Rational engineering of minimally immunogenic nucleases for gene therapy by Rumya Raghavan, Mirco J. Friedrich, Indigo King, Samuel Chau-Duy-Tam Vo, Daniel Strebinger, Blake Lash, Michael Kilian, Michael Platten, Rhiannon K. Macrae, Yifan Song, Lucas Nivon, Feng Zhang

“…Through MHC-associated peptide proteomics (MAPPs) analysis, we identify putative immunogenic epitopes on each nuclease. …”
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Detection of chimeric alpha-defensin transcripts and peptides in mouse Paneth cells by Steven Timmermans, Steven Timmermans, Charlotte Wallaeys, Charlotte Wallaeys, Somara De Beul, Somara De Beul, Natalia Garcia-Gonzales, Natalia Garcia-Gonzales, Claude Libert, Claude Libert

“…IntroductionIn mammals, Paneth cells, located in the crypts of the small intestine, produceantimicrobial peptides that serve to keep the intestinal microbiome under control. a-Defensins are the primary antimicrobial peptides produced by these cells.MethodsWe used 148 publicly available bulk RNA-seq samples on purified PCs, proteomics on enriched purified PC proteins and Defa peptide activity assays to detect all Defa transcrips, including potential chimeric transcrips.ResultsWe identified 28 expressed Defa genes in mice, with up to 85% of Paneth cell RNA reads mapping to these genes. …”
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Cardiac repair using regenerating neonatal heart tissue-derived extracellular vesicles by Hanjing Li, Yining Liu, Yuqing Lin, Sijia Li, Chenlu Liu, Ao Cai, Wei Li, Wanyu Zhang, Xinlu Gao, Zhongyu Ren, Haoyu Ji, Yang Yu, Xiuxiu Wang, Wenya Ma, Ning Wang, Dan Zhao, Tianlong Li, Yu Liu, Benzhi Cai

“…Here, we report that EVs from regenerating neonatal heart tissues, after apical resection surgery (AR-Neo-EVs), exhibit stronger pro-proliferative, anti-apoptotic, and pro-angiogenesis activities than EVs from neonatal mouse cardiac tissues (Neo-EVs), effects which are absent in adult mouse heart-derived EVs (Adu-EVs). Proteomic analysis reveals the expression of Wdr75 protein, a regulator of p53, is higher in AR-Neo-EVs than in Neo-EVs. …”
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Epitope mapping of recombinant Salmonella enterica serotype Heidelberg flagellar hook-associated protein by in silico and in vivo approaches by Hung-Yueh Yeh

“…The aim of the present study was to compare the epitope identification in the Salmonella enterica serotype Heidelberg FlgK protein by in silico prediction and in vivo experiment with mass spectrometry in association with immunoprecipitation proteomics. Results The Salmonella serotype Heidelberg FlgK protein contains 553 amino acids with a molecular mass of 61 kDa. …”
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TGF‐β regulates the release of breast cancer cell‐derived extracellular vesicles and the sorting of their protein cargo by downregulating RAB27B expression by Chao Li, Agustin Enciso‐Martinez, Roman I. Koning, Mona Shahsavari, Peter ten Dijke

“…Using click chemistry and quantitative proteomics, we found that TGF‐β increases the quantity of protein cargo and changes the composition of EVs by downregulating RAB27B expression. …”
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Harnessing Tumor Cell‐Derived Exosomes for Immune Rejection Management in Corneal Transplantation by Jieru Yang, Huanmin Kang, Yingyi Liu, Shan Lu, Huihui Wu, Bikui Zhang, Yan He, Wenhu Zhou

“…Utilizing murine corneal transplantation as a model, it is demonstrated that B16‐Exo significantly reduces immune rejection, evidenced by decreased corneal opacity, neovascularization, and immune dysregulation, while enhancing postoperative survival. Proteomic analyses reveal differential expression of pivotal proteins in B16‐Exo, notably the JAK2 protein within the JAK‐STAT signaling pathway, which has been mechanistically demonstrated to amplify the activity of myeloid‐derived suppressor cells (MDSCs) and inhibit T cell proliferation. …”
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<i>Helicobacter pylori</i> HP0135 Is a Small Lipoprotein That Has a Role in Outer Membrane Stability by Doreen Nguyen, Rachel G. Ivester, Kyle Rosinke, Timothy R. Hoover

“…The filament of the <i>H. pylori</i> flagellum is surrounded by a membranous sheath that is contiguous with the outer membrane. Proteomic analysis of isolated sheathed flagella from <i>H. pylori</i> B128 identified the lipoprotein HP0135 as a potential component of the flagellar sheath. …”
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Potential Pathways Involved in Elaidic Acid Induced Atherosclerosis in Human Umbilical Vein Endothelial Cells by Huahong Yu, Xiangmei Li, Zhongshang Liang, Bin Qiu, Siguang Li, Ting Luo, Jing Li, Hongyan Li, Zeyuan Deng

