Genes to Cells最新文献

RNA sequencing (RNA-seq) has become an essential technology for assessing gene expression profiles in biomedical research. However, the coding complexity of RNA-seq data analysis remains a significant barrier for students and researchers without extensive bioinformatics expertise. We present the Educational RNA-Seq Analysis tool (ERSAtool), a comprehensive R/Shiny interface that provides an intuitive graphical visualization of the complete RNA-seq analysis workflow. The application is built on established Bioconductor packages and upholds high standards in analyses while significantly reducing the technical expertise required to conduct sophisticated transcriptomic analyses. ERSAtool supports various input formats, such as raw count matrices and STAR alignment outputs. It generates sample information metadata through direct integration with the international public repository, Gene Expression Omnibus (GEO). The application guides users through normalization, data visualization, differential expression analysis, and functional interpretation using Gene Ontology and Gene Set Enrichment Analyses. All results can be compiled into comprehensive, downloadable reports that enhance reproducibility and knowledge sharing. The design targets features that support educational use, making it especially helpful for teaching transcriptomics in undergraduate to graduate-level bioinformatics courses and enhancing access to advanced transcriptomic analysis, potentially accelerating discoveries across various biological fields. ERSAtool is available for free at https://github.com/SuzukiLabTAMU/ERSAtool.

Signal regulatory protein (SIRP) α, an inhibitory receptor belonging to the immunoglobulin (Ig) superfamily is abundantly expressed in phagocytes such as macrophages. CD47, the ligand for SIRPα, is expressed in most healthy cells, and called “don't eat me” signal because it binds to SIRPα on the surface of macrophages and inhibits phagocytosis. SIRPα has multiple splice isoforms, but most functional analyses have been carried out using long SIRPα, the SIRPα isoform with three extracellular Ig domains. In this study, we analyzed the expression and function of short SIRPα, an SIRPα isoform with only one extracellular Ig domain. In resting mouse macrophage Raw 264.7 cells, the short and long SIRPα mRNA expression levels were similar, and the proportion of short SIRPα mRNA decreased substantially after endotoxin stimulation. Short SIRPα bound to CD47 as same as long SIRPα, however, did not suppress the phagocytosis of recombinant CD47-coated beads, unlike long SIRPα. These results suggest that short SIRPα may be a “don't eat me” signal regulator with different expression and function from long SIRPα.

Testis-specific gene regulatory mechanisms govern the differentiation of germ cells into mature sperm. However, the molecular underpinnings are not fully elucidated. Here, we show the subunits forming Paf1C, a transcription regulator complex conserved across eukaryotes, have their individual paralogs predominantly expressed in Drosophila testes. One of these, namely, Ctr9 paralog enriched in testes (Ctr9t) was found to play a critical and nonredundant role in postmeiotic spermatid differentiation and male fertility in D. melanogaster. A proximity proteome analysis provides evidence that Ctr9t prefers the interaction between paralog members. We show endogenous Ctr9t is expressed and functional in germ cells at spermatocyte stages, accumulating in a distinct compartment within the nucleolus. There, Ctr9t co-localizes with Spermatocyte arrest (Sa), a testis-specific paralog of TATA-binding protein (TBP)-associated factor 8 (TAF8). We further demonstrate that ctr9t function is crucial for maintaining Sa in the nucleolus, but not vice versa. Transcriptome profiling reveals that Ctr9t acts as an activator for the set of male fertility genes on the Y chromosome, but it also acts as a global repressor of X chromosome genes. Collectively, our results shed light on the nucleolus-associated, paralog-dependent regulation of gene expression from sex chromosomes, which ensures the terminal differentiation of male germ cells.

The 1st Asia & Pacific Bioinformatics Conference (APBJC) covers a wide range of scientific topics in the oral sessions (black) and workshops (red) as well as the poster session. The numbers in parentheses indicate the number of presentations in each session. AI-related topics were found to be connected to many of the session themes.

Retinal plays a key role in light absorption across prokaryotes and eukaryotes, both in rhodopsin and bacteriorhodopsin systems. The multicellular social amoeba Dictyostelium discoideum exhibits positive phototaxis. However, retinal binding proteins such as rhodopsin have not been found in the genome of Dictyostelium cells. Herein, we microscopically examined the effects of retinal on Dictyostelium cells. On adding all-trans-retinal to the medium, Dictyostelium cells retracted their pseudopodia and became rounded. This was unique to retinal among the tested vitamin A variants. Addition of all-trans-retinal at low concentrations did not cause cell rounding. However, it increased the frequency of cAMP signaling triggered during cell development. Results indicate that retinal acts on an unknown signaling pathway involving the cytoskeleton in Dictyostelium cells.

Diabetic retinopathy (DR) is known as a microvascular complication, in which various inflammatory symptoms, including activation of microglia, are observed. A model of hyperglycemia resembling type 1 diabetes mellitus (DM) induced in mice by intraperitoneal injection of streptozotocin (STZ) has been widely used. We examined the effects of anti- vascular endothelial growth factor A (VEGFA) and anti-angiopoietin-2 (ANGPT2) antibodies in addition to a bispecific antibody against VEGFA and ANGPT2 by intravitreously administrated to the eyes on early signs, especially the activation of microglia in STZ-treated mice eyes. After 14 weeks of STZ administration, alterations in activity by ERG and CD31 staining patterns were not observed. Although a difference in the number of microglia in the retina between normal and STZ-model retinas was not observed, the morphology of microglia had changed from ramified in control to amoeboid shape in STZ model at 4 days after the antibodies injection. Detailed morphological examination showed decreases in area, ramification index, and tree length in the STZ-model retinas compared with normal retinas. Recovery from these decreases was demonstrated mainly by the administration of the bispecific antibody. These results suggest that anti-VEGFA/ANGPT2 therapy may suppress the activation of microglia in the early stages of DR.

Corneal neovascularization (CNV) is frequently observed after various corneal injuries and corneal transplantation, leading to impairment of corneal transparency. Lymphangiogenesis and the inflammatory response often accompany CNV. Chemical injury is one of the most common causes of CNV, and alkali injury has been widely used as an animal model of this pathological state. We examined the effects of subconjunctival injection of an anti-VEGFA antibody (anti-VEGFA_ab), anti-ANGPT2 antibody (anti-ANGPT2_ab), and bispecific antibody against VEGFA and ANGPT2 (BsAb) in CNV using the alkali injury mouse model. The pathological indexes were examined using anterior segment optical coherence tomography (OCT) and whole-mount immunostaining, and gene expression patterns were examined using RT-qPCR. Treatment with anti-VEGFA_ab, anti-ANGPT2_ab, or BsAb did not affect the swelled thickness of the cornea; however, angiogenesis, but not lymphangiogenesis, was hampered by the treatment of either one of the antibodies. We observed an increase in the mRNA levels of Vegfa, Angpt2, Il1b, and Cx3cr1 following alkali injury. The administration of BsAb suppressed the induction of Vegfa and Cx3cr1. Additionally, BsAb treatment enhanced the mRNA levels of Angpt1 in this model. This study demonstrates the potential of dual VEGFA and ANGPT2 inhibition as a therapeutic strategy for CNV.