Article
Biochemistry & Molecular Biology
Abigail M. Schwind, Daniel J. Walsh, Cassandra M. Burke, Surachai Supattapone
Summary: Cofactor molecules are required for the generation of infectious mammalian prions in vitro. The study found that mouse and hamster prions have different cofactor preferences, with only hamster prions able to use single-stranded RNA as an alternative cofactor. The study also discovered that detergents solubilizing phosphatidylethanolamine inhibit mouse prion formation, while detergents unable to solubilize phosphatidylethanolamine have no effect. Furthermore, the inhibitory effect of solubilization requires post-translational modifications of the prion protein.
JOURNAL OF NEUROCHEMISTRY
(2023)
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)
Review
Spectroscopy
Jarne Pauwels, Daria Fijalkowska, Sven Eyckerman, Kris Gevaert
Summary: The surfaceome, consisting of plasma membrane proteins, plays crucial roles in cell communication, transport regulation, and immune responses. However, challenges such as inefficient extraction and lower abundance compared to intracellular proteins hinder comprehensive analysis. To address these issues, innovative analytical methodologies have been developed.
MASS SPECTROMETRY REVIEWS
(2022)
Article
Biochemistry & Molecular Biology
Heba Badr, Ron Blutrich, Kaitlin Chan, Jiefei Tong, Paul Taylor, Wen Zhang, Ran Kafri, Hannes L. Rost, Ming-Sound Tsao, Michael F. Moran
Summary: Proteome analysis revealed co-expressed upregulated metabolism proteins highly conserved between primary NSCLC and patient-derived xenograft tumors. The encoded genes of these proteins are associated with the survival of NSCLC patients, suggesting their role in driving NSCLC through metabolic processes.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Plant Sciences
Runmiao Tian, Jianjun Jiang, Shirong Bo, Hui Zhang, Xuehai Zhang, Sarah Jane Hearne, Jihua Tang, Dong Ding, Zhiyuan Fu
Summary: Through a multi-omic analysis, it was found that maize has 48 counterparts of human GPI synthesis and lipid remodeling genes. A null mutation in one of these genes resulted in defects in the basal endosperm transport layer. Proteomics analysis revealed two membrane proteins related to the endosperm transport layer that were significantly decreased in the mutant.
Article
Chemistry, Analytical
Francis Berthias, Dale A. Cooper-Shepherd, Frederik H. V. Holck, James I. Langridge, Ole N. Jensen
Summary: The combination of cyclic ion mobility spectrometry (cIM) and electron capture dissociation (ECD) allows for the complete separation and sequencing of large isomeric peptides, providing a new method for identifying biologically important proteoforms in complex mixtures.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemical Research Methods
Runmin Yang, Jingjing Ma, Shu Zhang, Yu Zheng, Lusheng Wang, Daming Zhu
Summary: This study introduces a new storage format called mzMD for MS datasets and presents an algorithm to query this format for summarizing a given data window. Experimental results demonstrate the high speed and stability of mzMD in retrieving high-quality data window summaries.
Article
Biochemical Research Methods
Xuan Guo, Lei Zhang, Zihan Lei, Zhe Hou, Hui Li, Xiaodong Li, Jing Dong, Ling Song, Dingding Chen, Dongyang Liu
Summary: The objective of this study was to develop a LC-MS/MS method for quantitation of seven cytochrome P450 (CYP450) enzymes. The method was validated for selectivity, linearity, stability, accuracy, and precision. The abundance of the enzymes in human liver microsomes and CYP3A4 in placenta was accurately determined using this method.
JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES
(2023)
Review
Food Science & Technology
A. Cimbalo, M. Frangiamone, G. Font, L. Manyes
Summary: This review highlights recent advances in using transcriptomics and proteomics as key tools to understand the molecular toxicity of mycotoxins. The most studied mycotoxin using transcriptomics is deoxynivalenol (DON), followed by aflatoxins (AFs) and zearalenone (ZEA). In contrast, proteomics mostly focuses on AFs, with some research on ZEA and DON. However, fewer studies have investigated the toxicological effects of emerging mycotoxins such as patulin, ochratoxin A, T-2 toxin, alternariol, and amino-14,16-dimethyloctadecan-3-ol. Transcriptomics commonly studies changes in gene expression related to the immune system, while proteomics focuses on cellular processes. The most commonly used techniques are RT-qPCR for gene expression analysis and liquid chromatography coupled with mass spectrometry for proteomics assays. The data gathered indicate an increased interest in using these omic approaches in the past five years. However, in vitro models are prioritized over in vivo and ex vivo models. Therefore, there is a need to enhance the use of in vivo models and alternative methods to better understand the mode of action of mycotoxins on animal and human health.
