CryoSCAPE: Scalable immune profiling using cryopreserved whole blood for multi-omic single cell and functional assays by Alexander T. Heubeck, Cole Phalen, Neel Kaul, Peter J. Wittig, Jessica Garber, Morgan Weiss, Palak C. Genge, Zachary Thomson, Claire Gustafson, Julian Reading, Peter J. Skene

“…We present CryoSCAPE (Cryopreservation for Scalable Cellular And Proteomic Exploration), a scalable method for immune studies of human PBMC with multi-omic single cell assays using direct cryopreservation of whole blood. …”
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Starvation-induced metabolic rewiring affects mTORC1 composition in vivo by Edgar Kaade, Simone Mausbach, Nina Erps, Marc Sylvester, Farhad Shakeri, Ron D. Jachimowicz, Volkmar Gieselmann, Melanie Thelen

“…Therefore, we investigated the changes of the proteome of liver lysosomes in mice starved short-term for 6h or long-term for 24h. …”
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Neuroprotective effects of curculigoside against Alzheimer’s disease via regulation oxidative stress mediated mitochondrial dysfunction in L-Glu-exposed HT22 cells and APP/PS1 mice... by Wenqi Wang, Yidi Qu, Siyu Li, Jinyu Chu, Hongxin Yang, Lirong Teng, Di Wang

“…Based on the screening of proteomic analysis on hippocampus, CCG were confirmed that it could regulate the expression levels of proteins related to mitochondrial dysfunction, mainly through activating on AMPK/Nrf2 signaling, in APP/PS1 mice and L-Glu-exposed HT22 cells. …”
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The triterpenoids-enriched extracts from Antrodia cinnamomea mycelia attenuate alcohol-induced chronic liver injury via suppression lipid accumulation in C57BL/6 mice by Yange Liu, Ronglong Chen, Lanzhou Li, Ruitao Dong, Hui Yin, Yawen Wang, Anhui Yang, Jianbin Wang, Changtian Li, Di Wang

“…Combining with the pathological observations, ACT displayed an anti-steatosis effects to restrain the progress of ALD. Based on proteomic analysis and enzyme-linked immunosorbent assay, ACT had been confirmed to regulate the levels of lipid biogeneration-related factors and depressed the over-accumulation of hepatic reactive oxygen species. …”
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Modulation of biological activities in adipose derived stem cells by histone deacetylation by Sallam Abdallah, Mouna Tabebi, Sawsan Qanadilo, Neserin Ali, Jing Wang, Pádraig D’Arcy, Wen Zhong, Folke Sjoberg, Moustafa Elmasry, Ahmed El-Serafi

“…Microarray analysis revealed 74 upregulated and 40 downregulated differentially expressed genes, including upregulation of P53 targets, CDKN1A and MDM2. Proteomic analysis identified 631 upregulated and 823 downregulated proteins compared to the vehicle. …”
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Comprehensive Enteroviral Serology Links Infection and Anti‐Melanoma Differentiation‐Associated Protein 5 Dermatomyositis by Sahana Jayaraman, Eleni Tiniakou, William R. Morgenlander, Miso Na, Lisa Christopher‐Stine, H. Benjamin Larman

“…Methods We employed Phage ImmunoPrecipitation Sequencing to profile serum antibodies against the human proteome, the human virome, and a comprehensive enterovirus library. …”
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Associations between accurate measures of adiposity and fitness, blood proteins, and insulin sensitivity among South Asians and Europeans by Pik Fang Kho, Pik Fang Kho, Laurel Stell, Shirin Jimenez, Shirin Jimenez, Daniela Zanetti, Daniela Zanetti, Daniela Zanetti, Daniel J. Panyard, Kathleen L. Watson, Ashish Sarraju, Ashish Sarraju, Ming-Li Chen, Ming-Li Chen, Lars Lind, John R. Petrie, Khin N. Chan, Holly Fonda, Kyla Kent, Kyla Kent, Jonathan N. Myers, Jonathan N. Myers, Jonathan N. Myers, Latha Palaniappan, Latha Palaniappan, Latha Palaniappan, Fahim Abbasi, Themistocles L. Assimes, Themistocles L. Assimes, Themistocles L. Assimes, Themistocles L. Assimes

“…We explored this possibility by investigating the relationship between ‘gold standard’ measures of adiposity, fitness, selected proteomic biomarkers, and insulin sensitivity among a cohort of SAs and Europeans (EURs).MethodsA total of 46 SAs and 41 EURs completed ‘conventional’ (lifestyle questionnaires, standard physical exam) as well as ‘gold standard’ (dual energy X-ray absorptiometry scan, cardiopulmonary exercise test, and insulin suppression test) assessments of adiposity, fitness, and insulin sensitivity. …”
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Platelet‐derived apoptotic vesicles ameliorate nonalcoholic fatty liver disease by regulating lipid metabolism via apolipoprotein A‐II by Yuhe Jiang, Yike Liao, Zeying Wang, Lei Zhu, Yunsong Liu, Ping Zhang, Yuan Zhu, Wenyue Li, Yongsheng Zhou, Xiao Zhang

