APMAT analysis reveals the association between CD8 T cell receptors, cognate antigen, and T cell phenotype and persistence by Jingyi Xie, Daniel G. Chen, William Chour, Rachel H. Ng, Rongyu Zhang, Dan Yuan, Jongchan Choi, Michaela McKasson, Pamela Troisch, Brett Smith, Lesley Jones, Andrew Webster, Yusuf Rasheed, Sarah Li, Rick Edmark, Sunga Hong, Kim M. Murray, Jennifer K. Logue, Nicholas M. Franko, Christopher G. Lausted, Brian Piening, Heather Algren, Julie Wallick, Andrew T. Magis, Kino Watanabe, Phil Mease, Philip D. Greenberg, Helen Chu, Jason D. Goldman, Yapeng Su, James R. Heath

“…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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Downregulation of S100 Calcium Binding Protein A9 in Esophageal Squamous Cell Carcinoma by Harsh Pawar, Srinivas M. Srikanth, Manoj Kumar Kashyap, Gajanan Sathe, Sandip Chavan, Mukul Singal, H. C. Manju, Kariyanakatte Veeraiah Veerendra Kumar, M. Vijayakumar, Ravi Sirdeshmukh, Akhilesh Pandey, T. S. Keshava Prasad, Harsha Gowda, Rekha V. Kumar

“…We had previously employed a quantitative proteomic approach to identify differentially expressed proteins in ESCC tumors. …”
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Characterization of the Protective HIV-1 CTL Epitopes and the Corresponding HLA Class I Alleles: A Step towards Designing CTL Based HIV-1 Vaccine by Sajib Chakraborty, Taibur Rahman, Rajib Chakravorty

“…High mutation rate in the viral genome underlying the antigenic variability of the viral proteome is the major hindrance as far as the antibody based vaccine development is concerned. …”
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How energy determines spatial localisation and copy number of molecules in neurons by Cornelius Bergmann, Kanaan Mousaei, Silvio O. Rizzoli, Tatjana Tchumatchenko

“…We combined our own data and experimental reports from five other large-scale mRNA and proteomics screens, comprising more than ten thousand molecular species to reveal the underlying computational principles of molecular localisation. …”
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Antimicrobial proteins from oyster hemolymph improve the efficacy of conventional antibiotics. by Kate Summer, Qi Guo, Lei Liu, Bronwyn Barkla, Sarah Giles, Kirsten Benkendorff

“…Effective HPE concentrations are comparable to AMPPs currently approved for use or in clinical trials pipelines. Proteomics analysis of HPE identified a number of proteins including abundant known AMPPs. …”
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Molecular Basis of GABA Hypofunction in Adolescent Schizophrenia-Like Animals by Xiaodan Wang, Ying Hu, Wenxin Liu, Yuanyuan Ma, Xi Chen, Ting Xue, Donghong Cui

“…Slice recording showed reduced GABA transmission and PVI+ hypofunction, indicating GABAergic hypofunction. Cortical proteomic evaluation combined with analysis of single cell data from the Allen Brain showed that various metabolic processes were enriched in top ranks and differentially altered in excitatory neurons, GABAergic interneurons, and glial cells. …”
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Comparative analysis of microbial contamination in diesel fuels using MALDI-TOF MS by Agnieszka Ludwiczak, Tomasz Zieliński, Ewelina Sibińska, Grażyna Czeszewska-Rosiak, Michał Złoch, Joanna Rudnicka, Andrzej Tretyn, Paweł Pomastowski

“…The 16 S rDNA sequencing confirmed proteomic identifications by the MALDI systems with high accuracy. …”
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Influence of Acute High Glucose on Protein Abundance Changes in Murine Glomerular Mesangial Cells by Michelle T. Barati, James C. Gould, Sarah A. Salyer, Susan Isaacs, Daniel W. Wilkey, Michael L. Merchant

“…The effects of acute exposure to high glucose levels as experienced by glomerular mesangial cells in postprandial conditions and states such as in prediabetes were investigated using proteomic methods. Two-dimensional gel electrophoresis and matrix assisted laser desorption ionization time of flight mass spectrometry methods were used to identify protein expression patterns in immortalized rat mesangial cells altered by 2 h high glucose (HG) growth conditions as compared to isoosmotic/normal glucose control (NG⁎) conditions. …”
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Biochemical characterization of the Escherichia coli surfaceome: a focus on type I fimbriae and flagella by Devon W. Kavanaugh, Adeline Sivignon, Yannick Rossez, Zina Chouit, Christophe Chambon, Christophe Chambon, Louane Béal, Mathilde Bonnet, Michel Hébraud, Michel Hébraud, Yann Guérardel, Hang Thi Thu Nguyen, Nicolas Barnich

“…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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Predicting the hub interactome of COVID-19 and oral squamous cell carcinoma: uncovering ALDH-mediated Wnt/β-catenin pathway activation via salivary inflammatory proteins by Pradeep Kumar Yadalam, Deepavalli Arumuganainar, Prabhu Manickam Natarajan, Carlos M. Ardila

