Review
Chemistry, Medicinal
Nabangshu Das, Colette Benko, Sean E. Gill, Antoine Dufour
Summary: Researchers are currently focusing on developing more selective MMP inhibitors by targeting other domains of MMPs through specific small molecule inhibitors or monoclonal antibodies. In addition, they are exploring unbiased global approaches, such as proteomics and N-terminomics, to discover new MMP substrates.
Article
Orthopedics
S. Bhutada, L. Li, B. Willard, G. Muschler, N. Piuzzi, S. S. Apte
Summary: This study investigated the proteolytic degradation of articular cartilage in osteoarthritis (OA) using terminomics strategies. The researchers identified the degradome of human knee OA cartilage and found that the protease HtrA1 played a significant role in cartilage proteolysis. The findings revealed widespread protein degradation in OA cartilage and suggested potential biomarkers for OA.
OSTEOARTHRITIS AND CARTILAGE
(2022)
Article
Agriculture, Dairy & Animal Science
Muhan Zhang, Daoying Wang, Xinglian Xu, Weimin Xu, Guanghong Zhou
Summary: The study identified 301 differentially expressed proteins in duck muscles related to lipid oxidation through iTRAQ analysis and confirmed by PRM. These proteins were found to be involved in lipid binding and metabolism, lipolysis, stress response, oxidative respiratory chain, and redox regulation, potentially impacting lipid oxidation in muscles.
Article
Biochemical Research Methods
Martin Ryden, Aleksandra Turkiewicz, Patrik Onnerfjord, Jon Tjornstrand, Martin Englund, Neserin Ali
Summary: This study aimed to characterize the degradome of knee osteoarthritis (OA) patients by analyzing proteolytic activity and differential abundance of cleavage products in synovial fluid (SF). Liquid chromatography mass spectrometry (LC-MS) was used to analyze SF samples from end-stage knee OA patients and controls, and a new database search was performed to identify non-tryptic and semi-tryptic peptides for degradomics studies in OA. Linear mixed models were used to estimate differences in peptide-level expression between the two groups. Known proteolytic events from the MEROPS peptidase database were mapped to the dataset to identify potential proteases and their substrates. A total of 429 differentially abundant peptides were identified, and metalloproteinases, chymase, and cathepsins were found to be the main proteolytic actors. The analysis indicated increased activity of these proteases regardless of their abundance.
Article
Plant Sciences
Kati Mielke, Raik Wagner, Laxmi S. Mishra, Fatih Demir, Andreas Perrar, Pitter F. Huesgen, Christiane Funk
Summary: FtsH12 plays a crucial role in seedling development of Arabidopsis thaliana, affecting plastid import machinery and chloroplast development. Changes in FtsH12 abundance lead to alterations in protein composition and structure of the chloroplast, impacting overall plant growth and leaf coloration.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Agriculture, Dairy & Animal Science
Xin Ma, Meng Wang, Jinglei Wang, Qian Zhang, Sisi Pu, Rui Wang, Sijiu Yu, Libin Wang, Yangyang Pan
Summary: In this study, the dynamic changes in yak oocytes during maturation were analyzed using iTRAQ technology. Differential proteomics sequencing revealed transient dynamic changes in the proteome and differences in physiological functions at different stages of oocyte maturation. Accurate identification of the differential proteins provides insights into the molecular regulatory mechanism of yak oocyte maturation.
Article
Agriculture, Multidisciplinary
Xue Luo, Mo Li, Henan Zhang, Danli Yan, Shuaiqi Ji, Rina Wu, Yongfu Chen
Summary: Proteomics and bioinformatics analysis of three strains of Lactobacillus plantarum under salt stress revealed differential expression of proteins related to protein biosynthesis, nucleotide metabolism, and sugar metabolism. Specific differentially expressed proteins were found between the strains in response to high salt conditions.
JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE
(2021)
Article
Biochemistry & Molecular Biology
Helena Laronha, Ines Carpinteiro, Jaime Portugal, Ana Azul, Mario Polido, Krasimira T. Petrova, Madalena Salema-Oom, Isabel Barahona, Jorge Caldeira
Summary: A new class of MMP inhibitors has been discovered, which can be co-polymerized with other vinyl compounds in commercial dental resins, limiting release and potential toxicity, and increasing safety. These inhibitors show unique properties towards various MMPs and did not significantly decrease cell viability at high concentrations.
