Article
Cell Biology
Tian-Yi Zhu, Shang-Tong Li, Dan-Dan Liu, Xiajun Zhang, Lianqi Zhou, Rong Zhou, Bing Yang
Summary: This study quantifies protein changes during aging in different individuals using single-worm mass spectrometry, and reveals the heterogeneity of aging by reconstructing the aging trajectory and proteomic landscape of C. elegans.
Article
Biochemical Research Methods
Dahang Yu, Zhe Wang, Kellye A. Cupp-Sutton, Yanting Guo, Qiang Kou, Kenneth Smith, Xiaowen Liu, Si Wu
Summary: A top-down TMT MS platform for confidently identifying and quantifying low molecular weight intact proteoforms in complex biological samples was developed by combining filter-SEC technique with high-performance size exclusion chromatography. This technique enables high-throughput analysis of intact proteoforms from Escherichia coli cell lysates, representing the first high-throughput TMT labeling-based, quantitative, top-down MS analysis suitable for complex biological samples.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Nutrition & Dietetics
Sarah Brajkovic, Nils Rugen, Carlos Agius, Nicola Berner, Stephan Eckert, Amirhossein Sakhteman, Claus Schwechheimer, Bernhard Kuster
Summary: Plants are crucial for sustainable global food supply, but the understanding of crop proteomes is limited. The presence of secondary metabolites in crop plants has hindered proteomic analyses, requiring individually optimized protein extraction protocols. In this study, a universal protein extraction protocol combined with an automated SP3 protocol and optimized micro-LC-MS/MS conditions was developed for high-quality proteomic analysis of crop plants. The workflow was successfully applied to analyze the proteomes of mature tomato fruits, demonstrating its robustness and potential for large-scale projects mapping crop tissue proteomes.
Article
Biochemical Research Methods
Meng Wang, Lihua Jiang, Ruiqi Jian, Joanne Y. Chan, Qing Liu, Michael P. Snyder, Hua Tang
Summary: The study focused on improving normalization methods in highly heterogeneous samples, developing a novel data-driven approach to correct systematic bias while maintaining biological heterogeneity. The results showed that this method achieved the greatest reduction in bias while preserving variation across samples.
Article
Chemistry, Multidisciplinary
Jan Leipert, Philipp T. Kaulich, Max K. Steinbach, Britta Steer, Konrad Winkels, Christine Blurton, Matthias Leippe, Andreas Tholey
Summary: Researchers have developed a sample preparation method based on protein aggregation and acidic elution, allowing for sensitive protein identification analysis of single nematodes on a digital microfluidics device. Compared to in-tube sample preparation, this method increases proteoform identifications by 46%. Label-free quantification also reveals changes in proteoform abundance that cannot be distinguished by bottom-up proteomics. This workflow facilitates proteoform-focused analysis on limited availability samples.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Review
Genetics & Heredity
Xiulan Chen, Yaping Sun, Tingting Zhang, Lian Shu, Peter Roepstorff, Fuquan Yang
Summary: Isobaric labeling technology has become a key tool for comparing protein expression in biological samples, although challenges remain in terms of quantitative accuracy and precision. The different types of isobaric mass tags and advantages and disadvantages of the labeling method are detailed, along with precautions needed at each step of the workflow for reliable quantification results. The broad applications of isobaric labeling technology in biological and clinical studies, with a focus on thermal proteome profiling and proteogenomics, are also discussed.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2021)
Review
Biochemistry & Molecular Biology
Joohyun Ryu, Stefani N. Thomas
Summary: Ovarian cancer is a deadly gynecologic malignancy with the need for new and more effective treatment strategies, while early detection and protein biomarkers play crucial roles. Targeted proteomics methods, including mass spectrometry, offer robust solutions for the development of ovarian cancer biomarkers.
Review
Chemistry, Analytical
Hanne Roberg-Larsen, Elsa Lundanes, Tuula A. Nyman, Frode S. Berven, Steven Ray Wilson
Summary: Single-cell analysis provides in-depth insights into diseases and diagnostics, with liquid chromatography playing a crucial role. The development of novel sample preparation techniques and improvements in mass spectrometry are enhancing the promise of single-cell analysis. However, technical challenges and the need for higher throughput and robustness may lead to the reinvention of alternative nano LC column formats.
