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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Differential regulation of apoptosis-related genes during long-term culture and differentiation of canine adipose-derived stem cells - a functional bioinformatical analysis by Maurycy Jankowski, Maurycy Jankowski, Maurycy Jankowski, Katarzyna Stefańska, Michał Suchodolski, Claudia Dompe, Claudia Dompe, Grzegorz Wąsiatycz, Bartosz Kempisty, Bartosz Kempisty, Bartosz Kempisty, Bartosz Kempisty, Michał Nowicki, Magdalena Roszak

“…A total of 17793 genes were detected and GO enrichment analysis was performed on the differentially expressed genes to identify significantly up- and downregulated Biological Process (BP) GO terms across each comparison.ResultsThe upregulation of apoptosis-regulating genes and genes related to circulatory system development suggest an induction of these processes, while the downregulation of neurogenesis and gliogenesis genes points to reciprocal regulation during osteogenic differentiation of canine ADSCs.DiscussionThese findings underscore the potential of ADSCs in bone regeneration and offer valuable insights for advancing tissue engineering, however further studies, including proteomic analyses, are needed to confirm these patterns and their biological significance.…”
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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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PADI4 Haplotypes in Association with RA Mexican Patients, a New Prospect for Antigen Modulation by Maria Guadalupe Zavala-Cerna, Norma Guadalupe Gonzalez-Montoya, Arnulfo Nava, Jorge I. Gamez-Nava, Maria Cristina Moran-Moguel, Roberto Carlos Rosales-Gomez, Susan Andrea Gutierrez-Rubio, Jose Sanchez-Corona, Laura Gonzalez-Lopez, Ingrid Patricia Davalos-Rodriguez, Mario Salazar-Paramo

“…Further evidence about proteomic expression of this gene will determine its participation in antigenic generation and autoimmunity.…”
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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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Conservative mechanism through various rapeseed (Brassica napus L.) varieties respond to heavy metal (Cadmium, Lead, Arsenic) stress by Lingyu Li, Zhanhuang Fan, Qingqin Gan, Gang Xiao, Mingbao Luan, Rilong Zhu, Zhenqian Zhang

“…Nevertheless, its ability to tolerate heavy metal stress at the molecular level remains unclear.MethodsHere, with 7-day seedlings as raw materials, we investigated physiological and biochemical indexes, analyzed the transcriptome sequencing for different treated materials (control, 50×, and 100×), combined with the results of transcriptome and proteome sequencing of the near-isogenic lines (F338 and F335) to reveal the response mechanism to heavy metal stress. …”
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LncRNA MIR210HG promotes the proliferation of colon cancer cells by inhibiting ferroptosis through binding to PCBP1 by Xiao-Qian Wang, A.-Qiang Fan, Liu Hong

“…We assessed MIR210HG expression in colon cancer cell lines and tissues, and examined the effects of its overexpression and knockdown on cell proliferation. Proteomic analysis was conducted to explore the interaction between MIR210HG and ferroptosis pathway components. …”
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Genome Structure of Bacillus cereus tsu1 and Genes Involved in Cellulose Degradation and Poly-3-Hydroxybutyrate Synthesis by Hui Li, Suping Zhou, Terrance Johnson, Koen Vercruysse, Ouyang Lizhi, Parthasarathy Ranganathan, Nsoki Phambu, Alexander J. Ropelewski, Theodore W. Thannhauser

“…The cellulolytic activity of tsu1 was detected using carboxymethylcellulose (CMC) plate Congo red assay and the shift towards low-molecular size forms of CMC revealed by gel permeation chromatography in CMC liquid culture and the identification of a cellulase in the secreted proteome.…”
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MSC-EXs inhibits uranium nephrotoxicity by competitively binding key proteins and inhibiting ROS production by Xinrui Yang, Jing Liu, Yaru Yin, Luxun Yang, Mingquan Gao, Zifei Wu, Binghui Lu, Shenglin Luo, Weidong Wang, Rong Li

