Article
Multidisciplinary Sciences
V. Dumrongprechachan, R. B. Salisbury, G. Soto, M. Kumar, M. L. MacDonald, Y. Kozorovitskiy
Summary: This study employed a genetically targeted APEX2-based proximity labeling approach to uncover proteome dynamics in two classes of striatal spiny projection neurons in the mouse brain. The findings were validated using imaging, electron microscopy, and mass spectrometry, providing important insights for understanding the development and functional organization of neural circuits in the brain.
NATURE COMMUNICATIONS
(2021)
Review
Computer Science, Information Systems
Sajid Ullah Khan, Mir Ahmad Khan, Muhammad Azhar, Faheem Khan, Youngmoon Lee, Muhammad Javed
Summary: Medical imaging has been widely used in diagnosing various disorders, but the challenge lies in accurate disease identification and improved therapies. Multi modal image fusion (MMIF) aims to combine complementary information from different imaging modalities to improve the quality and clear assessment of medical related problems. This review provides a detailed overview of medical imaging modalities, multimodal medical image databases, MMIF steps/rules, methods, performance evaluation, and future directions. It is expected to be valuable in developing more effective medical image fusion methods for clinical diagnosis.
JOURNAL OF KING SAUD UNIVERSITY-COMPUTER AND INFORMATION SCIENCES
(2023)
Review
Chemistry, Analytical
Ziyi Luo, Hao Xu, Liwei Liu, Tymish Y. Ohulchanskyy, Junle Qu
Summary: Alzheimer's disease is a multifactorial, irreversible neurodegenerative disease characterized by the abnormal accumulation of Aβ plaques in the brain, leading to neuronal dysfunction and cognitive impairment. Optical imaging, with its noninvasiveness and high sensitivity, is emerging as a promising tool for the diagnosis and study of Aβ buildup in AD research.
Article
Biochemical Research Methods
Md Inzamam Ul Haque, Debangshu Mukherjee, Sylwia A. Stopka, Nathalie Y. R. Agar, Jacob Hinkle, Olga S. Ovchinnikova
Summary: This study correlates H&E-stained biopsy data with MALDI mass-spectrometric imaging data to determine cancerous regions and their unique chemical signatures. The correlation between optical H&E features and chemical information in MSI allows for the prediction of prostate cancer with around 80% accuracy. Additionally, two chemical biomarkers were found to predict cancerous regions.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2023)
Review
Biology
Muhammad Adeel Azam, Khan Bahadar Khan, Sana Salahuddin, Eid Rehman, Sajid Ali Khan, Muhammad Attique Khan, Seifedine Kadry, Amir H. Gandomi
Summary: This article provides a comprehensive overview of multimodal medical image fusion methodologies, databases, and quality measurements. Medical imaging modalities are categorized based on radiation, visible-light imaging, microscopy, and multimodal imaging. Fusion techniques are classified into categories including frequency fusion, spatial fusion, decision-level fusion, deep learning, hybrid fusion, and sparse representation fusion. The associated diseases for each modality and fusion approach are presented, and quality assessment fusion metrics are also discussed.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Article
Biotechnology & Applied Microbiology
Marco Vicari, Reza Mirzazadeh, Anna Nilsson, Reza Shariatgorji, Patrik Bjaerterot, Ludvig Larsson, Hower Lee, Mats Nilsson, Julia Foyer, Markus Ekvall, Paulo Czarnewski, Xiaoqun Zhang, Per Svenningsson, Lukas Kaell, Per E. Andren, Joakim Lundeberg
Summary: We present a method that combines histology, mass spectrometry imaging, and spatial transcriptomics to measure mRNA transcripts and low-molecular-weight metabolites simultaneously across tissue regions. The potential of this method is demonstrated using mouse and human brain samples in the context of dopamine and Parkinson's disease.
