Article
Food Science & Technology
Jing Pu, Bingye Zhao, Xin Liu, Shugang Li, Beibei Wang, Di Wu, Jinqiu Wang, Fang Geng
Summary: This study comprehensively compared the protein profiles and properties of chicken egg white and its three components. The proteomes of thick and thin egg white are similar, but thick egg white has higher abundance of ovomucin subunits and lysozymes. The properties of thick and thin egg white are significantly different. Additionally, the chalaza component has higher abundance of insoluble proteins and lower abundance of soluble proteins, which explains its insolubility. These findings are important for further research and development of egg white, such as thinning of egg white, understanding changes in egg white properties, and differential application of thick and thin egg white.
FOOD RESEARCH INTERNATIONAL
(2023)
Article
Biochemical Research Methods
Antoine Lesur, Francois Bernardin, Ois Bernardin, Eric Koncina, Elisabeth Letellier, Gary Kruppa, Pierre-Olivier Schmit, Gunnar Dittmar
Summary: Blood analysis is a crucial part of clinical diagnostics, and mass spectrometry has made significant advancements in protein analysis in blood samples. The prm-PASEF method combines ion mobility as an additional separation dimension, increasing proteome coverage and allowing for shorter chromatographic gradients. An alternative method, g-dia-PASEF, is described as a less time-consuming approach.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Dianqin Xu, Xiaoyu Zhu, Ji Ren, Shan Huang, Ziwen Xiao, Hongmei Jiang, Yujie Tan
Summary: In this study, tandem mass tags-labeled quantitative proteomic technology and bioinformatics tools were used to analyze exfoliated cervical cells from normal and cervical cancer groups. A cancer-specific protein profile was established, leading to the identification of key proteins related to cervical cancer development. These differentially expressed proteins were found to be involved in various cellular processes and signaling pathways, laying the foundation for understanding the molecular mechanisms of cervical cancer.
JOURNAL OF PROTEOMICS
(2022)
Article
Chemistry, Multidisciplinary
Muzaffar Iqbal, Essam A. Ali, Mohd Abul Kalam, Sheikh F. Ahmad, Rashad Al-Salahi
Summary: A simple, selective and reliable ultra-performance liquid chromatography-tandem mass spectrometry assay has been developed for the quantitative analysis of 5-Aminoisoquinoline (5-AIQ) in plasma. The assay was linear in the concentration range of 1.0 to 666 ng/mL and showed good precision and bias. In silico ADME prediction showed that 5-AIQ is very soluble in water and has high gastrointestinal absorption and blood-brain barrier permeability. The validated method can be utilized for future pharmacokinetic and bio-distribution studies.
APPLIED SCIENCES-BASEL
(2022)
Article
Biochemical Research Methods
Jinjun Gao, Yuan Liu, Fan Yang, Xuemin Chen, Benjamin F. Cravatt, Chu Wang
Summary: ABPP is a powerful chemical proteomic method for studying protein activity, modifications, and interactions, where accurate quantification is crucial. CIMAGE is a specialized quantification software for ABPP data analysis, providing efficient and accurate quantification with the ability to visualize results conveniently.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Ophthalmology
Maite Lopez-Lopez, Uxia Regueiro, Susana B. Bravo, Maria del Pilar Chantada-Vazquez, Ruben Varela-Fernandez, Paulo Avila-Gomez, Pablo Hervella, Isabel Lema
Summary: Utilizing SWATH-MS for tear protein quantification, dysregulated proteins involved in iron homeostasis, inflammatory-immune response, oxidative stress, and other biological processes were identified in patients with keratoconus. The study sheds light on the molecular mechanisms underlying the disease and highlights the potential therapeutic targets related to iron accumulation and tissue damage in keratoconus pathophysiology.
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Anna A. Ivanova, Jon C. Rees, Bryan A. Parks, Michael Andrews, Michael Gardner, Eunice Grigorutsa, Zsuzsanna Kuklenyik, James L. Pirkle, John R. Barr
Summary: This study utilized quantitative lipidomics and proteomics to identify molecular changes associated with different metabolic risk categories, and established protein-lipid topological networks to analyze dysregulated proteins and lipids in relation to metabolic pathways.
Article
Biotechnology & Applied Microbiology
Juan J. Roman-Camacho, Juan C. Mauricio, Ines M. Santos-Duenas, Teresa Garcia-Martinez, Isidoro Garcia-Garcia
Summary: This study analyzed the protein profile of vinegar microbiota using liquid chromatography-tandem mass spectrometry, focusing on the Komagataeibacter species, particularly K. europaeus. The results showed that the majority of identified proteins involved in amino acid metabolism, protein biosynthesis, and energy production pathways increased their expression during the cycle loading phase and then decreased, with other proteins coming into play against acetic acid stress. These findings help predict the natural behavior of a microbial community in vinegar and contribute to obtaining a quality product.
