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

“…The IOPC cultured HIOs showed increased barrier integrity, and induced expression of immunomodulatory genes. A transcriptomic analysis suggests that HIOs from different donors show differences in the magnitude of their response to coculture with anaerobic bacteria. …”
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Role of laboratory biomarkers in monitoring and prediction of the effectiveness of treatment of rheumatic diseases using genetically engineered drugs by Elena Nikolayevna Aleksandrova, A A Novikov, E L Nasonov

“…The search for and validation of immunological predictors of the effective response to GE drug therapy make it possible to optimize and reduce the cost of therapy using these drugs in future.…”
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Expression of a humanized viral 2A-mediated lux operon efficiently generates autonomous bioluminescence in human cells. by Tingting Xu, Steven Ripp, Gary S Sayler, Dan M Close

“…Furthermore, the use of self-directed bioluminescent initiation in response to target detection was assessed to determine its amenability towards deployment as fully autonomous sensors. …”
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A multivariate cell-based liquid biopsy for lung nodule risk stratification: Analytical validation and early clinical evaluation by Jason D. Berndt, Fergal J. Duffy, Mark D. D'Ascenzo, Leslie R. Miller, Yijun Qi, G. Adam Whitney, Samuel A. Danziger, Anil Vachani, Pierre P. Massion, Stephen A. Deppen, Robert J. Lipshutz, John D. Aitchison, Jennifer J. Smith

“…In the platform, standardized cells are exposed to small volumes of patient serum, and the resulting transcriptomic response is analyzed using machine learning tools to develop disease classifiers. …”
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Machine learning models highlight environmental and genetic factors associated with the Arabidopsis circadian clock by Connor Reynolds, Joshua Colmer, Hannah Rees, Ehsan Khajouei, Rachel Rusholme-Pilcher, Hiroshi Kudoh, Antony N. Dodd, Anthony Hall

“…However, understanding clock function at the transcriptome level and its response to the environment requires assaying across high resolution time-course experiments. …”
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Evaluation of Beauvericin’s activity and mode of action against all life stages of L. tropica for cutaneous Leishmaniasis therapy by Lynn Al Samra, Mohamad El Nahas, Ilham Mneimneh, Aia Sinno, Sima Tokajian, Kelven Rahy, Sergio Thoumi, Lazo Ali, Wael Yammine, Charbel Al Khoury

“…Mechanistically, BEA acts as a calcium ionophore, inducing a marked increase in intracellular calcium levels, which serves as the primary cytotoxic event. Transcriptomic profiling further revealed that BEA-induced calcium dysregulation triggers secondary cellular responses involving calcium homeostasis, lipid metabolism, and stress response, contributing to its multifaceted mechanism of action. …”
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Harnessing cell size to separate genetically and functionally distinct dental pulp-derived mesenchymal stromal cell subpopulations by Yiyue Jiang, Zheng Zhang, Kangkang Ren, Shujuan Zhou, Yang Qiao, Weilu Huang, Nanyang Zhang, Hanyan Xu, Xinping Xu, Bing Wen, Wei Zhang, Lu Yin

“…The large- and medium-sized subpopulation upregulates genes involved in immune responses, calcium signaling, and ECM-receptor interaction, while the small-sized subpopulation downregulates genes associated with immune response pathways, cell cycle, and growth factor activities. …”
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Exercise-mobilized donor lymphocyte infusions enhanced with cytokine stimulation for the prevention and treatment of leukemic relapse after allogeneic hematopoietic cell transplant... by London M. McDougal, Forrest L. Baker, Forrest L. Baker, Forrest L. Baker, Michael P. Gustafson, Emmanuel Katsanis, Emmanuel Katsanis, Emmanuel Katsanis, Emmanuel Katsanis, Emmanuel Katsanis, Richard J. Simpson, Richard J. Simpson, Richard J. Simpson, Richard J. Simpson

