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361
APMAT analysis reveals the association between CD8 T cell receptors, cognate antigen, and T cell phenotype and persistence
Published 2025-02-01“…Starting with 951 putative antigens representing a comprehensive survey of the SARS-CoV-2 viral proteome, we utilize APMAT for the capture and single cell analysis of CD8 T cells from 62 HLA A*02:01 COVID-19 participants. …”
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362
Bioelectric stimulation outperforms brain derived neurotrophic factor in promoting neuronal maturation
Published 2025-02-01“…ES with large enough accumulated charge significantly enriched EV proteome associated with neural development and function. …”
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363
Discovery of a novel highly specific, fully human PSCA antibody and its application as an antibody-drug conjugate in prostate cancer
Published 2024-12-01“…The structure-based affinity maturation yielded a high-affinity binder, F12, which is highly specific and does not bind to 6,000 human membrane proteins based on a membrane proteome array assay. F12 targets PSCA amino acids 63–69 as tested by the peptide scanning microarray, and it cross-reacts with the murine PSCA. …”
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364
Biochemical characterization of the Escherichia coli surfaceome: a focus on type I fimbriae and flagella
Published 2025-02-01“…While the exact identity of the glycan(s) and their site of attachment currently elude detection by conventional glycomics/glycoproteomics, the current findings highlight a potential additional layer of complexity of the surface (glyco) proteome of the commensal or adhesive and invasive E. coli strains studied.…”
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365
Kaempferol protects against high-salt-induced hypertension and vascular endothelial injury by inhibiting ferroptosis through the ATF4/ACSL4 pathway
Published 2025-02-01“…Surface plasmon resonance and molecular docking analyses revealed that Kae directly binds to ATF4, while proteome microarray and co-immunoprecipitation assays demonstrated that ATF4 interacts with ACSL4 in HAECs. …”
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366
Extracellular vesicles (EVs) in seminal plasma of buffalo bulls possess spermatozoa specific fertility associated proteins and enzymes
Published 2023-11-01“…Finally, LC-MS/MS-based high throughput proteome was performed to identify the differential abundance of protein cargo in seminal EVs of contrasting fertility bulls. …”
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367
Benchmarking the identification of a single degraded protein to explore optimal search strategies for ancient proteins
Published 2024-11-01“…We tested different reference database choices, a targeted dairy protein one, and the whole bovine proteome and the three digestion options (tryptic-, semi-tryptic- and non-specific searches), in order to evaluate the effects of search space and the identification of peptides. …”
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368
Longitudinal omics data and preclinical treatment suggest the proteasome inhibitor carfilzomib as therapy for ibrutinib-resistant CLL
Published 2025-01-01“…A comparative analysis of exome, transcriptome and proteome of sorted leukemic murine cells during treatment and after relapse suggests alterations in the proteasome activity as a driver of ibrutinib resistance. …”
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369
Mitochondrial dysfunction-driven AMPK-p53 axis activation underpins the anti-hepatocellular carcinoma effects of sulfane sulfur
Published 2025-01-01“…We utilized bioinformatics algorithms for clustering, function enrichment, feature screening and survival analysis on proteomic data from the Cancer Proteome Atlas (CPTAC) and transcriptomic data from the Cancer Genome Atlas (TCGA). …”
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370
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371
Lipoxin A4 yields an electrophilic 15-oxo metabolite that mediates FPR2 receptor-independent anti-inflammatory signaling
Published 2025-01-01“…Rather, if present in sufficient concentrations, LXA4 and other mono- and poly-hydroxylated unsaturated fatty acids synthesized by macrophages would be readily oxidized to electrophilic α,β-unsaturated ketone products that modulate the redox-sensitive cysteine proteome via G-protein coupled receptor-independent mechanisms.…”
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372
Wilson and Walker's Principles and Techniques of Biochemistry and Molecular Biology /