ANALYTICA CHIMICA ACTA
(2021)
Article
Medicine, Research & Experimental
Lisa Schweizer, Tina Schaller, Maximilian Zwiebel, Oezge Karayel, Johannes Bruno Mueller-Reif, Wen-Feng Zeng, Sebastian Dintner, Thierry M. Nordmann, Klaus Hirschbuehl, Bruno Maerkl, Rainer Claus, Matthias Mann
Summary: SARS-CoV-2 can cause damage to lung tissue and other organs in the human body, and this study aimed to analyze these effects comprehensively. Using a mass spectrometry proteomics workflow, the researchers identified inflammatory responses as the initial reaction in all tissues. They also found specific patterns of damage in different organs, such as diffuse alveolar damage in the lungs and organ-specific changes in the kidneys, liver, and lymphatic and vascular systems. In the brain, secondary inflammatory effects were linked to neurotransmitter receptors and myelin degradation. These findings contribute to our understanding of the mechanisms of COVID-19 and provide insights for organ-specific therapeutic interventions.
EMBO MOLECULAR MEDICINE
(2023)
Review
Oncology
Elizabeth A. Connolly, Peter S. Grimison, Lisa G. Horvath, Phillip J. Robinson, Roger R. Reddel
Summary: Sarcoma, a rare and complex disease, faces challenges in diagnosis, disease classification, lack of effective treatment options, and identification of biomarkers and drug targets. Proteomics, the study of proteins, offers insights into cancer biology. This review discusses quantitative proteomic studies in sarcoma, highlighting the potential for diagnostic, prognostic, and therapeutic biomarkers. The application of proteomic methodologies in various sarcoma subtypes is described, with a focus on histological classification and understanding disease heterogeneity. The importance of proteomic research in addressing unmet needs in sarcoma is outlined.
FRONTIERS IN ONCOLOGY
(2023)
Article
Biochemical Research Methods
Kelly A. Dingess, Pauline van Dam, Jing Zhu, Marko Mank, Karen Knipping, Albert J. R. Heck, Bernd Stahl
Summary: Immunoglobulins in human milk, especially secretory immunoglobulin A (sIgA), play a crucial role in protecting breastfed infants from pathogens. Researchers developed a sIgA ELISA method for quantitative analysis of total sIgA in human milk, which showed strong correlation with mass spectrometry-detected IgA1, suggesting it as a superior indicator compared to standard serum IgA ELISA kits.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Chemistry, Analytical
Dong Hao Wang, Hui Gyu Park, Zhen Wang, R. J. Scott Lacombe, Vadim V. Shmanai, Andrei Bekish, Karsten Schmidt, Mikhail S. Shchepinov, J. Thomas Brenna
Summary: This study introduces a novel method for quantitatively determining the deuterium content along a hydrocarbon chain. By utilizing deuteration reactions and analysis techniques, the method enables accurate quantification of deuterium abundance at different positions of D-HUFA.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Paulina Czaplewska, Aleksandra E. Bogucka, Natalia Musial, Dmitry Tretiakow, Andrzej Skorek, Dominik Stodulski
Summary: The study aimed to explore protein components of human submandibular gland sialoliths matrix. Qualitative analysis was carried out using FASP methodology. By analyzing fragmentation spectra and using PEAKS Studio program, 254 human proteins and 393 bacterial proteins were identified in the sialolith extracts. The SWATH methodology was successfully applied for relative quantitative analysis of human proteins in deposits, providing a basis for further research.
