Journal: bioRxiv

Article Title: ABCE1-dependent translational control links Fe-S cluster biogenesis to parasite growth and lipid homeostasis in Toxoplasma gondii

doi: 10.64898/2026.07.01.735774

Figure Lengend Snippet: A. Electron micrograph of intracellular parasites treated with cycloheximide (CHX) for 6 h. Asterisks and square signs denote parasite and host lipid droplets (LDs), respectively. Pixel size: 10 nm. B. Immunofluorescence microscopy imaging of parasites untreated or treated for 6 h and 16 h with translation inhibitors cycloheximide and puromycin. LDs accumulate in both parasites and host cells. LDs were stained with Nile Red (orange), parasites were labeled with an anti-IMC3 antibody (green), and DNA was stained with DAPI. Scale bar = 5 μm. For this experiment, puromycin and CHX were used at 100 µg/ml. C, D. Quantification of lipid droplet number and area in cKD HA-TgABCE1 parasites grown in the absence or in the presence of CHX and puromycin for 6 h or 16 h. A total of 100 parasites were analyzed per condition. Values are represented as the mean ±standard deviation of n = 3 independent biological replicates (different symbols represent different series); ns: not significant ( p -value >0.05), **: p -value ≤0.01, ****: p -value ≤0.0001. p -value s from one-way ANOVA with Dunnett’s multiple comparison test. CHX: cycloheximide, puro: puromycin, SD: standard deviation. E. Immunofluorescence imaging of parasites from the cKD HA-TgZFP2 cell cycle mutant grown in the absence or presence of ATc 48 h, in which the ZFP2 depletion induces an accumulation of LDs (left). Immunofluorescence imaging of parasites pre-cultured for 24 h and then incubated for 48 h with the cell cycle inhibitor oryzalin (ory, 2.5 µM) results in the accumulation of LDs (middle). Ory was then washed out and parasites were left to recover for an extra 48 h : while some vacuoles remained blocked (arrowhead), parasites resuming cell division displayed less LDs (right). LDs were stained with BODIPY 493/503 (green), parasites are outlined, and DNA was stained with DAPI (blue). Scale bar = 5 μm. F, G. Quantification of LD number and area in parasites depleted of TgZFP2, or treated with ory, with or without washout. 100 parasites were analyzed per condition. Values are represented as the mean ± SD of n = 3 independent biological replicates (different symbols represent different replicates); **: p -value ≤0.01, ***: p -value ≤0.001, ****: p -value ≤0.0001, from Student’s t-test. H. Outline of the host cell lipid scavenging protocol: before infection with the parasites, HFF cells were treated for 18h with BODIPY 493/503 and oleic acid (OA, 0.4 mM) to stimulate the accumulation of host LDs. After washing, the HFFs were infected with cKD HA-TgABCE1 in the absence or presence of ATc for 48 h or treated with 2.5 µM ory. OA concentration was maintained at 0.2 mM to sustain host lipid droplets production. Immunofluorescence imaging shows, in both cases, the BODIPY 493/503 signal incorporated in the parasites’ LDs, illustrating scavenging from the host.

Article Snippet: HFF cells were pretreated with oleic acid (HY-N1446, MedChemExpress) at 400 μM and BODIPY 493/503 at 10 μM for 18h, washed five times with PBS and then incubated in complete DMEM medium for 30 min. Then, the cells were incubated with oleic acid at 200 μM and infected with cKD HA-ABCE1 tachyzoites either in the presence or absence of ATc for 48 h or with microtubule-disrupting agent oryzalin (HY-147092, MedChemExpress) at 2.5 μM for 48 h. Upon treatment with 2.5 μM of oryzalin for 48 h, the compound was removed by washes in HBSS and the parasites were then maintained in complete medium for 48 h. The parasites were fixed and permeabilized according to the IFA protocol, after which the LDs were stained with BODIPY493/503 for 30 min.

Techniques: Immunofluorescence, Microscopy, Imaging, Staining, Labeling, Standard Deviation, Comparison, Mutagenesis, Cell Culture, Incubation, Infection, Concentration Assay

Journal: BMC Cancer

Article Title: Targeting EpCAM expression via near-infrared fluorescent antibodies enables microscopic delineation of primary and recurrent HNSCC

doi: 10.1186/s12885-026-16172-2

Figure Lengend Snippet: Expression of EpCAM on cell lines of SCC-UADT, HNSCC-associated fibroblasts, and normal fibroblasts. A Representative histogram and quantitative data on the percentage of EpCAM-positive cells as well as on the expression level of EpCAM of the SCC-UADT cell lines KYSE-30 (ESCC) and FaDu (HNSCC), the HNSCC-associated fibroblast cell line CAF-4, and the normal fibroblast cell line HFF-1 as assessed by flow cytometry upon immunostaining with the AlexaFluor488-labeled anti-EpCAM antibody VU1D9 (high EpCAM-affinity) (mean ± SEM for n = 4; * p < .05 vs. CAF; # p < .05 vs. HFF; § p < .05 vs. KYSE-30; & p < .05 vs. FaDu). B Representative histogram and quantitative data on the percentage of EpCAM-positive cells as well as on the expression level of EpCAM of the SCC-UADT cell lines KYSE-30 and FaDu, the HNSCC-associated fibroblast cell line CAF-4, and the normal fibroblast cell line HFF-1 as assessed by flow cytometry upon immunostaining with the AlexaFluor488-labeled anti-EpCAM antibody MT201 (intermediate EpCAM-affinity; clinically validated) (mean ± SEM for n = 4; * p < .05 vs. CAF; # p < .05 vs. HFF; § p < .05 vs. KYSE-30; & p < .05 vs. FaDu)

Article Snippet: Human foreskin fibroblast cell line HFF-1 was purchased from ATCC (Manassas, USA; SCRC-1041).

