Article
Biochemistry & Molecular Biology
Jinit Masania, Patrick Wijten, Susanne Keipert, Mario Ost, Susanne Klaus, Naila Rabbani, Paul J. Thornalley
Summary: Mice with ectopic expression of UCP1 in skeletal muscle show a healthy aging phenotype and increased resistance to metabolic health impairment. Decreased protein glycation and oxidative damage, along with increased expression of heat shock proteins and mechanoprotection, were observed in aged HSA-mUCP1 mice compared to wildtype controls. These findings suggest that the decreased formation and increased clearance of MG-derived AGEs may contribute to the healthy aging phenotype in HSA-mUCP1 mice.
Article
Cell Biology
Diego Quintana-Torres, Alejandra Valle-Cao, Pablo Bousquets-Munoz, Sandra Freitas-Rodriguez, Francisco Rodriguez, Alejandro Lucia, Carlos Lopez-Otin, Alejandro Lopez-Soto, Alicia R. Folgueras
Summary: This study conducted a global plasma proteomic analysis in progeroid mouse models and found several upregulated proteins related to cardiovascular disease, the main cause of death in HGPS patients. The plasma proteome of progeroid mice exhibited an old signature, indicating accelerated aging. Furthermore, specific differences were observed in the circulating proteins between physiological and premature aging, highlighting potential biomarkers and therapeutic targets.
Article
Reproductive Biology
Chuanxin Zhang, Xueqi Dong, Xinyi Yuan, Jinzhu Song, Jiawei Wang, Boyang Liu, Keliang Wu
Summary: By analyzing the protein expression profile of fresh and aging metaphase II mouse oocytes using four-dimensional label-free quantification mass spectrometry, we identified differential expression of proteins related to gene expression and RNA metabolism. These findings provide a new perspective on the mechanisms of postovulatory aging.
JOURNAL OF OVARIAN RESEARCH
(2022)
Article
Neurosciences
Xin Wang, Xueyan Zhou, Jingyun Lee, Cristina M. Furdui, Tao Ma
Summary: This study investigated de novo proteome alterations in the hippocampus of aged Tg19959 AD model mice using the BONCAT method combined with unbiased large-scale proteomic analysis (BONSPEC). Multiple bioinformatics methods were applied to analyze the proteomics data, revealing an enrichment of proteins involved in synaptic function in the de novo proteome of AD mice. This study provides insights into the molecular signaling mechanisms underlying AD and related dementias (ADRDs).
JOURNAL OF ALZHEIMERS DISEASE
(2023)
Article
Biochemical Research Methods
Yanfang Chen, Severine Roselli, Nikita Panicker, Joshua S. Brzozowski, David A. Skerrett-Byrne, Heather C. Murray, Nicole M. Verrills
Summary: This article provides a comprehensive characterization of the proteome and phosphoproteome of wild-type primary MEFs from C57BL/6 mice. The study identifies abundant EIF2/4 and MTOR signaling pathways, as well as extracellular matrix and cytoskeleton associated pathways. Kinase enrichment analysis reveals the activation of P38A, P90RSK, P70S6K, and MTOR. This dataset serves as a valuable resource for future research in the field.
Article
Biochemistry & Molecular Biology
Francesco Demetrio Lofaro, Barbara Cisterna, Maria Assunta Lacavalla, Federico Boschi, Manuela Malatesta, Daniela Quaglino, Carlo Zancanaro, Federica Boraldi
Summary: This study characterized the matrisome in the aging skeletal muscle for the first time, demonstrating significant statistical differences in several matrisome proteins between aged and adult muscle. The findings provide new insights into the mechanisms regulating myocellular behavior in aging and their contribution to age-related muscle dysfunction.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemical Research Methods
Georgia Ntasi, Sara Sbriglia, Rossana Pitocchi, Roberto Vinciguerra, Chiara Melchiorre, Laura Dello Ioio, Giancarlo Fatigati, Emanuele Crisci, Ilaria Bonaduce, Andrea Carpentieri, Gennaro Marino, Leila Birolo
Summary: Animal glues are commonly used in restoration, and their performance is determined by the adhesive properties of collagen. Mass spectrometry techniques were used to characterize the protein components of homemade and commercial glues. The study identified the animal origin of the glues and distinguished between hide and bone glue based on the presence of collagen type III. The analysis of chemical modifications showed variations among different glues. These findings have analytical significance in the characterization of collagen-based materials and can assist restorers in selecting appropriate materials for conservation treatments.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemical Research Methods
John Q. Bettinger, Matthew Simon, Anatoly Korotkov, Kevin A. Welle, Jennifer R. Hryhorenko, Andrei Seluanov, Vera Gorbunova, Sina Ghaemmaghami
Summary: The oxidation of methionine is an important post-translational modification of proteins, with diverse effects on cell physiology. However, the large-scale investigation of methionine oxidation has been hindered by technical limitations. In this study, a new methodology called methionine oxidation by blocking (MobB) was developed, allowing for accurate quantification of low levels of methionine oxidation. Using this method, over 280 novel sites for in vivo methionine oxidation were identified in the brain tissues of mice. The results suggest that methionine oxidation may be a biologically regulated process rather than a result of stochastic chemical damage.
