Article
Plant Sciences
Patrick Willems, Elvis Ndah, Veronique Jonckheere, Frank Van Breusegem, Petra Van Damme
Summary: Alternative translation initiation can shape multiple protein forms from a single gene. This study provides evidence for the existence of ~90 N-terminal proteoform pairs shaped by alternative translation initiation in Arabidopsis thaliana. The study also suggests that alternative translation initiation may serve as a common mechanism to supply protein copies in multiple cellular compartments.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Radiology, Nuclear Medicine & Medical Imaging
Michael Lell, Marc Kachelriess
Summary: Computed tomography (CT) has greatly improved the capabilities of diagnostic and interventional radiology. It has evolved over the years, achieving significant advancements in scan speed, resolution, and dose reduction. Cardiac imaging requires high temporal and spatial resolution, while the transition of photon-counting detectors and the use of artificial intelligence have further enhanced CT technology. This article provides an overview of the technical specifications and future innovations of whole-body and dedicated CT systems.
INVESTIGATIVE RADIOLOGY
(2023)
Article
Multidisciplinary Sciences
Sigri Bakken Sperstad, Julie Caroline Saether, Marie Klevjer, Guro Fannelob Giskeodegard, Tone Frost Bathen, Ragnhild Rosbjorgen, Havard Dalen, Anja Bye
Summary: The study found that lipoprotein subfractions are closely associated with the risk of MI, especially in males. However, after adjusting for multiple testing, none of the lipoprotein subfractions were significantly associated with future MI.
Review
Biochemistry & Molecular Biology
Dmitry E. Andreev, Viktoriya V. Smirnova, Ivan N. Shatsky
Summary: Ribosome profiling, based on sequencing of ribosome-protected mRNA fragments, allows for accurate identification of translated reading frames and tracking of gene expression changes in response to stimuli. While classical ribosomal profiling has limitations, recent modifications enable analysis of elongating, scanning, and reinitiating ribosomes, as well as the discovery of new cotranslational assembly processes and isolation of ribosomal complexes associated with specific protein factors, providing a deeper understanding of translation regulation mechanisms and the roles of translational apparatus components.
BIOCHEMISTRY-MOSCOW
(2021)
Article
Biotechnology & Applied Microbiology
Shabbir Ahmad, Mujahid Mohammed, Lakshmi Prasuna Mekala, Rai Anusha, Chintalapati Sasikala, Chintalapati Venkata Ramana
Summary: Anoxygenic photosynthetic bacteria have metabolic versatility and can survive with a wide range of carbon and nitrogen sources. Rubrivivax benzoatilyticus JA2, a member of this group, can utilize L-tryptophan as a nitrogen source and produce indolic compounds with biotechnological significance. Studying the chemotrophic L-tryptophan metabolism of strain JA2 provides new insights into its metabolic potential.
WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY
(2023)
Article
Statistics & Probability
Zubair Ahmad, Eisa Mahmoudi, Rasool Roozegarz, G. G. Hamedani, Nadeem Shafique Butt
Summary: In recent years, statistical models have been widely used in applied areas for analyzing real data sets. However, traditional distributions are often not flexible enough to capture various aspects of real phenomena. To address this issue, this article investigates methods to generalize existing distributions and proposes nineteen new methods to extend classical distributions for modeling data in different fields. Comparative studies on three real data sets from reliability engineering, medical and financial sciences showcase the performance of the proposed methods and other well-known models.
PAKISTAN JOURNAL OF STATISTICS AND OPERATION RESEARCH
(2022)
Article
Public, Environmental & Occupational Health
Andreas Soehnel, Roland Frankenberger, Lars Kandsperger, Frank Wissing
Summary: The National Competence-Based Catalogue of Learning Objectives in Dentistry (NKLZ) is a crucial document for dental training in Germany, providing standardized objectives and ensuring quality and comparability. This article describes the background, history, structure, and development of NKLZ, emphasizing its importance in preparing future dentists for their profession.
BUNDESGESUNDHEITSBLATT-GESUNDHEITSFORSCHUNG-GESUNDHEITSSCHUTZ
(2023)
Article
Computer Science, Software Engineering
Fernando Renee Gonzalez Moraga, Stephanie Klein Tuente, Sean Perrin, Pia Enebrink, Kristina Sygel, Wim Veling, Marta Wallinius
Summary: Aggression is a known problem in forensic settings, and virtual reality has shown promise as an intervention for this issue. Virtual Reality Aggression Prevention Training (VRAPT) is a new psychological treatment that provides individuals with realistic and safe environments to practice managing aggression. By increasing awareness and control over aggression through social interactions in virtual environments, VRAPT aims to improve aggression management. Further research and development are needed to expand the scientific evidence for VR-assisted treatment of aggression in forensic settings.
