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Metabolomics data interpretation approach development

Metabolomics is a cutting-edge area that his been widely applied in various areas, especially in human disease mechanisms and potential biomarker studies. However, due to the interdisciplinary requirement among data scientists, analytical chemists, and biochemists, the biomarker validation methods are not very well-developed which significantly limits the application of metabolomics especially for researchers with limited instrumentation and data science expertise. In this project, we are working on developing novel algorithms on metabolomics biomarker discovery and validation.   Metabolomics is a cutting-edge area that can be a powerful tool for monitoring the environmental toxin's affections on animal and human health. However, the real-life applications are still in their infancy which is mainly due to the complexities of the metabolomics process. One of the main problems for metabolomics applications in health studies is the lack of models that considers the instrumentation errors and biological data into models, which lead to overfitting problems. We propose to develop novel automatic methods which will include all the data reliability information using machine learning methods and aim to develop novel approaches to apply metabolomics to monitor environmental problems. The study is also expected to predict potential problems under single and various combinational environmental toxins to animal and human health

 Selected publications: 

  1. Wang, B*.; Maldonado-Devincci A.; Jiang L., Evaluating line-broadening factors on a reference spectrum as a bucketing method for NMR-based metabolomics, Analytical Biochemistry, 2020, 606, 113872. (*Corresponding author)
  2. Jiang, L.; Howlett, K.; Patterson, K.; Wang, B*., Introduction of a new method for two-dimensional NMR quantitative analysis in metabolomics studies. Analytical Biochemistry, 2020, 597 (15), 113692. (*Corresponding author)
  3. Jiang, L.; Sullivan H, C.; Wang, B.* Evaluation of a new approach to analyzing the principal component analysis for multiple groups studies. Analytical Letters, 2022:DOI: 10.1080/00032719.2021.2019758 (*Corresponding author)
  4. Pollak, J., Mayonu, M., Jiang, L., & Wang, B. (2024). The development of machine learning approaches in two-dimensional NMR data interpretation for metabolomics applications. Analytical Biochemistry, 695, 115654. (*Corresponding author)
  5. Mayonu, M., Babaee, Deneyelle W, Jiang, L. & Wang, B. Evaluation of a new approach for principal component analysis application in metabolomics studies, Analytical Letters, submitted (*Corresponding author)

Grant: 

  • National Science Foundation (NSF), LEAPS-MPS: Artificial Intelligence Techniques for Automatic NMR Metabolomics Data Processing, 09/15/2021-10/31/2025, $248,613, (PI)
  • National Science Foundation (NSF), Collaborative Research: SCH: Therapeutic and Diagnostic System for Inflammatory Bowel Diseases: Integrating Data Science, Synthetic Biology, and Additive Manufacturing, 09/2023-08/2028, $168,690 (PI for FIT, leading PI Estrada Gomez, Purdue University)

Metabolomic studies on environmental science

Our project will develop a metabolomics model to discover the sea anemones metabolomics response to combinational environmental stress. It is expected that the synergistic harmful effect of two or more environmental factors to the health of sea anemones will be discovered in metabolomics studies. Therefore, our study will help to predict the potential serious environmental issue when several regular environmental factors appear simultaneously even in relatively low concentrations. The red tide blooms and Vibrio in the Gulf of Mexico have drawn wide concerns about environmental pollution and affect local residences via inhalation or ingestion . Red tide is caused by harmful algal blooms (HABs) and the Karenia Brevis which produces brevetoxins is the major concern of the Florida red tide. Traditionally, the cell monitoring of K. Brevis and the brevetoxins monitoring using shellfish extracts have been applied for environmental monitoring, but the red tide toxicity prediction remains difficult. An early warning system before the red tide blooms to monitor the brevetoxins and Vibrio is critical to red tide mitigation since prevention and early treatment are more effective than treatment methods after the blooms. Novel high omics methods such as metabolomics using big data approaches have been initialized in the environmental stressors studies, however, are rarely investigated in marine biology studies. 

