Picture from Dixon SJ et al. (2005) Development "Muscle arm development in Caenorhabditis elegans."

(D) The dorsal right (top) and dorsal left (bottom) BWMs that express MB::YFP from the trIs30 integrated transgene in a young adult. The Cpppaaa BWM is indicated (yellow arrow), along with four muscle arms (green arrows). (E) The ventral left (top) and ventral right (bottom) BWMs. The red asterisk indicates the position of the vulva. (F,G) Tracings of the dorsal and ventral BWMs, respectively. The identities of the distal muscles that express Mb::YFP at high levels are bright yellow, and those that express Mb::YFP at lower levels are light yellow. The head BWMs are shaded in dark grey, while the neck BWMs are shaded in light grey. The black X' in (G) represents the vulval muscles, which do not express Mb::YFP from trIs30 transgene. Anterior is to the left in all panels except in B and C. Scale bars: 50 μm. DHR, dorsal hypodermal ridge; LHR, lateral hypodermal ridge; VHR, ventral hypodermal ridge.

Picture from Dixon SJ et al. (2005) Development "Muscle arm development in Caenorhabditis elegans."

Figure 1. The muscle arms of C. elegans. (A) An illustration of the BWMs (red) of the left side of C. elegans. Each BWM quadrant is organized into two rows. (B) A cross-section of A adapted, with permission, from White et al. (White et al., 1986). Each muscle of the two dorsal BWM quadrants and each muscle of the two ventral quadrants (red) extends arms to the nearest nerve cord (dark green) in either the DHR or the VHR, respectively. Only the muscle arms of the ventral left quadrant are indicated by green arrows. The LHR is indicated. (C) A transmission electron micrograph by John White (with permission) of the boxed region in B. BWMs are shaded pink. (D) The dorsal right (top) and dorsal left (bottom) BWMs that express MB::YFP from the trIs30 integrated transgene in a young adult. The Cpppaaa BWM is indicated (yellow arrow), along with four muscle arms (green arrows). (E) The ventral left (top) and ventral right (bottom) BWMs. The red asterisk indicates the position of the vulva. (F,G) Tracings of the dorsal and ventral BWMs, respectively. The identities of the distal muscles that express Mb::YFP at high levels are bright yellow, and those that express Mb::YFP at lower levels are light yellow. The head BWMs are shaded in dark grey, while the neck BWMs are shaded in light grey. The black X' in (G) represents the vulval muscles, which do not express Mb::YFP from trIs30 transgene. Anterior is to the left in all panels except in B and C. Scale bars: 50 μm. DHR, dorsal hypodermal ridge; LHR, lateral hypodermal ridge; VHR, ventral hypodermal ridge.

Picture from Flibotte, Stephane et al. (2021) MicroPubl Biol

Figure 1. Chromosomes I and III in the hT2 balancer: (A) Breakpoint connections deduced by aligning split reads at the breakpoints. Identical strands indicates that the sequence on the left is connected directly to the sequence on the right, while 12/9/2021 - Open Accessdifferent strands denotes a change of strand. Genes affected by the breakpoints are listed in the third column. (B) A schematic representation of chromosomes I and III deduced for hT2 is shown. Each arrow represents the chromosomal segment of the reference sequence with the corresponding coordinates listed. The direction and color of each arrow represent the strand/direction of the sequence within the original reference chromosome. (C) Simplified representation (not at perfect scale) of wild-type (left two chromosomes) and the hT2 translocation (right two chromosomes) with standard marker genes indicated. Chromosome regions in magenta represent segments that are translocated in hT2, while those in black represent untranslocated segments responsible for correct meiotic pairing. For the wild-type chromosomes, the lines at 13.2 Mb (LG I) and 5.0 Mb (LG III) indicate approximate positions of translocation breakpoints from WGS data.

Picture from Phillips CM et al. (2005) Cell "HIM-8 binds to the X chromosome pairing center and mediates chromosome-specific ...."

