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
Functional proteomics reveals that Slr0237 is a SigE ‐regulated glycogen debranching enzyme pivotal for glycogen breakdown
AbstractThe group 2 σ factor for RNA polymerase SigE plays important role in regulating central carbon metabolism in cyanobacteria. However, the regulation of SigE for these pathways at a proteome level remains unknown. Using asigE-deficient strain ( ΔsigE) ofSynechocystis sp. PCC 6803 and quantitative proteomics, we found that SigE depletion induces differential protein expression for sugar catabolic pathways including glycolysis, oxidative pentose phosphate (OPP) pathway, and glycogen catabolism. Two glycogen debranching enzyme homologues Slr1857 and Slr0237 are found differentially expressed in ΔsigE. Glycogen determ...
Source: Proteomics - April 6, 2024 Category: Biochemistry Authors: Ye Liu,
Haitao Ge,
Dandan Lu 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 4, 2024 Category: Biochemistry Tags: FRONT COVER Source Type: research
Contents: Proteomics 7'24
(Source: Proteomics)
Source: Proteomics - April 4, 2024 Category: Biochemistry Tags: CONTENTS Source Type: research
Editorial Board: Proteomics 7'24
(Source: Proteomics)
Source: Proteomics - April 4, 2024 Category: Biochemistry Tags: EDITORIAL BOARD Source Type: research
Proteomic profiling of small extracellular vesicles derived from mouse pancreatic cancer and stellate cells: Role in pancreatic cancer
AbstractSmall extracellular vesicles (sEVs) are cell-derived vesicles evolving as important elements involved in all stages of cancers. sEVs bear unique protein signatures that may serve as biomarkers. Pancreatic cancer (PC) records a very poor survival rate owing to its late diagnosis and several cancer cell-derived proteins have been reported as candidate biomarkers. However, given the pivotal role played by stellate cells (PSCs, which produce the collagenous stroma in PC), it is essential to also assess PSC-sEV cargo in biomarker discovery. Thus, this study aimed to isolate and characterise sEVs from mouse PC cells and ...
Source: Proteomics - April 4, 2024 Category: Biochemistry Authors: Chamini J. Perera,
SM Zahid Hosen,
Tanzila Khan,
Haoyun Fang,
Alpha Raj Mekapogu,
Zhihong Xu,
Marco Falasca,
Suresh T. Chari,
Jeremy S. Wilson,
Ron Pirola,
David W. Greening,
Minoti V. Apte Tags: RESEARCH ARTICLE Source Type: research
Differential effects of physiological agonists on the proteome of platelet ‐derived extracellular vesicles
This study provides new information on the influence of physiological agonist stimuli on the biogenesis and proteome landscape of pEVs. (Source: Proteomics)
Source: Proteomics - April 2, 2024 Category: Biochemistry Authors: Mitchell J. Moon,
Alin Rai,
Prerna Sharma,
Haoyun Fang,
James D. McFadyen,
David W. Greening,
Karlheinz Peter Tags: RESEARCH ARTICLE Source Type: research
Open ‐source large language models in action: A bioinformatics chatbot for PRIDE database
ABSTRACTWe here present a chatbot assistant infrastructure (https://www.ebi.ac.uk/pride/chatbot/) that simplifies user interactions with the PRIDE database's documentation and dataset search functionality. The framework utilizes multiple Large Language Models (LLM): llama2, chatglm, mixtral (mistral), and openhermes. It also includes a web service API (Application Programming Interface), web interface, and components for indexing and managing vector databases. An Elo-ranking system-based benchmark component is included in the framework as well, which allows for evaluating the performance of each LLM and for improving PRIDE...
Source: Proteomics - April 1, 2024 Category: Biochemistry Authors: Jingwen Bai,
Selvakumar Kamatchinathan,
Deepti J. Kundu,
Chakradhar Bandla,
Juan Antonio Vizca íno,
Yasset Perez‐Riverol Tags: TECHNICAL BRIEF Source Type: research
The temporal protein signature analyses of developing human deciduous molar tooth germ
AbstractThe tooth serves as an exemplary model for developmental studies, encompassing epithelial-mesenchymal transition and cell differentiation. The essential factors and pathways identified in tooth development will help understand the natural development process and the malformations of mineralized tissues such as skeleton. The time-dependent proteomic changes were investigated through the proteomics of healthy human molars during embryonic stages, ranging from the cap-to-early bell stage. A comprehensive analysis revealed 713 differentially expressed proteins (DEPs) exhibiting five distinct temporal expression pattern...
Source: Proteomics - March 25, 2024 Category: Biochemistry Authors: Xiaohang Chen,
Gaochi Li,
Jian Zhang,
Liang Hu,
Guoqiang Zhao,
Buling Wu,
Fengxiang Wei,
Fu Xiong Tags: RESEARCH ARTICLE Source Type: research
A review of disease risk prediction methods and applications in the omics era
AbstractRisk prediction and disease prevention are the innovative care challenges of the 21st century. Apart from freeing the individual from the pain of disease, it will lead to low medical costs for society. Until very recently, risk assessments have ushered in a new era with the emergence of omics technologies, including genomics, transcriptomics, epigenomics, proteomics, and so on, which potentially advance the ability of biomarkers to aid prediction models. While risk prediction has achieved great success, there are still some challenges and limitations. We reviewed the general process of omics-based disease risk mode...
Source: Proteomics - March 24, 2024 Category: Biochemistry Authors: Chen Sun,
Xiangshu Cheng,
Jing Xu,
Haiyan Chen,
Junxian Tao,
Yu Dong,
Siyu Wei,
Rui Chen,
Xin Meng,
Yingnan Ma,
Hongsheng Tian,
Xuying Guo,
Shuo Bi,
Chen Zhang,
Jingxuan Kang,
Mingming Zhang,
Hongchao Lv,
Zhenwei Shang,
Wenhua Lv,
Ruiji Tags: REVIEW Source Type: research
