Article
Chemistry, Analytical
Liang Guo, Bin Wu, Xuhong Wang, Xiaoying Kou, Xiaohong Zhu, Kaijing Fu, Qian Zhang, Shaojun Hong, Xinjun Wang
Summary: Long-term low-dose ionizing radiation (LLIR) has potential pathogenic effects on cancer and cardiovascular diseases, but exploring the phenotypic changes caused by LLIR in human cohorts is technically and ethically challenging. This study found clear metabolic phenotypic differences between LLIR and non-LLIR exposed participants, and further categorized LLIR exposed workers into two types of metabolic phenotypes, corresponding to high and low damage types. 3-hydroxypropanoate and glycolaldehyde were identified as sensitive indicators to radiation damage, while taurine metabolism-related pathways were identified as the main differential metabolic pathway under LLIR induction.
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
(2022)
Article
Biochemical Research Methods
Evan L. Pannkuk, Evagelia C. Laiakis, Michael Girgis, Guy Y. Garty, Shad R. Morton, Monica Pujol-Canadell, Shanaz A. Ghandhi, Sally A. Amundson, David J. Brenner, Albert J. Fornace
Summary: A novel irradiation system, VADER, was used to expose mice to variable low-dose rate irradiation, identifying radiation markers through metabolomics analysis. A multiplex panel of urinary metabolites showed robust classification performance for radiation dose, suggesting dysregulated energy metabolism is associated with both low-dose rate and conventional radiation exposure.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Evan L. Pannkuk, Evagelia C. Laiakis, Guy Garty, Shivani Bansal, Brian Ponnaiya, Xuefeng Wu, Shanaz A. Ghandhi, Sally A. Amundson, David J. Brenner, Albert J. Fornace
Summary: This study compared the metabolite signatures in urine and serum after exposing mice to different dose rates of radiation. The results showed that individuals exposed to radiation could be distinguished at 1 day post-irradiation, but not at 7 days. The identical metabolite panels were able to identify exposed individuals regardless of dose rate.
Article
Multidisciplinary Sciences
Nicholas J. J. Morehouse, Trevor N. N. Clark, Emily J. J. McMann, Jeffrey A. A. van Santen, F. P. Jake Haeckl, Christopher A. A. Gray, Roger G. G. Linington
Summary: Spectral matching of MS2 fragmentation spectra has limitations due to instrument differences and limited spectral reference libraries. To overcome this challenge, SNAP-MS uses structural similarity network annotation to assign compound families to molecular networking subnetworks without using experimental or calculated reference spectra. SNAP-MS accurately annotates subnetworks built from both reference spectra and an in-house microbial extract library, and predicts compound families from published molecular networks acquired using different MS instruments.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Maria Pilar Giner, Stefan Christen, Simona Bartova, Mikhail Makarov, Marie E. Migaud, Carles Canto, Sofia Moco
Summary: NAD(+) and its reduced form NADH are essential coenzymes in hundreds of metabolic reactions, serving as substrates for key enzymes. Analyzing the NAD(+) metabolome using liquid chromatography-tandem mass spectrometry can provide insights into NAD(+) biology and its implications for health and disease.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Analytical
Chiara Maria Vitale, Arjen Lommen, Carolin Huber, Kevin Wagner, Borja Garlito Molina, Rosalie Nijssen, Elliott James Price, Marco Blokland, Frederike van Tricht, Hans G. J. Mol, Martin Krauss, Laurent Debrauwer, Olga Pardo, Nuria Leon, Jana Klanova, Jean-Philippe Antignac
Summary: A set of QA/QC criteria for nontargeted measurement of pesticide exposure markers in human urine has been proposed and applied in the HBM4EU project. The criteria include monitoring signal intensities, mass accuracy, and retention times of selected markers. The results show high repeatability and accuracy of the data. This is the first time that harmonized QA/QC criteria have been used to assess the quality of nontargeted analysis of human samples across multiple laboratories.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Vincent Hamani, Pascaline Ory, Pierre-Edouard Bodet, Laurence Murillo, Marianne Graber
Summary: This study investigated the impact of copper on the metabolism of the variegated scallop, identifying 28 metabolites clearly modulated by copper that reflect its effects on various biological functions such as osmoregulation, oxidative stress, reproduction, and energy metabolism.
