Phospho-seq: integrated, multi-modal profiling of intracellular protein dynamics in single cells by John D. Blair, Austin Hartman, Fides Zenk, Philipp Wahle, Giovanna Brancati, Carol Dalgarno, Barbara Treutlein, Rahul Satija

“…Abstract Cell signaling plays a critical role in neurodevelopment, regulating cellular behavior and fate. While multimodal single-cell sequencing technologies are rapidly advancing, scalable and flexible profiling of cell signaling states alongside other molecular modalities remains challenging. …”
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Novel Classification of Peroneal Tendon Disease Reveals Cellular and Molecular Phenotypes of the Tenosvnovium by Julia Matthias MD, Michael A. David PhD, Sara E. Buckley DO, Daniel J. Ross MD, Nathaniel Zona BA, Michael A. Hewitt B.A., Joshua Metzl MD, Daniel K. Moon MD, MS, MBA, Courtney Grimsrud MD, Douglas J. Adams PhD, Michael Zuscik PhD, Kenneth Hunt MD

“…Results: We observed distinct transcriptomic signatures between the tenosynovium graded by our classification system (Fig 1D). …”
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The role of B cell-activating factor system in autoimmune diseases: mechanisms, disease implications, and therapeutic advances by Liang Li, Shengxian Shen, Shuai Shao, Erle Dang, Gang Wang, Hui Fang, Hongjiang Qiao

“…Despite progress, mechanistic gaps in BAFF-mediated crosstalk between innate and adaptive immunity, as well as interspecies-specific pathogenesis warrant further investigation using humanized disease models and single-cell transcriptomic profiling. This review underscores the therapeutic potential of BAFF system modulation while advocating for disease-specific clinical trials to optimize precision-therapeutic targeting in autoimmune diseases.…”
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Graph-based pan-genome analysis reveals diversity of structural variations in native and commercial chicken by Yiming WANG, Zijia NI, Yinhua HUANG

“…The emergence of next-generation sequencing has enabled precise analysis of single nucleotide polymorphisms and insertions/deletions in chicken, while third-generation sequencing achieves the accurate structural variant identification. …”
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Identification and characterization of seminal fluid proteins in the Asian tiger mosquito, Aedes albopictus. by Kathryn E Boes, José M C Ribeiro, Alex Wong, Laura C Harrington, Mariana F Wolfner, Laura K Sirot

“…Despite the importance of Sfps on female reproductive behavior in mosquitoes and other insects, the identity of Sfps in Ae. albopictus has not previously been reported. We used transcriptomics and proteomics to identify 198 Sfps in Ae. albopictus. …”
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Widespread release of translational repression across Plasmodium's host-to-vector transmission event. by Kelly T Rios, James P McGee, Aswathy Sebastian, Sanjaya Aththawala Gedara, Robert L Moritz, Marina Feric, Sabrina Absalon, Kristian E Swearingen, Scott E Lindner

“…Therefore, female gametocytes proactively produce and translationally repress mRNAs that encode essential proteins that the zygote requires to establish a new infection. While the release of translational repression of individual mRNAs has been documented, the details of the global release of translational repression have not. …”
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Optimal Dual RNA-Seq Mapping for Accurate Pathogen Detection in Complex Eukaryotic Hosts by Infanta Eden M., Umashankar Vetrivel

“…Dual RNA-Seq technology has significantly advanced the study of biological interactions between two organisms by allowing parallel transcriptomic analysis. Existing analysis methods employ various combinations of open-source bioinformatics tools to process dual RNA-Seq data. …”
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Characterization of the major light-harvesting complexes (LHCBM) of the green alga Chlamydomonas reinhardtii. by Alberto Natali, Roberta Croce

“…LHCBM2/7 forms homotrimers while LHCBM1 seems to be present in heterotrimers. …”
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Studies on the antibacterial activity of the antimicrobial peptide Mastoparan X against methicillin-resistant Staphylococcus aureus by Zhangping Lu, Xiaofang Liang, Wenbo Deng, Qianqian Liu, Yulin Wang, Meng Liu, Fugui Lin, Zhihong Liu, Yu Zhang, Wenjie Wang, Yingying Sun, Yaozhou Wu, Lianhua Wei

“…In addition, Mastoparan X inhibited the formation of MRSA biofilm while destroying the mature bioepithelia already formed. …”
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RNAi effector diversity in nematodes. by Johnathan J Dalzell, Paul McVeigh, Neil D Warnock, Makedonka Mitreva, David McK Bird, Pierre Abad, Colin C Fleming, Tim A Day, Angela Mousley, Nikki J Marks, Aaron G Maule

