Analyzing domain features of small proteins using a machine ‐learning method
In this study, the InterPro tool and the maximum correlation method were utilized to analyze functional domains of SPs. The purpose was to identify important functional domains that can indicate the essential differences between small and large protein sequences. First, the small and large proteins were represented by their functional domains via a one-hot scheme. Then, the MaxRel method was adopted to evaluate the relationships between each domain and the target variable, indicating small or large protein. The top 36 domain features were selected for further investigation. Among them, 14 were deemed to be highly related t...
Source: Proteomics - January 23, 2024 Category: Biochemistry Authors: ShiJian Ding,
HuiPing Liao,
FeiMing Huang,
Lei Chen,
Wei Guo,
KaiYan Feng,
Tao Huang,
Yu ‐Dong Cai Tags: RESEARCH ARTICLE Source Type: research
Mycobacterium abscessus extracellular vesicles increase mycobacterial resistance to clarithromycin in vitro
In this study, we characterized the extracellular vesicles (EVs) released by drug-sensitiveM. abscessus untreated or treated with clarithromycin (CLR), one of the frontline anti-NTM drugs. Our data show that exposure to CLR increases mycobacterial protein trafficking into EVs as well as the secretion of EVs in culture. Additionally, EVs released by CLR-treatedM. abscessus increaseM. abscessus resistance to CLR when compared to EVs from untreatedM. abscessus. Proteomic analysis further indicates that EVs released by CLR-treatedM. abscessus carry an increased level of 50S ribosomal subunits, the target of CLR. Taken together...
Source: Proteomics - January 19, 2024 Category: Biochemistry Authors: Charlie A. Vermeire,
Xuejuan Tan,
Yurong Liang,
Stephen K. Kotey,
Janet Rogers,
Steven D. Hartson,
Lin Liu,
Yong Cheng 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 - January 16, 2024 Category: Biochemistry Tags: FRONT COVER Source Type: research
Contents: Proteomics 24 –1'2
(Source: Proteomics)
Source: Proteomics - January 16, 2024 Category: Biochemistry Tags: CONTENTS Source Type: research
Editorial Board: Proteomics 24 –1'2
(Source: Proteomics)
Source: Proteomics - January 16, 2024 Category: Biochemistry Tags: EDITORIAL BOARD Source Type: research
Standard abbreviations
(Source: Proteomics)
Source: Proteomics - January 16, 2024 Category: Biochemistry Tags: STANDARD ABBREVIATIONS Source Type: research
Secretome processing for proteomics: A methods comparison
In this study, we evaluated six secretome sample processing workflows coupled to single-shot mass spectrometry: (1) Protein concentration by ultrafiltration with a molecular weight cut-off (MWCO) filter and sample preparation through in-gel digestion (IGD); (2) Acetone protein precipitation coupled to IGD; (3) MWCO filter-based protein concentration followed by to in-solution digestion (ISD); (4) Acetone protein precipitation coupled to ISD; (5) Direct ISD; (6) Secretome lyophilization and ISD. To this end, we assessed workflow triplicates in terms of total number of protein identifications, unique identifications, reprodu...
Source: Proteomics - January 15, 2024 Category: Biochemistry Authors: Catarina Almeida ‐Marques,
Frank Rolfs,
Sander R. Piersma,
Irene V. Bijnsdorp,
Thang V. Pham,
Jaco C. Knol,
Connie R. Jimenez Tags: TECHNICAL BRIEF Source Type: research
HB ‐EGF‐loaded nanovesicles enhance trophectodermal spheroid attachment and invasion
AbstractThe ability of trophectodermal cells (outer layer of the embryo) to attach to the endometrial cells and subsequently invade the underlying matrix are critical stages of embryo implantation during successful pregnancy establishment. Extracellular vesicles (EVs) have been implicated in embryo-maternal crosstalk, capable of reprogramming endometrial cells towards a pro-implantation signature and phenotype. However, challenges associated with EV yield and direct loading of biomolecules limit their therapeutic potential. We have previously established generation of cell-derived nanovesicles (NVs) from human trophectoder...
Source: Proteomics - January 13, 2024 Category: Biochemistry Authors: Qi Hui Poh,
Alin Rai,
Jonathon Cross,
David W. Greening Tags: RESEARCH ARTICLE Source Type: research
Proteomics of urinary small extracellular vesicles in early diagnosis of kidney diseases in children ‐expectations and limitations
AbstractThe primary function of the kidneys is to maintain systemic homeostasis (disruption of renal structure and function results in multilevel impairment of body function). Kidney diseases are characterized by a chronic, progressive course and may result in the development of chronic kidney disease (CKD). Evaluation of the composition of the proteome of urinary small extracellular vesicles (sEVs) as a so-called liquid biopsy is a promising new research direction. Knowing the composition of sEV could allow localization of cellular changes in specific sections of the nephron or the interstitial tissue before fixed changes...
Source: Proteomics - January 12, 2024 Category: Biochemistry Authors: Klaudia Korecka,
Marta Gawin,
Agnieszka Pastuszka,
Miros ław Partyka,
Tomasz Koszutski,
Monika Pietrowska,
Lidia Hyla‐Klekot Tags: REVIEW Source Type: research