Article
Chemistry, Analytical
Daniel Eilertz, Michael Mitterer, Joerg M. Buescher
Summary: This study presents an automated tool automRm for preprocessing of liquid chromatography-mass spectrometry data, which includes features such as using machine learning for chromatographic peak detection and quality control of results. The tool is generally applicable to a wide range of analytical methods and outperforms other software solutions when applied to a HILIC-MS data set.
ANALYTICAL CHEMISTRY
(2022)
Article
Chemistry, Analytical
Teresa S. McMillen, Andrew Leslie, Kenneth Chisholm, Susanne Penny, Jeffrey Gallant, Alejandro Cohen, Arik Drucker, James P. Fawcett, Devanand M. Pinto
Summary: This study presents a comprehensive and quantitatively robust method for metabolomic analysis, using HILIC and RP stationary phases combined with positive and negative electrospray ionization. The method allows for complete analysis of a single sample in as little as 40 minutes and has been validated with clinical samples.
ANALYTICA CHIMICA ACTA
(2023)
Article
Biochemical Research Methods
John B. Coulton, James L. Edwards
Summary: The sample preparation technique described in the study involves online filter-assisted electroporation-based cell lysis and chilled organic solvent extraction for rapid preparation of metabolomic samples from suspended cells. By using isotopically labeled internal standards and C-13-glucose labeling experiments, the method ensures enzymatic quenching and successful incorporation of C-13 into organic acid metabolites. Analysis by nano-reverse-phase liquid chromatography-mass spectrometry (nano-RP-LC-MS) demonstrates the effectiveness of the technique in studying metabolites such as itaconate.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Biochemical Research Methods
Tusharkanti Ghosh, Daisy Philtron, Weiming Zhang, Katerina Kechris, Debashis Ghosh
Summary: The MaRR procedure was introduced to examine reproducibility in mass spectrometry-based metabolomics experiments, showing higher reproducibility for technical replicates compared to biological replicates across different datasets. The MaRR procedure tends to have high power for detecting reproducible metabolites in most situations, while in some cases it may perform less well.
BMC BIOINFORMATICS
(2021)
Article
Pharmacology & Pharmacy
Tongxi Zhuang, Xinhua Liu, Wen Wang, Jing Song, Le Zhao, Lili Ding, Li Yang, Mingmei Zhou
Summary: The study indicates that herbal polyphenols and flavonoids have multiple beneficial effects on obesity caused by chronic metabolic disorders, and the combination of CQR has significant therapeutic effects in combating obesity. Through urinary metabolomic analysis, it was found that CQR has a significant impact on the metabolites of HFD-induced obese rats.
FRONTIERS IN PHARMACOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Min Ji Bae, Min Kook Kang, Yong Uk Kye, Jeong-Hwa Baek, Ye-Ji Sim, Hae-June Lee, Yeong-Rok Kang, Wol Soon Jo, Joong Sun Kim, Chang Geun Lee
Summary: The study revealed that the radiation dose rate has different effects on the testes of mice. Low dose rate radiation caused more severe tissue toxicity and adverse effects on sperm production compared to high dose rate radiation. This suggests that the dose rate of radiation may have differential impacts on different organs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Analytical
Wen Lin, Yuping Chen, Yang Su, Xiaopin Lai, Kunbin Guo, Xin Wang, Siyu Chen, Kaiqing Liang, Keyuan Pu, Yue Wang, Jun Hu, Xiaolong Wei, Hongbiao Wang, Wenxiu Ni, Yan Lin, Janshon Zhu, Kwan-Ming Ng
Summary: This research successfully fabricated a covalently bonded AuNPs array for analyzing small biomolecules in human serum in high-salt environments. The covalently bonded array showed superior performances in stability, reproducibility, and sensitivity compared to the self-assembled array. Furthermore, the closely positioned AuNPs generated an enhanced electric field, thereby enhancing the detection sensitivity.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Masaru Yamaguchi, Yota Tatara, Eka Djatnika Nugraha, Yuki Tamakuma, Yoshiaki Sato, Tomisato Miura, Masahiro Hosoda, Shinji Yoshinaga, Mukh Syaifudin, Shinji Tokonami, Ikuo Kashiwakura
Summary: The high-level natural background radiation area in Mamuju, Indonesia provides an opportunity to study the effects of chronic low-dose radiation exposure on humans. Proteomic and oxidative modification profiling analyses were conducted to examine the serum components of residents. The findings suggest that specific protein expression alterations and oxidative modifications of serum albumin may serve as important indicators for estimating radiation dose.