“…Preclinical evidence suggests that these exercise-mobilized lymphocytes infiltrate tumors, exhibit enhanced leukemic control in xenogeneic mice, and display transcriptomic and proteomic profiles indicative of heightened anti-tumor immunity, migration potential and cytokine responsiveness. …”
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Circular Nucleic Acids Act as an Oncogenic MicroRNA Sponge to Inhibit Hepatocellular Carcinoma Progression by Qianyi Zhang, Pengcheng Sun, Guang Hu, Xuanyao Yu, Wen Zhang, Xuan Feng, Lan Yu, Pengfei Zhang

“…First, we identified tumor suppressor genes (TSGs) with abnormally low expression in hepatocellular carcinoma (HCC) tumor cells by transcriptomic analysis and targeted the upstream cancer miRNA clusters of these TSGs. …”
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Degenerated vision, altered lipid metabolism, and expanded chemoreceptor repertoires enable Lindaspio polybranchiata to thrive in deep-sea cold seeps by Yujie Yan, Inge Seim, Yang Guo, Xupeng Chi, Zhaoshan Zhong, Dantong Wang, Mengna Li, Haining Wang, Huan Zhang, Minxiao Wang, Chaolun Li

“…Over long-term adaptive evolution, genes associated with vision and biological rhythmicity were lost, which may indirectly benefit oligotrophy by eliminating energetically costly processes. Compared to its shallow-sea relatives, L. polybranchiata has a significantly higher proportion of polyunsaturated fatty acids (PUFAs) and expanded gene families involved in the biosynthesis of unsaturated fatty acids and chromatin stabilization, possibly in response to high hydrostatic pressure. …”
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Adaptation by stochastic switching of a monostable genetic circuit in Escherichia coli by Saburo Tsuru, Nao Yasuda, Yoshie Murakami, Junya Ushioda, Akiko Kashiwagi, Shingo Suzuki, Kotaro Mori, Bei‐Wen Ying, Tetsuya Yomo

“…Abstract Stochastic switching is considered as a cost‐saving strategy for adaptation to environmental challenges. …”
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A plasmid-chromosome crosstalk in multidrug resistant enterobacteria by Laura Toribio-Celestino, Alicia Calvo-Villamañán, Cristina Herencias, Aida Alonso-del Valle, Jorge Sastre-Dominguez, Susana Quesada, Didier Mazel, Eduardo P. C. Rocha, Ariadna Fernández-Calvet, Alvaro San Millan

“…Combining genetic engineering, transcriptomics, and CRISPRi gene silencing, we show that a pOXA-48-encoded LysR regulator is responsible for the plasmid-chromosome crosstalk. …”
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Inactivated Rothia nasimurium promotes a persistent antiviral immune status in porcine alveolar macrophages by Aida Tort-Miró, Aida Tort-Miró, Aida Tort-Miró, Uxía Alonso, Beatriz Martín-Mur, Beatriz Martín-Mur, Jordana Muñoz-Basagoiti, Jordana Muñoz-Basagoiti, Jordana Muñoz-Basagoiti, Yan Zeng, David Marín-Moraleda, David Marín-Moraleda, David Marín-Moraleda, Enrique Ezcurra, Enrique Ezcurra, Enrique Ezcurra, Sergio Montaner-Tarbes, Sergio Montaner-Tarbes, Sergio Montaner-Tarbes, María J. Navas, María J. Navas, María J. Navas, Marta Muñoz, Marta Muñoz, Marta Muñoz, Paula Monleón, Paula Monleón, Paula Monleón, Judith González-Oliver, Judith González-Oliver, Judith González-Oliver, Esmeralda Cano, Esmeralda Cano, Esmeralda Cano, Carles Vilalta, Carles Vilalta, Carles Vilalta, Marc Caballé, Lourdes Criado, Karl Kochanowski, Karl Kochanowski, Karl Kochanowski, Francesc Accensi, Francesc Accensi, Virginia Aragón, Virginia Aragón, Virginia Aragón, Florencia Correa-Fiz, Florencia Correa-Fiz, Florencia Correa-Fiz, Anna Esteve-Codina, Anna Esteve-Codina, Fernando Rodríguez, Fernando Rodríguez, Fernando Rodríguez, Jordi Argilaguet, Jordi Argilaguet, Jordi Argilaguet

