Development of Type 1 Diabetes Mellitus in Nonobese Diabetic Mice Follows Changes in Thymocyte and Peripheral T Lymphocyte Transcriptional Activity by Thais A. Fornari, Paula B. Donate, Claudia Macedo, Elza T. Sakamoto-Hojo, Eduardo A. Donadi, Geraldo A. Passos

“…The transcriptional activity of thymocytes developing into peripheral T lymphocytes revealed sequential participation of genes involved with CD4+/CD8+ T-cell differentiation (Themis), tolerance induction by Tregs (Foxp3), and apoptosis (Fasl) soon after T-cell activation (IL4), while the emergence of T1D coincided with the expression of cytotoxicity (Crtam) and inflammatory response genes (Tlr) by peripheral T lymphocytes.…”
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Transcriptional and cytokine signatures of Mycobacterium abscessus complex pulmonary disease during disease progression and treatment. by Ayesa Syenina, Yi Hern Tan, Danny Jian Hang Tng, Sandy Xue Qi Sim, Valerie Shyn Yun Chew, Jia Xin Yee, Eugenia Ziying Ong, Eng Eong Ooi, Jenny Guek Hong Low, Dorothy Hui Lin Ng

“…<h4>Methodology/principal findings</h4>To address the gaps in clinically relevant indicators, we profiled whole blood transcriptome and 45 plasma proteins of MABC-PD patients across different disease and treatment phases. …”
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Autophagy crosstalk with the immune microenvironment in chronic myeloid leukemia and serves as a biomarker for diagnosis and progression by Fangmin Zhong, Fangyi Yao, Jing Liu, Qun Fang, Xiajing Yu, Bo Huang, Xiaozhong Wang

“…Patients with high autophagy scores had a greater proportion of regulatory T-cell infiltration and greater cytokine–cytokine receptor interaction signaling pathway activity, while patients with low autophagy scores had greater γδT cell infiltration and PD-1 expression. …”
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Direct and indirect effects of spliceosome disruption compromise gene regulation by nonsense-mediated mRNA decay by Caleb M. Embree, Debadrita Paul, Andreas Stephanou, Guramrit Singh

“…Using publicly available RNA-seq datasets from K562 and HepG2 cells depleted of 18 different spliceosome components, we found that natural NMD-targeted mRNA isoforms were upregulated when catalytic spliceosome members were reduced. While some of this increase could be due to widespread pleiotropic effects of spliceosome dysfunction (e.g. reduced expression of NMD factors due to missplicing of their mRNAs), we identified that AQR, SF3B1, SF3B4, and CDC40 may have a more direct role in NMD. …”
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Expression of TAD1 (Tillering & Dwarf1) Gene in Hawara Bunar and IR64 Rice Cultivars by Vita Sindiya, Miftahul Huda Fendiyanto, Hamim Hamim, Miftahudin Miftahudin

“…Gene expression analysis was conducted using the qRT-PCR technique, while the phylogenetic tree was constructed based on the Neighbor-Joining method using PAUP4 software. …”
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Exogenous L-Cysteine and Its Transport Through CtaP Play a Role in Biofilm Formation, Swimming Motility, and Swarming Motility of <i>Listeria monocytogenes</i> by Mahide Muge Yilmaz Topcam, Nattanicha Prayoonwiwat, Carolina Bruschi, Kimon Andreas G. Karatzas

“…Furthermore, swimming motility of WT was enhanced with L-cysteine supplementation, while the swimming motility of Δ<i>ctaP</i> remained unaffected. …”
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Deciphering aging-associated prognosis and heterogeneity in gastric cancer through a machine learning-driven approach by Jiang Li, Chuanlai Yang, Yunxiao Zhang, Xiaoning Hong, Mingye Jiang, Zhongxu Zhu, Jiang Li

“…High AAI scores associated with poor prognosis and indicated potential benefits from adjuvant chemotherapy, while showing resistance to immunotherapy. Single-cell transcriptome analysis revealed that AAI was enriched in monocyte cells within the tumor microenvironment. …”
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A miR-219-5p-bmal1b negative feedback loop contributes to circadian regulation in zebrafish by Lianxin Wu, Meng Zhao, Xifeng Chen, Han Wang

“…Here, we showed that mature miR-219-5p, and its three pre-miRNAs, mir-219-1, mir-219-2, and mir-219-3, are rhythmically expressed primarily in Tectum opticum (TeO), Corpus cerebelli (CCe), and Crista cerellaris (CC) of the zebrafish brain. While mir-219-1 and mir-219-2 are regulated by the circadian clock through the E-like box, mir-219-3 is regulated by light via the D-box. …”
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Lysionotin promoted apoptosis of hepatocellular carcinoma cells via inducing autophagy by Xiaoxue Wang, Weiwei Zhong, Qin Wang, Peng Song, Xia Lin, Bohan Li, Yancun Yin, Chunyan Yang, Minjing Li

“…The molecular mechanism through which lysionotin induces autophagy and autophagy-induced apoptosis was ascertained by transcriptome sequencing, immunoblotting and Hoechst 33258 staining. …”
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Digital spatial profiling of segmental outflow regions in trabecular meshwork reveals a role for ADAM15. by Jennifer A Faralli, Mark S Filla, Yong-Feng Yang, Ying Ying Sun, Kassidy Johns, Kate E Keller, Donna M Peters, Donna M Peters