“…While RNA interference (RNAi) has been deployed to facilitate gene function studies in diverse helminths, parasitic nematodes appear variably susceptible. …”
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Contrasting transcriptional responses of a virulent and an attenuated strain of Mycobacterium tuberculosis infecting macrophages. by Alice H Li, Simon J Waddell, Jason Hinds, Chad A Malloff, Manjeet Bains, Robert E Hancock, Wan L Lam, Philip D Butcher, Richard W Stokes

“…We identified and compared adaptations of either strain upon encountering an intracellular environment, and also contrasted the transcriptomes of the two strains while inside macrophages. …”
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Akkermansia muciniphila helps in the recovery of lipopolysaccharide-fed mice with mild intestinal dysfunction by Yue Hu, Yue Hu, Jun Zhou, Xiaoqi Lin

“…Akkermansia muciniphila supplementation, particularly at higher doses, partially restored gut microbiota by increasing beneficial genera such as Muribaculum. Transcriptomics showed that LPS induced immune and inflammatory responses, while Akkermansia muciniphila reduced these effects by modulating pathways like TNF and NF-kappa B signaling.ConclusionAkkermansia muciniphila mitigates LPS-induced gut dysfunction by restoring microbiota balance and modulating immune responses, highlighting its potential as a therapeutic agent for gut health.…”
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Site-2 protease Sll0528 interacts with RbcR to regulate carbon/nitrogen homeostasis in the cyanobacterium Synechocystis sp. PCC 6803 by Shiqi Lin, Taotao Zheng, Yongyi Mo, Ge Zhang, Gu Chen

“…Transcriptomic analysis showed that the knockout of sll0528 led to a significant downregulation of the RbcR regulon, including the ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) operon rbcLXS. …”
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Target of Rapamycin is involved in root hair development in Phaseolus vulgaris by Hugo Alberto Monreal Contreras, Manoj-Kumar Arthikala, Miguel Lara, Kalpana Nanjareddy

“…Root hairs are essential for nutrient acquisition and rhizosphere interactions in vascular plants. While the Target of Rapamycin (TOR) kinase is a well established regulator of growth and metabolism, its role in root hair development in Phaseolus vulgaris remains underexplored. …”
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Isoscopoletin inhibits hepatocellular carcinoma cell proliferation via regulating glycolysis-related proteins. by Chenyao Ruan, Chen Wang, Jiawen Gu, Zhihui Zhu

“…In vitro results showed that isoscopoletin inhibited glucose consumption and lactate production, while regulating the levels of glycolysis-related proteins.…”
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Long-term benefits of TUDCA supplement in ARSACS zebrafish model by Valentina Naef, Stefania Della Vecchia, Michela Giacich, Rosario Licitra, Tiziana Bachetti, Gabriela Coronel Vargas, Marco Ponassi, Filippo Maria Santorelli

“…These results support the potential of further exploring TUDCA in future preclinical and clinical studies, while also emphasizing the need for additional investigations to better understand its mechanisms of action.…”
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Integrative Analysis of Shared Pathogenic Genes and Potential Mechanisms in Gardnerella vaginalis and Persistent HPV16 Infection by Ye Li, Yue Wang, Xianhua Liu, Huifeng Xue, Liying Wang, Maotong Zhang, Pengming Sun

“…This study integrated transcriptomic data from in vitro GV infection experiments and a GEO dataset (GSE75132) of HPV16 persistence to elucidate shared pathogenic mechanisms. …”
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Effects of exogenous sucrose on root nitrogen uptake in apple at sub-low root-zone temperature by Xiaoping Zhao, Hanyu Liu, Lijie Li, Deguo Lyu

“…Most of the genes associated with C and N metabolism (MdBMY3, MdSS3, MdPFK6, MdCS2, MdNPF4.4, MdGS and MdGDH1) were upregulated under sucrose treatment, as confirmed by transcriptomic data. Furthermore, the transcriptomic and metabolomic results suggested that sucrose may enhance N uptake by increasing the accumulation of luteolin and sinapyl alcohol in flavonoid metabolism. …”
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The bioactive sphingolipid playbook. A primer for the uninitiated as well as sphingolipidologists by Yusuf A. Hannun, Alfred H. Merrill, Jr., Chiara Luberto

“…Thus, it is not surprising that untargeted genetic/transcriptomic/pharmacologic/metabolomic screens have uncovered changes in sphingolipids and sphingolipid genes/proteins while studying physiological and pathological processes. …”
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Systematic identification and expression profiling of calmodulin-binding transcription activator genes reveal insights into their functional diversity against pathogens in sugarcan... by Talha Javed, Wenzhi Wang, Juan Li, Tingting Sun, Linbo Shen, San-Ji Gao, Shuzhen Zhang

“…Notably, eight SsnpCAMTA gene pairs displayed segmental duplication events, while CAMTA genes from S. spontaneum Np-X and Arabidopsis thaliana shared homology relationship. …”
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