Journal: Microbial Genomics

Article Title: Lifestyle-associated variation in type IV secretion systems between phytopathogenic and environmental Ralstonia

doi: 10.1099/mgen.0.001676

Figure Lengend Snippet: The T4SS gene clusters in Ralstonia have variable gene organization and composition. Clusters are ordered based on their phylogenetic distribution: found only in RSSC phytopathogens, found in both or found only in non-RSSC environmentals. Genes in each cluster are labelled based on F/P/I/GI-type classification conventions: tra / trb (F-type), virB / D4 (P-type), an independent tra / trb scheme (I-type), and tfc (GI-type). The virB4 homologues have a bolded name ( traC , virB4 , traU , and tfc16 ) and a bolded gene arrow border. The genes annotated as the type IV coupling protein gene are labelled ‘CP’. ‘LT’ indicates genes annotated as lytic transglycosylase genes. Genes marked with an asterisk (*) are T4SS genes that were not able to be annotated within the indicated F/P/I/GI-type convention. Gene clusters were defined using Operon-mapper, MacSyFinder v2 with CONJscan models, NCBI RefSeq annotations, and NCBI Conserved Domain Database. Gene clusters were visualized with clinker and labelled with Affinity Designer. Gaps are displayed where the representative cluster had regions without predicted T4SS genes; patterns of non-T4SS genes are not always consistent among all members of each cluster. The representative cluster j is found on two separate contigs in the only Ralstonia genome with cluster j. For additional details regarding genome, gene, and protein NCBI accessions, see and Files S10–S26.

Article Snippet: Bioinformatic analysis used sets of genomes: 394 RSSC phytopathogen genomes available as National Center for Biotechnology Information (NCBI) assemblies in 2023, 636 RSSC phytopathogen genomes available as NCBI assemblies or as raw reads on NCBI Sequence Read Archive (SRA) in 2024, 143 non-RSSC environmental genomes from 17 genomospecies available as NCBI assemblies in 2023, and 923 Burkholderiaceae family genomes that include the 394 RSSC phytopathogen genomes and 529 genomes from at least 252 genomospecies.

Techniques:

Journal: Frontiers in Genetics

Article Title: Functional characterization of MFSD3 in auditory system and zebrafish embryogenesis

doi: 10.3389/fgene.2025.1634493

Figure Lengend Snippet: Phenotypes of auditory system in mfsd3 zebrafish morphants. (A) Schematic of two MO targeting strategies: ATG-MO blocks translation initiation while E2I2-MO disrupts exon 2-intron 2 splicing. Primers pairs (1F/4R) detect wild-type transcripts or aberrant splicing products containing retained intron 2 or skipped exon 2. (B) Left: RT-PCR analysis of mfsd3 transcript from 1 dpf embryos injected with control-MO or E2I2-MO (4 ng). Aberrant splicing product (intron 2 retention and exon2 skipping) are indicated by shifted band patterns. Right: Sanger sequencing confirmation of wild-type sequence, intron 2-inserted transcript and exon2-skipped transcript. (C – Q) Gross morphology of head neuromasts and inner ear in Tg (Brn3c: mGFP) embryos at 3-dpf. Compared to control MO, Mfsd3 deficiency led to reduced hair cell numbers in head neuromasts ( (G,H), yellow arrowheads), hypoplastic otic vesicle (J,K) , malformed otoliths ( (J,K) , blue arrowheads) and damaged otic vesicle hair cells ( (M–N) , (P–Q) , asterisk). (R–T) Quantitative measurements demonstrated significant reduction in: otic vesicle area (R) , otoliths area (S) and mean otolith diameter (T) . ***P < 0.001 (n = 10; ANOVA). (U) Quantitative of hair cell numbers in head neuromasts showing significant decrease in morphants. Scale bar, 100 μm; Scatter plot with bars; ***P < 0.001 (n = 10; ANOVA). dpf, days post fertilization.

Article Snippet: The National Center for Biotechnology Information (NCBI) database annotations predict MFSD3 to function as a solute: proton symporter involved in proton transmembrane transport while serving as an integral membrane component.

Techniques: Reverse Transcription Polymerase Chain Reaction, Injection, Control, Sequencing

Journal: Frontiers in Genetics

Article Title: Functional characterization of MFSD3 in auditory system and zebrafish embryogenesis

doi: 10.3389/fgene.2025.1634493

Figure Lengend Snippet: Morphological defects and hair cells loss in Mfsd3-deficient zebrafish. (A–C) Compared with control MO, the mfsd3 knockdown MO showing significant body shortening (B,C) , axis curvature (B,C) and pericardial edema ( (B,C) , red arrowheads). (D – L) Live imaging of Brn3c: mGFP transgenic embryo at 3-dpf showed GFP expression from RGCs (retinal ganglion cells) and neuromasts (green dots) of the posterior lateral line and head. Zebrafish under control exhibited normal hair cells number (D) . Conversely, significantly decreased hair cells of the posterior lateral line were observed in mfsd3 morphants (E,F) . The white boxed regions are presented in amplified form in the lower panels (G – L) GFP fluorescence signal alone (G – I) and GFP fluorescence signal merged with bright field image (J – L) . Morphometric analyses were utilized to quantify the fluorescence particle signal of hair cells. (M) A time-course plot of survival rates in control vs. mfsd3 morphants for 3 days. (N) The percentage of embryos with development defects in control vs. mfsd3 morphants. (O,P) Quantitative analysis of body length (O) and curvature angle (P) of embryos. (n = 10; ANOVA; ***P < 0.001). (Q) Quantitative analysis of the pericardial area of embryos. (R) Quantitative analysis of the average number of hair cells at posterior lateral line. Scale bar, 100 μm; Scatter plot with bars (n = 10; ANOVA; **P < 0.0001). dpf, days post fertilization.