The HIM-8 Protein Localizes to the PC Region of the X Chromosome. All images show projections through fields of pachytene-region nuclei from animals of the indicated genotypes. The entire nuclear volume is shown in each projection. All scale bars represent 5 μm.(A) Wild-type hermaphrodite, revealing a single HIM-8 focus in each nucleus due to close association between the two binding sites detected in premeiotic and very early meiotic nuclei (Figure 3).(B) Wild-type male, which displays a single (unpaired) HIM-8 focus in each nucleus. In contrast to hermaphrodites, males also have one HIM-8 focus per nucleus in the premeiotic region of the gonad (data not shown). (E) HIM-8 immunostaining was performed in conjunction with FISH to two probes on the X chromosome, one from the left arm (1.5 Mb from the telomere) and one from a more medial position (7.4 Mb from the left end). The XL probe is closely associated with HIM-8 focus, while the XC probe is clearly more distant from the HIM-8 focus. Probes to the right end of the X and autosomal loci were also tested (data not shown) and did not correlate in their position with HIM-8 foci.

Picture from Phillips CM et al. (2005) Cell "HIM-8 binds to the X chromosome pairing center and mediates chromosome-specific ...."

Figure 4. The HIM-8 Protein Localizes to the PC Region of the X Chromosome. All images show projections through fields of pachytene-region nuclei from animals of the indicated genotypes. The entire nuclear volume is shown in each projection. All scale bars represent 5 μm.(A) Wild-type hermaphrodite, revealing a single HIM-8 focus in each nucleus due to close association between the two binding sites detected in premeiotic and very early meiotic nuclei (Figure 3).(B) Wild-type male, which displays a single (unpaired) HIM-8 focus in each nucleus. In contrast to hermaphrodites, males also have one HIM-8 focus per nucleus in the premeiotic region of the gonad (data not shown).(C) Hermaphrodite carrying two copies of the mnDp66 duplication of the X chromosome PC region. An additional HIM-8 focus is present in each nucleus, corresponding to the paired and synapsed duplication.(D) Hermaphrodite carrying both mnDp66 and the PC deficiency meDf2, which eliminates one of the two foci observed in (C).(E) HIM-8 immunostaining was performed in conjunction with FISH to two probes on the X chromosome, one from the left arm (1.5 Mb from the telomere) and one from a more medial position (7.4 Mb from the left end). The XL probe is closely associated with HIM-8 focus, while the XC probe is clearly more distant from the HIM-8 focus. Probes to the right end of the X and autosomal loci were also tested (data not shown) and did not correlate in their position with HIM-8 foci.

Picture from Trivedi M et al. (2023) MicroPubl Biol "CRISPR-mediated genome editing allows for efficient on demand creation of ...."

Figure 1. Methods and results on generating mini-deficiencies:A. Schematic showing the design for gRNA, ssDNA oligo repair, and genotyping primers for generating mini-deficiencies. H1 and H2 denote homology arms.B. Schematic showing the intended (black) and obtained (green) mini-deficiencies.C. Workflow for creating mini-deficiencies by injecting into balanced strains, and batch genotyping to detect successful edits. Agarose gel showing batch genotype result for dzDf1. Numbers on gel indicate lane/plate number.D. Workflow for creating mini-deficiencies by injecting into non-balanced strains, and a subsequent cross into balancer males to create a balanced strain.E. Agarose gel showing F1 single worm genotyping results of dzDf2 and dzDf3. Numbers above lanes indicate plate number with arrows marking lanes with PCR bands. Asterisks mark positive PCR results.F. Table summarizing the efficiency in generating the mini-deficiencies.G. Table summarizing efficiency of generating ChrI 2.0-2.1 Mb mini-deficiency under described conditions.H. Images of PVD neuron in wildtype, dz220 and dzDf1/dz220 background, showing non-complementation of dzDf1 with dz220.Created with BioRender.com (https://www.biorender.com/)

Picture from Dubois C et al. (2023) MicroPubl Biol "A QTL on chromosome IV explains a natural variation of QR.pap final position in ...."