NATURE BIOTECHNOLOGY
(2023)
Article
Neurosciences
Joakim Bastrup, Kathrine H. Hansen, Thomas B. G. Poulsen, Kenneth Kastaniegaard, Ayodeji A. Asuni, Soren Christensen, Dorthe Belling, Lone Helboe, Allan Stensballe, Christiane Volbracht
Summary: Chronic treatment with aducanumab significantly reduces the number of senile plaques in AD mouse model and alters the proteomic profile of surrounding tissue, potentially inhibiting Aβ toxicity and increase cell viability.
JOURNAL OF ALZHEIMERS DISEASE
(2021)
Article
Chemistry, Analytical
Austin B. Moyle, Nicole D. Wagner, Wesley J. Wagner, Ming Cheng, Michael L. Gross
Summary: Protein footprinting mass spectrometry is a technique that utilizes labeling of amino acids to study protein structure and dynamics. This study focused on a recently published nucleophile footprinter called benzoyl fluoride, and developed a workflow to assess its properties in terms of reactivity, reaction quenching, reagent considerations, kinetics, and modification sites characterization. The workflow provides a starting point for the discovery, validation, and introduction of improved footprinting reagents.
ANALYTICAL CHEMISTRY
(2023)
Article
Oncology
Laura Furia, Simone Pelicci, Federica Perillo, Maddalena M. Bolognesi, Pier Giuseppe Pelicci, Federica Facciotti, Giorgio Cattoretti, Mario Faretta
Summary: In situ multiplexing analysis and in situ transcriptomics are revolutionary tools for understanding the molecular basis of cancer and advancing personalized medicine. To achieve the best resolution and sensitivity, continuous interplay between different technologies is required. We propose a new experimental pipeline that alternates between automated and manual procedures to optimize the cost-to-benefit ratio in multiplexing experiments.
FRONTIERS IN ONCOLOGY
(2022)
Article
Multidisciplinary Sciences
Ayana Sugizaki, Keisuke Sato, Kazuyoshi Chiba, Kenta Saito, Masahiko Kawagishi, Yuri Tomabechi, Shalin B. Mehta, Hirokazu Ishii, Naoki Sakai, Mikako Shirouzu, Tomomi Tani, Sumio Terada
Summary: Biomolecular assemblies play a crucial role in cell physiology, with their function depending on the changes in molecular positions and orientations. Fluorescence polarization microscopy offers a promising solution by reporting the orientation of emission dipoles, providing insights into monitoring molecular orientation in real time within living cells.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Engineering, Electrical & Electronic
Jing Zhang, Yu Liu, Aiping Liu, Qingguo Xie, Rabab Ward, Z. Jane Wang, Xun Chen
Summary: Multimodal image fusion aims to synthesize informative images from multiple modalities, and self-supervised learning is a feasible technology to improve the performance. Existing methods ignore the domain discrepancy between training and test data, and lack the ability to capture long-range contextual relationships. Therefore, we propose a self-supervised transformer-based approach to address these issues.
IEEE SENSORS JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Elena Alvarez-Marimon, Hiram Castillo-Michel, Juan Reyes-Herrera, Jofre Seira, Ester Aso, Margarita Carmona, Isidre Ferrer, Josep Cladera, Nuria Benseny-Cases
Summary: Amyloid plaques in the cortex of patients with advanced Alzheimer's disease have been characterized into two types: fibrillary plaques with iron accumulation mainly in Fe2+ form, and nonfibrillary plaques with a mixture of beta-sheet and unordered structures where Fe3+ predominates over Fe2+. This distinction in plaque types and metal composition could play a key role in understanding the progression of Alzheimer's disease.
