummakupt, Elizabeth S., additional, Carmany, Daniel O., additional, McBride, Ethan M., additional, Busch, Michael W., additional, Demond, Paul S., additional, Rizzo, Gabrielle M., additional, Hollinshead, Donna E., additional, and Glaros, Trevor, additional

Published
2018
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32. Comparative Characterization of the Sindbis Virus Proteome from Mammalian and Invertebrate Hosts Identifies nsP2 as a Component of the Virion and Sorting Nexin 5 as a Significant Host Factor for Alphavirus Replication

Author

Schuchman, Ryan, primary, Kilianski, Andy, additional, Piper, Amanda, additional, Vancini, Ricardo, additional, Ribeiro, José M. C., additional, Sprague, Thomas R., additional, Nasar, Farooq, additional, Boyd, Gabrielle, additional, Hernandez, Raquel, additional, and Glaros, Trevor, additional

Published
2018
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35. MOESM4 of Development of a liquid chromatography high resolution mass spectrometry method for the quantitation of viral envelope glycoprotein in Ebola virus-like particle vaccine preparations

Author

Cazares, Lisa, Ward, Michael, Brueggemann, Ernst, Kenny, Tara, Demond, Paul, Mahone, Christopher, Martins, Karen, Nuss, Jonathan, Glaros, Trevor, and Bavari, Sina

Abstract

Additional file 4: Figure S3. LC-MS/MS protein identification of coomassie blue stained bands. (A) SDS-PAGE analysis using reducing conditions derived from a 5 Âľg aliquot of the eVLP lot â Bâ . The 10 highest intensity bands from a coomassie stained 4-12% NuPAGE Novex Bis-Tris gel were excised and digested with Trypsin/Lys-C. Each sample was analyzed on a 60 minute LC-MS/MS survey MS run and searched with MASCOT (v. 2.4) against the SProt (2014_02) database with human and Ebola zaire taxonomy specified. Locations of the 5 most prominent peptides are indicated as well as the total number of GP1 peptides observed for each sample (GP1 peptide counts). A minimum Expect score of 0.005 with an FDR of 1% was used for peptide validation. No N-terminal peptides downstream of AA 192 were observed in gel bands 7 thru 10. These data indicate that while the majority of the GP1 protein appears to be full-length, a significant number of N-terminal GP1 fragments are present. (B) An identical sample was analyzed via western blot using the H3D5 antibody showing immune-reactive bands of lower molecular weight.

Published
2016
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36. Direct Analysis of Aerosolized Chemical Warfare Simulants Captured on a Modified Glass-Based Substrate by “Paper-Spray” Ionization

Author

Dhummakupt, Elizabeth S., primary, Mach, Phillip M., additional, Carmany, Daniel, additional, Demond, Paul S., additional, Moran, Theodore S., additional, Connell, Theresa, additional, Wylie, Harold S., additional, Manicke, Nicholas E., additional, Nilles, J. Michael, additional, and Glaros, Trevor, additional

Published
2017
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41. Proteomic and Metabolomic Profiling Identify Plasma Biomarkers for Exposure to Ultra-low Levels of Carfentanil.

Author

Dhummakupt, Elizabeth S, Rizzo, Gabrielle M, Feasel, Michael, Mach, Phillip M, Tran, Bao Q, Carmany, Daniel O, Demond, Paul S, McBride, Ethan M, Maughan, Michele, Sekowski, Jennifer W, and Glaros, Trevor

Subjects
OPIOID analgesics, PROTEOMICS, METABOLOMICS, BIOLOGICAL tags, BLOOD plasma, LIQUID chromatography-mass spectrometry
Abstract

Despite the recent epidemic of fentanyl abuse, there are few validated assays capable of rapidly detecting these compounds. In order to improve the ability to detect carfentanil at physiologically relevant concentrations, we developed a systems biology approach to discover host-based markers which are specifically amplified upon exposure in a rabbit model. For this work, two "omics" pipelines utilizing mass spectrometry were developed and leveraged. First, a proteomics pipeline was developed to interrogate the blood plasma for protein-based biomarkers. Due to the incredible dynamic range of the plasma protein content, a multi-dimensional fractionation technique was used to partition and more accurately investigate the circulating plasma proteome. Isobaric tandem mass tags were integrated into the workflow to make quantitative assessments across all animals for an extended time course post-exposure. In addition to the proteomics efforts, blood plasma was also processed through an untargeted metabolomics pipeline. This approach allows for the identification of >800 small molecule features. By processing and analyzing data sets in parallel, we were able to identify a unique fingerprint of protein and metabolite perturbations that manifest following exposure to carfentanil. [ABSTRACT FROM AUTHOR]

Published
2019
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42. The Addition of Transcriptomics to the Bead-Enabled Accelerated Monophasic Multi-Omics Method: A Step toward Universal Sample Preparation

Author

Breidenbach, Joshua D., Rivera, Emilio S., Harvey, Tara, Mikolitis, Abigale S., Tseng, Chi Yen, Sanders, Claire K., Solomon, Emilia, Gleasner, Cheryl D., Thornhill, M. Grace, Luchini, Kes A., McBride, Ethan M., Blackwell, Brett R., LeBrun, Erick S., Mach, Phillip M., and Glaros, Trevor G.

