Journal: Journal of translational medicine

Article Title: METTL3 regulates Ambra1 expression in an m6A-YTHDF2-dependent manner to promote mantle cell lymphoma progression.

doi: 10.1186/s12967-025-06647-4

Figure Lengend Snippet: Fig. 8 METTL3/YTHDF2/Ambra1 promotes MCL progression. (A) Representative images of tumors from each group on day 28. (B-C) Changes in tumor size and weight in the indicated groups. (D) METTL3 and Ambra1 mRNA and protein expression in the tumor tissues of the indicated groups. (E) Immu noblots showing the expression of Bcl2, BAX, cleaved caspase-3, and PARP in the tumor tissues. (F-G) Representative IHC images showing expression of cyclin D1, CDK4, and CDK6 in the tumor tissues. n = 5, *P < 0.05 vs. sh-NC + sh-NC group, #P < 0.05 vs. sh-METTL3 + sh-NC group, &P < 0.05 vs. sh-NC + sh- Ambra1 group

Article Snippet: After blocking with 5% BSA, the sections were incubated overnight with rabbit polyclonal antibodies against cyclin D1 (AWA10518, Abiowell), CDK4 (11026-1-AP, ProteinTech), and CDK6 (14052-1-AP, ProteinTech) (dilution 1:200) at 4 °C.

Techniques: Expressing

Journal: bioRxiv

Article Title: Diatom ultrastructural diversity across controlled and natural environments

doi: 10.1101/2025.06.16.659906

Figure Lengend Snippet: (A) Maximum intensity projection showing NHS ester staining of a Coscinodiscus granii cell before and after expansion imaged using the same objective and microscope. The inset indicates the unadjusted pre-expansion size of the cell. Scale bars represent 20 µm (4.65 µm biological scale). (B) Measurements of the diameter of C. granii cells before and after expansion (n=37 and 13, respectively). The mean expansion factor was determined to be 4.3-fold. (C) Phylogenetic relation of diatom species used here indicated on the phylogram, adapted from (Medlin & and Kaczmarska, 2004). Clade colours are kept throughout the image. (D) Immunostaining for microtubules (magenta) and PSII combined with NHS ester pan-labelling (grey) and DAPI (blue) labelling the DNA and fragmented frustule (white arrow) of C. granii . Maximum intensity projections are shown spanning half a cell (i) and the central section (ii) allowing for a clear distinction of the MTOC (black arrow) and a microtubule cage spanning the nucleus in addition to the cortical bundles. NHS ester staining preferentially labels the triangular pyrenoid sitting roughly central in the manyfold chloroplasts which are found along the periphery and, in doublets, as single plastids in close proximity to the MTOC. Scale bars 100 µm (23.26 µm biological scale). (E - H) Exemplary maximum intensity projections of two pennate diatom cultures, Pleurosigma sp. (E) and Cylindrotheca sp. (F) as well as two more centric diatom cultures, Odontella sinensis (G) and Chaetoceros neogracillis (H). NHS ester (grey), microtubules (magenta and greyscale below), PSII (green and greyscale below), and DNA (blue) were stained for. Scale bars 50 µm (E, F, H), 100 µm (G) (Biological scale 13 µm in E, 18.5 µm in F, 28 µm in G, and 12 µm in H). (I-J) Environmental Chaetoceros sp. cells collected and fixed in Tallinn, Estonia, were observed in close association with (I) bacteria coating the outside of the frustule. Bacteria were stained with DAPI and readily segmented (BAC). (J) Another Chaetoceros cell was fixed in close association with two biflagellated cells (white arrows) containing distinct plastids. Scale bars 50 µm (12.5 µm biological scale).

Article Snippet: The following primary antibodies were used: mouse monoclonal anti-tubulin 12G10 (AB_1157911, IgG, DHSB USA, 1:1000), rabbit polyclonal anti-PsbA-D1 protein of Photosystem II (PS2; IgG, Agrisera Sweden; AS05084, 1:1000) used as proxy for thylakoid membranes ultrastructure, and rabbit polyclonal anti-RbcL (Agrisera Sweden ref AS03037, 1:1000).

Techniques: Staining, Microscopy, Immunostaining, Bacteria

Journal: bioRxiv

Article Title: Diatom ultrastructural diversity across controlled and natural environments