FOOD AND CHEMICAL TOXICOLOGY
(2022)
Article
Immunology
Haoran Guo, Qi Wang, Tao Li, Jingwen Chen, Chao Zhang, Ying Xu, Qing Chang, Hangyi Li, Weiqiang Sun, Ruidi Han, Chi Wang, Chengbin Wang
Summary: This study discovered that ascending to high altitude can lead to physiological and molecular changes, resulting in some individuals being unable to acclimatize. Predicting acute mountain sickness (AMS) prior to ascent remains a challenge. Proteomic analysis revealed significant differences in inflammatory and immune-related processes between AMS-susceptible and AMS-resistant groups. Potential biomarkers, such as SAP, AAT, LTF, and HSP90-alpha, were identified for the prediction of AMS at low altitudes.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Entomology
Yulica Santos-Ortega, Nabil Killiny
Summary: Controlling the vector Diaphorina citri is crucial for managing the devastating citrus disease, Huanglongbing. Targeting egg hatching of D. citri through RNA interference may effectively reduce vector population and disease transmission. Analyzing the chorion proteome of D. citri provides potential targets for better control of psyllid populations.
Article
Chemistry, Analytical
Yueting Xiong, Jun Yao, Yongtao Zheng, Fenglin Shen, Huanhuan Zhao, Jia Hu, Bing Leng, Pengyuan Yang, Xiaohui Liu
Summary: Protein biomarkers for intracranial aneurysm (IA) are crucial for early detection and diagnosis, and a comprehensive strategy involving tissue and serum analysis identified candidate biomarkers and established two diagnostic classifiers with high accuracy for IA and its rupture. The results suggest a valuable approach for biomarker discovery and patient stratification in IA.
Article
Biochemical Research Methods
Xintong Sui, Qiong Wu, Xiaozhen Cui, Xi Wang, Luobin Zhang, Nan Deng, Yangyang Bian, Ruilian Xu, Ruijun Tian
Summary: Capillary- and micro-flow liquid chromatography-tandem mass spectrometry (capLC-MS/MS and mu LC-MS/MS) offer an alternative to nano-flow LC-MS/MS with high robustness and throughput. In this study, the capLC-MS/MS and mu LC-MS/MS systems were compared in terms of sensitivity, analysis throughput, separation efficiency, and robustness. The results showed that capLC-MS/MS was more sensitive, while mu LC-MS/MS had higher analysis throughput and separation efficiency. Both systems demonstrated good reproducibility in long-term performance testing.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Plant Sciences
Jiankun Song, Jingsi Jiang, Le Kuai, Yue Luo, Meng Xing, Ying Luo, Yi Ru, Xiaoying Sun, Huiping Zhang, Taiyi Liu, Xin Li, Bin Li
Summary: Jueyin granules (JYG) may induce autophagy by up-regulating ApoA1 and inhibit the infiltration of CD4+ T cells and macrophages, thereby alleviating psoriatic inflammation.
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
Biochemistry & Molecular Biology
Laura Ceballos-Laita, Daisuke Takahashi, Matsuo Uemura, Javier Abadia, Ana Flor Lopez-Millan, Jorge Rodriguez-Celma
Summary: Iron and manganese are essential elements for plants, but they compete for the same uptake transporters and show conflicting interactions at the regulatory level. Proteomic techniques were used to study the proteome profiles of tomato roots grown under iron or manganese deficiency. The results showed that both deficiencies led to common cell wall remodelling, but differed greatly in terms of oxidative stress, coumarin production, protein, nitrogen, and energy metabolism.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Etsuko Watanabe, Mariko Kondo, Md Mostafa Kamal, Matsuo Uemura, Daisuke Takahashi, Yukio Kawamura
Summary: DRP1E plays a crucial role in plant freezing tolerance enhancement and PM reconstruction during cold acclimation, primarily by removing glycosylphosphatidylinositol-anchored proteins.