Article
Multidisciplinary Sciences
Kamendra Kumar, Kamal Datta, Albert J. Fornace, Shubhankar Suman
Summary: This study investigated the effects of proton and high-LET heavy-ion radiation on bone marrow cells and found that exposure to both types of radiation led to increased cell senescence and pro-osteoclastogenic activity. The effects were more pronounced with Fe-56 ions compared to protons. This study has important implications for understanding bone degeneration in deep-space astronauts and patients undergoing radiotherapy.
Article
Biology
Evan L. Pannkuk, Evagelia C. Laiakis, Jerry Angdisen, Meth M. Jayatilake, Pelagie Ake, Lorreta Yun-Tien Lin, Heng-Hong Li, Albert J. Fornace
Summary: Several diagnostic biodosimetry tools are being developed for radiological/nuclear emergency responses. Correlating changes in non-invasive biofluid small-molecule signatures to tissue damage from ionizing radiation exposure shows promise for predictive biodosimetry models. Genotypic variation in the general population may affect model performance in dose reconstruction.
RADIATION RESEARCH
(2022)
Article
Biology
Constantinos G. Broustas, Sanjay Mukherjee, Evan L. Pannkuk, Evagelia C. Laiakis, Albert J. Fornace, Sally A. Amundson
Summary: Radiation biodosimetry based on transcriptomic analysis of peripheral blood is a valuable tool for detecting radiation exposure, but confounding factors may affect its predictive power. The p38 signaling pathway plays an important role in the response to radiation, and its attenuation may protect blood cells from radiation-induced damage.
RADIATION RESEARCH
(2022)
Article
Genetics & Heredity
Jonathan P. Jacobs, Maryam Goudarzi, Venu Lagishetty, Dalin Li, Tytus Mak, Maomeng Tong, Paul Ruegger, Talin Haritunians, Carol Landers, Philip Fleshner, Eric Vasiliauskas, Andrew Ippoliti, Gil Melmed, David Shih, Stephan Targan, James Borneman, Albert J. Fornace, Dermot P. B. McGovern, Jonathan Braun
Summary: Crohn's disease patients in endoscopic remission show differences in the microbiome compared to unaffected controls, influenced by inflammation, genetic risk, and disease phenotype. Microbial profiling during endoscopic remission can predict disease behavior and progression, offering insight into CD pathogenesis and potential prognostic biomarkers.
Article
Biochemistry & Molecular Biology
Evan L. Pannkuk, Evagelia C. Laiakis, Guy Garty, Shivani Bansal, Brian Ponnaiya, Xuefeng Wu, Shanaz A. Ghandhi, Sally A. Amundson, David J. Brenner, Albert J. Fornace
Summary: This study compared the metabolite signatures in urine and serum after exposing mice to different dose rates of radiation. The results showed that individuals exposed to radiation could be distinguished at 1 day post-irradiation, but not at 7 days. The identical metabolite panels were able to identify exposed individuals regardless of dose rate.
Article
Biology
Shubhankar Suman, Santosh Kumar, Bhaskar V. S. Kallakury, Bo-Hyun Moon, Jerry Angdisen, Kamal Datta, Albert J. Fornace
Summary: This study provides experimental evidence that cancer risk after exposure to GCR could largely depend on doses received from constituent heavy ions.
RADIATION AND ENVIRONMENTAL BIOPHYSICS
(2022)
Article
Astronomy & Astrophysics
Kamendra Kumar, Bo-Hyun Moon, Kamal Datta, Albert J. Fornace Jr, Shubhankar Suman
Summary: This study examines the status of mammary cancer-associated preneoplasia markers in mice exposed to galactic cosmic radiation (GCR) and gamma-ray irradiation. The findings suggest that mice exposed to GCR have a higher risk of mammary cancer compared to those exposed to gamma-rays, as indicated by increased ductal outgrowth and cell proliferation in mammary tissues.
