Review
Plant Sciences
Julia Mergner, Bernhard Kuster
Summary: Proteins play essential roles in cellular processes, and studying protein expression, interactions, and modifications is crucial for understanding the molecular mechanisms underlying plant phenotypes. Mass spectrometry technology allows for the global identification and quantification of thousands of proteins, revealing dynamic changes in the plant proteome.
ANNUAL REVIEW OF PLANT BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Lin Bai, Guojian Yang, Zhaoyu Qin, Jiacheng Lyu, Yunzhi Wang, Jinwen Feng, Mingwei Liu, Tongqing Gong, Xianju Li, Zhengyang Li, Jixi Li, Jun Qin, Wenjun Yang, Chen Ding
Summary: This study used a novel method to analyze the binding activity of transcription factors under DNA modifications and identified potential readers for 5fC-modified DNA. By quantifying the modified DNA-binding activity of 1039 TFs, it revealed the hierarchical networks between the transcriptional protein machinery and modified DNA.
Article
Biology
Jonathan G. Van Vranken, Jiaming Li, Dylan C. Mitchell, Jose Navarrete-Perea, Steven P. Gygi
Summary: Recent advances in mass spectrometry have enabled quantitative proteomics to become a powerful tool in drug discovery, with the development of solvent shift assays allowing for the establishment of target engagement and increased efficiency. Using this approach, specific targets of compounds with known mechanisms of action can be readily identified, and combining solvent proteome profiling with other methods can expand the screening capabilities for evidence of ligand binding in the proteome.
Article
Chemistry, Analytical
Na Jiang, Yan Gao, Jia Xu, Fengting Luo, Xiangyang Zhang, Ruibing Chen
Summary: Data independent acquisition (DIA) has been shown to be a powerful proteomic technique for analyzing limited quantity samples. In this study, the performance of various DIA analysis strategies was systematically compared, and DIA-NN with gas-phase fractionation (GPF)-based libraries was found to outperform others in protein identification and retention time calibration. The optimized workflow was further validated by analyzing the proteome alteration in peripheral blood mononuclear cells (PBMCs) induced by lipopolysaccharide (LPS) stimulation, revealing activation of multiple signaling pathways. The results demonstrate the practicability of using DIA for scarce samples and its potential applications in biomarker discovery, immune status evaluation, and drug response monitoring.
JOURNAL OF PHARMACEUTICAL AND BIOMEDICAL ANALYSIS
(2022)
Review
Biochemistry & Molecular Biology
Yanmei Chen, Yi Wang, Jun Yang, Wenbin Zhou, Shaojun Dai
Summary: This paper reviews recent breakthroughs and strategies in unraveling the diversity of the plant proteome, focusing on the methods used to analyze posttranslational modifications (PTMs), protein localization, and the organization of proteins into functional modules. It also discusses PTM crosstalk, multiple PTMs temporally regulating protein life cycles, quantitative studies using MS to measure protein turnover rates, and future directions in the study of the plant proteome.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2021)
Article
Agriculture, Multidisciplinary
Mahya Bahmani, Angela Juhasz, Utpal Bose, Mitchell G. Nye-Wood, Malcolm Blundell, Crispin A. Howitt, Michelle L. Colgrave
Summary: In this study, the proteome profile of barley grain and malt samples was investigated using SWATH-MS proteomics. The results showed that the C-hordein-reduced lines had a more significant impact on proteome level changes during malting. Upregulated proteins in C-hordein-reduced lines were mainly involved in the tricarboxylic acid cycle and fatty acid peroxidation processes. Proteomics approaches in hordein-reduced barley lines after malting also revealed additional changes in the proteome driven by the genetic background. These findings provide valuable insights for barley breeders and maltsters to optimize gluten-free grains in malt products.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Oncology
Juliana Mueller Bark, Lucas Trevisan Franca de Lima, Xi Zhang, Daniel Broszczak, Paul J. Leo, Rosalind L. Jeffree, Benjamin Chua, Bryan W. Day, Chamindie Punyadeera
Summary: This study demonstrates the feasibility of isolating and characterizing small extracellular vesicles (EVs) from pre- and postoperative saliva samples from glioblastoma (GBM) patients for the first time. Preliminary findings encourage further large cohort validation studies on salivary small EVs to evaluate prognosis in GBM.
