Proteomic profiling of antibiotic ‐resistant Escherichia coli GW‐AmxH19 isolated from hospital wastewater treated with physical plasma
AbstractMicroorganisms which are resistant to antibiotics are a global threat to the health of humans and animals. Wastewater treatment plants are known hotspots for the dissemination of antibiotic resistances. Therefore, novel methods for the inactivation of pathogens, and in particular antibiotic-resistant microorganisms (ARM), are of increasing interest. An especially promising method could be a water treatment by physical plasma which provides charged particles, electric fields, UV-radiation, and reactive species. The latter are foremost responsible for the antimicrobial properties of plasma. Thus, with plasma it might...
Source: Proteomics - April 22, 2024 Category: Biochemistry Authors: Veronika Hahn,
Daniela Z ühlke,
Hauke Winter,
Annchristin Landskron,
Jörg Bernhardt,
Susanne Sievers,
Michael Schmidt,
Thomas von Woedtke,
Katharina Riedel,
Juergen F. Kolb Tags: RESEARCH ARTICLE Source Type: research
The tumour ‐derived extracellular vesicle proteome varies by endometrial cancer histology and is confounded by an obesogenic environment
AbstractEndometrial cancer, the most common gynaecological cancer worldwide, is closely linked to obesity and metabolic diseases, particularly in younger women. New circulating biomarkers have the potential to improve diagnosis and treatment selections, which could significantly improve outcomes. Our approach focuses on extracellular vesicle (EV) biomarker discovery by directly profiling the proteome of EVs enriched from frozen biobanked endometrial tumours. We analysed nine tissue samples to compare three clinical subgroups —low BMI (Body Mass Index) Endometrioid, high BMI Endometrioid, and Serous (any BMI)—identifyin...
Source: Proteomics - April 22, 2024 Category: Biochemistry Authors: Anastasiia Artuyants,
George Guo,
Marcella Flinterman,
Martin Middleditch,
Bincy Jacob,
Kate Lee,
Laura Vella,
Huaqi Su,
Michelle Wilson,
Lois Eva,
Andrew N. Shelling,
Cherie Blenkiron Tags: RESEARCH ARTICLE Source Type: research
Review of predicting protein stability changes upon variations
AbstractForecasting alterations in protein stability caused by variations holds immense importance. Improving the thermal stability of proteins is important for biomedical and industrial applications. This review discusses the latest methods for predicting the effects of mutations on protein stability, databases containing protein mutations and thermodynamic parameters, and experimental techniques for efficiently assessing protein stability in high-throughput settings. Various publicly available databases for protein stability prediction are introduced. Furthermore, state-of-the-art computational approaches for anticipatin...
Source: Proteomics - April 21, 2024 Category: Biochemistry Authors: Yiling Qiu,
Tao Huang,
Yu ‐Dong Cai Tags: REVIEW Source Type: research
Model fusion for predicting unconventional proteins secreted by exosomes using deep learning
In this study, we propose a novel approach to predict UPSEs by combining multiple deep learning models that incorporate both protein sequences and evolutionary information. Our approach utilizes a convolutional neural network (CNN) to extract protein sequence information, while various densely connected neural networks (DNNs) are employed to capture evolutionary conservation patterns.By combining six distinct deep learning models, we have created a superior framework that surpasses previous approaches, achieving an ACC score of 77.46% and an MCC score of 0.5406 on an independent test dataset. (Source: Proteomics)
Source: Proteomics - April 21, 2024 Category: Biochemistry Authors: Yonglin Zhang,
Lezheng Yu,
Ming Yang,
Bin Han,
Jiesi Luo,
Runyu Jing Tags: RESEARCH ARTICLE Source Type: research
Front Cover
Cover Image © Wiley-VCH GmbH. The image is part of a figure in the article DOI:10.1002/pmic.201900203 by Lei Li, Yong Jiang et al. (Source: Proteomics)
Source: Proteomics - April 17, 2024 Category: Biochemistry Tags: FRONT COVER Source Type: research
Contents: Proteomics 8'24
(Source: Proteomics)
Source: Proteomics - April 17, 2024 Category: Biochemistry Tags: CONTENTS Source Type: research
Editorial Board: Proteomics 8'24
(Source: Proteomics)
Source: Proteomics - April 17, 2024 Category: Biochemistry Tags: EDITORIAL BOARD Source Type: research
Standard abbreviations
(Source: Proteomics)
Source: Proteomics - April 17, 2024 Category: Biochemistry Tags: STANDARD ABBREVIATIONS Source Type: research
From data to discovery: The essential role of computational tools in proteomics
(Source: Proteomics)
Source: Proteomics - April 17, 2024 Category: Biochemistry Authors: Wout Bittremieux Tags: GUEST EDITORIAL Source Type: research
Intensity and retention time prediction improves the rescoring of protein ‐nucleic acid cross‐links
AbstractIn protein-RNA cross-linking mass spectrometry, UV or chemical cross-linking introduces stable bonds between amino acids and nucleic acids in protein-RNA complexes that are then analyzed and detected in mass spectra. This analytical tool delivers valuable information about RNA-protein interactions and RNA docking sites in proteins, both in vitro and in vivo. The identification of cross-linked peptides with oligonucleotides of different length leads to a combinatorial increase in search space. We demonstrate that the peptide retention time prediction tasks can be transferred to the task of cross-linked peptide reten...
