genome, transcript, and protein sequence data  (Beijing Genomics Institute Shenzhen)

Journal: The Plant Journal

Article Title: Chlamydomonas reinhardtii , Volvox carteri and related green algae accumulate ketocarotenoids not in vegetative cells but in zygospores

doi: 10.1111/tpj.17261

Figure Lengend Snippet: Phylogeny of BKT proteins from green algae and CrtW proteins from selected cyanobacteria and non‐photosynthetic bacteria. The maximum likelihood tree was inferred from an alignment of 70 protein sequences from 52 species and encompassing 245 amino acid positions and was rooted to a CrtW protein cluster from α‐proteobacteria. Nodes labeled with black dots had bootstrap support (100 replicates) ≥90%, white dots indicate support ≥60%. Green algal BKT proteins from species known to accumulate ketocarotenoids in the vegetative state are in red and labeled with an asterisk, those from species not known to accumulate ketocarotenoids but reported to generate reddish zygospores are in bold orange, and those for which we confirmed zygospore‐specific accumulation of ketocarotenoids are additionally underlined. See Table for sequence accessions and Figure for full tree with uncollapsed branches and bootstrap values.

Article Snippet: The amino acid sequence of the BKT from C. reinhardtii (GenBank accession AAX54908) was used for BLAST (Altschul et al., ) searches in (i) the PhycoCosm database at https://phycocosm.jgi.doe.gov/phycocosm/home (Grigoriev et al., ) and (ii) the protein sequence data of various cyanobacteria and proteobacteria in the GenBank microbial genomes to retrieve bacterial CrtW sequences used in previous phylogenetic analyses (Makino et al., ).

Techniques: Algae, Bacteria, Labeling, Sequencing

Journal: Redox Biology

Article Title: Androgen receptor deficiency-induced TUG1 in suppressing ferroptosis to promote benign prostatic hyperplasia through the miR-188-3p/GPX4 signal pathway

doi: 10.1016/j.redox.2024.103298

Figure Lengend Snippet: Disrupting Tug1 in mouse prostate luminal cells inhibits age-related glandular enlargement. a Analysis of Tug1 expression across various mouse tissues and its abundance in BPH tissues. The primary figure is derived from RT-qPCR analysis of Tug1 expression across various mouse tissues, with the top right figure showing Tug1 abundance using RNA-seq data from BPH tissues. b Examination of TUG1 expression in different cellular populations within human prostate tissues by using single-cell data from the HPA database. c A schematic representation of the anatomy of the mouse prostate. AP, anterior prostate; DLP, dorsolateral prostate; VP, ventral prostate. d RT-qPCR analysis of Tug1 expression in the AP, DLP, and VP of the mouse prostate. e FISH combined with IF analysis for the localization and quantification of Tug1 in different regions of the mouse prostate. Scale bars: 50 μm. f Construction and characterization of the mouse model with prostate luminal cell-specific knockout of Tug1. The primary figure outlines the construction and analysis process for the mouse model, with the top right figure presenting RT-qPCR analysis of Tug1 expression in the AP, DLP, and VP of the prostate in Pbsn-Cre4 Tug1 wt/wt or Pbsn-Cre4 Tug1 fl/fl mice at 12 months g Representative images of prostate tissues and H&E staining of the AP, DLP, and VP from Pbsn-Cre4 Tug1 wt/wt or Pbsn-Cre4 Tug1 fl/fl mice at 4, 8, and 12 months. The dashed line area represents the prostate tissue of mice. Scale bars: 1 cm for gross; 50 μm for H&E staining. h-i Comparison of the relative expansion (h) or weight (i) of the AP, DLP, and VP of the mouse prostate between Pbsn-Cre4 Tug1 wt/wt or Pbsn-Cre4 Tug1 fl/fl mice at 4, 8, and 12 months. * P < 0.05; ** P < 0.01; *** P < 0.001; n.s no significant.

Article Snippet: Single-cell sequencing data from the Human Protein Atlas (HPA) database of prostate tissues revealed that IL-1β is primarily derived from macrophages ( d).

Techniques: Expressing, Derivative Assay, Quantitative RT-PCR, RNA Sequencing, Knock-Out, Staining, Comparison

Journal: Redox Biology

Article Title: Androgen receptor deficiency-induced TUG1 in suppressing ferroptosis to promote benign prostatic hyperplasia through the miR-188-3p/GPX4 signal pathway

doi: 10.1016/j.redox.2024.103298

Figure Lengend Snippet: Downregulation of AR promotes TUG1 expression via IL-1β/MYC signaling in prostate luminal cells. a-c Correlation analyses between TUG1 expression and AR mRNA levels (a), IL1B mRNA levels (b), and IL-1β protein concentrations (c) in BPH tissues from our validation cohort. d Analysis of IL1B expression across different cellular populations within human prostate tissues using single-cell data from the HPA database. e CISH combined with IHC staining for the quantification of TUG1, AR, CD68, and IL-1β in BPH tissues. f Schematic representation of the experimental approach for AR inhibitor treatment in Pbsn-Cre4 Tug1 wt/wt or Pbsn-Cre4 Tug1 fl/fl mice. g-h Analysis of DLP weight (g) and H&E staining (h) in the prostate of Pbsn-Cre4 Tug1 wt/wt or Pbsn-Cre4 Tug1 fl/fl mice treated with PBS or MDV3100. i IF staining for AR and CD68 in the prostate of Pbsn-Cre4 Tug1 wt/wt mice treated with PBS or MDV3100. j RT-qPCR analysis of Il1b and Tug1 expression in the prostate of Pbsn-Cre4 Tug1 wt/wt mice treated with PBS or MDV3100. k FISH combined with IF for the quantification of Tug1 and AR expression in the prostate of Pbsn-Cre4 Tug1 wt/wt mice treated with PBS or MDV3100. l Integrative analysis of the JASPAR, PROMO, and AnimalTFDB databases along with TUG1-related genes to identify transcription factors involved in TUG1 regulation. m RT-qPCR analysis of Tug1 expression in RWPE-1 and BPH-1 cells transfected with siRNA targeting MYC or SP1, followed by treatment with PBS or IL-1β. n RT-qPCR analysis of TUG1 expression in RWPE-1 and BPH-1 cells treated with IL-1β and the MYC inhibitor 10058-F4. o IHC staining for MYC in the prostate of Pbsn-Cre4 Tug1 wt/wt mice treated with PBS or MDV3100. p Identification of MYC binding motifs within the human TUG1 promoter region. q-r ChIP-qPCR analysis of the MYC binding site at the TUG1 promoter region in RWPE-1 (q) and BPH-1 (r) cells. s-t Luciferase reporter assays of wild-type (WT) and mutant (MUT) TUG1 promoters in RWPE-1 (s) and BPH-1 (t) cells transfected with MYC siRNA and treated with IL-1β. All scale bars: 50 μm * P < 0.05; ** P < 0.01; *** P < 0.001; n.s no significant.

Article Snippet: Single-cell sequencing data from the Human Protein Atlas (HPA) database of prostate tissues revealed that IL-1β is primarily derived from macrophages ( d).

Techniques: Expressing, Biomarker Discovery, Immunohistochemistry, Staining, Quantitative RT-PCR, Transfection, Binding Assay, ChIP-qPCR, Luciferase, Mutagenesis