 Selected publications: 

  1. Jiang L, Sullivan H, Seligman C, Gilchrist S, Wang B*. An NMR-based metabolomics study on sea anemones Exaiptasia diaphana (Rapp, 1829) with atrazine exposure. Mol Omics. 2021 Dec 6;17(6):1012-1020. doi: 10.1039/d1mo00223f. PMID: 34633404. (*Corresponding author)
  2. Metabolomics study on southern hard clams (Mercenaria campechiensis) response to diclofenac exposure. Environmental Science: Advances, 2(1), 107-114. (*Co-Corresponding author)
  3. Wang, B., McKenna, N., Pollak, J., Mayonu, M., & Jiang, L. (2025). The investigation of early metabolic level perturbation of northern quahog (Mercenaria mercenaria) in response to brevetoxin. Molecular Omics. 2025
  4. Tran T, Babaee S, Wilson D, Mayonu M, Pollak J, Wang B, Comparative Study of Machine Learning Methods for Modeling Graphene-Based Adsorption in Water Treatment. (To be submitted)
  5. Wang, B., Habermehl, C. and Jiang, L., 2022. Metabolomic analysis of honey bee (Apis mellifera L.) response to glyphosate exposure. Molecular Omics, 18(7), pp.635-642.

Grant: 

  • Gulf of Mexico Alliance (GOMA), AI-Directed Tool Development for Pathogenic “Flesh-eating” Vibrio Bacteria Prediction and Control, 07/01/2024-6/30/2027, $200,000 (Leading PI)

Multi-omics in human health studies

Area 1: We built a team with experts in four different areas and developed a novel and highly practical approach to integrating data science, multi-omics, system biology, and additive manufacturing for the Theranostics of IBD. Our overarching hypothesis is that, by identifying key biomarkers of IBD and their interactions and progression, a theranostic engineered bacteria can be used as an effective mechanism to diagnose and treat IBD, and can be safely delivered to the human GI tract with the use of a smart 3D printed pill. The study is expected to develop an effective diagnosis tool and subsequent treatment to control the disease without side effects. The development of the theranostic will allow millions of people, including military, currently living with IBD to control their symptoms effectively and live a healthier and happier life.

Area 2: Metabolomics has been widely applied in human health studies. In collaboration with researchers at the health center at various universities, including University of South Florida, Florida State University, and Ohio University, we have combined metabolomics with microbiome and carried out various types of research on aging, obesity, diabetes, and Alzheimer's diseases.

Selected publications: 

  1. Ahmadi, S.; Wang, S.; Nagpal, R.; Wang, B.; Jain, S.; Razazan, A.; Mishra, S. P.; Zhu, X.; Wang, Z.; Kavanagh, K., A human-origin probiotic cocktail ameliorates aging-related leaky gut and inflammation via modulating microbiota-taurine-tight junction axis. JCI insight, 2020, 5(9), e132055.
  2. Ahmadi, S.; Razazan, A.; Nagpal, R.; Jain, S.; Wang, B.; Mishra, S. P.; Wang, S.; Justice, J.; Ding, J.; McClain, D. A., Metformin reduces aging-related leaky gut and improves cognitive function by beneficially modulating gut microbiome/goblet cell/mucin axis. The Journals of Gerontology: Series A, 2020, 75 (7), e9-e21.
  3. Wang, B., Jadhav, V., Odelade, A., Chang, E., Chang, A., Harrison, S. H., ... & Han, J. (2023). High fat diet reveals sex-specific fecal and liver metabolic alterations in C57BL/6J obese mice. Metabolomics, 19(12), 97.
  4. Kadyan, S., Park, G., Wang, B., Singh, P., Arjmandi, B., & Nagpal, R. (2023). Resistant starches from dietary pulses modulate the gut metabolome in association with microbiome in a humanized murine model of ageing. Scientific Reports, 13(1), 10566.
  5. Kadyan, S., Park, G., Wang, B., & Nagpal, R. (2023). Dietary fiber modulates gut microbiome and metabolome in a host sex-specific manner in a murine model of aging. Frontiers in Molecular Biosciences, 10, 1182643.
  6. Mishra, S. P., Wang, B., Jain, S., Ding, J., Rejeski, J., Furdui, C. M., ... & Yadav, H. (2023). A mechanism by which gut microbiota elevates permeability and inflammation in obese/diabetic mice and human gut. Gut 72 (10), 1848-1865