Review
Biochemistry & Molecular Biology
Miguel Angel Galvan-Morales
Summary: Proteomics in respiratory allergic diseases offers a wide range of techniques and programs for diagnosis, treatment, and immunotherapy. The main focus is on blocking cell diapedesis, modifying and blocking paratopes and epitopes, and inhibiting FceRI high-affinity receptors to prevent IgE binding. However, there is still a need for identifying allergens and cross-reactions through structural and epitope identification. The use of proteomics remains crucial for diagnostics and controlled immunotherapy systems. It is proposed to utilize this vision for treatment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Ophthalmology
Maite Lopez-Lopez, Uxia Regueiro, Susana B. Bravo, Maria del Pilar Chantada-Vazquez, Ruben Varela-Fernandez, Paulo Avila-Gomez, Pablo Hervella, Isabel Lema
Summary: Utilizing SWATH-MS for tear protein quantification, dysregulated proteins involved in iron homeostasis, inflammatory-immune response, oxidative stress, and other biological processes were identified in patients with keratoconus. The study sheds light on the molecular mechanisms underlying the disease and highlights the potential therapeutic targets related to iron accumulation and tissue damage in keratoconus pathophysiology.
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2021)
Article
Environmental Sciences
Tiago Simoes, Sara C. Novais, Tiago Natal-da-Luz, Bart Devreese, Tjalf de Boer, Dick Roelofs, Jose P. Sousa, Nico M. van Straalen, Marco F. L. Lemos
ENVIRONMENTAL POLLUTION
(2019)
Article
Microbiology
Andrea M. Sass, Stijn De Waele, Simon Daled, Bart Devreese, Dieter Deforce, Filip Van Nieuwerburgh, Tom Coenye
Article
Biotechnology & Applied Microbiology
Sofie Lodens, Sophie L. K. W. Roelants, Katarzyna Ciesielska, Robin Geys, Evelien Derynck, Karolien Maes, Filip Pattyn, Lisa Van Renterghem, Leopold Mottet, Sven Dierickx, Lynn Vanhaecke, Bart Devreese, Sofie L. De Maeseneire, Wim Soetaert
BIOTECHNOLOGY AND BIOENGINEERING
(2020)
Review
Microbiology
Jolien Vitse, Bart Devreese
FRONTIERS IN MICROBIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Benoit Deflandre, Noemie Thiebaut, Soren Planckaert, Samuel Jourdan, Sinaeda Anderssen, Marc Hanikenne, Bart Devreese, Isolde Francis, Sebastien Rigali
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2020)
Review
Entomology
Dirk C. de Graaf, Marcia Regina Brochetto Braga, Rusleyd Maria Magalhaes de Abreu, Simon Blank, Chris H. Bridts, Luc S. De Clerck, Bart Devreese, Didier G. Ebo, Timothy J. Ferris, Margo M. Hagendorens, Debora Lais Justo Jacomini, Iliya Kanchev, Zenon J. Kokot, Jan Matysiak, Christel Mertens, Vito Sabato, Athina L. Van Gasse, Matthias Van Vaerenbergh
Summary: Honey bees possess a sting used to inject venom, sparking interest in its potential therapeutic and allergenic properties. This paper provides insight into standardized methods for researching honey bee venom, covering collection techniques, biological activity determination, and application in biomedical research.
JOURNAL OF APICULTURAL RESEARCH
(2021)
Article
Environmental Sciences
Hugo R. Monteiro, Joao L. T. Pestana, Amadeu M. V. M. Soares, Bart Devreese, Marco F. L. Lemos
Article
Microbiology
Soren Planckaert, Benoit Deflandre, Anne-Mare De Vries, Maarten Ameye, Jose C. Martins, Kris Audenaert, Sebastien Rigali, Bart Devreese
Summary: The discovery of new rotihibin analogues in Streptomyces scabies, a major pathogen causing common scab disease, provides insights into their herbicidal activity and potential biotechnological production. Through genomic analysis, a cryptic biosynthetic gene cluster was identified, leading to a better understanding of the mechanism behind targeting the plant TORK pathway. The existence of other variants in plant-associated Streptomyces strains raises new questions about the function of this lipopeptide.