ACS CHEMICAL NEUROSCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Oshin D. Warerkar, Niyati H. Mudliar, Tanya Ahuja, Sailee D. Shahane, Prabhat K. Singh
Summary: The development of an accurate and sensitive sensor for detecting amyloid plaques is crucial for early diagnosis of protein disorders like Alzheimer's disease. The use of hemicyanine-based probe LDS730, belonging to the Near-Infrared Fluorescence family, provides higher precision, prevents photo-damage, and minimizes autofluorescence. The sensor exhibits a 110-fold increase in fluorescence turn-on emission when bound to insulin fibrils, making it highly sensitive with great potential for early detection and improving diagnostic accuracy.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Chemistry, Multidisciplinary
Ethan Yang, Xinyi Elaine Shen, Hoku West-Foyle, Tae-Hun Hahm, Maxime A. Siegler, Dalton R. Brown, Cole C. Johnson, Jeong Hee Kim, LaToya Ann Roker, Caitlin M. Tressler, Ishan Barman, Scot C. Kuo, Kristine Glunde
Summary: The authors report that co-crystallization of fluorophores with MALDI imaging matrices significantly enhances fluorophore brightness, enabling the amplification of innate tissue autofluorescence. This allows the development of FluoMALDI, which combines fluorescence microscopy and MALDI imaging to image the same biological sample. FluoMALDI has demonstrated the feasibility of imaging with endogenous and exogenous fluorophores, as well as autofluorescence-based imaging of brain and kidney tissue sections.
Article
Optics
Luis E. Villegas-Hernandez, Vishesh Dubey, Mona Nystad, Jean-Claude Tinguely, David A. Coucheron, Firehun T. Dullo, Anish Priyadarshi, Sebastian Acuna, Azeem Ahmad, Jose M. Mateos, Gery Barmettler, Urs Ziegler, Asa Birna Birgisdottir, Aud-Malin Karlsson Hovd, Kristin Andreassen Fenton, Ganesh Acharya, Krishna Agarwal, Balpreet Singh Ahluwalia
Summary: This study introduces a photonic chip as a high-throughput microscopy platform for super-resolution imaging of histological samples. It demonstrates diverse imaging capabilities and paves the way for the adoption of super-resolution high-throughput multimodal analysis of cryopreserved tissue samples.
LIGHT-SCIENCE & APPLICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Seong Su Kang, Lanxia Meng, Xingyu Zhang, Zhiping Wu, Ariana Mancieri, Boer Xie, Xia Liu, David Weinshenker, Junmin Peng, Zhentao Zhang, Keqiang Ye
Summary: DOPEGAL, a metabolite of norepinephrine, covalently modifies tau and accelerates its aggregation and propagation, leading to cognitive deficits in Alzheimer's disease. The selective vulnerability of noradrenergic locus ceruleus (LC) neurons in AD may be explained by oxidation of norepinephrine via monoamine oxidase A (MAO-A) into DOPEGAL, which modifies tau and facilitates its aggregation, toxicity, and propagation.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Monicah N. Bwayi, Efren Garcia-Maldonado, Sergio C. Chai, Boer Xie, Shirish Chodankar, Andrew D. Huber, Jing Wu, Kavya Annu, William C. Wright, Hyeong-Min Lee, Jayaraman Seetharaman, Jingheng Wang, Cameron D. Buchman, Junmin Peng, Taosheng Chen
Summary: The interactions between nuclear receptors can fundamentally change our understanding of their biology. In this study, the molecular basis of crosstalk between the pregnane X receptor (PXR) and constitutive androstane receptor (CAR) is revealed, demonstrating the formation of a novel heterodimer and mutual inhibition. These findings not only change the perceived functional relationship between PXR and CAR, but also provide new perspectives for elucidating their role and designing approaches to regulate them.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Neurosciences
David Labib, Zhen Wang, Priya Prakash, Matthew Zimmer, Matthew D. Smith, Paul W. Frazel, Lilianne Barbar, Maria L. Sapar, Peter A. Calabresi, Junmin Peng, Shane A. Liddelow, Valentina Fossati
Summary: The study investigated the surface marker profile and proteome of reactive astrocytes induced by proinflammatory factors and proposed several potential markers for this reactive sub-state. Colocalization of these markers with specific cells in post-mortem samples from Alzheimer's disease patients was observed. Proteomic analysis also identified proteins and pathways linked to potential engagement with peripheral immune cells.