Abstract

Omics-based measurements enable the study of biomolecules in a high-throughput fashion, leading to the characterization and quantification of biological systems. Multi-omics methods aim to incorporate several omics measurements for a more holistic approach, which is crucial for advancing our understanding of the diversity and redundancy of biological systems. Current multi-omics sample preparation methods have achieved proteomics, lipidomics, and metabolomics from individual samples; however, the bioinformatic tools currently available for interpreting data generated from these omics are limited. Alternately, transcriptomics has a wide arsenal of available bioinformatic tools offering intensive sample characterization but has yet to be incorporated into a unified, multi-omics sample preparation technique. Herein we describe the modified bead-enabled accelerated monophasic multi-omics (mBAMM) method, which incorporates RNA extraction for transcriptomics analysis. mBAMM was shown to enable RNA-seq without compromising the isolation of biomolecules for proteomics, lipidomics, and metabolomics. This methodology greatly improves sample characterization and represents a major innovation toward cohesive insights into biological systems.

Published
2024
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43. Direct Analysis of Aerosolized Chemical Warfare Simulants Captured on a Modified Glass-Based Substrate by ‘Paper-Spray’ Ionization

Author

Dhummakupt, Elizabeth, Mach, Phillip M, Carmany, Daniel, Demond, Paul, Moran, Theodore, Connell, Theresa, Wylie, Harold, Manicke, Nicholas E, Nilles, J. Michael, and Glaros, Trevor

Abstract

Paper spray ionization mass spectrometry (PS-MS) offers a rapid alternative platform requiring no sample preparation. Aerosolized CWA simulants, trimethyl phosphate, dimethyl methylphosphonate, and diisopropyl methylphosphonate, were captured by passing air through a glass fiber filter disk and simultaneously capturing it directly onto a disposable paper spray cartridge. CWA simulants were aerosolized at varying concentrations using an in-house built aerosol chamber. A custom 3D-printed holder was designed and built to facilitate the aerosol capture onto the paper spray cartridges. The air flow through each of the collection devices was maintained equally to assure the same volume of air sampled across methods. Each approach yielded linear calibration curves with R2 values between 0.98–0.99 for each compound and similar limits of detection in terms of disbursed aerosol concentration. While the glass fiber filter disk has a higher capture efficiency (≈40%), the paper spray method produces analogous results even with a lower capture efficiency (≈1%). Improvements were made to include glass fiber filters as the substrate within the paper spray cartridge consumable. Glass fiber filters were then treated with ammonium sulfate to decrease chemical interaction with the simulants. This allowed for improved direct aerosol capture efficiency (>40%). Ultimately, the limits of detection were reduced to levels comparable to current worker population limits of 1x10-6 mg/m3.

Published
2024
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44. Targeted Protein Detection Using an All-in-One Mass Spectrometry Cartridge

Author

Zhang, Chengsen, Glaros, Trevor, and Manicke, Nicholas E.

Abstract

We developed a simple 3D printed cartridge for mass spectrometry (MS) targeted detection of plasma proteins, including post-translational modifications (PTMs). The cartridge uses an integrated antibody enrichment column to preconcentrate the protein target as well as a novel built-in substrate to ionize the protein targets for MS detection. We show several examples of using this cartridge to perform rapid detection of clinically significant proteoforms from plasma samples.

Published
2024
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45. UNC2025 , a Potent and Orally Bioavailable MER/FLT3 Dual Inhibitor

Author

Lee, Minjung, Glaros, Trevor G., Zhang, Weihe, Zhang, Dehui, Cummings, Christopher T., Frye, Stephen V., Hunter, Debra, Sather, Susan, Wang, Xiaodong, and Newton, Dianne L.

Abstract

We previously reported a potent small molecule Mer tyrosine kinase inhibitor UNC1062. However, its poor PK properties prevented further assessment in vivo. We report here the sequential modification of UNC1062 to address DMPK properties and yield a new potent and highly orally bioavailable Mer inhibitor, 11, capable of inhibiting Mer phosphorylation in vivo, following oral dosing as demonstrated by pharmaco-dynamic (PD) studies examining phospho-Mer in leukemic blasts from mouse bone marrow. Kinome profiling versus more than 300 kinases in vitro and cellular selectivity assessments demonstrate that 11 has similar subnanomolar activity against Flt3, an additional important target in acute myelogenous leukemia (AML), with pharmacologically useful selectivity versus other kinases examined.