Grants: 

  • National Science Foundation (NSF), Collaborative Research: SCH: Therapeutic and Diagnostic System for Inflammatory Bowel Diseases: Integrating Data Science, Synthetic Biology, and Additive Manufacturing, 09/2023-08/2028, $168,690 (PI for FIT, leading PI Estrada Gomez, Purdue University)
  • National Institutes of Health (NIH) R01, Microbial therapy improves gut permeability to reduce cognitive decline and Alzheimer’s disease, 08/15/2021- 07/29/2026, $85,184.00, (PI for FIT, leading PI, Yadav, University of South Florida).
  • National Institutes of Health (NIH) R21, The role of gut microbiota in the efficacy of ketogenic diet to ameliorate Alzheimer's disease, 07/01/2021 – 06/30/2023, $17,000 (PI for FIT, leading PI, Yadav, University of South Florida)
  • National Institutes of Health (NIH), Adolescent alcohol exposure: impact on neuronal activation, steroids, and metabolomic profiles, 4/1/2024-3/31/2028, $10,000, (PI for FIT, leading PI, Maldonado-Devincci, North Carolina A&T State University )

Natural compounds in human health studies and environmental engineering

Area 1: Pharmaceuticals and personal care products (PPCPs) are receiving emerging concerns due to their wild usage all over the world and their persistent presence in the aquatic environment. The current commonly used wastewater treatment methods, such as nano-material adsorption and membranes process, are costly and difficult to scale up thus block the practical application. TiO2-based photocatalysis has shown great potential as a low-cost, sustainable, and green technology for wastewater treatment. However, TiO2 is mainly activated by UV lights (only 5-7% of the solar radiation), which is a critical limiting factor in increasing the photodegradation efficiency. Therefore, improving the energy conversion rate is one important approach to increase the photocatalytic performance in wastewater organic compounds treatment. Ruthenium dye N3 and other organic dyes were successfully utilized in dye-sensitized solar cells in the past decades, but only a few applications in wastewater treatment were reported which was also limited by the high toxicity of Ru and other organic dyes.

Area 2: Natural compounds have drawn high attention in cancer treatment due to their compelling performance and low toxicity. Though the synergism effect for the combination of natural compounds is critical in drug discovery, the traditional trial-and-error way to discover possible pure compound synergetic combinations has very low efficiency due to the high possibility of combinations. However, the synergistic combinations and potential toxicity combinations in plant extracts are hard to identify.  Garlic scape may have the potential to prevent development of diabetes by modulating carbohydrate digestion and glucose uptake in intestine. Measuring carbohydrate digestion and glucose uptake will produce the efficacy of garlic scape extract in intestine as the potential functional food that has anti-diabetic effect. One expected result is that the link between cancer metabolomic perturbation under different treatment and plant compounds profilings will provide directions to narrow down the most synergistic combinations in plant extract. 