Techniques: Expressing, Flow Cytometry, Immunostaining, Labeling

Journal: bioRxiv

Article Title: Super-resolved spatial organization of the nucleolar transcriptome

doi: 10.64898/2026.05.19.726041

Figure Lengend Snippet: a , Scheme of in situ reverse transcription used for transcriptome profiling in nucleolar subdomains. b , Representative epi-fluorescence images of nucleoli with each domain immunostained in HFF cells. c , Representative SMLM images of DF/DFC units by immunostaining within one nucleolus in HFF cells. d , Representative epi-fluorescence images of in situ RT-generated biotin-cDNAs stained by AF647-labeled streptavidin, together with each marker protein stained by CF568-labeled antibody in different nucleolar subdomains. Biotin signals in both FC and DFC regions were acquired under identical imaging conditions and displayed with the same contrast settings. Biotin signals in GC were imaged using a lower laser power to avoid image oversaturation. e , Representative SMLM images of biotin-cDNA and marker protein in FC/DFC units. Biotin-cDNAs were generated in DFC, while marker proteins of FC or DFC were simultaneously stained with the corresponding antibodies. f , Violin plot for cross-correlation distance between AF647 and CF568 channels. g , Violin plot of thickness of DFC ring, estimated by autocorrelation distance, D AF/AF, 1 or D CF/CF, 1 (Supplementary Text). h, Violin plot of DFC radius, estimated by autocorrelation distance, D AF/AF, 2 or D CF/CF, 2 . The fitted correlation distance (in the unit of pixels) was multiplied by the effective pixel size (26 nm). N in (f-h) reports the number of FC/DFC units in each plot, collected from 7 cells from two biological replicates. P -values were all calculated by unpaired two-tailed t test.

Article Snippet: HFF cells (ATCC, SCRC-1041) were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 15% (v/v) fetal bovine serum (FBS).

Techniques: In Situ, Reverse Transcription, Fluorescence, Immunostaining, Generated, Staining, Labeling, Marker, Imaging, Two Tailed Test

Journal: bioRxiv

Article Title: Super-resolved spatial organization of the nucleolar transcriptome

doi: 10.64898/2026.05.19.726041

Figure Lengend Snippet: a , Genome tracks of rRNA segments other than those shown in . b . RNA FISH images of rRNA fragments and junctions in HFF cells. Cell nuclei were outlined by yellow dashed lines.

Article Snippet: HFF cells (ATCC, SCRC-1041) were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 15% (v/v) fetal bovine serum (FBS).

Techniques:

Journal: bioRxiv

Article Title: Super-resolved spatial organization of the nucleolar transcriptome

doi: 10.64898/2026.05.19.726041

Figure Lengend Snippet: a , Venn diagram of enriched snoRNAs in nucleolar subdomains of HFF cells. b , Violin plot showing the log 2 (fold change) values of snoRNA in the FC, DFC and GC of HFF cells. c , RNA FISH images of snoRNAs, co-stained with DFC and GC markers. Nuclei stained with DAPI are outlined by dashed lines. d , Ratios of fluorescence intensities within DFC over GC for imaged snoRNAs. e , Schematic diagram of rRNA processing steps regulated by snoRNAs. f , Violin plot showing the log 2 (fold change) values of snoRNAs marked in (e) across three subdomains. g , RNA FISH images of GAS5 introns 4, 6, 9, and 11 (top panel) and the SNORD80 surrounding regions of GAS5 intron 8 (bottom panel) together with exons. h , Violin plot of distance between GAS5 focus and the boundary of nucleolus. i , Ratio of average fluorescence intensity of RNA intron signal in nucleus to that at the transcription site (marked by bright foci using exon targeting probes). j , Venn diagram of enriched snoRNAs in nucleolar subdomains in SH-SY5Y cells. k , Violin plot showing the log 2 (fold change) values of snoRNAs in SH-SY5Y cells. Enriched snoRNAs were selected using criteria of total reads ≥ 10, log 2 (fold change) > 1 and adjusted p -value < 0.05. N reports number of genes in (b) and (k), and number of imaged cells in (d), (h), and (i), from two biological replicates. P -values were calculated using two-sided t-test.

Article Snippet: HFF cells (ATCC, SCRC-1041) were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 15% (v/v) fetal bovine serum (FBS).

Techniques: Staining, Fluorescence