FRONTIERS IN MOLECULAR NEUROSCIENCE
(2022)
Article
Oncology
Rosa Nguyen, Hong Wang, Ming Sun, Dong Geun Lee, Junmin Peng, Carol J. Thiele
Summary: This study suggests a potential therapeutic benefit in using selinexor and alisertib to synergistically increase p53-mediated cytotoxicity of high-risk neuroblastoma.
Article
Biochemistry & Molecular Biology
Huan Sun, Ka Yang, Xue Zhang, Yingxue Fu, Jay Yarbro, Zhiping Wu, Ping-Chung Chen, Taosheng Chen, Junmin Peng
Summary: Chemoproteomics is a crucial platform for studying the mode of action of compounds. This study presents a pooling strategy to enhance throughput and applies it to a drug library. The findings demonstrate that pooling chemoproteomics screening is an efficient method for dissecting the molecular targets of compound libraries.
Article
Biochemistry & Molecular Biology
Giovanni Quarato, Fabien Llambi, Cliff S. Guy, Jaeki Min, Marisa Actis, Huan Sun, Shilpa Narina, Shondra M. Pruett-Miller, Junmin Peng, Zoran Rankovic, Douglas R. Green
Summary: The imbalance of intracellular Ca2+ and mitochondrial Ca2+ overload can lead to mitochondrial inner membrane permeabilization and cell death, which is distinct from Bcl-2 family-regulated mitochondrial outer membrane permeabilization. Cyclosporin A can prevent cell death by inhibiting Ca2+ release from endoplasmic reticulum stores.
CELL DEATH AND DIFFERENTIATION
(2022)
Article
Neurosciences
Chia-Chen Liu, Jing Zhao, Yuan Fu, Yasuteru Inoue, Yingxue Ren, Yuanxin Chen, Sydney V. Doss, Francis Shue, Suren Jeevaratnam, Ligia Bastea, Na Wang, Yuka A. Martens, Wenhui Qiao, Minghui Wang, Na Zhao, Lin Jia, Yu Yamazaki, Akari Yamazaki, Cassandra L. Rosenberg, Zhen Wang, Dehui Kong, Zonghua Li, Lindsey A. Kuchenbecker, Zachary A. Trottier, Lindsey Felton, Justin Rogers, Zachary S. Quicksall, Cynthia Linares, Joshua Knight, Yixing Chen, Aishe Kurti, Takahisa Kanekiyo, John D. Fryer, Yan W. Asmann, Peter Storz, Xusheng Wang, Junmin Peng, Bin Zhang, Betty Y. S. Kim, Guojun Bu
Summary: Peripheral apoE4 has detrimental effects on cognition and amyloid pathology by compromising vascular integrity and function. It impairs synaptic plasticity and cognition and influences functional pathways such as cell adhesion, lipoprotein metabolism, and complement activation. ApoE3 plasma from young mice improves cognition and reduces vessel-associated gliosis, while liver-expressed apoE4 exacerbates brain amyloid pathology.
NATURE NEUROSCIENCE
(2022)
Article
Biochemical Research Methods
Huan Sun, Suresh Poudel, David Vanderwall, Dong Geun Lee, Yuxin Li, Junmin Peng
Summary: Tandem mass tag (TMT) mass spectrometry is a popular labeling strategy for protein profiling. In this study, a 29-plex TMT method was developed and validated using pooled samples, demonstrating its ability to correct for noise and restore expected ratio values.
Article
Biochemical Research Methods
Suresh Poudel, David Vanderwall, Zuo-Fei Yuan, Zhiping Wu, Junmin Peng, Yuxin Li
Summary: A computational pipeline JUMPptm was presented to extract PTMs from unenriched whole proteome. The deep brain proteome of Alzheimer's disease (AD) was analyzed using JUMPptm, revealing dysregulated PTM peptides during AD progression and establishing a valuable pan-PTM profile for AD research.
