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.…”
Get full text

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.…”
Get full text

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. …”
Get full text

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. …”
Get full text

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. …”
Get full text

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. …”
Get full text

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. …”
Get full text

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. …”
Get full text

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. …”
Get full text

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 ).…”
Get full text

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. …”
Get full text

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. …”
Get full text

Isovitexin targets SIRT3 to prevent steroid-induced osteonecrosis of the femoral head by modulating mitophagy-mediated ferroptosis by Yinuo Fan, Zhiwen Chen, Haixing Wang, Mengyu Jiang, Hongduo Lu, Yangwenxiang Wei, Yunhao Hu, Liang Mo, Yuhao Liu, Chi Zhou, Wei He, Zhenqiu Chen

“…In this study, we analyzed clinical samples obtained from SIONFH patients using proteomic and bioinformatic approaches. We found an imbalance in mitochondrial homeostasis and ferroptosis-induced impairment of osteogenic capacity in SIONFH. …”
Get full text

Detection of HIV-1 and Human Proteins in Urinary Extracellular Vesicles from HIV+ Patients by Samuel I. Anyanwu, Akins Doherty, Michael D. Powell, Chamberlain Obialo, Ming B. Huang, Alexander Quarshie, Claudette Mitchell, Khalid Bashir, Gale W. Newman

“…Conclusion. Differences in the proteomic profile of EVs from HIV+ versus HIV− samples were found. …”
Get full text

Subclinical Inflammatory Status in Rett Syndrome by Alessio Cortelazzo, Claudio De Felice, Roberto Guerranti, Cinzia Signorini, Silvia Leoncini, Alessandra Pecorelli, Gloria Zollo, Claudia Landi, Giuseppe Valacchi, Lucia Ciccoli, Luca Bini, Joussef Hayek

“…., “pseudo-autistic”) RTT patients by routine haematology/clinical chemistry and proteomic 2-DE/MALDI-TOF analyses as a function of four major MECP2 gene mutation types (R306C, T158M, R168X, and large deletions). …”
Get full text

Integrating AI into Cancer Immunotherapy—A Narrative Review of Current Applications and Future Directions by David B. Olawade, Aanuoluwapo Clement David-Olawade, Temitope Adereni, Eghosasere Egbon, Jennifer Teke, Stergios Boussios

“…Results: AI has significantly contributed to identifying biomarkers that predict immunotherapy efficacy by analyzing genomic, transcriptomic, and proteomic data. It also optimizes combination therapies by predicting the most effective treatment protocols. …”
Get full text

Discovery of a novel highly specific, fully human PSCA antibody and its application as an antibody-drug conjugate in prostate cancer by Xiaojie Chu, Seungmin Shin, Du-San Baek, Liyong Zhang, Alex Conard, Megan Shi, Ye-Jin Kim, Cynthia Adams, Maggie Hines, Xianglei Liu, Chuan Chen, Zehua Sun, Dontcho V. Jelev, John W. Mellors, Dimiter S. Dimitrov, Wei Li

“…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. …”
Get full text

Benchmarking the identification of a single degraded protein to explore optimal search strategies for ancient proteins by Rodriguez Palomo, Ismael, Nair, Bharath, Chiang, Yun, Dekker, Joannes, Dartigues, Benjamin, Mackie, Meaghan, Evans, Miranda, Macleod, Ruairidh, Olsen, Jesper V., Collins, Matthew J.

“…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. …”
Get full text

Exploring BCL2 regulation and upstream signaling transduction in venetoclax resistance in multiple myeloma: potential avenues for therapeutic intervention by Rodrigo Fonseca, Yuan Xiao Zhu, Laura A. Bruins, Joseph Ahmann, Cecilia de Bonolo Campos, Esteban Braggio, Xianfeng Chen, Mariano Arribas, Susie Darvish, Seth Welsh, Erin Meermeier, Kiran K. Mangalaparthi, Richard K. Kandasamy, Greg Ahmann, J. Erin Wiedmeier-Nutor, Akhilesh Pandey, Marta Chesi, P. Leif Bergsagel, Rafael Fonseca

“…We conducted a multi-omic characterization of established VTX-resistant isogenic human myeloma cell lines (HMCL) and primary MM patient samples pre- and post-VTX treatment. Transcriptomic and proteomic analysis revealed that resistance was largely associated with BCL-2 family protein dysregulation, including upregulation of anti-apoptotic proteins such as MCL-1, BCL-XL, BCL-2, and downregulation of pro-apoptotic members. …”
Get full text

Inhibition of glutathione peroxidase 4 suppresses gastric cancer peritoneal metastasis via regulation of RCC2 homeostasis by Can Hu, Jingli Xu, Yanqiang Zhang, Ruolan Zhang, Siwei Pan, Jiahui Chen, Yan Wang, Qianyu Zhao, Yuqi Wang, Weiwei Zhu, Mengxuan Cao, Shengjie Zhang, Dan Zu, Zhiyuan Xu, Ji Jing, Xiangdong Cheng

“…GPx4 knockdown suppressed GC invasion, migration and peritoneal metastasis in vitro and in vivo. Proteomic analysis revealed that GPx4 expression regulated the Homeostasis of RCC2, an oncogene link to epithelial-mesenchymal transition (EMT). …”
Get full text