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Osteosarcoma is a highly aggressive bone tumor with a complex tumor microenvironment (TME) that contributes to its progression and therapeutic resistance. In this study, we integrated single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq datasets to …
Read PDFThe western painted turtle, Chrysemys picta bellii, has the greatest tolerance to anoxia of any tetrapod studied to date. These turtles reside in the northern United States and southern Canada, and survive months of anoxia …
Read PDFN<sup>6</sup>-methyladenosine (m<sup>6</sup>A), the most prevalent epitranscriptomic modification in plant mRNAs, functions as a critical regulatory layer governing environmental response. Refrigeration reduces transcripts of cell wall enzymes to delay softening, however whether m<sup>6</sup>A participated in this …
Read PDFThe <i>Lagerstroemia indica</i> (Crepe Myrtle) is an economically important ornamental and medicinal plant, with significant potential for functional genomics and breeding. However, there is no comprehensive, centralized database integrating multi-omics data. Therefore, it is of …
Read PDFObjectiveThis study investigated whether metastasis-associated protein 1 (MTA1) acts as an RNA-binding protein to directly regulate gene expression and alternative splicing in prostate cancer, thereby exploring its dual transcriptional and post-transcriptional roles.MethodsMTA1-stable-knockdown PC-3 cells were …
Read PDFOligodendrocytes produce myelin, a lipid-rich membrane that wraps neuronal axons in the central nervous system to provide metabolic and trophic support and allow for saltatory conduction. Developation requires precisely timed and localized neuron-oligodendrocyte communication. In …
Read PDFWhile cell hashing enhances single-cell RNA sequencing (scRNA-seq) efficiency and minimizes batch effects, commercial mouse hashtags often fail in FVB/N and several other strains due to antibody-epitope incompatibility. We describe a robust alternative utilizing biotinylated …
Read PDFDNA2 coordinates essential maintenance processes, including cell-cycle progression; however, its aberrant activity has been implicated in cancer cell survival under oncogene-induced replication stress. To date, no comprehensive pan-cancer investigation of DNA2 has been conducted. Employing …
Read PDFFungal pathogens represent a rising global concern with increasing impacts on human health and food security. Despite their significance, research on fungal infections continues to lag behind other infectious diseases, hindering diagnostic and treatment advances. …
Read PDFSpatial transcriptomics (ST) integrates gene expression with spatial context to study tissue pathology. We present SPaSE (spatially resolved pathology score), a protocol to quantify pathology by computing an optimal transport plan between ST spots of …
Read PDFIschemic stroke represents a significant global health hazard, causing substantial morbidity, mortality, and long-term disability worldwide. The brain's complexity necessitates targeting ischemic stroke dysfunction syndrome. Single-cell RNA sequencing (scRNA-seq) offers unbiased, high-resolution analysis of cell …
Read PDFComparative functional genomic studies are often affected by biased read mapping across species due to inter-species differences in genome structure, sequence composition, and annotation quality. We developed CrossFilt, a filtering strategy that retains only sequencing …
Read PDFBACKGROUND: This systematic review synthesizes applications of machine learning (ML) for multi-omics data integration in crop improvement, evaluating its dual potential to enhance predictive accuracy for selection (breeding utility) and to generate interpretable biological insights …
Read PDF<h4>Background</h4>Cervical cancer is among the most prevalent gynecological malignancies globally, and its inherent molecular heterogeneity remains a persistent obstacle to uniform treatment efficacy and patient survival. Lysosome-mediated cell death (LDCD) has recently emerged as a …
Read PDFOvarian cancer (OC) is a predominant cause of fatality amongst gynecological malignancies, frequently identified at its later stages owing to its asymptomatic characteristics and the absence of adequate screening techniques. Imaging techniques such as ultrasound …
Read PDFRecent advances in transcriptomics and regulatory genomics have expanded interest in the potential roles of alternative splicing and noncoding RNAs in the evolution of eusociality in bees. A recently published review by Brenman-Suttner and Zayed …
Read PDF<h4>Background</h4>Mucosal-associated invariant T (MAIT) cells are innate-like T lymphocytes involved in immune surveillance and tissue homeostasis. Yet, their transcriptional dynamics and functional crosstalk with macrophages at the time of myocardial injury are incompletely defined.<h4>Methods</h4>We used …
Read PDFCarcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1) is a multifunctional immunomodulatory protein involved in both immune activation and immune suppression across diverse cancer types. However, its biological significance and clinical relevance in sarcoma (SARC) remain …
Read PDFDrought stress is the most pervasive abiotic constraint on global crop productivity, with projected intensification under climate change threatening the yields of staple crops including wheat, rice, maize, and legumes. Conventional breeding approaches have delivered …
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