Journal: Scientific Reports

Article Title: Evidence for association of Vibrio echinoideorum with tissue necrosis on test of the green sea urchin Strongylocentrotus droebachiensis

doi: 10.1038/s41598-022-08772-2

Figure Lengend Snippet: Overview of putative virulence genes identified in the V. echinoideorum genome.

Article Snippet: traA, traB, traC, traD, traE, traF, traH, traI, traK, traL, traN, traU, traV traW, , IncF plasmid conjugative transfer protein.

Techniques: Chemotaxis Assay, Binding Assay, Membrane, Plasmid Preparation, Transduction

Journal: Frontiers in Molecular Biosciences

Article Title: A Functional oriT in the Ptw Plasmid of Burkholderia cenocepacia Can Be Recognized by the R388 Relaxase TrwC

doi: 10.3389/fmolb.2016.00016

Figure Lengend Snippet: Mobilization of plasmids carrying the Ptw- oriT by different conjugative plasmids between E. coli strains .

Article Snippet: pOX38 , IncF TraI TraD , pEF022 , Ptw - oriT + ptwA , 0.36 ± 0.37 , <2.2 × 10 −8.

Techniques:

Journal: Nature Communications

Article Title: Cellular sex throughout the organism underlies somatic sexual differentiation

doi: 10.1038/s41467-024-51228-6

Figure Lengend Snippet: a Diagrams displaying the genomic loci of tra , fru and dsx genes. A blue and red triangle indicates the male- and female-specific stop coding in the tra locus. b Expression pattern of dsx-Gal4 and fru-Gal4 ( P1 promoter) reporters in female tissues at the third larval stage (DNA labelled with DAPI, blue; the membrane-bound form of GFP, green). c Expression pattern of tra promoter-Gal4 reporter in male and female tissues at the third larval stage (DNA labelled with DAPI, blue; nucleus-targeted GFP, green). d Expression pattern of traF-Gal4 reporter in male and female tissues at the third larval stage (DNA labelled with DAPI, blue; nucleus-targeted GFP, green). e Expression pattern of traF-Gal4 reporter, combined with the dsx-Gal80 and fru-Gal80 ( P1 promoter) repressors, in female tissues at the third larval stage (DNA labelled with DAPI, blue; the nuclear form of GFP, green). The visualised cell populations and specific organs are green in the right and top diagrams. Diagrams of the new alleles generated are presented at the top of each panel. Immunohistochemical analyses were repeated at least three independent times.

Article Snippet: To generate the tra KO FRT traF knock-in allele, the following sequences were cloned into the RIV FRTnMCS1FRT white vector (DGRC: Plasmid#1333) using the EcoRI and BglII restriction sites by gene synthesis (Genscript): tra promoter -truncated tra cDNA –FRT site – traF cDNA.

Techniques: Expressing, Membrane, Generated, Immunohistochemical staining

Journal: Nature Communications

Article Title: Cellular sex throughout the organism underlies somatic sexual differentiation

doi: 10.1038/s41467-024-51228-6

Figure Lengend Snippet: a Expression pattern of cell-type specific reporters in the female midgut at the third larval stage (DNA labelled with DAPI, blue; the nuclear form of GFP, green). b Expression pattern of cell-type specific reporters, combined with the traF-LexA marker, in the female midgut at the third larval stage (DNA labelled with DAPI, blue; the nuclear form of GFP, green, the nuclear form of tdTomato, red). Arrowheads indicate examples of cells expressing both GFP and tdTomato. c Expression pattern of cell-type specific reporters, combined with the dsx-Gal80 and fru-Gal80 repressors, in the female midgut at the third larval stage (DNA labelled with DAPI, blue; the nuclear form of GFP, green). The visualised cell populations and specific cell types are yellow or green in the right and top diagrams. The TraF-expressing cells alone and co-expressing cell-type specific markers are depicted in red and yellow, respectively. Diagrams of the alleles used are presented on the top of each panel. Immunohistochemical analyses were repeated at least three independent times.

Article Snippet: To generate the tra KO FRT traF knock-in allele, the following sequences were cloned into the RIV FRTnMCS1FRT white vector (DGRC: Plasmid#1333) using the EcoRI and BglII restriction sites by gene synthesis (Genscript): tra promoter -truncated tra cDNA –FRT site – traF cDNA.