Published 2018Table of Contents: “…Biochemical and molecular biological methods in life sciences studies -- Basic principles -- Cell culture techniques -- Recombinant DNA techniques and molecular cloning -- Preparative protein biochemistry -- Electrophoretic techniques -- Immunochemical techniques -- Flow cytometry -- Radioisotope techniques -- Principles of clinical biochemistry -- Microscopy -- Centrifugation and ultracentrifugation -- Spectroscopic techniques -- Basic techniques probing molecular structure and interactions -- Mass spectrometric techniques -- Fundamentals of bioinformatics -- Fundamentals of chemoinformatics -- The python programming language -- Data analysis -- Fundamentals of genome sequencing and annotation -- Fundamentals of proteomics -- Fundamentals of metabolomics -- Enzymes and receptors -- Drug discovery and development.…”
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373
Wilson and Walker's Principles and Techniques of Biochemistry and Molecular Biology /
Published 2018Table of Contents: “…Biochemical and molecular biological methods in life sciences studies -- Basic principles -- Cell culture techniques -- Recombinant DNA techniques and molecular cloning -- Preparative protein biochemistry -- Electrophoretic techniques -- Immunochemical techniques -- Flow cytometry -- Radioisotope techniques -- Principles of clinical biochemistry -- Microscopy -- Centrifugation and ultracentrifugation -- Spectroscopic techniques -- Basic techniques probing molecular structure and interactions -- Mass spectrometric techniques -- Fundamentals of bioinformatics -- Fundamentals of chemoinformatics -- The python programming language -- Data analysis -- Fundamentals of genome sequencing and annotation -- Fundamentals of proteomics -- Fundamentals of metabolomics -- Enzymes and receptors -- Drug discovery and development.…”
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374
Results from an Australopithecus africanus dental enamel fragment confirm the potential of palaeoproteomics for South African Plio-Pleistocene fossil sites
Published 2025-02-01“…Palaeoproteomics can help improve our understanding of taxonomic variation, as demonstrated by the recently generated proteome of Paranthropus specimens from Swartkrans. …”
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375
The HFA‐PEFF score identifies ‘early‐HFpEF’ phenogroups associated with distinct biomarker profiles
Published 2022-06-01“…The aims of this pilot study are to (i) identify distinct phenogroups by cluster analysis of HFA‐PEFF domain scores in subjects that present with HF‐like symptoms and (ii) study whether these phenogroups may be associated with distinct blood proteome profiles. Methods and results Subjects referred to the Cardiology Centers of the Netherlands, location Utrecht, with non‐acute possibly cardiac‐related symptoms (such as dyspnoea or fatigue) were prospectively enrolled in the HELPFul cohort (N = 507) and were included in the current analysis. …”
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376
Transient lymphocyte count decrease correlates with oncolytic adenovirus efficacy in humans: mechanistic and biomarker findings from TUNIMO phase I trial
Published 2025-01-01“…More substantial lymphocyte count change was linked to stronger immune activation in plasma proteome after intravenous TILT-123 and the presence of TILT-123 mRNA in tumors. …”
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377
Brown Adipose Tissue undergoes pathological perturbations and shapes C2C12 myoblast homeostasis in the SOD1-G93A mouse model of Amyotrophic Lateral Sclerosis
Published 2025-02-01“…In this study, we employed a multi-omics approach, including RNA sequencing (GEO identifier GSE273052) and proteomics (ProteomeXchange identifier PXD054147), to investigate the alterations in BAT and its EVs in the SOD1-G93A mouse model of ALS. …”
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378
Clinical-grade extracellular vesicles derived from umbilical cord mesenchymal stromal cells: preclinical development and first-in-human intra-articular validation as therapeutics f...
Published 2025-01-01“…In silico studies confirmed sEV's immunosuppressive signature through miRNA and proteome analysis. In an OA mouse model, sEV injected intra-articularly (IA) induced hyaline cartilage regeneration, validated by histological and μCT analyses. …”
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379
Immune monitoring of trabectedin therapy in refractory soft tissue sarcoma patients - the IMMUNYON study
Published 2025-02-01“…Immune monitoring included deep immunophenotyping (200+ parameters), gene expression profiling (103 genes), and soluble proteome analysis (99 analytes). Using RECIST1.1 criteria, 68.2% of patients achieved stable disease (SD), while 31.8% exhibited progression disease (PD). …”
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380
Targeting eEF1A reprograms translation and uncovers broad-spectrum antivirals against cap or m6A protein synthesis routes
Published 2025-02-01“…Here we detect that plitidepsin decreases de novo cap-dependent translation of SARS-CoV-2 and non-viral RNAs but affects less than 13% of the host proteome, thus preserving cellular viability. In response to plitidepsin, cells upregulate EIF2AK3 and proteins that reduce translation, but also proteins that support proteostasis via ribosome synthesis and cap-independent translation by eIF4G2 and IGF2BP2. …”
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