“…The results showed that PLT‐apoVs exhibited superior effects in diminishing lipid accumulation in liver induced by high‐fat diet than MSC‐apoVs. Through proteomic analysis, we defined and validated apolipoprotein A‐II (APOA2) as a regulator for apoV‐mediated MSC adipogenesis, which could be used as a target to enhance apoV therapeutic potential in the lipid metabolism biomedical field. …”
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NERVE 2.0: boosting the new enhanced reverse vaccinology environment via artificial intelligence and a user-friendly web interface by Andrea Conte, Nicola Gulmini, Francesco Costa, Matteo Cartura, Felix Bröhl, Francesco Patanè, Francesco Filippini

“…Abstract Background Vaccines development in this millennium started by the milestone work on Neisseria meningitidis B, reporting the invention of Reverse Vaccinology (RV), which allows to identify vaccine candidates (VCs) by screening bacterial pathogens genome or proteome through computational analyses. When NERVE (New Enhanced RV Environment), the first RV software integrating tools to perform the selection of VCs, was released, it prompted further development in the field. …”
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Identifying optimal substrate classes of membrane transporters. by Andreas Denger, Volkhard Helms

“…Identifying all membrane transporters within a (meta-)proteome, along with their specific substrates, provides important information for various research fields, including biotechnology, pharmacology, and metabolomics. …”
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Altering the redox status of Chlamydia trachomatis directly impacts its developmental cycle progression by Vandana Singh, Scot P Ouellette

“…EBs and RBs have distinctive characteristics that distinguish them, including their size, infectivity, proteome, and transcriptome. Intriguingly, they also differ in their overall redox status as EBs are oxidized and RBs are reduced. …”
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Transcription factor TCF4: structure, function, and associated diseases by R. R. Savchenko, N. A. Skryabin

“…The biological role of approximately 20 % of human proteins has not been established yet, and the molecular functions of the known part of the proteome remain poorly understood. This hinders progress in basic and applied biological and medical sciences, especially in treating hereditary diseases, which are caused by mutations and polymorphic variants in individual genes. …”
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Robust ensemble of handcrafted and learned approaches for DNA-binding proteins by Loris Nanni, Sheryl Brahnam

“…Purpose – Automatic DNA-binding protein (DNA-BP) classification is now an essential proteomic technology. Unfortunately, many systems reported in the literature are tested on only one or two datasets/tasks. …”
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The molecular view of mechanical stress of brain cells, local translation, and neurodegenerative diseases by T. M. Khlebodarova

“…In further consideration of the role of the local translation system in the development of neuropsychic and neurodegenerative diseases, an original hypothesis was put forward that one of the possible causes of synaptopathies is impaired proteome stability associated with mTOR hyperactivity and formation of complex dynamic modes of de novo protein synthesis in response to synapse-stimulating factors, including chronic mechanical stress.…”
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IGFBP2 and IGFBP4 interact to activate complement pathway in diabetic kidney disease by Jieling Liang, Yangxiao Huang, Daping Peng, Yali Xie, Yifei Liu, Xiuxia Lu, Junfa Xu

“…Overactivation of the complement pathway in DKD remains poorly understood.Methods Blood samples were collected from patients for proteomic analysis, complemented by both in vitro and in vivo experiments to investigate the roles of IGFBP2, IGFBP4, and the complement pathway in DKD.Results Elevated levels of IGFBP2 and IGFBP4 were observed in DKD patients. …”
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Cytoplasmic male sterility and prospects for its utilization in breeding, genetic studies and seed production of potato by I. N. Anisimova, T. A. Gavrilenko

“…The main results of research on molecular mechanisms of CMS and fertility restoration obtained in the post-genomic era for various plant species using methods of transcriptomic and proteomic analyses are provided. As in many plant species, cytoplasmic male sterility in potato is of hybrid origin. …”
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Effect of Dietary Cholesterol, Phytosterol, and Docosahexaenoic Acid on Astaxanthin Absorption and Retention in Rainbow Trout by Yang Jin, Keshuai Li, Jon Olav Vik, Marie Hillestad, Rolf Erik Olsen

“…On the other hand, the transcriptomic and proteomic analyses found no changes of genes or proteins involved in Ax absorption, transport, or excretion in fish fed PS or DHA diets as compared to the control diet. …”
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Scrutinizing neurodegenerative diseases: decoding the complex genetic architectures through a multi-omics lens by Relu Cocoș, Bogdan Ovidiu Popescu

“…Additionally, we emphasize the importance of multi-omics layers including genomic, transcriptomic, proteomic, epigenetic, and metabolomic data in elucidating the molecular mechanisms underlying neurodegeneration. …”
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Cbf11 and Mga2 function together to activate transcription of lipid metabolism genes and promote mitotic fidelity in fission yeast. by Anna Marešová, Michaela Grulyová, Miluše Hradilová, Viacheslav Zemlianski, Jarmila Princová, Martin Převorovský

“…Deletion of either gene results in a similar array of defects, including slow growth, dysregulated lipid homeostasis, impaired cell cycle progression (cut phenotype), abnormal cell morphology, perturbed transcriptomic and proteomic profiles, and compromised response to the stressors camptothecin and thiabendazole. …”
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Identification of GBN5 as a molecular biomarker of pan-cancer species by integrated multi-omics analysis by Qian Guo, Xinxin Zhong, Zihan Dang, Baiquan Zhang, Zixin Yang

“…Materials and methods We employed a multi-omics approach, including transcriptomic, genomic, proteomic, single-cell cytomic, spatial transcriptomic, and genomic data, to explore the prognostic value and potential oncogenic mechanisms of GBN5 across pan-cancers from multiple perspectives. …”
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