Techniques: Expressing, Marker, Immunohistochemical staining

Journal: Nature Communications

Article Title: Cellular sex throughout the organism underlies somatic sexual differentiation

doi: 10.1038/s41467-024-51228-6

Figure Lengend Snippet: a Diagrams representing the specific cell population with tra knock-out in females, the allele generated and the genotypes used. b Diagrams representing the specific cell population with traF knock-in in males, the allele generated and the genotypes tested. c – e Adult wing size ( c ), adult weight ( d ), female fertility ( e ) quantifications following tra knock-out specifically in dsx - and fru -negative cells. In all figures, the wing size and the weight of control females are set at 100%. All other sexes and genotypes are shown as a percentage of this female control. f Ovaries of control females and females with tra knock-out specifically in dsx- and fru-negative cells (DNA labelled with DAPI, blue; Actin stained with phalloidin, red). g – i Adult wing size ( g ), adult weight ( h ), and male fertility ( i ) quantifications following traF knock-in specifically in dsx - and fru -negative cells. j Testes of control males and males with traF knock-in specifically in dsx- and fru-negative cells (DNA labelled with DAPI, blue; Actin stained with phalloidin, red). k – m Adult wing size quantifications following tra knock-out and gain-of-function specifically in wing pouch cells ( k ), tra knock-down and overexpression in wing pouch cells ( l ), and tra knock-down specifically in wing cells outside the pouch ( m ). In this and all subsequent figures, boxplots display the minimum, the maximum, the sample median, and the first and third quartiles. Data was combined from at least three independent experiments. n = wing number measured per genotype in ( c ), ( g ), ( k ), ( l ), and ( m ), number of replicates (each repeat containing five flies) in ( d ) and ( h ) and number of flies in ( e ) and ( i ). Asterisks highlighting significant comparisons across sexes are displayed in grey boxes at the bottom of graphs; those highlighting significant comparisons within female and male datasets are displayed in red and blue boxes, respectively. When significant, the difference compared to the median of the controls is indicated. For all panels, p -values from one-sided Mann-Whitney-Wilcoxon tests are *** p < 0.0001, ** p = 0.0043, * p = 0.035, (ns) p = 0.7322.

Article Snippet: To generate the tra KO FRT traF knock-in allele, the following sequences were cloned into the RIV FRTnMCS1FRT white vector (DGRC: Plasmid#1333) using the EcoRI and BglII restriction sites by gene synthesis (Genscript): tra promoter -truncated tra cDNA –FRT site – traF cDNA.

Techniques: Knock-Out, Generated, Knock-In, Control, Staining, Knockdown, Over Expression, MANN-WHITNEY

Journal: Nature Communications

Article Title: Cellular sex throughout the organism underlies somatic sexual differentiation

doi: 10.1038/s41467-024-51228-6

Figure Lengend Snippet: a TraF protein sequence divergence between Drosophila species and the red flour beetle Tribolium castaneum . b Sex transformations of abdominal pigmentation and genitalia induced by tra knock-out and knock-in of D. sechellia and D. virilis tra genes. c , d Adult wing size ( c ), and female fertility ( d ) quantifications following D. sechellia and D. virilis TraF protein expressions. e Diagrams representing the specific cell population with D. virilis tra expression, the allele generated, and the genotypes tested. f Female fertility quantifications following D. virilis TraF protein expression specifically in fru - or dsx -positive cells. Data was combined from at least three independent experiments. n = wing number measured per genotype in ( c ) and number of flies in ( d ) and ( f ). Asterisks highlighting significant comparisons across sexes are displayed in grey boxes at the bottom of graphs; those highlighting significant comparisons within female datasets are displayed in red. For all panels, p -values from one-sided Mann-Whitney-Wilcoxon tests are *** p < 0.0001, (ns) p > 0.066.

Article Snippet: To generate the tra KO FRT traF knock-in allele, the following sequences were cloned into the RIV FRTnMCS1FRT white vector (DGRC: Plasmid#1333) using the EcoRI and BglII restriction sites by gene synthesis (Genscript): tra promoter -truncated tra cDNA –FRT site – traF cDNA.

Techniques: Sequencing, Knock-Out, Knock-In, Expressing, Generated, MANN-WHITNEY