Article
Chemistry, Analytical
Bo-Jhang Lin, Tien-Chueh Kuo, Hsin-Hsiang Chung, Ying-Chen Huang, Ming-Yang Wang, Cheng-Chih Hsu, Po-Yang Yao, Yufeng Jane Tseng
Summary: Mass spectrometry imaging (MSI) is a powerful tool for investigating the spatial distribution of molecules in samples. However, analyzing complex biological systems often requires multiple analytical techniques. Image registration is a critical step for combining MSI with other imaging techniques, but it can be challenging due to differences in spatial resolution and image characteristics. In this study, a web service called MSI Registrar (MSIr) was developed for automatic registration between MSI and histology, providing a more objective and efficient way to analyze molecular components in tissues.
ANALYTICAL CHEMISTRY
(2023)
Article
Food Science & Technology
Suraphan Panyod, Wei-Kai Wu, Sin-Yi Peng, Yea-Jing Tseng, Ya-Chi Hsieh, Rou-An Chen, Huai-Syuan Huang, Yi-Hsun Chen, Hsiao-Li Chuang, Cheng-Chih Hsu, Ting-Chin David Shen, Kai-Chien Yang, Chi-Tang Ho, Ming-Shiang Wu, Lee-Yan Sheen
Summary: Recently, the role of gut microbiota in diseases, including cardiovascular disease, has gained research attention. Ginger essential oil (GEO) and its bioactive compound citral have shown anti-atherosclerotic effects by improving lipid profile, blood sugar, insulin resistance, and reducing TMAO levels and inflammatory cytokines. They also modulate gut microbiota diversity and composition.
NPJ SCIENCE OF FOOD
(2023)
Article
Biochemistry & Molecular Biology
Yun-Ju Huang, Min-Shiuan Tsai, Suraphan Panyod, Po-Yu Liu, Kuan-Hung Lu, Cheng-Yu Weng, Huai-Syuan Huang, Cheng-Chih Hsu, Lee-Yan Sheen
Summary: This study found that garlic essential oil and its active constituent diallyl disulfide have therapeutic effects on depressive behavior in an unpredictable chronic mild stress model by attenuating neuroinflammation, modulating intestinal barrier function, and influencing gut microbiota.
Article
Chemistry, Multidisciplinary
Cheng-Hua Ma, Chih-Lin Chen, Cheng-Chih Hsu
Summary: This study presents a simple and rapid online digestion platform called online microdroplet-assisted enzymatic digestion (MAED), which combines intact protein separation with enzymatic digestion in microdroplets. The method allows for rapid bottom-up analysis of protein mixtures and provides a more comprehensive characterization, particularly for low molecular weight proteins.
CHEMICAL COMMUNICATIONS
(2023)
Article
Agriculture, Multidisciplinary
Wei-Chieh Wang, Hsin-Hsiang Chung, Ewelina P. Dutkiewicz, Jhih-Ying Wong, Wen-Chin Yang, Cicero Lee-Tian Chang, Cheng-Chih Hsu
Summary: Coccidiosis is a common parasitic disease in poultry that is typically diagnosed in a laboratory and observed 4 days after infection. Researchers have developed an on-site diagnostic platform using mass spectrometry to differentiate healthy chickens from those infected with Eimeria tenella. The platform achieved high accuracy and can diagnose infection 2 days earlier than current methods.
ACS AGRICULTURAL SCIENCE & TECHNOLOGY
(2022)
Article
Chemistry, Analytical
Ko-Keng Chang, Yi-Hong Cai, Chih-Hao Hsiao, Cheng-Chih Hsu, Yi-Sheng Wang
Summary: A miniature mass spectrometer suitable for high m/z region is described, which shows superior performance in terms of mass resolving power and sensitivity for microbial, protein conjugate, and polymer analyses.