PTEN as a prognostic factor for radiotherapy plus immunotherapy response in nasopharyngeal carcinoma by Jiaxing Guo, Ming Zhang, Xiaoli Li, Jiashuo Wang

“…Flow cytometry of cells and exosomal analysis were performed to examine these proteins. …”
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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

“…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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OperonSEQer: A set of machine-learning algorithms with threshold voting for detection of operon pairs using short-read RNA-sequencing data. by Raga Krishnakumar, Anne M Ruffing

“…A number of methods have used transcriptomics data to predict operons, based on the premise that contiguous genes in an operon will be expressed at similar levels. …”
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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

“…Transcriptomic analysis showed that 851 genes were significantly altered and ABC transport protein, amino acid biosynthesis, glycolysis and tricarboxylic acid (TCA) cycle were inhibited after 16μg/mL Mastoparan X treatment.ConclusionOur study demonstrated that Mastoparan X has potent bactericidal activity against MRSA and is expected to provide new potential peptides for the clinical treatment of MRSA.…”
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Constructing a tumor immune microenvironment-driven prognostic model in acute myeloid leukemia using bioinformatics and validation data by Amir Abbas Navidinia, Ali Keshavarz, Bentol Hoda Kuhestani Dehaghi, Reza Khayami, Najibe Karami, Vahid Amiri, Mehdi Allahbakhshian Farsani

“…TIME analysis revealed associations between high-risk scores and immunosuppressive cell subsets, including Tregs and M2 macrophages. …”
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Physiological Responses and Histopathological Changes in Narrow-Clawed Crayfish (<i>Pontastacus leptodactylus</i>) Under Acute Thermal Stress by Xia Zhu, Bin Li, Yuzhen Liu, Shujian Chen, Yangfang Ye, Ronghua Li, Weiwei Song, Changkao Mu, Chunlin Wang, Ce Shi

“…Similarly, the T25 group displayed increased MDA and CAT levels but decreased T-AOC. Comparative transcriptomic analysis demonstrated that differentially expressed genes (DEGs) in the control vs. …”
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Assessment and Monitoring of the Wound Micro-Environment in Chronic Wounds Using Standardized Wound Swabbing for Individualized Diagnostics and Targeted Interventions by Julian-Dario Rembe, Waseem Garabet, Jan-Wilm Lackmann, Sadaf Alizadehrahrouei, Matthias Augustin, Joachim Dissemond, Wiebke Ibing, Karl Köhrer, Klaus Pfeffer, Anna Rommerskirchen, Sebastian Alexander Scharf, Tobias Wienemann, Thorsten Wachtmeister, Hubert Schelzig, Ewa Klara Stuermer

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Unraveling the Heterogeneity of CD8+ T-Cell Subsets in Liver Cirrhosis: Implications for Disease Progression by Kepu Zheng, Leiyang Dai, Shengning Zhang, Yingpeng Zhao, Wang Li, Yang Gao, Yuanyi Mang, Lingfeng Jiao, Yu Tang, Jianghua Ran

“…Tex cells, defined by PDCD1, LAG3, and CXCL13 expression, were increased in cirrhosis, while Tem cells were decreased. Lineage tracing and differential analysis highlighted CXCL13+ Tex cells as a terminal, exhausted subtype of cells with roles in PD-1 signaling, glycolysis, and T-cell regulation. …”
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Gut microbiota regulates innate anxiety through neural activity of medial prefrontal cortex in male mice by Jing Ren, Xiao-Ying Lian, Wan-Qian Ye, You-Lu Wen, Cheng-Lin Lu, Xiong Cao

“…Neural activation mapping revealed elevated c-FOS expression in the medial prefrontal cortex (mPFC), basolateral amygdala (BLA), and central amygdala (CeA) of HA-FMT recipients. Transcriptomic analysis of mPFC tissue in HA- and LA-FMT recipients demonstrated microbiota driven regulation of transcriptional reprogramming, protein modification, and synapse modulation, indicating mechanistic connections along the microbiota gut-brain axis. …”
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Kynu inhibition mitigates bile duct ischemic injury by rewiring tryptophan metabolism to restore tight junction integrity by Guoqing Bao, Siliang Zhang, Zhengchen Ye, Ding Luo, Pinduan Bi, Bin Yang

“…In vivo, post-ischemia Kynu blockade reduced bile duct damage, inflammation, and biliary barrier permeability. Proteome analysis revealed that Kynu inhibition decreased 3-HAA, AA and QA levels while increased XA level. …”
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Ketomimetic nutrients remodel the glycocalyx and trigger a metabolic defense in breast cancer cells by Mohini Kamra, Yuan-I Chen, Paula C. Delgado, Erin H. Seeley, Stephanie K. Seidlits, Hsin-Chih Yeh, Amy Brock, Sapun H. Parekh

“…Single cell label-free metabolic imaging has been performed, coupled with measurement of cellular proliferative and migratory abilities, and MS-based metabolomic screens. Transcriptomic analysis of crucial enzymes was performed using total RNA extraction and rt-qPCR. …”
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RAB5B: explore its carcinogenic potential and understand its role, prognostic value and biological significance in pan-cancer by Jing Zhu, Chun Yu, Xin Xu, Chu Zou, Jiaqi Li, Rui Wang, Xinchao Li, Aijun Sun, Shiyan Wang, Chao Jiang

