NERVE 2.0: boosting the new enhanced reverse vaccinology environment via artificial intelligence and a user-friendly web interface by Andrea Conte, Nicola Gulmini, Francesco Costa, Matteo Cartura, Felix Bröhl, Francesco Patanè, Francesco Filippini

“…Abstract Background Vaccines development in this millennium started by the milestone work on Neisseria meningitidis B, reporting the invention of Reverse Vaccinology (RV), which allows to identify vaccine candidates (VCs) by screening bacterial pathogens genome or proteome through computational analyses. When NERVE (New Enhanced RV Environment), the first RV software integrating tools to perform the selection of VCs, was released, it prompted further development in the field. …”
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Mycobacterium bovis BCG Surface Antigens Expressed under the Granuloma-Like Conditions as Potential Inducers of the Protective Immunity by Yingyu Chen, Lia Danelishvili, Sasha J. Rose, Luiz E. Bermudez

“…In attempts to identify novel surface antigens of Mycobacterium bovis as a proof-of-concept for potential inducers of protective immunity, we investigated surface proteome of M. bovis BCG strain that was cultured under the granuloma-like condition. …”
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Decorin, an exercise-induced secretory protein, is associated with improved prognosis in breast cancer patients but does not mediate anti-tumorigenic tissue crosstalk in mice by Marit Hjorth, Casey L. Egan, Guilherme D. Telles, Martin Pal, David Gallego-Ortega, Oliver K. Fuller, Emma D. McLennan, Ryan D. Gillis, Tae Gyu Oh, George E.O. Muscat, Surafel Tegegne, Michael S.M. Mah, Joanna Skhinas, Emma Estevez, Timothy E. Adams, Matthew J. McKay, Mark Molloy, Kevin I. Watt, Hongwei Qian, Paul Gregorevic, Thomas R. Cox, Pernille Hojman, Julie Midtgaard, Jesper F. Christensen, Martin Friedrichsen, Renato V. Iozzo, Erica K. Sloan, Brian G. Drew, Jørgen F.P. Wojtaszewski, Martin Whitham, Mark A. Febbraio

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Profiling protease cleavage patterns in plasma for pancreatic cancer detection by Morgan R. Stewart, Arnaud Quentel, Elise Manalo, Jose Montoya Mira, Srivathsan Ranganathan, Bruce P. Branchaud, Jared M. Fischer, Eugene Tu, Fehmi Civitci, Yu-Jui Chiu, Adem Yildirim

“…However, the complexity of the human proteome makes it challenging to develop sensitive and selective tests against a specific protease biomarker. …”
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Identifying MTHFD1 and LGALS4 as Potential Therapeutic Targets in Prostate Cancer Through Multi-Omics Mendelian Randomization Analysis by Huan Han, Hanwen Su, Zhihua Lv, Chengliang Zhu, Jingtao Huang

“…<b>Methods:</b> We integrated eQTL data from the eQTLGen Consortium and pQTL data from UK Biobank Proteome Plasma Proteins (UKB-PPP) and deCODE health datasets. …”
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Nanobody-thioesterase chimeras to specifically target protein palmitoylation by Chien-Wen Kuo, Caglar Gök, Hannah Fulton, Eleanor Dickson-Murray, Samuel Adu, Emily K. Gallen, Sheon Mary, Alan D. Robertson, Fiona Jordan, Emma Dunning, William Mullen, Godfrey L. Smith, William Fuller

“…Abstract The complexity of the cellular proteome is massively expanded by a repertoire of chemically distinct reversible post-translational modifications (PTMs) that control protein localisation, interactions, and function. …”
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Zika virus modulates human fibroblasts to enhance transmission success in a controlled lab-setting by Raimondas Mozūraitis, Karsten Cirksena, Mohammad Raftari, Melika Hajkazemian, Musa Mustapha Abiodun, Juela Brahimi, Sandra Radžiutė, Violeta Apšegaitė, Rasa Bernotienė, Lech Ignatowicz, Tessy Hick, Andreas Kirschning, Annasara Lenman, Gisa Gerold, S. Noushin Emami

“…The findings are complemented by an extensive meta-proteome analysis. Overall, we demonstrate a multifaceted role of virus-host interaction and shed light on how arboviruses may influence the behaviour of their vectors as an evolved means of improving transmission-success.…”
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Proximity Labeling-Based Identification of MGAT3 Substrates and Revelation of the Tumor-Suppressive Role of Bisecting GlcNAc in Breast Cancer via GLA Degradation by Bowen Wang, Xin He, Yue Zhou, Zengqi Tan, Xiang Li, Feng Guan, Lei Lei

“…This approach enriched 116 and 189 proteins, respectively, identifying 17 common substrates shared with bisecting GlcNAc-bearing proteome obtained via intact glycopeptide enrichment methods. …”
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Staphylococcus warneri dampens SUMOylation and promotes intestinal inflammation by Léa Loison, Marion Huré, Benjamin Lefranc, Jérôme Leprince, Christine Bôle-Feysot, Moïse Coëffier, David Ribet

“…Many of these effectors remodel the host proteome, either by altering transcription or by regulating protein post-translational modifications. …”
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3D‐Printed Bioceramic Scaffolds Reinforced by the In Situ Oriented Growth of Grains for Supercritical Bone Defect Reconstruction by Boqing Zhang, Kaixin Wang, Xingyu Gui, Wenzhao Wang, Ping Song, Lina Wu, Likun Guo, Changchun Zhou, Yujiang Fan, Xingdong Zhang