MICROBIOLOGY SPECTRUM
(2021)
Article
Genetics & Heredity
Benoit Deflandre, Nudzejma Stulanovic, Soren Planckaert, Sinaeda Anderssen, Beatrice Bonometti, Latifa Karim, Wouter Coppieters, Bart Devreese, Sebastien Rigali
Summary: In this study, it was found that cello-oligosaccharides can induce the production of various toxins, siderophores, and antibiotics in pathogenic Streptomyces scabiei, while reducing the production of spore germination inhibitors. Additionally, several cryptic biosynthetic gene clusters were discovered to be activated by cello-oligosaccharides, suggesting the presence of undiscovered metabolites that may contribute to the pathogenicity of S. scabiei.
MICROBIAL GENOMICS
(2022)
Review
Microbiology
Ronnie G. Willaert, Yeseren Kayacan, Bart Devreese
Summary: This article discusses the adhesion of fungal pathogens to host tissue cells or abiotic surfaces during infections, with a focus on the roles of the Flo adhesin family. The authors reviewed the domain architectures, functions, and classifications of Flo adhesins, as well as detailed discussions on the structure, function, and adhesion mechanisms of those with solved structures. They also identified yeasts expressing Flo adhesins from the Pfam database and discussed their adhesion characteristics and involvement in infections.
Article
Multidisciplinary Sciences
Ganna Saelens, Soren Planckaert, Victoria Martinez-Sernandez, Florencio M. Ubeira, Bart Devreese, Sarah Gabriel
Summary: This study investigated the presence of Anisakis-like allergens in both crushed and excretory/secretory (E/S) protein extract of P. decipiens. The results confirmed the existence of at least five A. simplex allergens in P. decipiens, highlighting the importance of including E/S protein extracts in proteomic studies. This suggests that P. decipiens could also be a potential source of allergens causing hypersensitivity reactions in humans.
SCIENTIFIC REPORTS
(2022)
Article
Microbiology
Benoit Deflandre, Cedric Jadot, Soren Planckaert, Noemie Thiebaut, Nudzejma Stulanovic, Raphael Herman, Bart Devreese, Frederic Kerff, Sebastien Rigali
Summary: Plant decaying biomass is a rich carbon source for soil microorganisms, and they possess hydrolytic enzymes to utilize polysaccharides, oligosaccharides, and monosaccharides. This study reveals the existence of an enzyme, BcpE2, that can retrieve glucose from various plant-derived substrates. This enzyme provides microorganisms with a versatile tool to scavenge nutrients from any type of plant material.
Article
Microbiology
Forough Nazar Pour, Bruna Pedrosa, Micaela Oliveira, Catia Fidalgo, Bart Devreese, Gonzalez Van Driessche, Carina Felix, Nuno Rosa, Artur Alves, Ana Sofia Duarte, Ana Cristina Esteves
Summary: This study investigated the pathogen-host interactions between Neofusicoccum parvum and Eucalyptus, revealing that under host mimicry conditions, N. parvum produced a large number of proteins involved in plant cell wall degradation, adhesion, penetration, pathogenesis, and oxidative stress, further elucidating the pathogen's infection strategy and lifestyle.
Article
Chemistry, Applied
Ganna Saelens, Soren Planckaert, Bart Devreese, Sarah Gabriel
Summary: This study conducted a controlled feeding trial using Anisakidae-contaminated feed on chickens and found that peptides from Anisakis simplex allergens can be transferred from the feed to the chicken meat and blood. If future experiments confirm the allergenic potency of these peptides in humans, it would expand the risk of Anisakis and Pseudoterranova infections beyond fishborne food.
JOURNAL OF FOOD COMPOSITION AND ANALYSIS
(2023)
Article
Biotechnology & Applied Microbiology
Vjera Radonicic, Charlotte Yvanoff, Maria Ines Villalba, Bart Devreese, Sandor Kasas, Ronnie G. Willaert
Summary: Candida albicans is an emerging multidrug-resistant opportunistic pathogen that causes invasive disease in humans, resulting in high healthcare costs worldwide. A microfluidic chip incorporating microwells and optical nanomotion detection (ONMD) was developed for rapid antifungal susceptibility testing (AFST). The chip allows for rapid exchange of growth medium and antifungals, enabling single-cell ONMD measurements before and after treatment. This simple and label-free technique can potentially be used as a routine AFST device in hospitals globally.
FERMENTATION-BASEL
(2023)