PHYSIOLOGIA PLANTARUM
(2022)
Article
Plant Sciences
Tatsuya Kutsuno, Sushan Chowhan, Toshihisa Kotake, Daisuke Takahashi
Summary: Plants adapt to freezing stress through cold acclimation and deacclimation, which are regulated by changes in cell wall structure and monosaccharide composition. The balance between freezing tolerance and growth is crucial for plant development in changing environments. Arabinogalactan proteins and pectic galactan play important roles in freezing tolerance and growth, while arabinan and xyloglucan stabilize at cold acclimation levels during deacclimation.
PHYSIOLOGIA PLANTARUM
(2023)
Article
Multidisciplinary Sciences
Kazusato Oikawa, Shino Goto-Yamada, Yasuko Hayashi, Daisuke Takahashi, Yoshitaka Kimori, Michitaro Shibata, Kohki Yoshimoto, Atsushi Takemiya, Maki Kondo, Kazumi Hikino, Akira Kato, Keisuke Shimoda, Haruko Ueda, Matsuo Uemura, Keiji Numata, Yoshinori Ohsumi, Ikuko Hara-Nishimura, Shoji Mano, Kenji Yamada, Mikio Nishimura
Summary: Pexophagy plays a pivotal role in selectively removing ROS-generating peroxisomes under high-intensity light, which protects plants from oxidative damage during photosynthesis.
NATURE COMMUNICATIONS
(2022)
Article
Plant Sciences
Aina Kikuchi, Katsuya Hara, Yoshihisa Yoshimi, Kouichi Soga, Daisuke Takahashi, Toshihisa Kotake
Summary: The study shows that long β-1,6-galactan side chains are necessary for normal cellulose synthesis and cell growth in plants, contributing to a better understanding of the physiological importance of arabinogalactan-proteins (AGPs).
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Chemistry, Physical
Hozumi Takahashi, Tatsuya Kono, Kosuke Sawada, Satoru Kumano, Yuka Tsuri, Mihoko Maruyama, Masashi Yoshimura, Daisuke Takahashi, Yukio Kawamura, Matsuo Uemura, Seiichiro Nakabayashi, Yusuke Mori, Yoichiroh Hosokawa, Hiroshi Y. Yoshikawa
Summary: Focused irradiation with ultrashort laser pulses allows precise control of ice crystallization in supercooled water. The laser-induced shockwaves and bubbles act as an impulse for ice crystal nucleation. This method enables observation of ice crystallization with micrometer and microsecond resolution and can be applied to study ice crystallization dynamics in natural and biological phenomena.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Editorial Material
Plant Sciences
Guillaume Charrier, Ian R. Willick, Daisuke Takahashi
PHYSIOLOGIA PLANTARUM
(2023)
Article
Plant Sciences
Andrew Lonsdale, Laura Ceballos-Laita, Daisuke Takahashi, Matsuo Uemura, Javier Abadia, Melissa J. Davis, Antony Bacic, Monika S. Doblin
Summary: Plant proteins that lack classical signal peptide leader sequences, known as leaderless secretory proteins (LSPs), play roles in plant development and stress responses. Identifying LSPs in plant proteomics experiments is challenging due to possible contamination during purification, and machine learning algorithms also lack sufficient validated examples. This study establishes criteria for identifying potential plant LSPs based on experimental observations and trains random forest classifiers to predict LSPs. The resulting database LSPDB and bioinformatic prediction tools LSPpred and SPLpred provide a method for predicting and identifying plant putative LSPs until more validated LSPs are established.
Article
Biochemistry & Molecular Biology
Kanika Ghosh, Daisuke Takahashi, Toshihisa Kotake
Summary: Type II arabinogalactans (AGs) are diverse plant polysaccharides found in cell walls and plasma membranes as carbohydrate moieties in arabinogalactan-proteins (AGPs). The main structure of type II AG is a 1,3-beta-D-galactan main chain with 1,6-beta-D-galactan side chains decorated with sugars like alpha-L-arabinose and beta-D-glucuronic acid. Determining the structures of these complex AGs is challenging, but their modification offers scientific and commercial opportunities. This review outlines the chemical structures of type II and type II related AGs, compares structural analysis techniques, and highlights structural modifications for enhanced functionality.
CARBOHYDRATE RESEARCH
(2023)