Source: Proteomics - April 17, 2024 Category: Biochemistry Authors: Arslan Siraj,
Robbin Bouwmeester,
Arthur Declercq,
Luisa Welp,
Aleksandar Chernev,
Alexander Wulf,
Henning Urlaub,
Lennart Martens,
Sven Degroeve,
Oliver Kohlbacher,
Timo Sachsenberg Tags: RESEARCH ARTICLE Source Type: research
DREAMweb: An online tool for graph ‐based modeling of NMR protein structure
AbstractThe value of accurate protein structural models closely conforming to the experimental data is indisputable. DREAMweb deploys an improved DREAM algorithm, DREAMv2, that incorporates a tighter bound in the constraint set of the underlying optimization approach. This reduces the artifacts while modeling the protein structure by solving the distance-geometry problem. DREAMv2 follows a bottom-up strategy of building smaller substructures for regions with a larger concentration of experimental bounds and consolidating them before modeling the rest of the protein structure. This improves secondary structure conformance i...
Source: Proteomics - April 17, 2024 Category: Biochemistry Authors: Niladri Ranajan Das,
Kunal Narayan Chaudhury,
Debnath Pal Tags: TECHNICAL BRIEF Source Type: research
Characterization of a chromatin ‐associated TCF7L1 complex in human embryonic stem cells
AbstractHuman embryonic stem cells (hESCs) resemble the pluripotent epiblast cells found in the early postimplantation human embryo and represent the “primed” state of pluripotency. One factor that helps primed pluripotent cells retain pluripotency and prepare genes for differentiation is the transcription factor TCF7L1, a member of a small family of proteins known as T cell factors/Lymphoid enhancer factors (TCF/LEF) that act as downstream c omponents of the WNT signaling pathway. Transcriptional output of the WNT pathway is regulated, in part, by the activity of TCF/LEFs in conjunction with another component of the W...
Source: Proteomics - April 17, 2024 Category: Biochemistry Authors: Linh M. Vuong,
Songqin Pan,
Robert A. Sierra,
Marian L. Waterman,
Paul D. Gershon,
Peter J. Donovan Tags: DATASET BRIEF Source Type: research
Polyglutamine disease proteins: Commonalities and differences in interaction profiles and pathological effects
We present insights from AlphaFold-predicted structural models and discuss the biological roles of polyQ-containing proteins. Lastly, we explore reported protein –protein interaction networks to highlight shared protein interactions and their potential relevance in disease development. (Source: Proteomics)
Source: Proteomics - April 15, 2024 Category: Biochemistry Authors: Megan Bonsor,
Orchid Ammar,
Sigrid Schnoegl,
Erich E. Wanker,
Eduardo Silva Ramos Tags: REVIEW Source Type: research
Differential expression of N ‐glycopeptides derived from serum glycoproteins in mild cognitive impairment (MCI) patients
AbstractMild cognitive impairment (MCI) is an early stage of memory loss that affects cognitive abilities with the aging of individuals, such as language or visual/spatial comprehension. MCI is considered a prodromal phase of more complicated neurodegenerative diseases such as Alzheimer's. Therefore, accurate diagnosis and better understanding of the disease prognosis will facilitate prevention of neurodegeneration. However, the existing diagnostic methods fail to provide precise and well-timed diagnoses, and the pathophysiology of MCI is not fully understood. Alterations of the serumN-glycoproteome expression could repres...
Source: Proteomics - April 12, 2024 Category: Biochemistry Authors: Cristian D. Gutierrez Reyes,
Mojgan Atashi,
Mojibola Fowowe,
Sherifdeen Onigbinde,
Oluwatosin Daramola,
David M. Lubman,
Yehia Mechref Tags: RESEARCH ARTICLE Source Type: research
Imputation of missing values in lipidomic datasets
In this study, we investigate commonly used methods such as zero, half-minimum, mean, and median imputation, as well as more advanced techniques such as k-nearest neighbor and random forest imputation. We employ a combination of simulation-based approaches and application to real datasets to assess the performance and effectiveness of these methods. Shotgun lipidomics datasets exhibit high correlations and missing values, often due to low analyte abundance, characterized as MNAR. In this context, k-nearest neighbor approaches based on correlation and truncated normal distributions demonstrate best performance. Importantly,...
Source: Proteomics - April 11, 2024 Category: Biochemistry Authors: Nicolas Fr ölich,
Christian Klose,
Elisabeth Widén,
Samuli Ripatti,
Mathias J. Gerl Tags: RESEARCH ARTICLE Source Type: research