“…Although studies have revealed the functional mechanisms of RAB5B in specific tumor types, its role in pan-cancer and the underlying molecular mechanisms still lack in-depth analysis.MethodsA comparative analysis of RAB5B gene expression was conducted using transcriptomic datasets from Cancer Genome Map (TCGA) and Genotype-Tissue Expression (GTEx), followed by tissue distribution profiling via Human Protein Atlas (HPA) and GeneMANIA to map its expression across human tissues. …”
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The effect of dietary chitin on Atlantic salmon (Salmo salar) chitinase activity, gene expression, and microbial composition by Matilde Mengkrog Holen, Simen Rød Sandve, Thomas Nelson Harvey, Yang Jin, Inga Leena Angell, Knut Rudi, Matthew Peter Kent

“…Here we use a combination of chitinase activity assays, transcriptomics, and 16S rRNA bacterial analysis to assess the effect of chitin supplementation on Atlantic salmon gene expression and microbial community composition. …”
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Fish MicroRNA Responses to Thermal Stress: Insights and Implications for Aquaculture and Conservation Amid Global Warming by Ting Lin, Madhava Meegaskumbura

“…In the context of global warming, heat tolerance is becoming a crucial physiological trait influencing fish species’ distribution and survival. While our understanding of fish heat tolerance and stress has expanded from behavioral studies to transcriptomic analyses, knowledge at the transcriptomic level is still limited. …”
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Genome-wide identification of the regulatory network of mitogen-activated protein kinase signaling cascades gene families in Hevea Brasiliensis by Xiaojuan Huang, Manman Sun, Xiaoyu Du, Lin Quan, Jinquan Chao, Xiaomin Deng, Hongze Liao

“…Furthermore, expression profiling analysis based on public transcriptomic data revealed that these genes were differentially expressed in various tissues and differentially regulated in response to different stresses. …”
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To verify the biological characteristics of disulfidptosis associated gene ADORA2B in esophageal cancer by Yixiao Cui, Yuhan Deng, Zhenhua Wu, Xiaohong Sun

“…Utilizing integrated transcriptomics and single-cell proteomics, the involvement of immune cells in the tumor microenvironment was examined, while bioinformatics was used to investigate the expression, function, and survival data of ADORA2B. …”
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Addressing the tissue specificity of U5 snRNP spliceosomopathies by Rahmat Azhari Kemal, Rahmat Azhari Kemal, Raymond T. O’Keefe

“…We propose that future research could benefit from models originating from patient-derived induced pluripotent stem cells (iPSCs) and isogenic controls to compare the coding and non-coding transcriptomic perturbations. Analysis of spliceosomal protein complexes and their interactome could also uncover novel insights on molecular pathogenesis. …”
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The glutamate receptor gene GLR3.3: A bridge of calcium-mediated root development in poplar by Yi An, Ya Geng, Yu Liu, Xiao Han, Lichao Huang, Wei Zeng, Jin Zhang, Mengzhu Lu

“…In this study, we analyzed the morphological and transcriptomic variations of 84K poplar (Populus alba × P. glandulosa) in response to different calcium concentrations and found that low Ca2+ (1 mmol · L−1) promoted lateral root development, while deficiency (0.1 mmol · L−1 Ca2+) inhibited lateral root development. …”
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Bisphenol S interrupted axonogenesis on a human embryonic stem cells derived neural differentiation model: Conserved axon guidance and WNT signaling pathway involved by Wanqing Guo, Wei Xiong, Liang Wang, Xiaoya Wang, Yongru Zhou, Yili Chen, Xiaomeng Li, Lishi Zhang, Mengmei Ni, Jinyao Chen

“…The results revealed that BPS exposure interrupted axonogenesis, manifesting a trend of initial stimulating followed by inhibition, and peaked at the intermediate dose (3.75 μM) significantly, then reached the nadir at the high dose (375 μM) significantly in the precursor to maturation stage and the whole differentiation stage. Transcriptomics analysis showed that the main interrupted pathway enriched in axonogenesis, myelination, and neurotransmitter secretion by the GO function analysis and immune-related pathway by the KEGG analysis, besides, conserved axon guidance (Slit-Robo, Netrin-DCC, Semaphorin-Plexin) and WNT signaling pathway was also enriched in KEGG pathway analysis, which previously proved to regulate axonogenesis by directly acting on growth cones and inhibit axon growth by neuroinflammatory responses. …”
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Evaluating methods for integrating single-cell data and genetics to understand inflammatory disease complexity by Hope A. Townsend, Hope A. Townsend, Kaylee J. Rosenberger, Kaylee J. Rosenberger, Lauren A. Vanderlinden, Lauren A. Vanderlinden, Jun Inamo, Jun Inamo, Fan Zhang, Fan Zhang, Fan Zhang

“…Conversely, large genome-wide association studies (GWAS) are commonly accessible.MethodsWe present a 3-step robust benchmarking analysis of integrating GWAS and scRNA-seq to identify genetically relevant cell states and genes in inflammatory diseases. …”
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