“…In the presented study, two-dimensional electrophoresis based proteomics was used to discover the role of elaidic acid in atherosclerosis. …”
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An updated reference genome of Barbatula barbatula (Linnaeus, 1758) by Levente Laczkó, Nikoletta Andrea Nagy, Ágnes Nagy, Ágnes Maroda, Péter Sály

“…We identified 23270 protein-coding genes, and the proteome exhibited high completeness with BUSCO (93.1%) and OMArk (90.81%). …”
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Analysis of Toll-Like Receptors in Human Milk: Detection of Membrane-Bound and Soluble Forms by Chiara Cattaneo, Alice Caramaschi, Elena Uga, Michela Braghin, Gianluca Cosi, Chiara Peila, Maria C. Strozzi, Miriam Sabatini, Diego Gazzolo, Marcello Manfredi, Maria Cavaletto

“…Here, we investigated the presence of Toll-like receptors TLR1/2/4/6 in colostrum and mature milk of women who delivered before (preterm) or after (term) 37 weeks of gestational age, integrating classical immune-related techniques with proteomic LC-MS/MS analysis. We have detected immunoreactivity for TLRs mostly in preterm samples, even for TLR1 and TLR6, until now not described in human milk. …”
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Molecular Characterization of the Onset and Progression of Colitis in Inoculated Interleukin-10 Gene-Deficient Mice: A Role for PPARα by Bianca Knoch, Matthew P. G. Barnett, Janine Cooney, Warren C. McNabb, Diane Barraclough, William Laing, Shuotun Zhu, Zaneta A. Park, Paul MacLean, Scott O. Knowles, Nicole C. Roy

“…The aims were to (1) characterize colitis onset and progression using a histopathological, transcriptomic, and proteomic approach and (2) investigate links between PPARα and IL10 using gene network analysis. …”
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Targeting protein-protein interactions in drug discovery: Modulators approved or in clinical trials for cancer treatment by Cristina Camps-Fajol, Debora Cavero, Jordi Minguillón, Jordi Surrallés

“…Despite the development of PPI modulators is challenging, advances in the genetic, proteomic and computational level have facilitated their discovery and optimization. …”
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A split-GAL4 driver line resource for Drosophila neuron types by Geoffrey W Meissner, Allison Vannan, Jennifer Jeter, Kari Close, Gina M DePasquale, Zachary Dorman, Kaitlyn Forster, Jaye Anne Beringer, Theresa Gibney, Joanna H Hausenfluck, Yisheng He, Kristin Henderson, Lauren Johnson, Rebecca M Johnston, Gudrun Ihrke, Nirmala A Iyer, Rachel Lazarus, Kelley Lee, Hsing-Hsi Li, Hua-Peng Liaw, Brian Melton, Scott Miller, Reeham Motaher, Alexandra Novak, Omotara Ogundeyi, Alyson Petruncio, Jacquelyn Price, Sophia Protopapas, Susana Tae, Jennifer Taylor, Rebecca Vorimo, Brianna Yarbrough, Kevin Xiankun Zeng, Christopher T Zugates, Heather Dionne, Claire Angstadt, Kelly Ashley, Amanda Cavallaro, Tam Dang, Guillermo A Gonzalez III, Karen L Hibbard, Cuizhen Huang, Jui-Chun Kao, Todd Laverty, Monti Mercer, Brenda Perez, Scarlett Rose Pitts, Danielle Ruiz, Viruthika Vallanadu, Grace Zhiyu Zheng, Cristian Goina, Hideo Otsuna, Konrad Rokicki, Robert R Svirskas, Han SJ Cheong, Michael-John Dolan, Erica Ehrhardt, Kai Feng, Basel EI Galfi, Jens Goldammer, Stephen J Huston, Nan Hu, Masayoshi Ito, Claire McKellar, Ryo Minegishi, Shigehiro Namiki, Aljoscha Nern, Catherine E Schretter, Gabriella R Sterne, Lalanti Venkatasubramanian, Kaiyu Wang, Tanya Wolff, Ming Wu, Reed George, Oz Malkesman, Yoshinori Aso, Gwyneth M Card, Barry J Dickson, Wyatt Korff, Kei Ito, James W Truman, Marta Zlatic, Gerald M Rubin, FlyLight Project Team

“…These tools enable functional, transcriptomic, and proteomic studies based on precise anatomical targeting. …”
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TGF-β induces cholesterol accumulation to regulate the secretion of tumor-derived extracellular vesicles by Dorival Mendes Rodrigues-Junior, Chrysoula Tsirigoti, Konstantina Psatha, Dimitris Kletsas, Michalis Aivaliotis, Carl-Henrik Heldin, Aristidis Moustakas