LIFE SCIENCES IN SPACE RESEARCH
(2023)
Review
Astronomy & Astrophysics
Janice L. Huff, Floriane Poignant, Shirin Rahmanian, Nafisah Khan, Eleanor A. Blakely, Richard A. Britten, Polly Chang, Albert J. Fornace, Megumi Hada, Amy Kronenberg, Ryan B. Norman, Zarana S. Patel, Jerry W. Shay, Michael M. Weil, Lisa C. Simonsen, Tony C. Slaba
Summary: For missions to the moon or Mars, space explorers will face a complex radiation field with various ion species and energies. The NASA Space Radiation Laboratory (NSRL) has developed an innovative galactic cosmic ray simulator (GCRsim) to simulate the space radiation environment and study biological risks. The GCRsim consists of 33 ion beams that simulate the primary and secondary GCR fields encountered in space. A recent virtual workshop assessed the status of the GCRsim, discussing its design and beam selection strategies. This information is important for advancements in space radiobiology.
LIFE SCIENCES IN SPACE RESEARCH
(2023)
Article
Biochemical Research Methods
Evan L. Pannkuk, Nicole A. S. -Y. Dorville, Shivani Bansal, Sunil Bansal, Yvonne A. Dzal, Quinn E. Fletcher, Kaleigh J. O. Norquay, Albert J. Fornace Jr, Craig K. R. Willis
Summary: This study investigates the lipidomic changes in bats with white-nose syndrome (WNS) and suggests that oxidative stress occurs in the early stages of WNS before fat depletion, but not inflammatory response. The study compared WNS-susceptible Myotis lucifugus to WNS-resistant Eptesicus fuscus and found altered splenic lipid levels only in M. lucifugus.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Santosh Kumar, Shubhankar Suman, Bo-Hyun Moon, Albert J. Fornace Jr, Kamal Datta
Summary: This study reveals that radiation exposure induces long-term oxidative stress in colonic epithelial cells, which is associated with colon carcinogenesis. The NADPH oxidase pathway may play a critical role in propagating this oxidative stress after radiation exposure.
MOLECULAR BIOLOGY REPORTS
(2023)
Article
Biochemical Research Methods
Lewis Y. Y. Geer, Joel Lapin, Douglas J. J. Slotta, Tytus D. D. Mak, Stephen E. E. Stein
Summary: By using a neural network to predict complete spectra, we created predicted spectral libraries that were used to rescore sequence search results, resulting in improved peptide identification accuracy and increased number of identifications, particularly for modified and phosphorylated peptides.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Oncology
Elaina Kwiatkowski, Shubhankar Suman, Bhaskar V. S. Kallakury, Kamal Datta, Albert J. Fornace Jr, Santosh Kumar
Summary: This study assessed the expression of multiple stem cell markers in premalignant tumors after low- and high-LET radiation. The results showed a correlation between increased levels of stemness markers and fi-catenin activation in premalignant tumors, particularly in tumors induced by high-LET radiation. The study highlights the complex relationship between radiation types and stem cell phenotypes, and their potential influence on carcinogenesis processes.
Review
Oncology
Kamendra Kumar, Santosh Kumar, Kamal Datta, Albert J. J. Fornace Jr, Shubhankar Suman
Summary: High-energy heavy ions can cause DNA damage, leading to cellular responses such as cell cycle arrest, cell death, and cellular senescence. Prolonged exposure to high-energy ions in space radiation increases the risk of gastrointestinal (GI) carcinogenesis. Alterations in DNA damage response (DDR) can result in gene mutations and pro-inflammatory, pro-oncogenic signaling, accelerating adenoma-to-carcinoma progression during radiation-induced GI cancer development.
Article
Medicine, Research & Experimental
Di Cui, Jianneng Li, Ziqi Zhu, Michael Berk, Aimalie Hardaway, Jeffrey McManus, Yoon-Mi Chung, Mohammad Alyamani, Shelley Valle, Ritika Tiwari, Bangmin Han, Maryam Goudarzi, Belinda Willard, Nima Sharifi
Summary: After androgen deprivation, prostate cancer frequently becomes castration resistant (CRPC), involving intratumoral androgen production. Cancer-associated fibroblasts (CAFs) increase 3 beta HSD1 expression and induce androgen synthesis, leading to CRPC.
JOURNAL OF CLINICAL INVESTIGATION
(2023)
Article
Medicine, Research & Experimental
Renxiang Chen, Yun-Tien Lin, Albert J. Fornace, Heng-Hong Li
Summary: The increasing number of compounds and chemicals that require safety assessments pose a serious challenge for regulatory agencies. In vitro screening using toxicogenomic biomarkers has been proposed as a solution, and a highly automated, multiplexed, and high-throughput genotoxicity testing assay has been developed to increase screening efficiency.
ALTEX-ALTERNATIVES TO ANIMAL EXPERIMENTATION
(2022)