Sodium butyrate is incorporated into central metabolism in fly head while inducing oxygen consumption increase. by Annika Müller-Eigner, Benedikt Gille, Frederik Dethloff, Chen Meng, Christina Ludwig, John T Heiker, Patrick Giavalisco, Shahaf Peleg

“…Here we show that while head oxygen consumption is increased by the addition of butyrate, no apparent changes are observed on the proteome and acetylome. Instead, we show that butyrate is metabolized and incorporated into the tricarboxylic acid (TCA) cycle. …”
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Alu Mobile Elements: From Junk DNA to Genomic Gems by Sami Dridi

“…Alu RNAs embedded in Pol II transcripts can promote evolution and proteome diversity, which further indicates that these mobile retroelements are in fact genomic gems rather than genomic junks.…”
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α-catenin phosphorylation is elevated during mitosis to resist apical rounding and epithelial barrier leak by Phuong M. Le, Jeanne M. Quinn, Annette S. Flozak, Adam W. T. Steffeck, Che-Fan Huang, Cara J. Gottardi

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Results from an Australopithecus africanus dental enamel fragment confirm the potential of palaeoproteomics for South African Plio-Pleistocene fossil sites by Palesa P. Madupe, Fazeelah Munir, Marc Dickinson, Alberto J. Taurozzi, Meaghan Mackie, Mirriam Tawane, Catherine Mollereau, Nomawethu Hlazo, Kirsty Penkman, Lauren Schroeder, Clément Zanolli, Jesper V. Olsen, Rebecca R. Ackermann, Enrico Cappellini

“…Palaeoproteomics can help improve our understanding of taxonomic variation, as demonstrated by the recently generated proteome of Paranthropus specimens from Swartkrans. …”
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Preparation, Structural Characterization and Antioxidant Activity of Extracellular Nanovesicles from Hericium erinaceus by Xueli YANG, Ben NIU, Hangjun CHEN, Weijie WU, Guannan WANG, Xiangjun FANG, Honglei MU, Haiyan GAO

“…Based on the analysis of lipidomics and proteomics, 346 lipids species and 52 proteins were identified in HEDENVs. …”
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Alcohol intake exacerbates experimental autoimmune prostatitis through activating PI3K/AKT/mTOR pathway-mediated Th1 differentiation by Shun Xu, Shun Xu, Shun Xu, Jing Chen, Jing Chen, Jing Chen, Shaoyu Yue, Shaoyu Yue, Shaoyu Yue, Yifan Zhang, Yifan Zhang, Yifan Zhang, Shengyu Zhao, Shengyu Zhao, Shengyu Zhao, Yongtao Hu, Yongtao Hu, Yongtao Hu, Cheng Zhang, Cheng Zhang, Cheng Zhang, Wenrui Guan, Wenrui Guan, Wenrui Guan, Li Zhang, Li Zhang, Li Zhang, Ligang Zhang, Ligang Zhang, Ligang Zhang, Chaozhao Liang, Chaozhao Liang, Chaozhao Liang

“…Proteomic and KEGG pathway analyses showed that abnormal Th1 differentiation and PI3K/AKT/mTOR pathway were significantly enriched. …”
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Mesenchymal stem cell‐derived exosomes mitigate amyloid β‐induced retinal toxicity: Insights from rat model and cellular studies by Amanda Qarawani, Efrat Naaman, Rony Ben‐Zvi Elimelech, Michal Harel, Shahaf Sigal‐Dror, Tali Ben‐Zur, Tamar Ziv, Daniel Offen, Shiri Zayit‐Soudry

“…Fluorescent labelling demonstrated increased migration of AT‐MSC‐Exosomes towards retinal cells under conditions of amyloid‐related toxicity. Proteomic analysis indicated a decrease in the retinal levels of heat‐shock proteins activated by pathogenic Aβ fibrils following AT‐MSC‐Exosome treatment. …”
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Co-occurrence of direct and indirect extracellular electron transfer mechanisms during electroactive respiration in a dissimilatory sulfate reducing bacterium by Liyuan Hou, Rebecca Cortez, Michael Hagerman, Zhiqiang Hu, Erica L.-W. Majumder

“…We also conducted untargeted proteomics and metabolomics profiling, offering insights into how DvH adapts metabolically to different electron donors and acceptors. …”
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Karyopherin Alpha 2-Expressing Pancreatic Duct Glands and Intra-Islet Ducts in Aged Diabetic C414A-Mutant-CRY1 Transgenic Mice by Satoshi Okano, Akira Yasui, Shin-ichiro Kanno, Kennichi Satoh, Masahiko Igarashi, Osamu Nakajima

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Functional mass spectrometry indicates anti-protease and complement activity increase with COVID-19 severity by Douglas D. Fraser, Douglas D. Fraser, Swapan Roy, Matt Kuruc, Maritza Quintero, Logan R. Van Nynatten, Gediminas Cepinskas, Gediminas Cepinskas, Haiyan Zheng, Amenah Soherwardy, Devjit Roy