Article Snippet: The National Center for Biotechnology Information (NCBI) database annotations predict MFSD3 to function as a solute: proton symporter involved in proton transmembrane transport while serving as an integral membrane component.

Techniques: Control, Knockdown, Imaging, Transgenic Assay, Expressing, Amplification, Fluorescence

Journal: Frontiers in Genetics

Article Title: Functional characterization of MFSD3 in auditory system and zebrafish embryogenesis

doi: 10.3389/fgene.2025.1634493

Figure Lengend Snippet: Locomotor capacity was reduced in mfsd3 zebrafish morphants. (A,B) The digital tracks and heatmap image in larvae from control-MO and mfsd3 -MO injected groups at 5-dpf. Each behavioral test consisted of ten larvae each placed into individual wells. (C–F) The statistical analyses showed significantly reduced total movement distance (C) , velocity (D) , mobility (E) and maximum acceleration (F) in mfsd3 morphants compared to control-MO injected groups (n = 10; ANOVA; ***P < 0.001). dpf, days post fertilization.

Article Snippet: The National Center for Biotechnology Information (NCBI) database annotations predict MFSD3 to function as a solute: proton symporter involved in proton transmembrane transport while serving as an integral membrane component.

Techniques: Control, Injection

Journal: Frontiers in Genetics

Article Title: Functional characterization of MFSD3 in auditory system and zebrafish embryogenesis

doi: 10.3389/fgene.2025.1634493

Figure Lengend Snippet: Zebrafish with Mfsd3 deficiency exhibited upregulated Wnt/β-catenin signaling activity. (A) Schematic diagram depicting the potential regulatory action of mfsd3 on the Wnt/β-catenin signaling pathway. (B) Wnt/β-catenin signaling pathway was upregulated in mfsd3 morphants. Endogenous dkk1b , wnt8a , wnt9a , lrp5 , lrp6 , frzb , fzd7a , fzd7b , gsk-3β , axin1 , axin2 , mycn , lef1 , myca , β-catenin and COX2 in control and mfsd3 morphants measured by qRT-PCR assay (n = 6–10 individual embryos). The dkk1b , wnt8a, lrp6, frzb and COX2 were all upregulated significantly in the mfsd3 morphants group. ***P < 0.001; **P < 0.01; *P < 0.05.

Article Snippet: The National Center for Biotechnology Information (NCBI) database annotations predict MFSD3 to function as a solute: proton symporter involved in proton transmembrane transport while serving as an integral membrane component.

Techniques: Activity Assay, Control, Quantitative RT-PCR

Journal: Nature Microbiology

Article Title: Dynamic expression of candidalysin facilitates oral colonization of Candida albicans in mice

doi: 10.1038/s41564-025-02122-4

Figure Lengend Snippet: a , Competitive colonization of C57BL/6 WT mice with 101 WT_mCherry and 101 ece1 Δ/Δ at a 1:50 ratio for 7 days before fluorescent and non-fluorescent tongue CFU were enumerated. One group of mice was treated with ampicillin in the drinking water from day −4 and −3 until the end of the experiment. Tongue CFU of either strain were determined based on the presence or absence of fluorescence, n = 7 per group. Connected symbols are 101 WT and 101 ece1 Δ/Δ CFU per individual animal (left) and fold differences between the two strains per animal (right) in a . Data are presented as mean per group ± s.e.m. b , c , Differentially regulated genes (log 2 (fold changes)) linked to antifungal immune response ( b ) and epidermal keratinization and antimicrobial activity ( c ) in the tongue of C57Bl/6 WT mice colonized with 101 WT for the indicated period of time compared with naive mice. Data are extracted from a previously published RNAseq dataset . d , Differential expression of the genes shown in c in Il17rc − / − compared with those in Il17rc +/ − mice colonized with 101 WT for 3 days. Data are from an RNAseq dataset deposited in the NCBI GEO repository with accession number GSE280210 . e , Il17rc − / − mice were associated with 101 WT (1/50 inoculum) or 101 ece1 Δ/Δ , and tongue CFU were enumerated on day 19; n = 4 or 12 per group; mean ± s.e.m. f , Competitive colonization of Il17rc − / − and Il17rc +/ − mice with 101 WT_mCherry and 101 ece1 Δ/Δ at a 1:50 ratio for 7 days; n = 7 per group. Fluorescent and non-fluorescent tongue CFU were enumerated and fold differences between the two strains per animal are shown as in a ; data presented as mean per group ± s.e.m. Data in a , e and f are pooled from at least two independent experiments. Paired datapoints in competitive colonization experiments ( a , f ) are connected with a line. The statistical significance of differences between groups was determined by two-way ANOVA ( a , f (left)), unpaired two-tailed t -test ( a (right), e ), two-sided Mann–Whitney test ( f (right panel)).

Article Snippet: To determine differentially expressed genes in the colonized tongues of C57Bl/6 WT mice over time, we explored a published dataset available via National Center for Biotechnology Information (NCBI) BioProject accession number PRJNA491801 (ref. ).

Techniques: Fluorescence, Activity Assay, Quantitative Proteomics, Two Tailed Test, MANN-WHITNEY