 

Selected publications: 

  1. Patterson, K.; Howlett, K.; Patterson, K.; Wang, B*.; Jiang, L*., Photodegradation of Ibuprofen and four other pharmaceutical pollutants on natural pigments sensitized TiO2 Water Environment Research, 2020, 92 (8), 1152-1161. (Co-Corresponding author)
  2. Sullivan H., Wang B; Jiang L. (2022). Investigation of tropical plant‐based natural dyes combination and adsorption optimization for natural dye‐sensitized solar cell. Environmental Progress & Sustainable Energy, 41(4), e13809. (*Co-Corresponding author)
  3. Tran T, Babaee S, Wilson D, Mayonu M, Pollak J, Wang B, Comparative Study of Machine Learning Methods for Modeling Graphene-Based Adsorption in Water Treatment. Water Environment Research, submited

Grant: 

  • S. Department of Agriculture, Capacity Building Grants Program (CBGP), Investigation of garlic scape nutraceuticals as an anti-diabetic food, 09/01/2022 – 08/31/2025, $20,370 (PI for FIT, PI for FIT, leading PI, Kang, North Carolina A&T State University)

Summary of Research grants

  • Gulf of Mexico Alliance (GOMA), AI-Directed Tool Development for Pathogenic “Flesh-eating” Vibrio Bacteria Prediction and Control, 07/01/2024-6/30/2027, $200,000 (Leading PI)
  • National Science Foundation (NSF), LEAPS-MPS: Artificial Intelligence Techniques for Automatic NMR Metabolomics Data Processing, 09/15/2021-10/31/2025, $248,613, (PI)
  • National Science Foundation (NSF), Collaborative Research: SCH: Therapeutic and Diagnostic System for Inflammatory Bowel Diseases: Integrating Data Science, Synthetic Biology, and Additive Manufacturing, 09/2023-08/2028, $168,690 (PI for FIT, leading PI Estrada Gomez, Purdue University)
  • National Institutes of Health (NIH), Adolescent alcohol exposure: impact on neuronal activation, steroids, and metabolomic profiles, 4/1/2024-3/31/2028, $10,000, (PI for FIT, leading PI, Maldonado-Devincci, North Carolina A&T State University )
  • S. Department of Agriculture, Capacity Building Grants Program (CBGP), Investigation of garlic scape nutraceuticals as an anti-diabetic food, 09/01/2022 – 08/31/2025, $20,370 (PI for FIT, PI for FIT, leading PI, Kang, North Carolina A&T State University)
  • National Institutes of Health (NIH) R01, Microbial therapy improves gut permeability to reduce cognitive decline and Alzheimer’s disease, 08/15/2021- 07/29/2026, $85,184.00, (PI for FIT, leading PI, Yadav, University of South Florida).
  • National Institutes of Health (NIH) R21, The role of gut microbiota in the efficacy of ketogenic diet to ameliorate Alzheimer's disease, 07/01/2021 – 06/30/2023, $17,000 (PI for FIT, leading PI, Yadav, University of South Florida)
  • National Science Foundation (NSF), MRI: Acquisition of a liquid chromatography with tandem mass spectrometer for interdisciplinary research and education on the campus of North Carolina A&T State University, Co-PI (Leading PI Renzun Zhao), $679,703, 09/01/2022 - 08/31/2024
  • Department of Defense (DoD) Army Research Laboratory (ARL), Center for Detection and Monitoring of Chemical and Biological Threat Agents through Deployment of an Integrated Microengineered Organ Equivalent System, Co-PI, $8,000,000 09/01/2021 – 08/31/2022
  • Travel Grant, Florida Coastal Challenges, NSF funded, Nova Southeastern University (NSU), 2022
  • NC A&T TraCS Interdisciplinary Team Science Award, An integrative study of translation and molecular mechanisms of the neuroprotective effect of the Mediterranean diet on Parkinson’s disease, Co-PI, $20,000.00, 01/03/2021-06/30/2021
  • NC TraCS, Junior Faculty Supplies Awards, PI, $3,000.00, 04/2020
  • Cancer Prevention Research Institute of Texas (CPRIT), training grant, metabolic modulation by combinatorial intervention with natural compounds for cancer, awardee postdoc fellow, 03/01/2015-02/09/2016