Journal: Genome Research

Article Title: Reevaluation of the Toxoplasma gondii and Neospora caninum genomes reveals misassembly, karyotype differences, and chromosomal rearrangements

doi: 10.1101/gr.262832.120

Figure Lengend Snippet: Comparative analysis of genome assemblies of Neospora caninum and Toxoplasma gondii using third-generation sequencing data reveals misassembly and karyotype differences. ( A ) Comparative analysis of the T. gondii type II ( Tg ME49) genome assembly and the N. caninum Liverpool ( Nc Liv) strain genome assembly, obtained based on Sanger technology sequencing data. ( B ) Comparative alignment of the Nc Liv genome assemblies using Sanger and third-generation (long-read) technology. ( C ) Comparative alignment of the T. gondii type II ( Tg ME49) genome assemblies based on Sanger technology sequencing data or third-generation (long-read) technology of T. gondii type I ( Tg RH). ( D ) Comparative alignment of the T. gondii type I ( Tg RH) and the Nc Liv genome assemblies based on third-generation (long-read) sequencing technology. ( E ) Chromosomal layout of N. caninum . Karyotype, chromosome length, telomeres, putative centromeres, and large repeats are shown.

Article Snippet: Nonetheless, examination of available T. gondii PRU RNA sequence data from Oxford Nanopore has revealed numerous reads capable of encoding full-length cytochrome transcripts.

Techniques: Sequencing

Journal: Genome Research

Article Title: Reevaluation of the Toxoplasma gondii and Neospora caninum genomes reveals misassembly, karyotype differences, and chromosomal rearrangements

doi: 10.1101/gr.262832.120

Figure Lengend Snippet: Regions of synteny breaks between N. caninum and T. gondii are populated by three conserved domains. ( A ) Sequence identity of domains identified at regions where chromosomal rearrangements have occurred. ( B ) Graphical representation of Chromosome VIII of Nc Liv. Comparative alignment to the T. gondii chromosomes. Percentages of sequence identity are shown. Regions examined for the presence of motifs are indicated (light green). The position of the putative centromere is indicated in orange. Note that large repetitive regions were not identified in this chromosome. 5′ (light purple) and 3′ (dark purple) telomeres are indicated. The identity and number of domains found per region, in Chromosome VII, are indicated.

Article Snippet: Nonetheless, examination of available T. gondii PRU RNA sequence data from Oxford Nanopore has revealed numerous reads capable of encoding full-length cytochrome transcripts.

Techniques: Sequencing

Journal: Genome Research

Article Title: Reevaluation of the Toxoplasma gondii and Neospora caninum genomes reveals misassembly, karyotype differences, and chromosomal rearrangements

doi: 10.1101/gr.262832.120

Figure Lengend Snippet: Comparative analysis of mitochondrial genome structures and annotations of Neospora and Toxoplasma reveals gene fragmentation and reshuffling between species and strains. ( A ) The repetitive nature of the gene structure in a 32-kb mitochondrial DNA contig of Nc Liv is graphically represented in a YASS plot. ( B ) The repetitive nature of the gene structure in a 16-kb mitochondrial DNA contig of Nc Liv is graphically represented in a YASS plot. ( C ) Comparative alignment between two Nc Liv mitochondrial contigs of 16 and 32 kb, respectively. ( D ) Comparative alignment between a Nc Liv mitochondrial contig of 32 kb and a Nc Uru1 mitochondrial contig of 38 kb. ( E ) Comparative alignment between two Nc Uru1 mitochondrial contigs of 16 and 38 kb, respectively. ( F ) The repetitive nature of the gene structure in a 16-kb mitochondrial DNA contig of Nc Uru1 is graphically represented in a YASS plot. ( G ) Comparative alignment between a Nc Liv mitochondrial contig of 32 kb and a T. gondii mitochondrial contigs of 39 kb.

Article Snippet: Nonetheless, examination of available T. gondii PRU RNA sequence data from Oxford Nanopore has revealed numerous reads capable of encoding full-length cytochrome transcripts.

Techniques:

Journal: BMC Cancer

Article Title: The landscape of coding RNA editing events in pediatric cancer

doi: 10.1186/s12885-021-08956-5

Figure Lengend Snippet: The StrongArm RNA-Seq mapping and RNA editing detection pipelines. A Schematic workflow of StrongArm RNA-seq mapping pipeline. The pipeline starts with competitive mapping of 5 different combinations of mapper and database, followed by further local refinement. B RNA editing identification pipeline. RNA-Seq BAM files are aligned with StrongArm as shown in (A), and germline and somatic DNA variants are also called from the same patient using WGS or WES of matched tumor and germline DNA. The pipeline searches for RNA-specific (RNA editing) variants in coding (CDS) regions by comparing RNA-Seq reads to DNA-Seq. A series of false editing filters is then employed to remove RNA editing artifacts, followed by manual review of the BAM alignment. The RNA editing candidates are then used to evaluate the editing levels cross the whole cohort

Article Snippet: Fig. 1 The StrongArm RNA-Seq mapping and RNA editing detection pipelines.

