Mechanism for microbial population collapse in a fluctuating resource environment by Serdar Turkarslan, Arjun V Raman, Anne W Thompson, Christina E Arens, Mark A Gillespie, Frederick von Netzer, Kristina L Hillesland, Sergey Stolyar, Adrian López García de Lomana, David J Reiss, Drew Gorman‐Lewis, Grant M Zane, Jeffrey A Ranish, Judy D Wall, David A Stahl, Nitin S Baliga

“…We have characterized the mechanism for collapse by conducting RNA‐seq analysis, proteomics, microcalorimetry, and single‐cell transcriptome analysis. …”
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Proteostasis and Mitochondrial Role on Psychiatric and Neurodegenerative Disorders: Current Perspectives by Pablo Olivero, Carlo Lozano, Ramón Sotomayor-Zárate, Nicolás Meza-Concha, Marcelo Arancibia, Claudio Córdova, Wilfredo González-Arriagada, Ricardo Ramírez-Barrantes, Ivanny Marchant

“…Proteostasis alterations in the prefrontal cortex implicate proteome instability and accumulation of misfolded proteins. …”
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Alternative 3′ UTR polyadenylation is disrupted in the rNLS8 mouse model of ALS/FTLD by Randall J. Eck, Paul N. Valdmanis, Nicole F. Liachko, Brian C. Kraemer

“…Here, we identify significant disruptions to 3` UTR polyadenylation in the ALS/FTLD-TDP mouse model rNLS8 that correlate with changes in gene expression and protein levels through the re-analysis of published RNA sequencing and proteomic data. A subset of these changes are shared with TDP-43 knock-down mice suggesting depletion of endogenous mouse TDP-43 is a contributor to polyadenylation dysfunction in rNLS8 mice. …”
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Biological Aging and Venous Thromboembolism: A Review of Telomeres and Beyond by Rafaela Vostatek, Cihan Ay

“…Techniques such as high-throughput genomics, epigenomics, transcriptomics, proteomics, and metabolomics analyses identified and quantified numerous epigenetic markers, transcripts, proteins, and metabolites. …”
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Cytokine Patterns in Brain Tumour Progression by Radu Albulescu, Elena Codrici, Ionela Daniela Popescu, Simona Mihai, Laura Georgiana Necula, Daniel Petrescu, Mihaela Teodoru, Cristiana Pistol Tanase

“…The body’s response to cancer has many parallels with inflammation and repair; the inflammatory cells and cytokines present in tumours are more likely to contribute to tumour growth, progression, and immunosuppression, rather than in building an effective antitumour defence. Using new proteomic technology, we have investigated serum profile of pro- (IL-1β, IL-6, IL-8, IL-12, GM-CSF, and TNF-α) and anti-inflammatory cytokines (IL-4, IL-10), along with angiogenic factors (VEGF, bFGF) in order to assess tumoural aggressiveness. …”
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Molecular correlates for HPV-negative head and neck cancer engraftment prognosticate patient outcomes by Matthew Waas, Christina Karamboulas, Benson Z. Wu, Shahbaz Khan, Stephanie Poon, Jalna Meens, Meinusha Govindarajan, Amanda Khoo, Salvador Mejia-Guerrero, Annie Ha, Lydia Y. Liu, Kevin C. J. Nixon, Joseph Walton, Scott V. Bratman, Shao Hui Huang, David Goldstein, Federico Gaiti, Laurie Ailles, Thomas Kislinger

“…Here, we perform transcriptomic and proteomic profiling of 88 HNSCC patients and find the relationship between engraftment and clinical outcomes is recapitulated by molecular phenotype. …”
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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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Activators of the 26S proteasome when protein degradation increases by Donghoon Lee

“…Abstract In response to extra- and intracellular stimuli that constantly challenge and disturb the proteome, cells rapidly change their proteolytic capacity to maintain proteostasis. …”
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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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