“…Calcium sulfate improves the release of active calcium ions from calcium phosphate ceramics, further enhancing their bioactivity and osteoinductivity in vivo. Transcriptome and proteome sequencing reveals that the in situ whisker‐reinforced ceramics increase the expression of proteins related to calcium ion binding and promote the expression of osteogenesis‐related proteins. …”
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Proteostasis and Mitochondrial Role on Psychiatric and Neurodegenerative Disorders: Current Perspectives by Pablo Olivero, Carlo Lozano, Ramón Sotomayor-Zárate, Nicolás Meza-Concha, Marcelo Arancibia, Claudio Córdova, Wilfredo González-Arriagada, Ricardo Ramírez-Barrantes, Ivanny Marchant

“…Proteostasis alterations in the prefrontal cortex implicate proteome instability and accumulation of misfolded proteins. …”
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Post-Translational Modifications of Proteins Orchestrate All Hallmarks of Cancer by Pathea Shawnae Bruno, Aneeta Arshad, Maria-Raluca Gogu, Natalie Waterman, Rylie Flack, Kimberly Dunn, Costel C. Darie, Anca-Narcisa Neagu

“…Aberrant PTMs can be considered as enabling characteristics of cancer as long as they orchestrate all malignant modifications and variability in the proteome of cancer cells, cancer-associated cells, and tumor microenvironment (TME). …”
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Amyloids in bladder cancer hijack cancer-related proteins and are positive correlated to tumor stage by Diego Alem, César X. García-Laviña, Francisco Garagorry, Dardo Centurión, Joaquina Farias, Hany Pazos-Espinosa, María Noel Cuitiño-Mendiberry, Carolina Villadóniga, Susana Castro-Sowinski, Martín Fló, Federico Carrión, Brenda Iglesias, Kevin Madauss, Lucía Canclini

“…Subsequently, the amyloid proteome of the RT4 non-invasive and HT1197 invasive bladder cancer cell lines was identified and included oncogenes, tumor suppressors, and highly expressed cancer-related proteins. …”
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Phylogenetic and pangenomic analyses of members of the family <i>Micrococcaceae</i> related to a plant-growth-promoting rhizobacterium isolated from the rhizosphere of potato (<i>S... by S. Yu. Shchyogolev, G. L. Burygin, L. A. Dykman, L. Yu. Matora

“…Similar results were obtained in a full-scale AAI test against the UniProt database (about 250 million records), by using the AAI-profiler program and the proteome of K. rosea strain ATCC 186T as a query. According to the AAI &gt; 65 % criterion, members of the genus Arthrobacter and several other genera belonging to the class Actinomycetes, with a very wide geographical and ecological range of sources of isolation, should be placed into the same genus as Kocuria. …”
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SHASI-ML: a machine learning-based approach for immunogenicity prediction in Salmonella vaccine development by Ottavia Spiga, Ottavia Spiga, Ottavia Spiga, Anna Visibelli, Francesco Pettini, Bianca Roncaglia, Annalisa Santucci, Annalisa Santucci, Annalisa Santucci

“…When applied to the Salmonella enterica serovar Typhimurium proteome, the model identified 292 novel immunogenic protein candidates. …”
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Salivary Protein Profile and Food Intake: A Dietary Pattern Analysis by Teresa Louro, Carla Simões, Wilmara Lima, Laura Carreira, Paula Midori Castelo, Henrique Luis, Pedro Moreira, Elsa Lamy

“…Our results support the association of salivary proteomics and different dietary patterns and highlight the need of considering food consumption habits in studies using saliva, since this is a factor associated with variations in the composition of this fluid.…”
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Effect of potato glycoside alkaloids on mitochondria energy metabolism of Fusarium solani, the root rot pathogen of Lycium barbarum by Ruiyun Li, Bin Wang, Wei Chen, Chongqing Zhang, Nan Li, Yupeng Wang, Yuke Yan, Yuyan Sun, Jing He, Jing He

“…The results from both parallel reaction monitoring (PRM) and real-time RT-qPCR were consistent with the overall trends observed in TMT proteomics, thereby confirming the validity of the TMT proteomics analysis. …”
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p18 encoded by FgGMTV1 is responsible for asymptomatic infection in Fusarium graminearum by Lihang Zhang, Pengfei Li, Yanfei Wang, Shuangchao Wang, Lihua Guo

“…This work not only expands our knowledge of the genomovirus proteome but also provides insights into the strategies of viral evolution and adaptation. …”
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In vitro effect of hCG on cryptorchid patients’ gubernacular cells: a predictive model for adjuvant personalized therapy by Andrea Errico, Giulia Ambrosini, Sara Vinco, Emanuela Bottani, Elisa Dalla Pozza, Nunzio Marroncelli, Jessica Brandi, Daniela Cecconi, Ilaria Decimo, Filippo Migliorini, Nicola Zampieri, Ilaria Dando

“…Furthermore, from the proteomic analysis, we show that hCG regulates the intra- and extra-cellular organization of gubernacular cells together with a massive regulation of the antioxidant response. …”
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