FRONTIERS IN VIRTUAL REALITY
(2022)
Article
Cell Biology
Johannes Krumm, Keisuke Sekine, Patroklos Samaras, Agnieska Brazovskaja, Markus Breunig, Ryota Yasui, Alexander Kleger, Hideki Taniguchi, Mathias Wilhelm, Barbara Treutlein, J. Gray Camp, Bernhard Kuster
Summary: This study utilizes quantitative proteomics to follow the molecular processes of induced pluripotent stem cell differentiation into hepatocytes, revealing stage-specific markers and important molecular switches in hepatocyte development. The findings provide valuable resources for future research.
Correction
Biochemistry & Molecular Biology
Severin Lechner, Martin Ian P. Malgapo, Christian Graetz, Raphael R. Steimbach, Agnes Baron, Patrick Ruether, Simon Nadal, Carmen Stumpf, Christina Loos, Xin Ku, Polina Prokofeva, Ludwig Lautenbacher, Tino Heimburg, Vivian Wuerf, Chen Meng, Mathias Wilhelm, Wolfgang Sippl, Karin Kleigrewe, Josch K. Pauling, Karl Kramer, Aubry K. Miller, Michael W. Pfaffl, Maurine E. Linder, Bernhard Kuster, Guillaume Medard
NATURE CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Sergi Rodriguez-Calado, Petra Van Damme, Francesc Xavier Aviles, Ana Paula Candiota, Sebastian Tanco, Julia Lorenzo
Summary: The cellular role of CCP6 was assessed using BioID, and 37 putative interactors of CCP6 were identified. CCP6 was found to be present in the pericentriolar material and involved in centrosome and centriole functions, as well as in the formation and maintenance of primary cilia. The CCP6 proximal partner list also included proteins associated with cilium assembly and Joubert syndrome.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Petra Van Damme, Camilla Osberg, Veronique Jonckheere, Nina Glomnes, Kris Gevaert, Thomas Arnesen, Henriette Aksnes
Summary: N-terminal acetylation of proteins is a conserved modification in eukaryotes, and the yeast Saccharomyces cerevisiae is a valuable model for studying this process. The bulk of N-terminal acetylation in S. cerevisiae is catalyzed by NatA, NatB, and NatC. In this study, the authors identified 57 yeast NatC substrates using a combination of techniques. They also uncovered some non-NatC NAT activity, suggesting redundancy between NatC and NatE/Naa50. Furthermore, the authors demonstrated the evolutionary conservation of NatC from yeast to humans and its potential implications for studying pathogenic variants. Overall, this work provides valuable insights into NatC-mediated N-terminal acetylation.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Lore Gryffroy, Evi Ceulemans, Nicolas Manosalva Perez, Jhon Venegas-Molina, Ana Cristina Jaramillo-Madrid, Savio D. Rodrigues, Liesbeth De Milde, Veronique Jonckheere, Marc Van Montagu, Barbara De Coninck, Klaas Vandepoele, Petra Van Damme, Alain Goossens
Summary: Rhizogenic Agrobacterium strains are biotrophic pathogens that infect hydroponically grown Solanaceae and Cucurbitaceae crops, causing hairy root disease (HRD). They are also widely used for hairy root cultures to produce specialized plant metabolites. The development of hairy roots is regulated by genes encoded on the T-DNA of the root-inducing (Ri) plasmid, including the important rolB gene. In this study, through proximity labeling in tomato hairy roots, the repressor proteins TOPLESS (TPL) and Novel Interactor of JAZ (NINJA) were identified as direct interactors of RolB. The interactions between RolB, TPL, and NINJA were found to play a role in the transcriptional regulation and reprogramming of phytohormone signaling, immunity, growth, and developmental processes in the host plants.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
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
Benjamin A. Neely, Viktoria Dorfer, Lennart Martens, Isabell Bludau, Robbin Bouwmeester, Sven Degroeve, Eric W. Deutsch, Siegfried Gessulat, Lukas Kaell, Pawel Palczynski, Samuel H. Payne, Tobias Greisager Rehfeldt, Tobias Schmidt, Veit Schwaemmle, Julian Uszkoreit, Juan Antonio Vizcaino, Mathias Wilhelm, Magnus Palmblad
Summary: In recent years, machine learning has made significant progress in modeling mass spectrometry data for proteomics analysis. A workshop was conducted to evaluate and explore machine learning applications in multidimensional mass spectrometry-based proteomics analysis. The workshop helped identify knowledge gaps, define needs, and discuss the possibilities, challenges, and future opportunities. The summary of the discussions conveys excitement about the potential of machine learning in proteomics and aims to inspire future research.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Multidisciplinary Sciences
Jana Zecha, Florian P. Bayer, Svenja Wiechmann, Julia Woortman, Nicola Berner, Julian Mueller, Annika Schneider, Karl Kramer, Mar Abril-Gil, Thomas Hopf, Leonie Reichart, Lin Chen, Fynn M. Hansen, Severin Lechner, Patroklos Samaras, Stephan Eckert, Ludwig Lautenbacher, Maria Reinecke, Firas Hamood, Polina Prokofeva, Larsen Vornholz, Chiara Falcomata, Madeleine Dorsch, Ayla Schroeder, Anton Venhuizen, Stephanie Wilhelm, Guillaume Medard, Gabriele Stoehr, Juergen Ruland, Barbara M. Gruener, Dieter Saur, Maike Buchner, Benjamin Ruprecht, Hannes Hahne, Matthew The, Mathias Wilhelm, Bernhard Kuster
Summary: A proteomic assay called decryptM is introduced to quantify drug-regulated posttranslational modifications (PTMs) for thousands of PTMs in cells, providing insights into target engagement and drug mechanisms. The approach is shown to be applicable across 31 cancer drugs and 13 cell lines. The resulting 1.8 million dose-response curves are provided as an interactive molecular resource in ProteomicsDB, expanding the utility of the research.
