Opportunities and Prospects for Preclinical Drug Safety Assessment Using Alternative Methods: Experience from the Toxicology in the 21st Century (Tox21) Programme in the USA by V. N. Perfilova

“…Thus, new tools and technologies provide an opportunity for switching from in vivo toxicity testing of candidate medicinal products to in silico and in vitro methods.…”
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Single cell analysis of diverse immune cell in pneumococcal meningitis by Yujie Zhang, Jing Duan, Sufang Lin, Jialun Wen, Jianxiang Liao

“…In conclusion, our study provides a comprehensive single-cell transcriptomic landscape of immune responses in PM. …”
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Identification of a terpene synthase arsenal using long-read sequencing and genome assembly of Aspergillus wentii by Richard Olumakaiye, Christophe Corre, Fabrizio Alberti

“…Conclusion These results provide a scaffold for the future exploration of terpenoid biosynthetic pathways for bioactive molecules in A. wentii. …”
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Machine learning explores the prognostic and immuno-oncological impact of mitochondrial unfolded protein response in CESC by Keh-Sen Liu, Yen-Hsiang Chang, Hsing-Ju Wu, Hung-Yu Lin

“…These insights into UPRmt’s role in CESC provide new directions for developing personalized treatment strategies.…”
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Enhancing anti-CD3 mAb-mediated diabetes remission in autoimmune diabetes through regulation of dynamin-related protein 1(Drp1)-mediated mitochondrial dynamics in exhausted CD8+T-c... by Ruiling Zhao, Zhangyao Su, Junjie Gu, Hang Zhao, Lingling Bian, Yin Jiang, Yun Cai, Tao Yang, Yong Gu, Xinyu Xu

“…T-cell receptor (TCR) diversity and Bulk RNA sequencing provided insights into the transcriptomic profiles and TCR reactivity of these cells. …”
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Sulfated dietary fiber protects gut microbiota from antibiotics by Fuqing Wu, Xiaoqian Annie Yu, David Angeles-Albores, Susan E. Erdman, Eric J. Alm

“…Result In this study, we found that fucoidan, a marine polysaccharide derived from brown seaweed, provides broad-spectrum growth protection against multiple classes of antibiotics for human gut microbial isolates in vitro and for fecal communities ex vivo. …”
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BBSome deficiency in Lotmaria passim reveals divergent functions in trypanosomatid parasites by Xuye Yuan, Tatsuhiko Kadowaki

“…Studying the BBSome in flagellated protists can provide insights into these ancestral functions and their subsequent adaptations. …”
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A novel system to culture human intestinal organoids under physiological oxygen content to study microbial-host interaction. by Tatiana Y Fofanova, Umesh C Karandikar, Jennifer M Auchtung, Reid L Wilson, Antonio J Valentin, Robert A Britton, K Jane Grande-Allen, Mary K Estes, Kristi Hoffman, Sashirekha Ramani, Christopher J Stewart, Joseph F Petrosino

“…Thus, the IOPC system provides a robust coculture setup for investigating host-microbe interactions in complex, patient-derived intestinal tissues, that can facilitate the study of mechanisms underlying the role of the microbiome in health and disease.…”
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Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast. by Emanuel Gonçalves, Zrinka Raguz Nakic, Mattia Zampieri, Omar Wagih, David Ochoa, Uwe Sauer, Pedro Beltrao, Julio Saez-Rodriguez

“…We extended our analysis to two studies containing transcriptomics, phosphoproteomics and metabolomics measurements across a comprehensive panel of kinases/phosphatases knockouts and time-resolved perturbations to the nitrogen metabolism. …”
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Multi-task benchmarking of spatially resolved gene expression simulation models by Xiaoqi Liang, Marni Torkel, Yue Cao, Jean Yee Hwa Yang

“…Abstract Background Computational methods for spatially resolved transcriptomics (SRT) are often developed and assessed using simulated data. …”
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Therapeutic potential of a choline-zinc-vitamin E nutraceutical complex in ameliorating thioacetamide-induced nonalcoholic fatty liver pathology in zebrafish. by Bingbing Cao, Jiali Zhou, Bo Xia, Xiaoqing Li, Rui Wang, Yiqiao Xu, Chunqi Li