JOURNAL OF PROTEOME RESEARCH
(2022)
Review
Genetics & Heredity
Ruike Wang, Yingying Wu, Rundong Liu, Mengchen Liu, Qiong Li, Yue Ba, Hui Huang
Summary: This paper provides an up-to-date evaluation of the neuroprotective mechanisms of SIRT1 in modulating neurodegeneration, highlighting the importance of protein homeostasis, aging-related signaling pathways, neurogenesis, and synaptic plasticity. The potential of targeting SIRT1 to block the occurrence and progression of neurodegenerative diseases is also discussed.
JOURNAL OF MOLECULAR MEDICINE-JMM
(2022)
Review
Biochemistry & Molecular Biology
Rachel E. Lacoursiere, Dania Hadi, Gary S. Shaw
Summary: Ubiquitination is a complex process controlled by a series of enzymes. Recent studies have shown that these enzymes can be further modified through acetylation or phosphorylation, and alterations in these modifications have been observed in different diseases.
Article
Microbiology
Natan Nagar, Noa Ecker, Gil Loewenthal, Oren Avram, Daniella Ben-Meir, Dvora Biran, Eliora Ron, Tal Pupko
Summary: The degradation of intracellular proteins in Gram-negative bacteria is regulated through various cellular processes and serves as a mechanism for quality control. By employing a quantitative pulsed-SILAC method followed by mass spectrometry analysis, this study identified fast-degrading novel proteins and developed a machine learning classifier to discriminate them from the rest of the proteome. These findings expand the understanding of protein degradation in bacteria and have implications for protein engineering, potentially aiding in the identification of new antibacterial drug targets.
Article
Chemistry, Applied
Man-Man Yu, Ying-Chen Fan, Xin-Ran Zhang, De-Yang Li, Yu-Xin Liu, Da-Yong Zhou, Bei-Wei Zhu
Summary: Quantitative proteomic analysis revealed that texture changes in abalone muscles during boiling were caused by protein oxidation, denaturation, aggregation, and degradation, with the degradation of structural proteins leading to decreases in shear force and hardness.
Article
Biochemical Research Methods
Akila Wijerathna-Yapa, Elke Stroeher, Ricarda Fenske, Lei Li, Owen Duncan, A. Harvey Millar
Summary: Autophagy is a catabolic process that plays a crucial role in degrading cytoplasmic proteins and organelles in a lysosome or vacuole-dependent manner. Proteomic studies have helped uncover the protein regulatory mechanisms of autophagy, including the identification of receptor and cargo proteins and protein-protein interactions.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Neurosciences
Arunabh Sarkar, Aamir Nazir
Summary: Maintaining cellular homeostasis through efficient clearance of aberrant proteins is crucial for health. Aging poses challenges to the proteostasis network, impacting fundamental physiological processes. Strategies to improve proteostasis may help delay age-related pathological consequences and promote healthy aging.
MOLECULAR NEUROBIOLOGY
(2022)
Review
Developmental Biology
Nikolai Slavov
Summary: Robust single-cell mass spectrometry methods allow accurate quantification of proteins and their modification, providing insights into post-transcriptional regulatory mechanisms and their role in developmental cell fate specification. These methods also enable the analysis of protein conformations and activities, linking protein functions to developmental processes in single cells.
Article
Immunology
Conrad M. Freuling, Elisa Eggerbauer, Stefan Finke, Christiane Kaiser, Christian Kaiser, Antje Kretzschmar, Tobias Nolden, Steffen Ortmann, Charlotte Schroeder, Jens P. Teifke, Peter Schuster, Ad Vos, Thomas C. Mettenleiter, Thomas Mueller
Article
Virology
Emmanuel Heilmann, Janine Kimpel, Stephan Geley, Andreas Naschberger, Carles Urbiola, Tobias Nolden, Dorothee von Laer, Guido Wollmann
Article
Biotechnology & Applied Microbiology
Nikolaus F. Zwickl, Nancy Stralis-Pavese, Christina Schaeffer, Juliane C. Dohm, Heinz Himmelbauer
Article
Plant Sciences
Matteo Schiavinato, Marina Marcet-Houben, Juliane C. Dohm, Toni Gabaldon, Heinz Himmelbauer
Article
Multidisciplinary Sciences
Verena te Kamp, Conrad M. Freuling, Ad Vos, Peter Schuster, Christian Kaiser, Steffen Ortmann, Antje Kretzschmar, Sabine Nemitz, Elisa Eggerbauer, Reiner Ulrich, Jan Schinkoethe, Tobias Nolden, Thomas Mueller, Stefan Finke
SCIENTIFIC REPORTS
(2020)
Article
Cell Biology
Madlin Potratz, Luca Zaeck, Michael Christen, Verena te Kamp, Antonia Klein, Tobias Nolden, Conrad M. Freuling, Thomas Mueller, Stefan Finke
Article
Plant Sciences
Matteo Schiavinato, Alexandrina Bodrug-Schepers, Juliane C. Dohm, Heinz Himmelbauer
Summary: Polyploidization is a common mechanism for speciation and adaptation, especially in plants. The analysis of hybrid plant genomes revealed biased subgenome fractionation in hybrids with different ages and levels of subgenomic intermixing. Domestication may either encourage or hinder subgenome intermixing, depending on the evolutionary context.