Article
Engineering, Biomedical
Amish Asthana, Riccardo Tamburrini, Deborah Chaimov, Carlo Gazia, Stephen J. Walker, Mark Van Dyke, Alice Tomei, Sandrine Lablanche, John Robertson, Emmanuel C. Opara, Shay Soker, Giuseppe Orlando
Summary: Interactions between pancreatic ECM and islet cells play a crucial role in islet physiology, and combining engineering approaches with mass spectrometry techniques can provide a more comprehensive analysis of the proteome for creating physiologically relevant pancreatic microenvironments.
Article
Cell Biology
Charles Banliat, Coline Mahe, Regis Lavigne, Emmanuelle Com, Charles Pineau, Valerie Labas, Benoit Guyonnet, Pascal Mermillod, Marie Saint-Dizier
Summary: A comprehensive study of proteome dynamics in non-rodent mammalian embryos developed in vivo was conducted. Proteomic changes in bovine embryos at different developmental stages were analyzed, and distinct patterns were observed. Proteins that increased in abundance during development were associated with RNA metabolism, protein translation, and ribosome biogenesis, while proteins that decreased in abundance were involved in Golgi vesicle transport and protein processing in endoplasmic reticulum. The results provide valuable insights into the molecular mechanisms underlying early embryo development.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Environmental Sciences
Benjamin Trotter, Magdalena Wilde, Julian Brehm, Evdokia Dafni, Arlinda Aliu, Georg J. Arnold, Thomas Froehlich, Christian Laforsch
Summary: Research on the effects of microplastics on freshwater organisms, particularly Daphnia, has shown that chronic exposure to polystyrene microplastics can lead to decreased body length and offspring numbers in Daphnia magna. Proteomic analysis revealed changes in protein abundance, including alterations in enzymes and important physiological pathways. This study highlights the potential impact of long-term exposure to microplastics on the fitness of aquatic organisms.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Biochemical Research Methods
Sergio Ciordia, Gloria Alvarez-Sola, Maria Rullan, Jesus M. Urman, Matias A. Avila, Fernando J. Corrales
Summary: The analysis of biological fluids for disease-related proteins is an important field of research. However, challenges exist, especially in complex matrices like bile. A new procedure described in this study significantly improves protein recovery from rat bile, providing valuable resources for further understanding disease molecular markers.
JOURNAL OF PROTEOMICS
(2021)
Review
Immunology
Laura A. Solt
Summary: T cells transition from a quiescent state to active proliferation and effector function upon exposure to cognate antigen, a process tightly controlled by signal transduction pathways. Dysregulation of these events can mediate disease, and recent sequencing advances at the single-cell level have improved our understanding of T cell biology.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Diana Valeria Rossetti, Ilaria Inserra, Alessia Nestico, Federica Vincenzoni, Federica Iavarone, Irene Messana, Massimo Castagnola, Luca Massimi, Gianpiero Tamburrini, Massimo Caldarelli, Claudia Desiderio
Summary: The study aimed to explore the intact proteome of pediatric brain tumors of different WHO grades and localizations to understand the molecular mechanisms underlying the onset and progression of these pathologies. Proteomic analysis revealed statistically significant differences in protein/peptide levels between tumor histotypes, as well as the identification of naturally occurring fragments and post-translational modifications. This study contributes to elucidating the molecular profiles of the most common solid tumors affecting children.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Agriculture, Dairy & Animal Science
Mohan Kiran, Naveena B. Maheswarappa, Rituparna Banerjee, Venkatesh Ch, Srikanth Rapole
Summary: The study showed that slaughtering of sheep without stunning resulted in changes in protein abundance related to various physiological processes. These protein alterations have the potential to serve as indicators for assessing animal welfare.
ANIMAL BIOTECHNOLOGY
(2021)
Article
Ophthalmology
Maite Lopez-Lopez, Uxia Regueiro, Susana Belen Bravo, Maria del Pilar Chantada-Vazquez, Carmen Pena, Elio Diez-Feijoo, Pablo Hervella, Isabel Lema
Summary: This study utilized a qualitative approach to explore the tear proteome of patients with keratoconus (KC), finding that the expression of certain proteins in tears of KC patients differed from the control group. These differences were linked to processes such as cell death, oxidative damage, and inflammation.
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2022)