“…The results of this study provide evidence for the application of the nutraceutical complex in the improvement of NAFLD.…”
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Characterization of MreCD in Streptococcus mutans by Victor Chan, Tessa Holcomb, Justin R. Kaspar, Robert C. Shields

“…Assays included cell morphology imaging, protein interaction analysis, transcriptomics, proteomics, and biofilm studies to generate a comprehensive understanding of the role of MreCD in S. mutansResults Consistent with mreCD participating in cell elongation, cells lacking these genes were found to be rounder than wild-type cells. …”
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Single-Cell RNA Sequencing Reveals the Interaction of Injected ADSCs with Lung-Originated Cells in Mouse Pulmonary Fibrosis by Mamatali Rahman, Zhao-Yan Wang, Jun-Xiang Li, Hao-Wei Xu, Rui Wang, Qiong Wu

“…The ADSC treatment drastically changed the transcriptomic profile and composition of lung cells, especially macrophages. …”
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Listeria monocytogenes infection rewires host metabolism with regulatory input from type I interferons. by Duygu Demiroz, Ekaterini Platanitis, Michael Bryant, Philipp Fischer, Michaela Prchal-Murphy, Alexander Lercher, Caroline Lassnig, Manuela Baccarini, Mathias Müller, Andreas Bergthaler, Veronika Sexl, Marlies Dolezal, Thomas Decker

“…Moreover, FA oxidation inhibition provides protection from L. monocytogenes infection, explaining part of the protection of Irf9-/- and Ifnar1-/- mice. …”
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Non-reciprocal Interspecies Hybridization Barriers in the Capsella Genus Are Established in the Endosperm. by Carolin A Rebernig, Clément Lafon-Placette, Marcelinus R Hatorangan, Tanja Slotte, Claudia Köhler

“…These results provide strong support for the theory that crosses between plants of different mating systems will be unbalanced, with the outcrosser behaving like a plant of increased ploidy, evoking a response that resembles an interploidy-type seed failure. …”
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Understanding Atherosclerotic Plaque Cellular Composition: Recent Advances Driven by Single Cell Omics by Esra Cetin, Anne-Catherine Raby

“…With the development of single-cell transcriptomic and proteomic technologies, a previously inconceivable wealth of data has been generated in an attempt to better understand the pathophysiology of the disease and identify novel avenues for the development of targeted therapeutic interventions. …”
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Data-driven model discovery and model selection for noisy biological systems. by Xiaojun Wu, MeiLu McDermott, Adam L MacLean

“…We demonstrate the potential to learn models from sparse, noisy data in application to a canonical cell state transition using data derived from single-cell transcriptomics. Overall, this approach provides a practical framework for model discovery in biology in cases where data are noisy and sparse, of particular utility when the underlying biological mechanisms are partially but incompletely known.…”
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Inhibition of FLT1 ameliorates muscular dystrophy phenotype by increased vasculature in a mouse model of Duchenne muscular dystrophy. by Mayank Verma, Yuko Shimizu-Motohashi, Yoko Asakura, James P Ennen, Jennifer Bosco, Zhiwei Zhou, Guo-Hua Fong, Serene Josiah, Dennis Keefe, Atsushi Asakura

“…Recently, the vasculature has also shown to be perturbed in DMD and DMD model mdx mice. Recent DMD transcriptomics revealed the defects were correlated to a vascular endothelial growth factor (VEGF) signaling pathway. …”
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Utilisation of mucin glycans by the human gut symbiont Ruminococcus gnavus is strain-dependent. by Emmanuelle H Crost, Louise E Tailford, Gwenaelle Le Gall, Michel Fons, Bernard Henrissat, Nathalie Juge

“…Comparative genomic analysis of the two R. gnavus strains highlighted potential clusters and glycoside hydrolases (GHs) responsible for the breakdown and utilization of mucin-derived glycans. Transcriptomic and functional activity assays confirmed the importance of specific GH33 sialidase, and GH29 and GH95 fucosidases in the mucin utilisation pathway. …”
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The multi-omics analysis identifies a novel endoplasmic reticulum stress and immune related genes signature in lung adenocarcinoma by Danhe Huang, Yuying Liu, Mingyu Yuan, Xiongwei Wang, Lianqing Hong

“…Methods Utilizing transcriptomic and clinical data from the TCGA-LUAD cohort, we developed an ERS-immune prognostic signature through Least Absolute Shrinkage and Selection Operator algorithm. …”
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