Article
Biochemistry & Molecular Biology
Heng Wee Tan, Yan-Ming Xu, Zhan-Ling Liang, Na-Li Cai, Yu-Yao Wu, Andy T. Y. Lau
Summary: This study explores the proteomic landscape of cells with impaired ZIP8 and uncovers the potential relationships between essential micronutrients and uncharacterized proteins C9orf85 and CXorf38. The differentially expressed proteins identified in ZIP8-KO cells could be potential targets for diagnosing and/or treating human ZIP8-associated diseases, including but not limited to malnutrition, viral infection, and cancers.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Agronomy
Xiaoli Zhang, Maoyan Tang, Hui Wang, Wei Tao, Qiang Wang, Lei Chen, Guoqing Gao, Ronghua Lv, Tianfeng Liang
Summary: This study found that the Southeast Asian germplasm resource C1 has a higher photosynthetic efficiency compared to G164, as evidenced by better tissue structure, chloroplast ultrastructure, and photosynthetic physiological indicators. Proteomics analysis also revealed higher activity of key photosynthetic enzymes in C1. These findings provide an important foundation for breeding high light efficiency varieties and further understanding photosynthesis.
Article
Plant Sciences
Yong Gao, Xia Shi, Yongyuan Chang, Yingbo Li, Xuehang Xiong, Hongmei Liu, Mengyuan Li, Weihua Li, Xuehai Zhang, Zhiyuan Fu, Yadong Xue, Jihua Tang
Summary: Narrowing down a single putative target gene and constructing the regulation network by proteomic method for a leaf senescence mutant. Leaf senescence mutant is an important resource for exploring molecular mechanism of aging. Proteomics analysis of the mutant and its wild type revealed differentially accumulated proteins mainly enriched in regulation pathways such as photosynthesis, ribosome, and chlorophyll metabolism. The interaction networks constructed by transcriptome data showed that ZmELS5 likely repaired several key factors in the photosynthesis system. These results provide a fundamental basis and new insights for further research on the molecular mechanism of leaf senescence in maize.
PLANT CELL REPORTS
(2023)
Article
Agriculture, Dairy & Animal Science
Mingxing Cao, Lin Huang, Suyu Jin, Mengbo Zhao, Yucai Zheng
Summary: The study compared the milk protein compositions of standard lactation and prolonged lactation yaks using iTRAQ technique, revealing degeneration characteristics in the milk proteins of prolonged lactation yaks. Metabolic pathway differences were mainly centered around carbohydrate metabolism and amino acid biosynthesis pathways.
Article
Plant Sciences
Jialiang Li, Rui Yang, Yonglei Jiang, Shubin Sun, Junying Li, Hao Gu, Ying Lin, Xianxue Luo, Chenggang He, Yi Chen
Summary: This study provides insights into the responses of tobacco roots to different soil types, showing that red soil promotes the coordination of chemical composition of tobacco leaves and the growth and activity of the root system, while limestone soil and paddy soil have relatively weaker effects.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Medicine, Research & Experimental
Jie Zhu, Ling Han, Ruilai Liu, Zhenghua Zhang, Qiong Huang, Xu Fang, Ke Yang, Guiqin Huang, Zhizhong Zheng, Nikhil Yawalkar, Hui Deng, Kexiang Yan
Summary: By analyzing the proteome profile of PBMCs from patients with PsA, PsO, and healthy controls, this study identified 14 potential biomarkers for PsA diagnosis. Additionally, the expression of SIRT2 was significantly higher in PsA patients compared to PsO and healthy controls, and was negatively correlated with the phosphorylation of p38MAPK.
JOURNAL OF TRANSLATIONAL MEDICINE
(2021)
Article
Reproductive Biology
Xiangping Li, JiaHui Yao, Jiaying Hu, ChunHua Deng, Yun Xie, Zhu Wang
Summary: This study identified 1477 proteins in murine TIF, with 706 proteins showing a linear change trend with age and 45 age-related DEPs identified. Bioinformatic analyses revealed that these proteins were involved in actin cytoskeleton organization, intrinsic apoptotic signaling pathway, and regulation of protein transport. Comparative analysis with relevant proteomes further revealed the characteristics of mouse TIF proteome.
