Picture from Cotra F et al. (2023) MicroPubl Biol "Molecular basis of essential and morphological variations across 12 balancer ...."

Figure 1. Molecular basis of balanced mutations and morphological markers across 12 balancer strains:A) Table summarizing balanced mutations (TOP) and morphological markers (BOTTOM) resolved at a molecular level (genomic position and variant effect) in this study. *Amino Acid change. Between parenthesis is the transcript used as reference. For frameshift mutations, we indicated the amino acid after which the frameshift occurs. ** The flanking sequences were retrieved from Sanger sequencing for bn126, md2415, tm9709, and tm9723. B) Visualization of the genomic position of four morphological markers or balanced mutations in the Illumina short-read whole genome sequencing data using the Integrative Genomics Viewer v2.16 (IGV) in the control genome (N2) and the strain of interest. For each sample, the information is displayed on two different tracks. The histogram of the top track represents the coverage per base. A sudden drop in the coverage can signal a deletion. The arrows in the bottom track represent the reads aligned along the reference genome. A grey read is a read aligned to the reference genome with limited differences. At a deletion breakpoint, reads colored in red have their mate aligned on the reference genome at a larger distance than the inner distance initially used during the library preparation. The reference sequence and corresponding annotation is displayed at the very bottom of each screenshot. From left to right: unc-93(e1500) in MT690, dpy-2(tm9710) in FX30144, klp-19(bn126) in SS746, and unc-54(h1040) in KR2839.

Picture from Lee, Bo Yun et al. (2022) MicroPubl Biol

Figure 1. The structure of TALT1 arrays in CB4856 and DL226(A) Schematic representation of chromosome V right arm regions in N2, CB4856, and DL226. Locations of TALT sequences are V:21149554-21162688 in the CB4856 genome and V:21278369-21293965 in the DL226 genome. Six raw reads covered the 6-copy TALT array of DL226. DL226-specific TALT insertion was indicated by a gray horizontal line. The six raw-read sequences are available in Extended Data 2. (B) The comprehensive structure of duplicated regions. The new telomeric repeat and TALT (the long purple line) are right next to the original copy (the long green line). Besides, a duplicated part of telomeric repeat (the short purple line) is also in the repeat.

Picture from Aghayeva, Ulkar et al. MicroPubl Biol

Figure 1: daf-16 alleles generated by CRISPR/Cas9 genome engineering and their expression patterns in starvation/crowding-induced dauer stage animals. The relative signal strength of the image is not directly comparable because different microscope settings had to be used. The absolute signal intensity is GFP>mNeonGreen>mKate2>mNeptune2.5. Scale bars are 10 um.

Picture from Zdraljevic S et al. (2023) MicroPubl Biol "Heritable Cas9-induced nonhomologous recombination in C. elegans"

Figure 1. Heritable Cas9-induced nonhomologous recombination in C elegans:A) Overview of the workflow used to induce nonhomologous recombination. A cartoon depiction of the genome composition of the QX2501 NIL used in this study is shown, where yellow represents QX1211 and purple represents XZ1516. Genomic coordinates (with XZ1516 as the reference genome) of the three gRNAs used in this study are shown below the genome representation of the NIL. Genomic coordinates of two indel variants used to differentiate between the parental genotypes are shown in red and labeled A and B. Young adult QX1211/QX2501 heterozygotes are injected with a gRNA that targets Cas9 to the desired location, along with a co-injection marker (dpy-10 gRNA + ssODN repair template). The progeny of the injected animals that express the co-injection phenotype are singled to wells of a 96-well plate and allowed to self. A subset of the worms is genotyped with the A and B primer pairs. Individuals displaying loss of heterozygosity (LOH) such that both parental genotypes are still represented (i.e. individuals heterozygous at one marker and homozygous on the other, or homozygous at both markers) are marked with a green plus sign and recovered to agar plates for further characterization.B) Overview of the Cas9-induced nonhomologous recombination results. The table shows the PCR genotypes of rol/dpy progeny in this study. Left-most column depicts the expected strain genotypes based on PCR genotyping of the A and B indel variants. Within this column, recombinant genotypes are indicated by "LOH" in the upper-right corner. Dotted red lines indicate the marker where the LOH event occurred. The next three columns-one for each guide-show the number of genotyped rol/dpy progeny with the corresponding genotype. Black dots in the upper left corner correspond to the strains with whole-genome sequence data. The right-most column shows the F2 progeny genotypes when QX2501/QX1211 heterozygous animals were allowed to self without injection The last row of the table shows the total number of recombinants identified over the total number of F2 individuals genotyped for each gRNA.

Picture from Hao JC et al. (2010) Dev Cell "The tripartite motif protein MADD-2 functions with the receptor UNC-40 (DCC) in ...."

(A) Comma stage (bottom) and 1.5-fold stage (top) embryos. The anterior cells that express madd-2::gfp include developing neurons of the nerve ring. Expression is also detected in the ventral and posterior embryo, including motor neurons and hypodermal cells.(B) L1 stage larva. Expression is high in head neurons that project into the nerve ring (arrow). Muscles of the head also express the transgene (arrowhead).(C) L3 stage larva. The HSN motor neuron expresses the madd-2::gfp transgene. Scale bars equal 5 um.