Article
Biochemistry & Molecular Biology
Ghaith M. Hamza, Eric Miele, Don M. Wojchowski, Paul Toran, Camilla R. Worsfold, Tamil S. Anthonymuthu, Vladislav B. Bergo, Andrew X. Zhang, Jeffrey C. Silva
Summary: The Affi-BAMS™ epitope-directed affinity bead capture/MALDI MS platform is effective in quantitatively defining complex PTM marks of H3 and H4 histones. The platform achieves a range of >3 orders of magnitude with a technical precision CV of <5%. It can resolve heterogeneous histone N-terminal PTMs with as little as 100 μg of starting material.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Alexia Grangeon, Valerie Clermont, Azemi Barama, Fleur Gaudette, Jacques Turgeon, Veronique Michaud
Summary: This study quantified the protein expression levels of 16 major CYP450 isoforms in various sections of the human small intestine using LC-MS/MS, revealing seven detected isoforms and observing wide inter-subject variability. The study found that CYP450 protein levels were better correlated with specific isoform activities than with mRNA levels, which could provide new data for improving physiologically based pharmacokinetic models.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Environmental Sciences
Cong-Cong Shen, Mo-Xian Chen, Tian Xiao, Cheng Zhang, Jun Shang, Kai-Lu Zhang, Fu-Yuan Zhu
Summary: The study utilized SWATH-MS technology to analyze the proteome changes in poplar seedling roots following Pb treatment. Results showed that the lignin and flavonoid biosynthesis pathways were activated upon Pb exposure, while cell wall-related proteins exhibited increased abundances. Glutathione metabolism pathway may play a protective role in mitigating Pb-induced oxidative damages.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2021)
Article
Chemistry, Applied
Sridevi Muralidharan, Yan Yee Poon, Graeme C. Wright, Paul A. Haynes, Nanju A. Lee
Summary: This study used mass spectrometry-based proteomic analysis on Australian peanut recombinant inbred lines and found significant protein expression differences between high and low polyphenol expressing RILs. Metabolic changes, including increased enzymatic breakdown of sugars and phenylalanine biosynthesis, were observed in polyphenol-rich RILs. The study also revealed overexpression of phenylpropanoid pathway and antioxidant enzymes, such as catalase, in the polyphenol-rich peanut phenotype.
Article
Biochemical Research Methods
Vincent R. Richard, Claudia Gaither, Robert Popp, Daria Chaplygina, Alexander Brzhozovskiy, Alexey Kononikhin, Yassene Mohammed, Rene P. Zahedi, Evgeny N. Nikolaev, Christoph H. Borchers
Summary: This study used multiplexed targeted mass spectrometry assays to determine the concentrations of hundreds of substances in the plasma of hospitalized COVID-19 patients. The researchers found clear distinctions between COVID-19 patients and controls, as well as significant differences between survivors and nonsurvivors. Using a machine learning model, they were able to predict patient survival with high accuracy based on the concentrations of a limited number of substances on the day of hospitalization.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Biochemical Research Methods
Huu-Quang Nguyen, Dabin Lee, Yeoseon Kim, Geul Bang, Kun Cho, Young-Sun Lee, Jong Eun Yeon, David M. Lubman, Jeongkwon Kim
Summary: This study utilized LC-MS/MS to analyze the protein expression profiles of extracellular vesicles from serum samples of patients with various fatty liver diseases, revealing significant differences in protein expression levels of apolipoproteins, immunoglobulins, and other markers. Through principal component analysis, a clear differentiation between ALD and NAFLD was achieved. The up-regulation of alpha-2-macroglobulin in alcoholic hepatitis and apolipoprotein C3 in NAFLD were identified as significant findings.
JOURNAL OF PROTEOMICS
(2021)
Article
Biochemistry & Molecular Biology
Jingfang Bian, Ying-Hon Sze, Dennis Yan-Yin Tse, Chi-Ho To, Sally A. McFadden, Carly Siu-Yin Lam, King-Kit Li, Thomas Chuen Lam
Summary: Most of the previous myopic animal studies used lower resolution proteomics approaches and single-candidate methods, making it difficult to detect minor changes. This study utilized SWATH proteomic analysis to identify significant protein changes in pigmented guinea pigs after induced myopia, highlighting lipid metabolism as a top function associated with differentially expressed proteins. The study provides new insights for further research in myopia control.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Medicinal
Raju Khatri, Natasha Kulick, Rebecca J. B. Rementer, John K. Fallon, Craig Sykes, Amanda P. Schauer, Melina M. Malinen, Merrie Mosedale, Paul B. Watkins, Angela D. M. Kashuba, Kim A. Boggess, Philip C. Smith, Kim L. R. Brouwer, Craig R. Lee
Summary: Pregnancy-related hormones have been shown to significantly increase CYP3A4 protein concentrations and nifedipine metabolism, as well as alter the expression of other key CYP proteins in a concentration-dependent manner. There is a positive correlation between CYP3A4 mRNA levels in hepatocyte-derived exosomes and CYP3A4 protein levels and dehydronifedipine formation. These findings offer mechanistic insight into the changes in nifedipine metabolism observed in pregnant women.