“…Notably, the protective effects of MSC-EXs exceed those of MSCs and are comparable to those of sodium bicarbonate, as confirmed by various analytical techniques. Proteomic studies have shown that MSC-EXs reduce uranyl ion deposition in renal tubule cells through competitive binding with transferrin, osteopontin, and albumin. …”
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Emodin Ameliorates Intestinal Dysfunction by Maintaining Intestinal Barrier Integrity and Modulating the Microbiota in Septic Mice by Mina Zhang, Bo Lian, Rui Zhang, Yuhong Guo, Jingxia Zhao, Shasha He, Yunjing Bai, Ning Wang, Yan Lin, Xuerui Wang, Qingquan Liu, Xiaolong Xu

“…Intestinal barrier function was also improved by emodin through enhancing ZO-1 and occludin expression, which prevented the secondary translocation of Escherichia coli. By proteome microarray investigation, JNK2 was identified as a direct target of emodin. …”
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Profiling Proteins in the Hypothalamus and Hippocampus of a Rat Model of Premenstrual Syndrome Irritability by Mingqi Qiao, Peng Sun, Yang Wang, Sheng Wei, Xia Wei, Chunhong Song, Fushun Wang, Jibiao Wu

“…This study employed two-dimensional gel electrophoresis (2DE) for proteomic map analysis of the hypothalamus and hippocampus of rat models of premenstrual syndrome (PMS) irritability. …”
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Difference in the Vitreal Protein Profiles of Patients with Proliferative Diabetic Retinopathy with and without Intravitreal Conbercept Injection by Chen Zou, Minjie Zhao, Jingjing Yu, Dandan Zhu, Yunzhi Wang, Xinping She, Yanan Hu, Zhi Zheng

“…Liquid chromatography-tandem mass spectrometry- (LC-MS/MS-) based proteomic methods were used to determine the protein profiles of the vitreous humor in patients with PDR treated with (IVC group; n=9) and without (PDR group; n=8) preoperative IVC. …”
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Unlocking biological complexity: the role of machine learning in integrative multi-omics by Ravindra Kumar, Rajrani Ruhel, Andre J. van Wijnen

“…Integrative multi-omics approaches use multi-layered datasets such as genomic, transcriptomic, proteomic, and metabolomic data to understand biological processes much more comprehensively compared to the single-omics analysis and to provide a comprehensive view of cellular and molecular processes. …”
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A high coverage reference transcriptome assembly of pea (<i>Pisum sativum</i> L.) mycorrhizal roots by A. M. Afonin, I. V. Leppyanen, O. A. Kulaeva, O. Y. Shtark, I. A. Tikhonovich, E. A. Dolgikh, V. A. Zhukov

“…As transcriptomic and proteomic approaches are being implemented for studying the mutualistic symbioses of pea, a need for a reference transcriptome of genes expressed under these specific conditions for increasing the resolution and the accuracy of other methods arose. …”
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Don't die like me: Which proteins are responsible for the selective neuronal vulnerability within the substantia nigra? by Simone Steinbach, Mariana Molina, Lea T Grinberg, Luisa Aring, Annika Guntermann, Katrin Marcus, Helmut Heinsen, Renata E Paraizo Leite, Caroline May

“…For this purpose, the neurons from the ventral as well as dorsal tier of the substantia nigra were specifically isolated out of neuropathologically unremarkable human substantia nigra sections with laser microdissection. Following, their proteome was analyzed by data independent acquisition mass spectrometry. …”
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Molecular and Cellular Mechanisms of Immunosenescence: Modulation Through Interventions and Lifestyle Changes by Luca Pangrazzi, Andreas Meryk

“…We will examine the current understanding of immunosenescence at the genomic, epigenomic, and proteomic levels, and discuss how various lifestyle factors can potentially mitigate or partially reverse aspects of immune aging. …”
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Prediction of inhibitory peptides against E.coli with desired MIC value by Nisha Bajiya, Nishant Kumar, Gajendra P. S. Raghava

“…Additionally, we screened anti-E. coli proteins in the proteomes of three probiotic bacterial strains and created a web-based platform, “EIPpred”, enabling users to design peptides with desired MIC values ( https://webs.iiitd.edu.in/raghava/eippred ).…”
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First identification report for amino acid composition of red algae Gracilaria spp. obtained from Central Java, Indonesia by Klara Kharisma Bunga Chandra, Tri Rini Nuringtyas, Tri Joko Raharjo

“…The unique protein expressions have never been analyzed using a proteomic approach, and no reports are available on Gracilaria spp. amino acid sequences in Central Java. …”
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