Journal: Nucleic Acids Research

Article Title: The GT1 domain of RNase J ensures RNA quality control through dsRNA binding in Arabidopsis plastids

doi: 10.1093/nar/gkag033

Figure Lengend Snippet: RNJ protein domains and structure. ( A ) RNJ linear structures from Arabidopsis thaliana, Populus trichocarpa, Chlamydomonas reinhardtii, Synechocystis sp. PCC 6803, Bacillus subtilis , and Methanocaldococcus jannaschii . Domains drawn to scale are the cTP, chloroplast target peptide; MBL, Metallo-β-lactamase domain; β-CASP, β-CASP domain; CTD, C-terminal domain; GT1, GT1 domain. On the right, protein length is indicated. ( B ) AlphaFold predicted structures as accessible from the AlphaFold Protein Structure Database ( https://alphafold.ebi.ac.uk/ ). Arabidopsis (At, AF- Q84W56 -F1), Chlamydomonas (Cr, AF-B2YFW5-F1), Synechocystis (Sy, AF- P54123 -F1), and Bacillus (Bs, AF- Q45493 -F1). Domains are colored as in panel (A) and as labeled for AtRNJ. The N-terminal region upstream of the MBL domain is hidden for easier viewing. The proline-rich helix unique to the Chlamydomonas linker region is indicated.

Article Snippet: Spectra were searched against the A. thaliana UniProt reference proteome (Taxon ID 3702, downloaded Jan 5, 2025; 39 396 sequences) supplemented with common contaminants and decoy sequences.

Techniques: Labeling

Journal: Computational and Structural Biotechnology Journal

Article Title: A global view of altered ligand-receptor interactions in bone marrow aging based on single-cell sequencing

doi: 10.1016/j.csbj.2024.06.020

Figure Lengend Snippet: Different LR interactions involving hematopoietic stem cells in old and young bone marrow. A. Left, the number of significantly different LR interactions with hematopoietic stem cells (HSC) as sender cell between the old and young group; Right, the number of significantly different LR interactions with HSC as receiver cell between the old and young group. MS> 0.1 and MS< −0.1 indicate up-regulation and down-regulation in the old group respectively. B．KEGG pathways enriched by receptors in the significantly different LR interactions with HSC as receiver cells. C, D. HEK293T cells were used to overexpress the three ligands Igfbp4, Mmp9 and Selenop respectively. Then the supernatant was then collected to incubate HSCs. WT is the supernatant of wild-type HEK293T without overexpressed protein. Then SPiDER-βGal flow cytometry was used to detect the fluorescence intensity of HSCs (C) and RT-qPCR was used to detect the expression of p16 and p21 in HSCs (D). * P value < 0.05, ** P value< 0.01.

Article Snippet: Mouse Igfbp4 (Refseq ID: 16010), Mmp9 (Refseq ID: 17395), and Selenop (Refseq ID: 20363) were cloned into protein expression plasmids (Sino Biological Inc., Beijing, China).

Techniques: Flow Cytometry, Fluorescence, Quantitative RT-PCR, Expressing