JOURNAL OF PHARMACEUTICAL SCIENCES
(2021)
Article
Chemistry, Medicinal
Jacqueline Bezencon, Chitra Saran, Janine Hussner, James J. Beaudoin, Yueping Zhang, Hong Shen, John K. Fallon, Philip C. Smith, Henriette E. Meyer zu Schwabedissen, Kim L. R. Brouwer
Summary: Recent studies have focused on the impact of loss of Mrp2 function on the routes of excretion of endogenous CPs. The results showed that CPs are substrates of rodent Oatp1b2 and Oatp2b1. The concentrations of CP-I and CP-III were elevated in TR- rat liver, while biliary clearance was decreased.
JOURNAL OF PHARMACEUTICAL SCIENCES
(2021)
Article
Chemistry, Medicinal
Rani J. Qasem, John K. Fallon, Manisha Nautiyal, Merrie Mosedale, Philip C. Smith
Summary: This study evaluated the efficiency of sequential digitonin and Triton-X-100 fractionation of membrane protein from limited samples for QTAP of DMEs and transporters. Results showed that DDF produced linear membrane protein yields with better permeabilization compared to other methods, making it an efficient and cost-effective approach.
JOURNAL OF PHARMACEUTICAL SCIENCES
(2021)
Article
Medicine, Research & Experimental
Anam Hammid, John K. Fallon, Toni Lassila, Giulia Salluce, Philip C. Smith, Ari Tolonen, Achim Sauer, Arto Urtti, Paavo Honkakoski
Summary: This study analyzed the esterase activity and expression in ocular tissues of rabbits and pigs, revealing significant species and tissue differences in ocular hydrolytic enzymes, which can be important for the design of prodrugs and drug conjugates, evaluation of ocular effects of systemic drugs, and translational and toxicity studies.
MOLECULAR PHARMACEUTICS
(2021)
Article
Toxicology
Manisha Nautiyal, Rani J. Qasem, John K. Fallon, Kristina K. Wolf, Jingli Liu, Darlene Dixon, Philip C. Smith, Merrie Mosedale
Summary: This study demonstrated successful long-term culture of mouse hepatocytes as spheroids using 3D methodology, highlighting their utility in supporting investigations of drug-induced liver injury (DILI).
TOXICOLOGY IN VITRO
(2021)
Article
Pharmacology & Pharmacy
Bridget L. Morse, Lisa Hong Chen, John T. Catlow, John K. Fallon, Philip C. Smith, Kathleen M. Hillgren
Summary: Research on the organic cation transporter 1 (OCT1) in humans has shown its significance in physiology, drug exposure, and drug response, particularly in variant carriers. Studies using cell lines and Oct knockout mice reveal the impact of Oct1 deficiency on drug pharmacokinetics, especially in the liver. Substrate-dependent activity of OCT1 contributes to the complexity of understanding its role in pharmacokinetics.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Pharmacology & Pharmacy
Bridget L. Morse, John K. Fallon, Anil Kolur, Andrew T. Hogan, Philip C. Smith, Kathleen M. Hillgren
Summary: Hepatic clearance may be limited by organic anion transporting polypeptides (OATPs) and organic cation transporter 1 (OCT1), with little reported on OCT1 activity across species. Expression of transporters, including Oatps and Octs, varies between tissues in mice and rats, with higher Octs expression in the kidney compared to the liver. Liver partitioning of OCT1 substrates is lower in rodents compared to monkeys, reflecting species-dependent OCT1 activity.
Article
Pharmacology & Pharmacy
Heather Eng, Elaine Tseng, Matthew A. Cerny, Theunis C. Goosen, R. Scott Obach
Summary: Time-dependent inhibition of CYP3A is a key mechanism in drug-drug interactions, but measurements in human liver microsomes can often lead to overestimations. This study evaluated TDI of 50 drugs in HLMs and suspended human hepatocytes, providing appropriate boundary lines for the parameter rate constant for inhibition. Values of k(obs) in HHEPs were consistently lower than those in HLMs, offering practical guidance for early drug discovery research on CYP3A.