Techniques: RNA Sequencing, DNA Sequencing

Journal: Nature Communications

Article Title: Medium from human iPSC-derived primitive macrophages promotes adult cardiomyocyte proliferation and cardiac regeneration

doi: 10.1038/s41467-025-58301-8

Figure Lengend Snippet: a Schematic diagram of the protocols to generate hiPMs from human iPSCs. Relevant growth factors and duration of differentiation steps are as indicated. Cartoon elements used in the schematic diagram were created using BioRender. b Flow cytometry analysis of cells double positive for KDR and CD235 during hemogenic epithelium (HE) specification at day 5 after the start of hiPM differentiation. c Flow cytometry analysis of cells positive for CD45 during myeloid progenitor generation at day 11 after the start of hiPM differentiation. d Flow cytometry analysis of hiPMs positive for CD11b and CD14 at day 32 after the start of hiPM differentiation. e Immunofluorescence images for CD11b and CD14 expression in hiPMs. iPSCs were used as a negative control. Cells were stained with CD11b (red) and CD14 (green); nuclei were counterstained with Hoechst (blue). Scale bar, 10 µm. The experiment was repeated three times independently with similar results. f Phagocytosis assessment of hiPMs with FITC-conjugated Dextran (green). Human iPSC-derived cardiac fibroblasts (hiCFs) were used as a negative control. Scale bar, 50 μm. g Flow cytometry analysis of CCR2 expression in hiPMs. THP-1Ms were used as a positive control. The experiment was repeated three times independently with similar results. h Principal component analysis of RNA sequencing data revealing in-group clusters with minimal overlap between hiPMs and THP-1Ms. n = 4 biological repeats per group. i Barplot of differentially expressed genes (hiPMs vs THP-1Ms) specific to primitive macrophages. Differentially expressed genes were identified with a cutoff of |Fold change | > 2 and adjusted p -value < 0.05. j Measurement of LYVE1 , FOLR2 , CD163 , and MAF mRNA levels in hiPMs and THP-1Ms via qPCR analysis. β-actin was used as a control. n = 3 biological repeats per group. k Representative immunofluorescence images for LYVE1 expression in hiPMs. THP-1Ms were used as a negative control. Cells were stained with LYVE1 (green); nuclei were counterstained with Hoechst (blue). Scale bar, 20 μm. Quantitative data are presented as the mean ± SEM. Groups were compared using a two-tailed unpaired Student’s t test ( j ) or ANOVA ( i ). Source data are provided as a Source Data file.

Article Snippet: All the RNA sequencing data have been deposited to the National Center for Biotechnology Information Sequence Read Archive (SRA) under accession number PRJNA1154450 and PRJNA1154419 .

Techniques: Flow Cytometry, Immunofluorescence, Expressing, Negative Control, Staining, Derivative Assay, Positive Control, RNA Sequencing, Control, Two Tailed Test

Journal: Nature Communications

Article Title: Medium from human iPSC-derived primitive macrophages promotes adult cardiomyocyte proliferation and cardiac regeneration

doi: 10.1038/s41467-025-58301-8

Figure Lengend Snippet: a Immunofluorescence staining of Ki67-positive human cardiomyocytes treated with FM, hiPM-cm, hiPM-cm components retained by or passing through 3-kDa filters. Human cardiomyocytes were labeled with cTnT (red) and Ki67 (green); nuclei were counterstained with Hoechst (blue). Scale bar, 10 μm. n = 3 biological repeats per group. b Experimental strategy for analyzing protein components from hiPMpre-cm or hiPM-cm collected in RPMI medium by LC/MS. Cartoon elements used in the schematic diagram were created using BioRender. c Venn diagram showing the overlap between upregulated proteins identified in hiPM-cm versus hiPMpre-cm by LC/MS and upregulated genes encoding secreted proteins in CCR2 - human cardiac tissue-resident macrophages versus CCR2 + human monocyte-derived macrophages in the heart. d Unsupervised clustering analysis of relative pro-proliferative potentials of pairwise protein combinations evaluated by the percentages of Ki67-positive human cardiomyocytes. e Immunofluorescence staining of Ki67-positive human cardiomyocytes treated with a five-protein combination including C1QB, NRP1, PLTP, FUCA1, and SERPING1 (5-P combo). Scale bar, 10 μm. n = 3 biological repeats per group. f Principal component analysis of RNA sequencing data from human cardiomyocytes treated with FM and hiPM-cm. n = 3 biological repeats per group. g Volcano plot illustrating DEGs between human cardiomyocytes treated with FM and hiPM-cm. h Representative KEGG terms of cell proliferation-related genes upregulated in cardiomyocytes incubated with hiPM-cm versus FM. i Immunoblotting analysis showing the phosphorylated and total protein levels of AKT, ERK, and STAT3 in human cardiomyocytes treated with FM and hiPM-cm. GAPDH was used as a loading control. n = 3 biological repeats per group for phosphorylated and total ERK; n = 6 biological repeats per group for the other proteins. j Quantification of Ki67-positive human cardiomyocytes treated with hiPM-cm and inhibitors for PI3K-AKT (A-674563), ERK (PD0325901), and JAK-STAT (Stattic) pathways in single or in combination. n = 3 biological repeats per group. Quantitative data are presented as the mean ± SEM. Groups were compared using a two-tailed unpaired Student’s t test ( i ) or one-way ANOVA followed by post hoc Tukey test ( a , e , and j ). Source data are provided as a Source Data file.

Article Snippet: All the RNA sequencing data have been deposited to the National Center for Biotechnology Information Sequence Read Archive (SRA) under accession number PRJNA1154450 and PRJNA1154419 .

Techniques: Immunofluorescence, Staining, Labeling, Liquid Chromatography with Mass Spectroscopy, Derivative Assay, RNA Sequencing, Incubation, Western Blot, Control, Two Tailed Test