Article
Multidisciplinary Sciences
E. Heilmann, J. Kimpel, B. Hofer, A. Roessler, I. Blaas, L. Egerer, T. Nolden, C. Urbiola, H. G. Kraeusslich, G. Wollmann, D. von Laer
Summary: This study presents a regulatory switch for RNA viruses that allows control over viral activity using clinically approved HIV protease inhibitors.
NATURE COMMUNICATIONS
(2021)
Article
Biotechnology & Applied Microbiology
Reinhard Lehner, Lisa Blazek, Andre E. Minoche, Juliane C. Dohm, Heinz Himmelbauer
Summary: This study presents a genome assembly of chard, revealing its genome characteristics and gene space completeness. Comparison with sugar beet and wild beets identified gene relationships and shared genomic regions. Genomic variants distinguishing sugar beet and chard were also determined, showing extensive haplotype sharing between the two cultivars.
JOURNAL OF BIOTECHNOLOGY
(2021)
Article
Agronomy
Alexandrina Bodrug-Schepers, Nancy Stralis-Pavese, Hermann Buerstmayr, Juliane C. Dohm, Heinz Himmelbauer
Summary: This study suggests utilizing natural variation between individuals of a population for genome assembly scaffolding, demonstrating the potential value of haplotype information from distantly related individuals in grouping and ordering contigs for generating pseudomolecules.
THEORETICAL AND APPLIED GENETICS
(2021)
Article
Multidisciplinary Sciences
Krishna Das, Elodie Belnoue, Matteo Rossi, Tamara Hofer, Sarah Danklmaier, Tobias Nolden, Liesa-Marie Schreiber, Katharina Angerer, Janine Kimpel, Sandra Hoegler, Bart Spiesschaert, Lukas Kenner, Dorothee von Laer, Knut Elbers, Madiha Derouazi, Guido Wollmann
Summary: The combination of a self-adjuvanting protein vaccine and an antigen-expressing oncolytic virus significantly enhances T cell immunogenicity, potentially making non-inflamed tumors proinflammatory and less resistant to checkpoint blockade therapy. Therapeutic cancer vaccination in combination with oncolytic viruses can elicit tumor-specific cytotoxic T cells that offer opportunities to address resistance to checkpoint blockade therapy.
NATURE COMMUNICATIONS
(2021)
Article
Microbiology
Kanika Vanshylla, Chengcheng Fan, Marie Wunsch, Nareshkumar Poopalasingam, Matthijs Meijers, Christoph Kreer, Franziska Kleipass, Denis Ruchnewitz, Meryem S. Ercanoglu, Henning Gruell, Friederike Muenn, Kai Pohl, Hanna Janicki, Tobias Nolden, Simone Bartl, Saskia C. Stein, Max Augustin, Felix Dewald, Lutz Gieselmann, Philipp Schommers, Thomas F. Schulz, Leif Erik Sander, Manuel Koch, Marta Luksza, Michael Laessig, Pamela J. Bjorkman, Florian Klein
Summary: This study analyzed single B cells from 10 COVID-19 convalescent individuals and identified 126 monoclonal antibodies. Some of these antibodies showed cross-reactivity to SARS-CoV-1 and other related coronaviruses. Multiple broadly neutralizing antibodies were found to effectively neutralize different variants of SARS-CoV-2, including emerging escape variants.
CELL HOST & MICROBE
(2022)
Article
Virology
Sabine Nitschel, Luca M. Zaeck, Madlin Potratz, Tobias Nolden, Verena te Kamp, Kati Franzke, Dirk Hoeper, Florian Pfaff, Stefan Finke
Summary: The study investigated the adaptation of field rabies virus to cell culture replication, revealing that adaptive mutations could be acquired through passages to overcome replication bottlenecks in cell culture. The limited release of infectious virus at the plasma membrane was identified as a defined characteristic of highly virulent field rabies viruses.
Article
Plant Sciences
Giuseppe Andolfo, Juliane C. Dohm, Heinz Himmelbauer
Summary: The activation of plant immunity relies on R-gene receptors, but traditional methods of identifying these genes may be imprecise. A new method called HRP has been developed to better identify and annotate NB-LRR genes in plant genomes, showing increased efficiency and accuracy in comparison to previous approaches. This high-performance method has the potential to lead to the discovery of novel R-genes and the development of improved plant cultivars.
Article
Multidisciplinary Sciences
Felix L. Wascher, Nancy Stralis-Pavese, J. Mitchell McGrath, Britta Schulz, Heinz Himmelbauer, Juliane C. Dohm
Summary: The phylogeny of wild and cultivated beets is clarified using genomic analysis and it is found that Greece is the domestication site of sugar beet. This study provides comprehensive insights into the evolutionary relationships of beets.
NATURE COMMUNICATIONS
(2022)