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Identification of Maltase Glucoamylase as a Biomarker of Acute Kidney Injury in Patients with Cirrhosis by Linda Awdishu, Shirley Tsunoda, Michelle Pearlman, Chanthel Kokoy-Mondragon, Majid Ghassemian, Robert K. Naviaux, Heather M. Patton, Ravindra L. Mehta, Bhavya Vijay, Satish P. RamachandraRao

“…Urine exosome protein content was analyzed, and proteomic data were validated by immunoblotting. Statistical analysis included partial least squares-discriminant analysis coupled with variable importance in projection identification. …”
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ADAM-10 Regulates MMP-12 during Lipopolysaccharide-Induced Inflammatory Response in Macrophages by Yan Jiang, Qiming Gong, Jinmei Huang, Yuanxun Gong, Qiang Tang, Dalong Wei, Qianli Tang, Jingjie Zhao, Jian Song, Lingzhang Meng

“…Differentially expressed or regulated proteins were identified in interfered ADAM-10 (sh ADAM-10) macrophages using tandem mass tag (TMT) proteomics. The changes and regulatory role of ADAM-10 during LPS-induced inflammatory response in normal, interfering, and overexpressing ADAM-10 (EX ADAM-10) cells were determined. …”
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Deoxycholic Acid-Mediated Sphingosine-1-Phosphate Receptor 2 Signaling Exacerbates DSS-Induced Colitis through Promoting Cathepsin B Release by Shengnan Zhao, Zizhen Gong, Xixi Du, Chunyan Tian, Lingyu Wang, Jiefei Zhou, Congfeng Xu, Yingwei Chen, Wei Cai, Jin Wu

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Diagnosis of Parasitic Diseases: Old and New Approaches by Momar Ndao

“…These include immunoassays, molecular-based approaches, and proteomics using mass spectrometry platforms technology. …”
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Investigating the role of intratumoral Streptococcus mitis in gastric cancer progression: insights into tumor microenvironment by Ping Yang, Gaoli Liang, Yangyue Ni, Xiaojie Chu, Xiaoshan Zhang, Zhongyu Wang, Adeel Khan, Fangfang Jin, Han Shen, Miao Li, Zhipeng Xu

“…Here, using 16 S rRNA sequencing, tumor tissue proteomics and serum cytokines analysis, we identified enrichment of specific microbial communities within tumors of gastric cancer patients, possibly affecting the tumor microenvironment by immune modulation, metabolic processes, and inflammatory responses. …”
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Cervical mucus in linked human Cervix and Vagina Chips modulates vaginal dysbiosis by Ola Gutzeit, Aakanksha Gulati, Zohreh Izadifar, Anna Stejskalova, Hassan Rhbiny, Justin Cotton, Bogdan Budnik, Sanjid Shahriar, Girija Goyal, Abidemi Junaid, Donald E. Ingber

“…By integrating human Cervix and Vagina Chips, we demonstrated that cervical mucus significantly reduces inflammation and epithelial damage caused by a dysbiotic microbiome commonly associated with BV. Proteomic analysis of the Vagina Chip, following exposure to mucus from the Cervix Chip, revealed differentially abundant proteins, suggesting potential biomarkers and therapeutic targets for BV management. …”
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Helicobacter pylori: Genomic Insight into the Host-Pathogen Interaction by Kathryn P. Haley, Jennifer A. Gaddy

“…Infectious disease research in particular has experienced an explosion of bacterial genomic, transcriptomic, and proteomic data complementing the phenotypic methods employed in traditional bacteriology. …”
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State of the interactomes: an evaluation of molecular networks for generating biological insights by Sarah N Wright, Scott Colton, Leah V Schaffer, Rudolf T Pillich, Christopher Churas, Dexter Pratt, Trey Ideker

“…Abstract Advancements in genomic and proteomic technologies have powered the creation of large gene and protein networks (“interactomes”) for understanding biological systems. …”
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Advances in multi-omics integrated analysis methods based on the gut microbiome and their applications by Dongdong Duan, Mingyu Wang, Jinyi Han, Mengyu Li, Zhenyu Wang, Shenping Zhou, Wenshui Xin, Xinjian Li, Xinjian Li

“…With the emergence of new technologies including next-generation sequencing (NGS) and advanced techniques such as microbial community sequencing, people have begun to explore the interaction mechanisms between microorganisms and hosts at various omics levels such as genomics, transcriptomics, metabolomics, and proteomics. With the enrichment of multi-omics integrated analysis methods based on the microbiome, an increasing number of complex statistical analysis methods have also been proposed. …”
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Protocol for transcriptomic and epigenomic analyses of tip-like endothelial cells using scRNA-seq and ChIP-seq by Shintaro Funasaki, Yuri Miyamura, Shunsuke Kamei, Akhinur Rahman, Masaya Yamazaki, Shingo Usuki, Keiichiro Yasunaga, Yorifumi Satou, Hiroto Ohguchi, Takashi Minami

“…This scalable protocol is also applicable to diverse omics studies, including proteomics and metabolomics.For complete details on the use and execution of this protocol, please refer to Miyamura et al.1 : Publisher’s note: Undertaking any experimental protocol requires adherence to local institutional guidelines for laboratory safety and ethics.…”
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