Article
Dermatology
Fabio Sabino, Fabian E. Egli, Simonas Savickas, Joerg Holstein, Daniela Kaspar, Mika Rollmann, Jayachandran N. Kizhakkedathu, Tim Pohlemann, Hans Smola, Ulrich Auf Dem Keller
JOURNAL OF INVESTIGATIVE DERMATOLOGY
(2018)
Article
Cell Biology
Kristin Seltmann, Michael Meyer, Jitka Sulcova, Tobias Kockmann, Ulrike Wehkamp, Stephan Weidinger, Ulrich auf dem Keller, Sabine Werner
SCIENCE TRANSLATIONAL MEDICINE
(2018)
Article
Food Science & Technology
Konstantinos Kalogeropoulos, Andreas Frederik Treschow, Ulrich Auf Dem Keller, Teresa Escalante, Alexandra Rucavado, Jose Maria Gutierrez, Andreas Hougaard Laustsen, Christopher T. Workman
Review
Biochemistry & Molecular Biology
Elizabeta Madzharova, Philipp Kastl, Fabio Sabino, Ulrich Auf Dem Keller
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2019)
Review
Biochemistry & Molecular Biology
Simonas Savickas, Philipp Kastl, Ulrich auf dem Keller
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2020)
Review
Medicine, General & Internal
S. Holm Nielsen, L. Jonasson, K. Kalogeropoulos, M. A. Karsdal, A. L. Reese-Petersen, U. Auf Dem Keller, F. Genovese, J. Nilsson, I Goncalves
JOURNAL OF INTERNAL MEDICINE
(2020)
Article
Biochemistry & Molecular Biology
Stefania L. Wunderli, Ulrich Blache, Agnese Beretta Piccoli, Barbara Niederost, Claude N. Holenstein, Fabian S. Passini, Unai Silvan, Louise Bundgaard, Ulrich Auf Dem Keller, Jess G. Snedeker
Editorial Material
Biochemistry & Molecular Biology
Magnus S. Agren, Ulrich auf dem Keller
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2020)
Article
Food Science & Technology
Christoffer V. Sorensen, Cecilie Knudsen, Ulrich Auf Dem Keller, Konstantinos Kalogeropoulos, Cristina Gutierrez-Jimenez, Manuela B. Pucca, Eliane C. Arantes, Karla C. F. Bordon, Andreas H. Laustsen
Article
Pharmacology & Pharmacy
Manuela B. Pucca, Shirin Ahmadi, Felipe A. Cerni, Line Ledsgaard, Christoffer Sorensen, Farrell T. S. McGeoghan, Trenton Stewart, Erwin Schoof, Bruno Lomonte, Ulrich auf dem Keller, Eliane C. Arantes, Figen Caliskan, Andreas H. Laustsen
FRONTIERS IN PHARMACOLOGY
(2020)
Article
Oncology
Kerstin A. Kessel, Marco M. E. Vogel, Carmen Kessel, Henning Bier, Tilo Biedermann, Helmut Friess, Peter Herschbach, Ruediger von Eisenhart-Rothe, Bernhard Meyer, Marion Kiechle, Ulrich Keller, Christian Peschel, Florian Bassermann, Roland Schmid, Markus Schwaiger, Stephanie E. Combs
CLINICAL AND TRANSLATIONAL RADIATION ONCOLOGY
(2018)
Meeting Abstract
Cell Biology
L. B. Bundgaard, M. S. Agren, P. Holstein, S. Savickas, F. Sabino, U. Auf Dem Keller
WOUND REPAIR AND REGENERATION
(2018)
Review
Biochemistry & Molecular Biology
Simonas Savickas, Ulrich Auf Dem Keller
BIOLOGICAL CHEMISTRY
(2018)
Article
Cell Biology
Marc Bachofner, Tobias Speicher, Roman L. Bogorad, Sukalp Muzumdar, Carina P. Derrer, Fabrizio Hurlimann, Friederike Bohm, Paolo Nanni, Tobias Kockmann, Ekaterina Kachaylo, Michael Meyer, Susagna Padrissa-Altes, Rolf Graf, Daniel G. Anderson, Victor Koteliansky, Ulrich auf dem Keller, Sabine Werner
DEVELOPMENTAL CELL
(2017)
Article
Multidisciplinary Sciences
Ulrich Eckhard, Pitter F. Huesgen, Oliver Schilling, Caroline L. Bellac, Georgina S. Butler, Jennifer H. Cox, Antoine Dufour, Verena Goebeler, Reinhild Kappelhoff, Ulrich auf dem Keller, Theo Klein, Philipp F. Lange, Giada Marino, Charlotte J. Morrison, Anna Prudova, David Rodriguez, Amanda E. Starr, Yili Wang, Christopher M. Overall