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. …”
Get full text

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. …”
Get full text

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. …”
Get full text

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. …”
Get full text

A novel two-component system contributing the catabolism of c-di-GMP influences virulence in Aeromonas veronii by Chaolun Liu, Jia Shao, Xiang Ma, Yanqiong Tang, Juanjuan Li, Hong Li, Xue Chi, Zhu Liu

“…The roles of ArrS/ArrR in Aeromonas veronii were investigated using RT-qPCR, murine model, and proteomics.ResultsArrS and ArrR constituted a two-component system in Aeromonas veronii and were transcriptionally repressed by ArgR. …”
Get full text

Impact of developmental state, p53 status, and interferon signaling on glioblastoma cell response to radiation and temozolomide treatment. by Artem Berezovsky, Oluwademilade Nuga, Indrani Datta, Kimberly Bergman, Thais Sabedot, Katherine Gurdziel, Susan Irtenkauf, Laura Hasselbach, Yuling Meng, Claudius Mueller, Emanuel F Petricoin, Stephen Brown, Neeraja Purandare, Sidhesh Aras, Tom Mikkelsen, Laila Poisson, Houtan Noushmehr, Douglas Ruden, Ana C deCarvalho

“…In this study, we employed an integrative multi-omics approach, including targeted proteomics, transcriptomics, genomics, and DNA methylation profiling, to investigate the response of a representative panel of GBM patient-derived cancer stem cells (CSCs) to astrocytic differentiation and RT and TMZ treatments. …”
Get full text

A review of leishmaniasis: current knowledge and future directions of heterocyclic molecules by Tejaswini Masne, Dileep Kumar, Deepali Bansode

“…It emphasizes the importance of interdisciplinary research and integrating emerging technologies, such as genomics and proteomics, to identify new drug targets and strategies for disease control. …”
Get full text

Multi-modal investigation reveals pathogenic features of diverse DDX3X missense mutations. by Federica Mosti, Mariah L Hoye, Carla F Escobar-Tomlienovich, Debra L Silver

“…Here, we integrate transcriptomics, proteomics, and live imaging to demonstrate clinically diverse DDX3X missense mutations perturb neural development via distinct cellular and molecular mechanisms. …”
Get full text

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.…”
Get full text

Rehabilomics Strategies Enabled by Cloud-Based Rehabilitation: Scoping Review by Sejun Oh, SangHeon Lee

“… BackgroundRehabilomics, or the integration of rehabilitation with genomics, proteomics, metabolomics, and other “-omics” fields, aims to promote personalized approaches to rehabilitation care. …”
Get full text

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. …”
Get full text

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. …”
Get full text

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. …”
Get full text

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. …”
Get full text

Endothelial Progenitor Cell Migration-Enhancing Factors in the Secretome of Placental-Derived Mesenchymal Stem Cells by Witchayaporn Kamprom, Pakpoom Kheolamai, Yaowalak U-Pratya, Aungkura Supokawej, Methichit Wattanapanitch, Chuti Laowtammathron, Sittiruk Roytrakul, Surapol Issaragrisil

Get full text

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. …”
Get full text

The histone methyltransferase DOT1B is dispensable for stage differentiation and macrophage infection of Leishmania mexicana by Nicole Eisenhuth, Elisa Theres Rauh, Melina Mitnacht, Andrea Debus, Ulrike Schleicher, Falk Butter, Katerina Pruzinova, Petr Volf, Christian J. Janzen

Get full text

Gut microbiota drives colon cancer risk associated with diet: a comparative analysis of meat-based and pesco-vegetarian diets by Carlotta De Filippo, Sofia Chioccioli, Niccolò Meriggi, Antonio Dario Troise, Francesco Vitali, Mariela Mejia Monroy, Serdar Özsezen, Katia Tortora, Aurélie Balvay, Claire Maudet, Nathalie Naud, Edwin Fouché, Charline Buisson, Jacques Dupuy, Valérie Bézirard, Sylvie Chevolleau, Valérie Tondereau, Vassilia Theodorou, Claire Maslo, Perrine Aubry, Camille Etienne, Lisa Giovannelli, Vincenzo Longo, Andrea Scaloni, Duccio Cavalieri, Jildau Bouwman, Fabrice Pierre, Philippe Gérard, Françoise Guéraud, Giovanna Caderni

Get full text

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. …”
Get full text

Methods of yeast genome editing by A. S. Rozanov, V. N. Shlyahtun, L. A. Tekutieva, O. M. Son, S. V. Sizova, S. E. Peltek

“…Many high­throughput methods were developed in the second decade of the XXI century, including those used in genomics, transcriptomics, proteomics, metabolomics, interactomics, etc. Modern bioinformatic databases now allow one to rapidly process the increasing flow of information and model cellular processes. …”
Get full text