Figure 1. A main QTL on chromosome IV underlies the difference in QRpap final position between CB4932 and JU1242:(A) Nomarski micrographs of late L1 larvae showing examples of QR.paa and QR.pap positions in JU1242 (top) and CB4932 (bottom). (B) Distribution of QR.paa and QR.pap positions in JU1242 and CB4932, replotted from data in Dubois et al., 2021. n=50 per line. Large dots and error bars represent the mean ± s.d. Statistical differences were assessed using a Wilcoxon's rank sum test (***p-value<0.001). (C) Distribution of QR.paa and QR.pap positions in the F1 progeny of JU1242 and CB4932. n=50 per condition. Letters (a-d) represent groups with similar mean (Dunn's test with Bonferroni adjustment post-hoc comparison). For instance, "ab" means that this condition is not significatively different from either "a" or "b", which are different from each other. (D) Generation of Recombinant Inbred Lines (RILs). A single pair of chromosomes is represented for clarity. (E) Distribution of QR.pap final position in the 200 RILs. The parental genotypes CB4932 (dark blue) and JU1242 (dark orange) were phenotyped independently three times. The 40 RILs with the most anterior QR.pap position (light blue) were pooled for sequencing, as well as the 40 with the most posterior position (light orange). Dots and error bars represent the mean ± c.i. (95%); n=20 per line. A histogram of the phenotypic distribution is shown on the right. (F) Bulk Segregant Analysis: JU1242 allele frequency in the Posterior pool (orange) and the Anterior Pool (Blue). Thin horizontal black lines represent the threshold for a significant difference between log-odd ratios at p = 0.001. The JU1242 allele frequency is fixed in the Posterior Pool between 4.5 Mb to 6 Mb, revealing a QTL associated to the variation in QR.pap final position. (G) Validation of the chromosome IV effect on QR.pap final position. Near isogenic Lines were generated using successive backcrosses to exchange chromosome IV between CB4932 and JU1242. The chromosomes from CB4932 are represented in Blue and those from JU1242 in Orange. n>40 scored animals per line. Dots and error bars represent the mean ± s.d. Letters (a-c) represent groups of genotypes with a similar QR.pap mean (Dunn's test with Bonferroni adjustment post-hoc comparison).

Picture from Jang S et al. (2016) Neuron "Glycolytic Enzymes Localize to Synapses under Energy Stress to Support Synaptic ...."

Figure S2, related to Figure 1and Figure 2. Genetic lesions in pfk-1.1 mutants and endogenous expression pattern(A-B) Schematic of the genomic region of pfk-1.1 and locations of the genetic lesions of the pfk1.1 alleles examined in this study (marked with arrows) (A); and percentage of animals displaying a diffuse distribution of synaptic vesicle proteins in rescuing backgrounds (B). Single Nucleotide Polymorphism (SNP) mapping was performed and the ola72 lesion was determined to be located between 2.77 Mb and 3.16 Mb on chromosome X (A). Fosmid WRM0616aB04, which contains the pfk-1.1 genomic region (as well as un-named gene, Y41G9A.5), was shown to rescue the diffuse distribution of synaptic vesicle protein phenotype in pfk-1.1(ola72) mutant animals exposed to 10 minutes of hypoxic conditions (induced by mounting on glass slide with coverslip (Pitts and Toombs, 2004)) (B). The pfk-1.1 promoter driving pfk-1.1 cDNA also rescues the synaptic vesicle clustering phenotype in pfk-1.1(ola72) mutant animals exposed to 10 minutes of hypoxic conditions (B). Number of animals scored is indicated at the bottom of each column. pfk-1.1(ola72) is the same as shown in Figure 1J for (B).(C) Percentage of animals displaying a diffuse distribution of synaptic vesicle proteins after 10 minutes of hypoxic treatment (induced by mounting on glass slide with coverslip (Pitts and Toombs, 2004)). Note that all three independent pfk-1.1 alleles phenocopy pfk-1.1(ola72), and that pfk-1.1(gk549413) fails to complement pfk-1.1(ola72). Number of animals scored is indicated at the bottom of each column. Wild-type control and pfk-1.1 (ola72) is the same as shown in Figure 1J. (D-G) Expression of the pfk-1.1 promoter is observed in neurons of the ventral and dorsal nerve cords (arrows) (D); and in head neurons, including the NSM neurons (E-G).(H) Schematic of the glycolysis pathway and mutants examined in this study. Enzymes are shown in black, while substrates are in blue. Numbers inside parentheses indicate the number of identified C. elegans homologs for each given enzyme in the pathway. Solid red arrow denotes enzymatic reactions in the glycolysis pathway. Dashed arrows denote regulatory steps: (+) for activation and (-) for inhibition. Asterisk marks genes examined in this study. We selected the specific enzymes for analyses based on availability of identified alleles from the Caenorhabditis Genomic Center (CGC). With the exception of 6-phosphofructokinase/pfk-1.1, which was identified in our forward genetic screen, all other enzymes were selected based on theavailability of deletion alleles. Scale bar represents 25um for (D), and 5um for (E). Error bars denote SEM. *, p < 0.05. **, p <0.01. ***, p < 0.001 between indicated groups.

Picture from Tu H et al. (2015) BMC Evol Biol "Membrane-associated collagens with interrupted triple-helices (MACITs): ...."