doi: 10.1101/2025.06.16.659906

Figure Lengend Snippet: (A) Maximum intensity projection showing NHS ester staining of a C. neogracilis cell before and after expansion imaged using the same objective and microscope. The inset indicates the unadjusted pre-expansion size of the cell. Scale bars 20 µm (B) Measurements of the width of C. neogracilis cells before and after expansion (n= 30, respectively). The mean expansion factor was determined to be 4.1-fold. (C) Overview of a coverslip collected and fixed in Plentzia, Spain shortly after collection and stained with NHS ester. Several different species and cells including a fragmented copepod can be distinguished. The scale bar represents 500 µm and zoom in on two example cells from C shown with NHS ester and DAPI staining before and after expansion. Note that an air bubble introduced a large halo effect in NHS ester staining in the top right. Scale bars represent 50 µm. (D & E) Higher magnification acquisition of features from C showing two distinct areas within a chain of Chaetoceros sp. , with (D) showing a small spherical cell devoid of PSII staining but showing a elaborate microtubule (magenta) network and centriolar MTOC (inset and arrows, scale bar 2 µm). The neighbouring cell in the chain in (E) presents an expected morphology with a polar, nuclear (blue) associated centriole-less MTOC, lobes of plastids (green) with central pyrenoids (grey). The scale bars represent 20 µm. (F) Close up of microflagellates from show distinct nuclei, two chloroplasts per cell, with discernible pyrenoids. Scale bar 20 µm.

Article Snippet: The following primary antibodies were used: mouse monoclonal anti-tubulin 12G10 (AB_1157911, IgG, DHSB USA, 1:1000), rabbit polyclonal anti-PsbA-D1 protein of Photosystem II (PS2; IgG, Agrisera Sweden; AS05084, 1:1000) used as proxy for thylakoid membranes ultrastructure, and rabbit polyclonal anti-RbcL (Agrisera Sweden ref AS03037, 1:1000).

Techniques: Staining, Microscopy

Journal: bioRxiv

Article Title: Diatom ultrastructural diversity across controlled and natural environments

doi: 10.1101/2025.06.16.659906

Figure Lengend Snippet: (A) Left panel Coscinodiscus granii overview, expanded scale bar 50 µm, biological scale bar 11,52 µm. The three right panels zoom into the orange square with merged RuBisCo and NHS, RuBisCo, NHS ester, expanded scale bar 10 µm, biological scale bar 2,30 µm. (B) Rhizosolenia sp. Merge, DNA, PSII, tubulin, NHS ester, expanded scale bar 50 µm, biological scale bar 16,29 µm. (C) P. tricornutum triradiate and fusiform morphotype. Merge, DNA, PSII, tubulin, NHS ester, expanded scale bar 50 µm, biological scale bar 26,74 µm. (D) P. tricornutum oval morphotype. Merge, DNA, PSII, tubulin, NHS ester, expanded scale bar 50 µm, biological scale bar 26,74 µm.

Article Snippet: The following primary antibodies were used: mouse monoclonal anti-tubulin 12G10 (AB_1157911, IgG, DHSB USA, 1:1000), rabbit polyclonal anti-PsbA-D1 protein of Photosystem II (PS2; IgG, Agrisera Sweden; AS05084, 1:1000) used as proxy for thylakoid membranes ultrastructure, and rabbit polyclonal anti-RbcL (Agrisera Sweden ref AS03037, 1:1000).

Techniques:

Journal: bioRxiv

Article Title: Diatom ultrastructural diversity across controlled and natural environments

doi: 10.1101/2025.06.16.659906

Figure Lengend Snippet: From left to right: a composite image showing NHS-Ester in grey, PSII in green, Tubulin in magenta, and DNA in blue. A greyscale image of just the NHS, PSII and Tubulin channels are on the right. Expanded scale bars are 10 µm and biological scale bars are 2.25 µm.

Article Snippet: The following primary antibodies were used: mouse monoclonal anti-tubulin 12G10 (AB_1157911, IgG, DHSB USA, 1:1000), rabbit polyclonal anti-PsbA-D1 protein of Photosystem II (PS2; IgG, Agrisera Sweden; AS05084, 1:1000) used as proxy for thylakoid membranes ultrastructure, and rabbit polyclonal anti-RbcL (Agrisera Sweden ref AS03037, 1:1000).

Techniques:

Journal: bioRxiv

Article Title: Diatom ultrastructural diversity across controlled and natural environments

doi: 10.1101/2025.06.16.659906

Figure Lengend Snippet: (A) Left panel is an overview of the env. Chaetoceros sp. isolated in Tallinn, Estonia, expanded scale bar 10 µm; biological scale bar 2.5 µm. PSII and NHS ester are shown as single slices, DNA and Tubulin are max projections. Three panels on the right are a montage of the z-stack showing the thylakoid membranes and PPTs. expanded scale bar 10 µm; biological scale bar 2.5 µm. (B) Left panel is a 3D segmentation of C. neogracilis, expanded scale bar 20 µm, biological scale bar 4.9 µm. Three panels on the right are a montage of the z-stack showing the thylakoid membranes and PPTs, expanded scale bar 10 µm, biological scale bar 2,46 µm.

Article Snippet: The following primary antibodies were used: mouse monoclonal anti-tubulin 12G10 (AB_1157911, IgG, DHSB USA, 1:1000), rabbit polyclonal anti-PsbA-D1 protein of Photosystem II (PS2; IgG, Agrisera Sweden; AS05084, 1:1000) used as proxy for thylakoid membranes ultrastructure, and rabbit polyclonal anti-RbcL (Agrisera Sweden ref AS03037, 1:1000).

Techniques: Isolation