The caterpillar Manduca sexta brain shows changes in gene expression and protein abundance correlating with parasitic manipulation of behaviour by McMillan LEM, Herbison RH, Biron DG, A Barkhouse, DW Miller, N Raun, Adamo SA

“…The host’s behaviour remains unchanged until the wasps exit the caterpillar, and then the caterpillar becomes a non-feeding “bodyguard” for the wasp cocoons. Using proteomic, transcriptomic and qPCR studies, we discovered an increase in antimicrobial peptide gene expression and protein abundance in the host central nervous system at the time of wasp emergence, correlating with the change in host behaviour. …”
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Allergen degradation of bee pollen by lactic acid bacteria fermentation and its alleviatory effects on allergic reactions in BALB/c mice by Shuting Yin, Qiangqiang Li, Yuxiao Tao, Enning Zhou, Kun Wang, Wanwen Chen, Xiangxin Li, Liming Wu

“…Four novel allergens (glutaredoxin, oleosin-B2, catalase and lipase) were identified with significant decreases in LAB-fermented BP (FBP) than natural BP by proteomics. Meanwhile, metabolomics analysis showed significant increases of 28 characteristic oligopeptides and amino acids in FBP versus BP, indicating the degradation of LAB on allergens. …”
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Opportunities for predictive proteogenomic biomarkers of drug treatment sensitivity in epithelial ovarian cancer by Trudy J. Philips, Britt K. Erickson, Stefani N. Thomas

“…Proteogenomics is the integration of genomics, transcriptomics, epigenomics and proteomics data. This review paper provides novel insight into the role of proteogenomics as an analytical approach to identify predictive biomarkers of drug treatment response in epithelial ovarian cancer. …”
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Noncanonical roles of ATG5 and membrane atg8ylation in retromer assembly and function by Masroor Ahmad Paddar, Fulong Wang, Einar S Trosdal, Emily Hendrix, Yi He, Michelle R Salemi, Michal Mudd, Jingyue Jia, Thabata Duque, Ruheena Javed, Brett S Phinney, Vojo Deretic

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Post-genomic approaches to understanding interactions between fungi and their environment by R.P. de Vries, I. Benoit, G. Doehlemann, T. Kobayashi, J.K. Magnuson, E.A. Panisk, S.E. Baker, M.-H. Lebrun

“…The availability of fungal genomes and development of postgenomic technologies for fungi, such as transcriptomics, proteomics and metabolomics, have enabled more detailed studies into this topic resulting in new insights. …”
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High-Dimensional Cox Regression Analysis in Genetic Studies with Censored Survival Outcomes by Jinfeng Xu

“…With the advancement of high-throughput technologies, nowadays high-dimensional genomic and proteomic data are easy to obtain and have become ever increasingly important in unveiling the complex etiology of many diseases. …”
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Analysis of glutamate-dependent mechanism and optimization of fermentation conditions for poly-gamma-glutamic acid production by Bacillus subtilis SCP017-03. by Caiyun Wu, Yutao Gou, Shuai Jing, Wei Li, Fanglan Ge, Jiao Li, Yao Ren

“…In this study, we first systematically analyzed the response of Bacillus subtilis SCP017-03 to glutamate addition by comparing transcriptomics and proteomics. The introduction of glutamate substantially altered gene expression within the central metabolic pathway of cellular carbon. …”
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Diagnostic and Prognostic Significance of Exosomes and Their Components in Patients With Cancers by Zinnat Ara Moni, Zahid Hasan, Md. Shaheen Alam, Nitai Roy, Farhadul Islam

“…On the contrary, tumor cells release more exosomes than normal cells, and these tumor‐specific exosomes can carry the genomic and proteomic signature contents of the tumor cells, which can act as tools for the diagnosis and prognosis of patients with cancers. …”
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Total synthesis and target identification of marine cyclopiane diterpenes by Tian Li, Shan Jiang, Yuanhao Dai, Xia Wu, Huihui Guo, Liang Shi, Xueli Sang, Li Ren, Jie Wang, Lili Shi, Wenming Zhou, Houhua Li, Hong-Dong Hao

“…Herein, we report our synthetic and chemical proteomics studies of cyclopiane diterpenes which culminate in the asymmetric total synthesis of conidiogenones C, K and 12β-hydroxy conidiogenone C, and identification of Immunity-related GTPase family M protein 1 (IRGM1) as a cellular target. …”
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INSIHGT: an accessible multi-scale, multi-modal 3D spatial biology platform by Chun Ngo Yau, Jacky Tin Shing Hung, Robert A. A. Campbell, Thomas Chun Yip Wong, Bei Huang, Ben Tin Yan Wong, Nick King Ngai Chow, Lichun Zhang, Eldric Pui Lam Tsoi, Yuqi Tan, Joshua Jing Xi Li, Yun Kwok Wing, Hei Ming Lai

“…With INSIHGT, we map undescribed podocyte-to-parietal epithelial cell microfilaments in mouse glomeruli and neurofilament-intensive inclusion bodies in the human cerebellum, and identify NPY-proximal cell types defined by spatial morpho-proteomics in mouse hypothalamus. We anticipate that INSIHGT can form the foundations for 3D spatial multi-omics technology development and holistic systems biology studies.…”
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Integrated multi-omics profiling reveals neutrophil extracellular traps potentiate Aortic dissection progression by Yu-Fei Zhao, Zi-Ang Zuo, Zhe-Yun Li, Ye Yuan, Shi-Chai Hong, Wei-Guo Fu, Bin Zhou, Li-Xin Wang

“…It is imperative to delve into the exploration of prognostic indicators to streamline the identification of individuals at elevated risk for postoperative AAEs, and therapeutic targets to optimize the efficacy of TEVAR for patients with AD. Here, we perform proteomic and single-cell transcriptomic analyses of peripheral blood and aortic lesions, respectively, from patients with AD and healthy subjects. …”
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Secretomes from Mesenchymal Stem Cells against Acute Kidney Injury: Possible Heterogeneity by Kenji Tsuji, Shinji Kitamura, Jun Wada

“…Over the past few decades, many studies identified trophic factors from MSCs, which attenuate renal injury in a variety of animal acute kidney injury models, including renal ischemia-reperfusion injury and drug-induced renal injury, using microarray and proteomic analysis. Nevertheless, these studies have revealed the heterogeneity of trophic factors from MSCs that depend on the cell origins and different stimuli including hypoxia, inflammatory stimuli, and aging. …”
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Foodomics as a Tool for Evaluating Food Authenticity and Safety from Field to Table: A Review by Shuchen Zhang, Jianan Chen, Fanhui Gao, Wentao Su, Tiejing Li, Yuxiao Wang

“…This review also addresses crucial aspects of fully processing food, such as verifying the origin, processing techniques, label authenticity, and detecting adulterants, by summarizing the omics technologies of proteomics, lipidomics, flavoromics, metabolomics, genomics, and their analytical methodologies, recent developments, and limitations. …”
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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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