“…To this end, we used a large number of cancer cell models, coupled to EV cell biological assays, unbiased proteomic and transcriptomic screens, followed by signaling and cancer biology analyses, including drug resistance assays. …”
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Improving serum redox balance, inflammatory status, physical function, and cognitive ability through dual-task resistance training and detraining in nursing home residents by Erivaldo Machado Araújo, Hélio José Coelho-Júnior, Caio Victor Sousa, Thiago dos Santos Rosa, Ivo Vieira Sousa Neto, Emanuele Marzetti, Octávio Luiz Franco, Samuel da Silva Aguiar

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NLRP3 activation maintains intestinal epithelial barrier and reduces liver injury in alcoholic liver disease mice by Shi‐Qing Li, Ya‐Ru Wang, Zhong‐Liang Xie, Yan Wang, Zi‐Han Feng, Jian‐Hao Xu, Bing Yuan, Yi‐Tong Zhang, Guan Yang, Jing‐Lin Wang, Yuan Yuan

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Paracrine activity of Smurf1-silenced mesenchymal stem cells enhances bone regeneration and reduces bone loss in postmenopausal osteoporosis by Alberto González-González, Itziar Álvarez-Iglesias, Daniel García-Sánchez, Monica Dotta, Ricardo Reyes, Ana Alfonso-Fernández, Alfonso Bolado-Carrancio, Patricia Díaz-Rodríguez, María Isabel Pérez-Núñez, José Carlos Rodríguez-Rey, Jesús Delgado-Calle, Flor M. Pérez-Campo

“…Ex vivo, human bone explants were treated with hCM-Smurf1 to assess anti-resorptive effects. Proteomic analysis of the soluble and vesicular CM fractions identified key proteins involved in bone regeneration. …”
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CAR-CIK vs. CAR-T: benchmarking novel cytokine-induced killer cells as solid tumor immunotherapy in ErbB2+ rhabdomyosarcoma by Laura M. Moser, Laura M. Moser, Laura M. Moser, Laura M. Moser, Laura M. Moser, Catrin Heim, Sebastian E. Koschade, Sebastian E. Koschade, Sebastian E. Koschade, Sebastian E. Koschade, Sebastian E. Koschade, Philipp Wendel, Philipp Wendel, Philipp Wendel, Philipp Wendel, Süleyman Bozkurt, Sabine Harenkamp, Hermann Kreyenberg, Hermann Kreyenberg, Michael Merker, Michael Merker, Christian Münch, Christian Münch, Christian Münch, Elise Gradhand, Meike Vogler, Meike Vogler, Meike Vogler, Evelyn Ullrich, Evelyn Ullrich, Evelyn Ullrich, Evelyn Ullrich, Evelyn Ullrich, Halvard Bönig, Halvard Bönig, Jan-Henning Klusmann, Jan-Henning Klusmann, Jan-Henning Klusmann, Jan-Henning Klusmann, Peter Bader, Peter Bader, Peter Bader, Peter Bader, Peter Bader, Winfried S. Wels, Winfried S. Wels, Winfried S. Wels, Eva Rettinger, Eva Rettinger, Eva Rettinger, Eva Rettinger, Eva Rettinger

“…Modes of action were assessed by comparing cytokine secretion profiles using bead-based multiplexed flow cytometry and by liquid chromatography mass spectrometry whole cell proteomics. Finally, we used an in vivo model of RMS mimicking minimal metastatic residual disease to compare anti-tumor potency of CAR-CIK vs. …”
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Brucella suis ΔmapB outer membrane vesicles as an acellular vaccine against systemic and mucosal B. suis infection by Florencia Muñoz González, Florencia Muñoz González, Magali G. Bialer, Maria L. Cerutti, Silvia M. Estein, Lila Y. Ramis, Pablo C. Baldi, Pablo C. Baldi, Ángeles Zorreguieta, Ángeles Zorreguieta, Mariana C. Ferrero, Mariana C. Ferrero

“…To determine the level of protection conferred by immunization, mice were challenged with virulent B. suis via intraperitoneal or intratracheal routes, and the bacterial load was quantified post-challenge.ResultsDynamic Light Scattering of the OMVs from both strains revealed the presence of spherical structures of 90-130 nm. Proteomic analysis identified 94 and 95 proteins in the wt and ΔmapB OMVs, respectively, including several known Brucella immunogens. …”
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SMAP3-ID for Identification of Endogenous Protein–Protein Interactions Reveals Regulation of Mitochondrial Activity by Lamins by Julia Warren, Jian Wang, Francis Dhoro, Bo Chao, Ashok Reddy, Stefanie Kaech Petrie, Larry L. David, Xiangshu Xiao, Bingbing X. Li

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