Picture from Blanchette CR et al. (2015) PLoS Biol "Glypican Is a Modulator of Netrin-Mediated Axon Guidance."

Fig 3. unc-6/netrin signaling via the unc-5/UNC5 receptor requires lon-2/glypican. (A) The axon of PVM normally migrates ventrally in the wild type, but it can be forced to migrate dorsally by misexpressing the repulsive receptor unc-5/UNC5. We quantified PVM since AVM could not be reliably identified (bothAVM and neighboring ALMR axons project dorsally in Pmec-7::unc-5 transgenic animals.)

Picture from Mahadik SS et al. (2025) MicroPubl Biol "Transcripts from the src-1(cj293) mutant can encode a SRC-1 molecule ...."

Figure 1. Transcripts from the src-1 locus in src-1(+) and src-1(cj293)/+: Alignments of RNA seq to the src-1 locus in A) src-1(+) and B) src-1(cj293). At the top are representative alignments from the Integrated Genome Viewer. The asterisk in src-1(cj293)/+ indicates a group of exon 3 to exon 6 splices, which did not occur in src-1(+). Shown below the alignments are Sashimi plots of splicing at the src-1 locus, generated in the Integrated Genome Viewer. The 318 exon 3 to exon exon 6 splices are indicated with an asterisk. The structure of the src-1 locus is shown at the bottom. The extent of the src-1(cj293) deletion is indicated with a red bar. 5' to 3' orientation of the locus is indicated. The src-1(cj293)-specific exon 3 to 6 splice is indicated with a dashed red line below the gene model. C) The sequence of the src-1 locus from exon 3 to exon 6 (bases 1,570,337 to 1,577,868 on LGI). The region deleted in src-1(cj293) is red, and the exons are cyan. Exons 4 and 5 are removed by the src-1(cj293) deletion.

Picture from Hobson RJ et al. (2011) Curr Biol "Complexin maintains vesicles in the primed state in C. elegans."

(b). cpx-2 is expressed in the nervous system. Above, gene model and regions deleted in C.elegans complexin mutants. Red bars indicate regions deleted in the mutants. The black line represents the region of the genome used to create the GFP construct. Below, a reporter construct consisting of the cpx-2 gene fused with GFP is expressed in approximately 30 head, midbody and tail neurons and the coelomocytes. Images were taken with a confocal microscope and are of young adult hermaphrodites oriented dorsal up, and anterior to the left. Images are a stitch of multiple confocal Z-projections along the length of the animal.

Picture from Johnson RP et al. (2006) Development "C. elegans dystroglycan DGN-1 functions in epithelia and neurons, but not ...."

Figure 3. dgn-1 is expressed in epithelia and neurons. (A) In early embryos, dgn-1::GFP is expressed in epithelial and neural precursors in the outer layer of cells. (B) As elongation begins, expression becomes prominent in pharyngeal epithelia (pe), the excretory cell (exc), the two somatic gonad precursors in the gonad primordium (gp), and in rectal epithelia (rect). Weaker expression is seen in a number of hypodermal and neural precursors. (C) In early larvae, expression persists in the e2 and marginal (mc) cells of the pharyngeal epithelium, the excretory cell, the gonad primordium and the rectal epithelium. Strong expression is seen in the PVP neurons. (D-G) Enlarged images showing expression in: (D) the pharyngeal epithelium and hypodermal cell hyp5 (hyp); (E) somatic gonad precursors, which project processes (arrowheads) around the primordial germ cells (asterisks); (F) PVP neurons; (G) rectal epithelial cells, which project processes (arrowhead) around the rectal sphincter. (H) Transient expression during late L1 stage in P-cell-derived ventral cord neurons (arrowheads). (I) A L3 stage animal showing expression in the distal tip cell and gonad epithelium (arrowheads). (J) Strong expression in L4/adult stage gonad, including the uterus (ut), spermatheca (st) and sheath (sh). (K) Expression in late L4 stage vulval epithelium. Scale bar: 10μm.

Picture from Ferdousy, Sakia et al. (2022) MicroPubl Biol

Figure 1. Comparison of genome editing efficiency between wild type Cas9 and SuperFi-Cas9 in C elegans:(A) Representative images of wild type and different mutant worms. Worms were grown under identical conditions and the images were taken at young adult stage for all the strains. Scale bar = 100 µm. (B) Efficiencies of Cas9- and SuperFi-Cas9-mediated mutagenesis through non-homologous end joining. Note that in F1 worms harboring the wild type Cas9, the mutagenesis rates for unc-9 and phm-2 were much higher than that for dpy-11, which was likely due to the presence of a GG motif at the 3' end of the protospacer sequences for unc-9 and phm-2 but not for dpy-11 (see methods). This observation is consistent with a previous report showing that a GG motif at the 3' end of the protospacer sequence dramatically enhances genome editing by CRISPR/Cas9 (Farboud and Meyer, 2015). (C) Efficiencies of Cas9- and SuperFi-Cas9-mediated mutagenesis through homology-directed repair. Mutagenesis rate = (number of F1s yielding mutants/number of transgenic F1s) x 100.