“…The gradient boosting model outperformed all models with an accuracy of 95% and class accuracy of 95%. Salivary proteomic interactome analysis revealed novel hub proteins as potential common biomarkers.…”
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Inflammatory disease progression shapes nanoparticle biomolecular corona-mediated immune activation profiles by Jacob R. Shaw, Nicholas Caprio, Nhu Truong, Mehari Weldemariam, Anh Tran, Nageswara Pilli, Swarnima Pandey, Jace W. Jones, Maureen A. Kane, Ryan M. Pearson

“…Integrated multi-omics analysis of proteomics, lipidomics, metabolomics, and cytokine datasets highlight a set of differentially enriched TLR4 ligands that correlate with dynamic NP corona-mediated immune activation. …”
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Adipose-Derived Mesenchymal Stem Cells Enhance Ovarian Cancer Growth and Metastasis by Increasing Thymosin Beta 4X-Linked Expression by Yijing Chu, Min You, Jingjing Zhang, Guoqiang Gao, Rendong Han, Wenqiang Luo, Tingting Liu, Jianxin Zuo, Fuling Wang

“…However, the underlying mechanism has not yet been revealed. In this study, a proteomics analysis was performed to compare protein expression treated with and without ADSCs in ovarian cancer cells. …”
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Anti-colon cancer activity of water-soluble polysaccharides extracted from Gloeostereum incarnatum via Wnt/β-catenin signaling pathway by Jiawei He, Anhui Yang, Xuyu Zhao, Yang Liu, Shuyan Liu, Di Wang

“…Eight-week administration with GIPS at doses of 30 or 90 mg/kg strongly inhibited tumor growth including the reduction on numbers and the suppression of the size without influencing the animals’ body weight and organ functions. According to the proteomics performing by antibody array, among 308 detected cytokines, GIPS significantly regulated 89 of them. …”
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Expression Profiling of Long Noncoding RNA Splice Variants in Human Microvascular Endothelial Cells: Lipopolysaccharide Effects In Vitro by Imran H. Chowdhury, Hema P. Narra, Abha Sahni, Kamil Khanipov, Casey L. C. Schroeder, Jignesh Patel, Yuriy Fofanov, Sanjeev K. Sahni

“…Endothelial cell interactions with lipopolysaccharide (LPS) involve both activating and repressing signals resulting in pronounced alterations in their transcriptome and proteome. Noncoding RNAs are now appreciated as posttranscriptional and translational regulators of cellular signaling and responses, but their expression status and roles during endothelial interactions with LPS are not well understood. …”
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Diet-derived urolithin A is produced by a dehydroxylase encoded by human gut Enterocloster species by Reilly Pidgeon, Sacha Mitchell, Michael Shamash, Layan Suleiman, Lharbi Dridi, Corinne F. Maurice, Bastien Castagner

“…Here, we use a combination of untargeted bacterial transcriptomics, proteomics, and comparative genomics to uncover an inducible uroC dehydroxylase (ucd) operon in Enterocloster species. …”
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PMA1-containing extracellular vesicles of Candida albicans triggers immune responses and colitis progression by Zhen Xu, Shuping Qiao, Zelin Wang, Chen Peng, Yayi Hou, Baorui Liu, Guochun Cao, Tingting Wang

“…Compared to WT-C.a, ΔPMA1-C.a could not aggravate colitis. Proteomic analysis showed that PMA1 was transported by extracellular vesicles (EVs) of C. albicans. …”
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Applying the Concept of Peptide Uniqueness to Anti-Polio Vaccination by Darja Kanduc, Candida Fasano, Giovanni Capone, Antonella Pesce Delfino, Michele Calabrò, Lorenzo Polimeno

“…Proteins from poliovirus type 1, strain Mahoney, were analyzed for amino acid sequence identity to the human proteome at the pentapeptide level, searching for sequences that (1) have zero percent of identity to human proteins, (2) are potentially endowed with an immunologic potential, and (3) are highly conserved among poliovirus strains. …”
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PaleoProPhyler: a reproducible pipeline for phylogenetic inference using ancient proteins by Patramanis, Ioannis, Ramos-Madrigal, Jazmín, Cappellini, Enrico, Racimo, Fernando

“…The pipeline can not only process various forms of proteomic data, but also easily harness genetic data in different formats (CRAM, BAM, VCF) and translate it, allowing the user to create reference panels for phyloproteomic analyses. …”
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Identification and Characterization of TEX101 in Bovine Epididymal Spermatozoa by Subir K. Nagdas, Eric L. McLean, Leeá P. Richardson, Samir Raychoudhury

“…The 38 kDa RCA binding polypeptide of cauda sperm PM was purified and exhibited a charge train of three distinct spots with isoelectric points (pH 5.3 and 5.8). Proteomic identification yielded ten peptides that matched the sequence of Testis Expressed 101 protein (TEX101). …”
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Drug Target Identification and Elucidation of Natural Inhibitors for : An Study by Surya Narayan Rath, Manisha Ray, Animesh Pattnaik, Sukanta Kumar Pradhan

“…In this study, bioinformatics tools and technology have been applied to suggest a potential drug target by screening the proteome information of B. petrii DSM 12804 (accession No. …”
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