“…In this study we used a spatial transcriptomics approach to identify genes specifically associated with either high or low outflow regions in the trabecular meshwork (TM) that could potentially affect aqueous humor outflow in vivo. …”
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Functional Analysis of Promoters, mRNA Cleavage, and mRNA Secondary Structure on <i>esxB-esxA</i> in <i>Mycolicibacterium smegmatis</i> by Ryan G. Peters, Jessica M. Kelly, Sarah Bibeau, Ying Zhou, Scarlet S. Shell

“…EsxB (CFP-10) and EsxA (ESAT-6) are secreted effectors required for the function of ESX-1 systems. While some transcription factors regulating the expression of <i>esxB</i> and <i>esxA</i> have been identified, little work has addressed their promoter structures or other determinants of their expression. …”
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Identification of telomere maintenance-driven molecular subtypes in hepatocellular carcinoma: implications for prognosis and targeted therapy via KPNA2 by Zhicheng Xu, Hanyu Wang, Haixia Tian, Weijing Wang, Dong Hua

“…Results TC1 demonstrated a significant correlation with cellular differentiation and the fatty acid metabolism pathway, while also predicting a low tumor mutation burden (TMB) alongside favorable prognostic outcomes. …”
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Impact of Oxygen Availability on the Organelle‐Specific Redox Potentials and Stress in Recombinant Protein Producing Komagataella phaffii by Aliki Kostopoulou, Corinna Rebnegger, Borja Ferrero‐Bordera, Matthias Mattanovich, Sandra Maaß, Dörte Becher, Brigitte Gasser, Diethard Mattanovich

“…It was found that the transition from normoxic to hypoxic conditions affected the redox potential of all investigated organelles, while the exposure to hyperoxic conditions did not impact them. …”
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CDKN2D-WDFY2 is a cancer-specific fusion gene recurrent in high-grade serous ovarian carcinoma. by Kalpana Kannan, Cristian Coarfa, Kimal Rajapakshe, Shannon M Hawkins, Martin M Matzuk, Aleksandar Milosavljevic, Laising Yen

“…The parental gene, CDKN2D, is a cell-cycle modulator that is also involved in DNA repair, while WDFY2 is known to modulate AKT interactions with its substrates. …”
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Multiple changes in peptide and lipid expression associated with regeneration in the nervous system of the medicinal leech. by Céline Meriaux, Karim Arafah, Aurélie Tasiemski, Maxence Wisztorski, Jocelyne Bruand, Céline Boidin-Wichlacz, Annie Desmons, Delphine Debois, Olivier Laprévote, Alain Brunelle, Terry Gaasterland, Eduardo Macagno, Isabelle Fournier, Michel Salzet

“…Exposing nervous tissues to Transient Receptor Potential Vanilloid (TRPV) receptor agonists resulted in enhanced neurite outgrowth from a cut nerve, while exposure to antagonists blocked such outgrowth.…”
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N6-methyladenosine-mediated upregulation of MANF promotes ER stress resistance in renal cell carcinoma by Junjie Cen, Dongliang Zhao, Xin Shi, Jinlong Chen, Hang Zhou, Yanping Liang, Chengpeng Gui, Wei Chen, Junhang Luo, Xu Chen

“…This study identifies an unprecedented mechanism by which mesencephalic astrocyte-derived neurotrophic factor (MANF) contributes to RCC progression. From single-cell transcriptome, we observed a significant upregulation of MANF in RCC compared to its progenitor cells, the proximal tubular cells. …”
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A Novel Ferroptosis-Related Gene Prognosis Signature and Identifying Atorvastatin as a Potential Therapeutic Agent for Hepatocellular Carcinoma by Ling Wang, Xiaoqin He, Yang Shen, Jiayu Chen, Yukai Chen, Zhuolin Zhou, Ximing Xu

“…Through experiments conducted in vivo and in vitro, we demonstrated that Atorvastatin can induce ferroptosis in HCC cells while inhibiting their growth and migration. In conclusion, this research targets ferroptosis therapy and provides new insights for improving the prediction and prevention of HCC.…”
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Fusobacterium nucleatum as an oral bacteria promotes the carcinogenesis of laryngeal cancer via upregulating YWHAZ by Yiyue Ren, Jing Ye, Liuhong Shi, Kehao Le, Yifan Wang

“…Background and purpose F. nucleatum, a gram-negative oral bacteria, is abundant in laryngeal cancer (LC). While specific 14-3-3 proteins act as LC oncogenes, the link between F. nucleatum and 14-3-3 proteins dysregulation remains unknown.Materials and methods Transcriptome data from 520 HNSC patients were obtained from TCGA. …”
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Proteomic Analysis Reveals the Protective Effects of Selenomethionine Against Liver Oxidative Injury in Piglets by Kai Zhang, Shuhui Yan, Junhong Miao, Wen Li, Zhenxu Li

“…The control (CON) and diquat (DQ) groups were fed a basal diet supplemented with 0.3 mg Se/kg Se, while the SeMet group received a basal diet supplemented with 1.0 mg Se/kg. …”
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Unveiling the heterogeneity and immunotherapy potency of tumor-associated neutrophils in the tumor microenvironment of gastric cancer by Tong-tong Qi, Si-jiang Zhou, Zhu Yu, Yong Li, Jun-qiang Chen

“…Epithelial cells were classified into ten subclusters, while TANs were grouped into five subclusters. In gastric primary tumors, epithelial cell subtypes included primarily MUC16 + and stem-like populations. …”
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