Review
Plant Sciences
Naomi Stuer, Petra Van Damme, Sofie Goormachtig, Judith Van Dingenen
Summary: Both pathogenic and symbiotic microorganisms can manipulate the immune response and physiology of their host by releasing effector proteins. Recent studies challenge the conventional notion that effectors are secreted proteins translocated by primary amino acid sequence motifs, and propose unconventional secretion and effector structures. Additionally, advanced proteomics approaches offer potential for the comprehensive characterization of fungal and oomycete effectomes.
TRENDS IN PLANT SCIENCE
(2023)
Review
Microbiology
Joren De Ryck, Petra Van Damme, Sofie Goormachtig
Summary: The type III secretion system (T3SS) is a well-studied pathogenicity determinant used by bacteria to translocate effectors (T3Es) into host cells for immune evasion and niche establishment. This article explores different approaches to functionally characterize T3Es, including host localization studies, virulence screenings, biochemical activity assays, and large-scale omics studies. Using Ralstonia solanacearum species complex (RSSC) as a case study, the advances in these methods and understanding of effector biology are discussed. Complementary data obtained from these methods offer crucial insights into the entire function of effectors and contribute to a better understanding of phytopathogens, presenting opportunities for tackling them.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Liping Liu, Jakob Trendel, Guojing Jiang, Yanhui Liu, Astrid Bruckmann, Bernhard Kuester, Stefanie Sprunck, Thomas Dresselhaus, Andrea Bleckmann
Summary: RNA binding proteins play multiple and essential roles in the regulation of gene expression in all living organisms. However, little is known about their function in reproductive processes in plants. Through RNA interactome capture experiments, 728 proteins associated with poly(A(+))-RNA were identified in the egg cells of Arabidopsis. These findings provide a valuable resource to study the function of RBPs in egg cell development, fertilization, and early embryogenesis.
BIOLOGICAL CHEMISTRY
(2023)
Article
Microbiology
Ursula Fels, Patrick Willems, Margaux De Meyer, Kris Gevaert, Petra Van Damme
Summary: By applying dual proteome profiling, this study obtained a detailed and holistic proteomic perspective on host-pathogen interactions during Salmonella infection. Data-independent acquisition (DIA) proteomics outperformed data-dependent acquisition (DDA) in identifying the downregulated bacterial proteome response during early stages of infection. This study revealed specific proteomic signatures and interdependent host/pathogen responses, as well as potential novel infection markers and signaling responses.
Article
Mathematical & Computational Biology
Klaudia Adamowicz, Lis Arend, Andreas Maier, Johannes R. Schmidt, Bernhard Kuster, Olga Tsoy, Olga Zolotareva, Jan Baumbach, Tanja Laske
Summary: Proteomics technologies are important for biomarker identification and disease mechanism research. However, leveraging publicly available proteomics data for these purposes is challenging due to the heterogeneity of data generated by different research groups using different organisms and assay systems. To address this issue, researchers have developed ProHarMeD, a tool that harmonizes and compares proteomics data from multiple studies and extracts disease mechanisms and drug repurposing candidates.
NPJ SYSTEMS BIOLOGY AND APPLICATIONS
(2023)
Article
Genetics & Heredity
Jim Clauwaert, Zahra McVey, Ramneek Gupta, Gerben Menschaert
Summary: The correct mapping of the proteome is crucial for understanding biological systems and advancing drug discovery and disease understanding. In this study, we propose TIS Transformer, a deep learning model that accurately determines translation start sites using only sequence information. Our method outperforms previous approaches and can detect key features of the translation process and multiple coding sequences on a transcript, including micropeptides encoded by short Open Reading Frames. We demonstrated the application of our method by remapping the full human proteome.
NAR GENOMICS AND BIOINFORMATICS
(2023)
Review
Microbiology
Laure Simoens, Igor Fijalkowski, Petra Van Damme
Summary: The development of genomic techniques has expanded our understanding of the diversity and richness of prokaryotic genomes. Recent studies have revealed the existence of small open reading frames (sORFs) encoding small proteins in bacterial genomes and highlighted their important biological roles. However, there are still many challenges to fully understand these small proteins.
FEMS MICROBIOLOGY REVIEWS
(2023)