DRUG METABOLISM AND DISPOSITION
(2021)
Article
Pharmacology & Pharmacy
Liberta Cuko, Zofia Duniec-Dmuchowski, Elizabeth A. Rondini, Asmita Pant, John K. Fallon, Elizabeth M. Wilson, Nicholas J. Peraino, Judy A. Westrick, Philip C. Smith, Thomas A. Kocarek
Summary: The squalestatin 1 inhibitor Squal1 induces rat hepatic CYP2B expression indirectly through the constitutive androstane receptor (CAR), but does not similarly induce CYP2B6 expression in human hepatocytes due to interference with CAR activation caused by inhibitory effect on cholesterol biosynthesis.
DRUG METABOLISM AND DISPOSITION
(2021)
Article
Pharmacology & Pharmacy
Raju Khatri, John K. Fallon, Craig Sykes, Natasha Kulick, Rebecca J. B. Rementer, Taryn A. Miner, Amanda P. Schauer, Angela D. M. Kashuba, Kim A. Boggess, Kim L. R. Brouwer, Philip C. Smith, Craig R. Lee
Summary: Pregnancy-related hormones have been shown to influence the expression and function of UGT proteins, particularly enhancing UGT1A1-mediated metabolism of labetalol in human hepatocytes. This findings provide mechanistic insight into the increased clearance of labetalol observed in pregnant individuals.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Medicine, Research & Experimental
Olumide B. Gbolahan, Bert H. O'Neil, Autumn J. McRee, Hanna K. Sanoff, John K. Fallon, Philip C. Smith, Anastasia Ivanova, Dominic T. Moore, Julie Dumond, Gary N. Asher
Summary: This study aimed to evaluate the safety and efficacy of concurrent administration of curcumin and irinotecan. The results showed that the combination therapy was well-tolerated and did not significantly affect the pharmacokinetic properties of irinotecan. There was no apparent increase in the incidence of toxicities associated with irinotecan. Although the objective response rate was relatively low, further studies are needed to evaluate the efficacy of this combination therapy.
CTS-CLINICAL AND TRANSLATIONAL SCIENCE
(2022)
Article
Cell Biology
Yuling Zhao, Matthew J. Haney, John K. Fallon, Myosotys Rodriguez, Carson J. Swain, Camryn J. Arzt, Philip C. Smith, Matthew Shane Loop, Emily B. Harrison, Nazira El-Hage, Elena Batrakova
Summary: Extracellular vesicles (EVs), derived from macrophages transfected ex vivo to express neurotrophic factors, show promising therapeutic potential for Parkinson disease (PD). In this study, EVs carrying glial-cell-line-derived neurotrophic factor (GDNF) were collected and characterized. Intranasal administration of EV-GDNF significantly improved locomotor functions, increased neuronal survival, and decreased neuroinflammation in PD mice. No offsite toxicity caused by EV-GDNF administration was detected. EV-based approach provides a versatile and potent therapeutic intervention for PD.
Article
Pharmacology & Pharmacy
Anam Hammid, John K. Fallon, Toni Lassila, Paula Vieiro, Anusha Balla, Francisco Gonzalez, Arto Urtti, Philip C. Smith, Ari Tolonen, Paavo Honkakoski
Summary: Novel and comprehensive data on the protein expression and activities of carboxylesterases from individual human eye tissues are generated. In combination with previous reports on preclinical species, this study will improve the understanding of interspecies differences in ocular drug metabolism and aid the development of ocular pharmacokinetics models.
DRUG METABOLISM AND DISPOSITION
(2022)
Article
Multidisciplinary Sciences
Chitra Saran, Dong Fu, Henry Ho, Abigail Klein, John K. Fallon, Paavo Honkakoski, Kim L. R. Brouwer
Summary: Hepatic cell lines can be used as cost-effective and reproducible alternatives to primary human hepatocytes. However, their usefulness in studying bile acid homeostasis and cholestatic toxicity is limited due to abnormal expression and function of bile acid-metabolizing enzymes, transporters, and the absence of canalicular formation. This study demonstrates that culturing HuH-7 human hepatoma cells with dexamethasone and dimethyl sulfoxide can improve the differentiation process and increase the expression and function of bile acid transporters. The differentiated HuH-7 cells display altered bile acid composition and induction of bile acid-metabolizing enzymes, making them a suitable model for studying cholestatic hepatotoxicity.
SCIENTIFIC REPORTS
(2022)
Article
Engineering, Biomedical
Matthew J. Haney, Yuling Zhao, John K. Fallon, Yue Wang, Samuel M. Li, Emily E. Lentz, Dorothy Erie, Philip C. Smith, Elena V. Batrakova
Summary: Extracellular vesicles (EVs) are considered a promising drug delivery system due to their nanoparticle size, ability to cross biological barriers, and low immunogenicity. EVs released by cells of different origin show potential for drug delivery to the brain for treatment of neurodegenerative disorders.
ADVANCED NANOBIOMED RESEARCH
(2021)