“…In particular, the capability of bacterial-based immunostimulants to modulate innate immune cells functionality makes them cost-effective candidates as vaccine adjuvants, antimicrobials, or preventive immunostimulators inducing long-term innate immune memory in livestock. …”
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Facile construction of mechanically robust and highly osteogenic materials for bone regeneration by Song Chen, Dachuan Liu, Qianping Guo, Li Dong, Huan Wang, Jiaxu Shi, Weicheng Chen, Caihong Zhu, Weishan Wang, Wei Xia, Miodrag J. Lukic, Helmut Cölfen, Bin Li

“…Although various strengthening strategies have been applied, the achieved mechanical response of hydrogels still lags behind the mechanics of natural bone. …”
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FB5P-seq-mAbs: monoclonal antibody production from FB5P-seq libraries for integrative single-cell analysis of B cells by Sakina Ado, Chuang Dong, Noudjoud Attaf, Myriam Moussa, Agathe Carrier, Agathe Carrier, Pierre Milpied, Jean-Marc Navarro

“…Parallel analysis of phenotype, transcriptome and antigen receptor sequence in single B cells is a useful method for tracking B cell activation and maturation during immune responses. …”
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Multiomic Analysis of Environmental Effects and Nitrogen Use Efficiency of Two Potato Varieties Under High Nitrogen Conditions by Shuo Gao, Guowei Wei, Yuan Chang, Yanbin Yin, Qiaorong Wei, Ying Shi

“…Excessive use of nitrogen (N) fertilizer in potato production has increased costs and environmental pollution. In this study, the N use efficiency (NUE) of two potato varieties (DXY and DN310) was determined under high nitrogen conditions. …”
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Ursolic Acid Regulates Intestinal Microbiota and Inflammatory Cell Infiltration to Prevent Ulcerative Colitis by Qinsong Sheng, Fei Li, Guanping Chen, Jiacheng Li, Jing Li, YiFan Wang, Yingyan Lu, Qun Li, Mingqian Li, Kequn Chai

“…Ulcerative colitis (UC) is a chronic and relapsing inflammatory bowel disorder in the colon and rectum leading to low life-quality and high societal costs. Ursolic acid (UA) is a natural product with pharmacological and biological activities. …”
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Single-cell technology for drug discovery and development by Anzhuo Zhang, Jiawei Zou, Yue Xi, Lianchong Gao, Fulan Deng, Yujun Liu, Pengfei Gao, Henry H. Y. Tong, Lianjiang Tan, Xin Zou, Xin Zou, Jie Hao

“…The success rate of drug development today remains low, with long development cycles and high costs, especially in areas such as oncology, neurology, immunology, and infectious diseases. …”
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Building digital histology models of transcriptional tumor programs with generative deep learning for pathology-based precision medicine by Hanna M. Hieromnimon, James Dolezal, Kristina Doytcheva, Frederick M. Howard, Sara Kochanny, Zhenyu Zhang, Robert L. Grossman, Kevin Tanager, Cindy Wang, Jakob Nikolas Kather, Evgeny Izumchenko, Nicole A. Cipriani, Elana J. Fertig, Alexander T. Pearson, Samantha J. Riesenfeld

“…However, the costs of such assays can be prohibitive for clinical translation at scale. …”
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Lysosome-Associated Membrane Protein Targeting Strategy Improved Immunogenicity of Glycoprotein-Based DNA Vaccine for Marburg Virus by Xiyang Zhang, Yubo Sun, Junqi Zhang, Hengzheng Wei, Jing Wang, Chenchen Hu, Yang Liu, Sirui Cai, Qinghong Yuan, Yueyue Wang, Yuanjie Sun, Shuya Yang, Dongbo Jiang, Kun Yang

“…Moreover, DNA vaccines have unique advantages, such as simple construction processes, low production costs, and few adverse reactions, but their immunogenicity may decrease due to the poor absorption rate of plasmids. …”
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