Published
2014
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46. Development of a liquid chromatography high resolution mass spectrometry method for the quantitation of viral envelope glycoprotein in Ebola virus-like particle vaccine preparations

Author

Cazares, Lisa H., primary, Ward, Michael D., additional, Brueggemann, Ernst E., additional, Kenny, Tara, additional, Demond, Paul, additional, Mahone, Christopher R., additional, Martins, Karen A. O., additional, Nuss, Jonathan E., additional, Glaros, Trevor, additional, and Bavari, Sina, additional

Published
2016
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48. Molecular Mechanisms Governing Persistent Induction of Pro-Inflammatory Genes by Lipopolysaccharide

Author

Glaros, Trevor Griffiths, Biology, Li, Liwu, Capelluto, Daniel G. S., Liu, Dongmin, and Tyson, John J.

Subjects
Inflammation, Low Dose, Macrophage, Priming, Lipopolysaccharide, Interleukin-1 Receptor-Associated Kinase 1, Endotoxemia
Abstract

Low dose endotoxemia is caused by several health conditions including smoking, alcohol abuse, high fat diets, and aging. Several studies have correlated low dose endotoxemia with increased risks of atherosclerosis, diabetes, and Parkinson's disease. Unlike high doses of endotoxin which induce a strong but transient induction of pro-inflammatory mediators, low doses of endotoxin result in a mild but chronic induction of pro-inflammatory genes. The central hypothesis of our study was that if low doses of endotoxin are capable of inducing mild prolonged inflammation, then a unique signaling circuit must be utilized. In the first study, the molecular mechanisms for the persistent induction of lipocalin 2 (LCN2) in response to 100 ng/mL of lipopolysaccharide (LPS) in kidney fibroblasts was examined. It appears that the intracellular signaling network responsible for the persistent induction of LCN2 requires both activator protein-1 (AP-1) and CCAAT/enhancer binding protein delta (C/ebpδ). Interleukin-1 receptor-associated kinase 1 (IRAK-1) is critical for LCN2 expression. In the second study, the molecular mechanisms governing the persistent induction of interleukin 6 (IL-6) upon a 50 pg/mL challenge of LPS in macrophages was examined. At this dose, only the persistent activation of cJun N-terminal kinase (JNK) and C/ebpδ was observed. IL-6 transcription requires the transient recruitment of activating transcription factor 2 (ATF2) and the persistent recruitment of C/ebpδ to the IL-6 promoter. In the third study, the molecular mechanisms that mediate LPS-induced priming was examined. The results demonstrate that macrophages are able to sense their prior history of exposure to LPS that result in either a priming or tolerance phenotype upon a secondary challenge of LPS. Results suggest that this sensing mechanism involves cross-talk between IRAK-1 and phosphoinositide-3-kinase (PI3K). Collectively, these studies indicate that JNK and C/ebpδ are the primary players responsible for the persistent expression of pro-inflammatory genes during low dose endotoxemia. IRAK-1 is a key intracellular signaling kinase that mediates signaling at low doses of LPS. IRAK-1 is not only critical for low dose induced expression, but also for LPS-induced priming. This research has revealed a novel signaling pathway that could provide new molecular targets for drug development against chronic inflammatory diseases. Ph. D.

Published
2011

49. Histone modification analysis by chromatin immunoprecipitation from a low number of cells on a microfluidic platform

Author

Geng, Tao, Bao, Ning, Litt, Michael D., Glaros, Trevor G., Li, Liwu, and Lu, Chang

Subjects
MU-CHIP, EPIGENETIC CHARACTERIZATION, DNA, ACETYLATION, ASSAY, PROTOCOL, DEVICE, MAPS, Nanoscience and Nanotechnology
Abstract

Histone modifications are important epigenetic mechanisms involved in eukaryotic gene regulation. Chromatin immunoprecipitation (ChIP) assay serves as the primary technique to characterize the genomic locations associated with histone modifications. However, traditional tube-based ChIP assays rely on large numbers of cells as well as laborious and time-consuming procedures. Here we demonstrate a novel microfluidics-based native ChIP assay which dramatically reduces the required cell number and the assay time by conducting cell collection, lysis, chromatin fragmentation, immunoprecipitation, and washing on a microchip. Coupled with real-time PCR, our assay permits the analysis of histone modifications from as few as similar to 50 cells within 8.5 h. We envision that our method will provide a new approach for the analysis of epigenetic regulations and protein-DNA interactions in general, based on scarce cell samples such as those derived from animals and patients.

Published
2011

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