Journal: Developmental biology

Article Title: Role of BMP signaling during early development of the annelid Capitella teleta.

doi: 10.1016/j.ydbio.2021.06.011

Figure Lengend Snippet: Fig. 1. List of exogenous BMP4 treatments performed. Solid black line: Animals raised in ASW þ PS þ BMP4 protein. Blue dashed line: Animals raised in ASW þ PS. Blue tissue in stages 4–6 larvae: neural tissue.

Article Snippet: Ct-BMP2/4 protein (Kenny et al., 2014) has a 42% sequence identity and 58% sequence similarity with the recombinant zebrafish BMP4 protein (R&D Systems, cat. 1128-BM-010) used; the sequence alignment was performed by T-Coffee (Di Tommaso et al., 2011).

Techniques:

Journal: bioRxiv

Article Title: Usherin in the pineal gland: altered sleep in zebrafish models of Usher syndrome type 2a

doi: 10.64898/2026.03.09.710525

Figure Lengend Snippet: A) Mid-sagittal H&E-stained section from the Zebrafish BioAtlas of a 6 dpf larva ( ; ). The pineal gland (indicated by the box) is located on the dorsal side of the brain, situated between the telencephalon and mesencephalon. B) Corresponding mid sagittal section from 5 dpf wild-type larva labelled with DAPI (blue), anti-usherin C-terminus (red), and anti-rhodopsin (green). The white box indicates the pineal gland region, which is shown at higher magnification in panel C. C) Higher magnification of the pineal gland in AB wild-type and ush2a b1245 mutant larvae. Usherin localises to the pineal gland in wild-type but is absent in ush2a mutants. Scale bar: 20 µm.

Article Snippet: The following primary antibodies were used: rabbit anti-usherin (C-terminal, 1:1000, DZ01481, Boster Bio) and mouse anti-rhodopsin (1:5000, NBP2-59690, Novus Biologicals) or mouse anti-centrin (1:500, 04-1624, Sigma-Aldrich).

Techniques: Staining, Mutagenesis

Journal: iScience

Article Title: The microcephaly-associated protein YIPF5 differentially regulates ER export

doi: 10.1016/j.isci.2026.114791

Figure Lengend Snippet: YIPF5 regulates the secretome composition (A) Schematic representation of the experimental workflow for analyzing the glycoprotein secretome. MCF10A cells were metabolically labeled with the clickable sugar analog ManNAz, followed by a biotin-azide click reaction to tag glycoproteins ( n = 4). Secreted glycoproteins were concentrated from the culture medium, selectively purified, and identified using mass spectrometry. The image was created with BioRender.com . (B) Quantitative comparison of protein abundance in the secretome versus the total proteome of MCF10A cells. Proteins with secretion changes reflecting a similar change in total expression (“explained by proteome”) (q value ≤ 0.05) are shown in green. Proteins with increased or decreased secretion independent of total proteome changes are highlighted in red and blue, respectively. Gray (not affected) represents unchanged proteins. (C) Analysis of protein abundance changes in the secretome of YIPF5 KO versus control MCF10A cells (WT). Proteins significantly upregulated (red) or downregulated (blue) in the YIPF5 KO secretome are shown. Proteins with secretion changes explained by total proteome abundance are shown in green, while unaffected proteins are in gray. The vertical axis represents –log10(q value), and the horizontal axis represents log2(fold change). (D and E) Heatmap depicting proteins showing increased secretion in the YIPF5 KO secretome with a gene ontology (GO) annotation for the ER (GO: 0007029) and the Golgi apparatus (GO: 0005794) (D) or that contain a KDEL-ER retrieval sequence (E). (F) MCF10A WT and YIPF5 KO cells stably expressing the inducible ER-Ca 2+ sensor GCampER were analyzed using live fluorescence microscopy at identical settings. (G) Mean ± SD fluorescence intensity of GCampER was quantified in MCF10A WT and YIPF5 KO cells in 72 wells per cell line from n = 3 independent experiments. Unpaired t test, two-tailed p < 0.0001. (H) HeLa cells stably expressing shScramble or shRNAs against YIPF5 were transiently transfected with CNPY3-mCherry, supernatants were collected and cell lysates prepared after 24 h followed by western blot analysis using a CNPY3 antibody. A representative blot of n = 3 independent experiments is shown. For full size blot see C. (I) Quantification of CNPY3-secretion from (H). Displayed are arbitrary units normalized to the values of shScramble-expressing cells from n = 3 independent experiments. One-way ANOVA with Tukey’s multiple comparisons test, with ∗ indicating p < 0.05. (J) Analysis of protein abundance changes in the secretome of YIPF5 KO re-expressing YIPF5 I98S mutant versus control MCF10A cells (WT). Proteins significantly upregulated (red) or downregulated (blue) in the YIPF5 I98S secretome are shown ( n = 4). Proteins with secretion changes explained by total proteome abundance are denoted in green, while unaffected proteins are in gray. (K) Venn Diagram of protein abundance changes in YIPF5-KO cells and YIPF5-KO re-expressing YIPF5 I98S cells. Proteins with decreased (blue) or increased (red) secretome abundance are shown. See also and , , , , and .

Article Snippet: CNPY3 rabbit polyclonal , Proteintech , Cat# 15215-1-AP; RRID: AB_11182172.

Techniques: Metabolic Labelling, Labeling, Purification, Mass Spectrometry, Comparison, Quantitative Proteomics, Expressing, Control, Sequencing, Stable Transfection, Fluorescence, Microscopy, Two Tailed Test, Transfection, Western Blot, Mutagenesis