Fig. 8 Localization of COL-99::EGFP::FLAG at NMJs and in other tissues. a) Detection of COL-99::EGFP::FLAG expression in the head part of an adult C. elegans. Whole mount immunofluorescence staining was performed with a rabbit anti-GFP antibody and AlexaFluor 488-conjugated anti-rabbitIgG. c) Detection of COL-99::EGFP::FLAG in the middle body part. The specimen was prepared by a freeze-crack treatment and a mild PFA fixation.The detection antibody was rabbit anti-GFP. e Staining of methanol/acetone fixed tail (TA) section of a col-99::egfp::flag worm with rabbit anti-GFP(white) and DAPI (blue). The green fluorescence detected with AlexaFluor 488-conjugated secondary antibody was converted to white to enhance the sensitivity. g Double staining of an L1 larva with rabbit anti-GFP (green) and mouse anti-myosin (magenta). The image was converted from a3D Z-scan and signal was adjusted by Image J software. I) Whole-mount immunofluorescent staining of a col-99::egfp::flag adult worm with rabbitanti-GFP (green) and mouse anti-myosin (magenta). k Immunofluorescent staining of a freeze-crack section of worm muscle after mild PFA fixationwith rabbit anti-GFP (green) and mouse anti-myosin (magenta). m-o Immunofluorescent staining of a col-99::egfp::flag worm after freezecracktreatment with rabbit anti-GFP (green in m and o) and alpha-bungarotoxin (magenta in n and o) showing NMJ localization. o Mergedfrom (m) and (n). q-s Immunofluorescent staining of col-99 embryos with rabbit anti-GFP (green in q and s) and alpha -bungarotoxin (magentain r and s). b, d, f, h, j, l, p, and t are negative control staining of unc-119 worms for (a), (c), (e), (g), (i), (k), (o), and (s) respectively. Bars, 5 um in a-h, k-l and m-p, 10 um in i-j, and 20 um in q-t. HE, head; MB, middle body; TA, tail; BM, body muscle; NMJ, neuromuscular junction

Picture from Kim J et al. (2017) MicroPubl Biol "A quantitative trait locus for nictation behavior on chromosome V"

Lee et al., 2017 showed that CB4856 has a lower nictation ratio (the number of nictating dauers over the number of moving dauers on a micro-dirt chip) than N2, and that a genetic locus (nict-1) on chromosome IV mediates this phenotype difference. Although this paper had no evidence of any other genetic loci for nictation behavior, we have studied other quantitative trait loci (QTL) using different linkage-based mapping strategies. Here, we report another genetic locus that was identified using introgression lines on chromosome V. N2 x CB4856 introgression lines were tested using a population nictation assay (Lee et al., 2015). We measured the nictation ratios of the ewIR65, ewIR67, ewIR68, and ewIR70 lines, which contain N2-type genome in all chromosomes except for CB4856-type chromosome V segments (Figure 1A). Among them, only ewIR70 line showed significant lower nictation ratio. Therefore, we narrowed down the chromosome V right region. We also measured nictation ratios of ysIR50, ewIR74, and ysIR51 lines (Figure 1B). ysIR50 and ysIR51 were derived from N2 x ewIR70. ysIR50, ewIR74, and ysIR51 lines showed significantly lower nictation ratios than that of N2. Because the putatively responsible QTL region is covered by another near-isogenic region, eanIR158, which was made independently by Erik Andersen's laboratory, we measured the nictation ratios of eanIR158 and jyIR3 lines and found that they did not show any significant difference from N2 (Figure 1C). eanIR158 and jyIR3 lines were built with QX1430 x N2 (personal communication) and QX217 x N2 (Balla et al., 2015), respectively, and QX1430 and QX217 were made by Leonid Kruglyak's laboratory (Andersen et al., 2015; Rockmen and Kruglyak, 2009). However, ewIR70 and ewIR74 were built by Jan Kammenga's laboratory (Doroszuk et al., 2009). Thus, we concluded that the two laboratories may have used different N2 or CB4856 strain derivatives, which may have altered genetic variations in the introgression lines. A take-home lesson is that it is important to examine NILs derived from common original strains in order to follow QTL without being affected by differences in background genotypes. Jan Kammenga kindly provided their N2 x CB4856 introgression lines for chromosome V, which include ewIR65, ewIR67, ewIR68, ewIR70, and ewIR74, and Erik Andersen also gave us many introgression lines, which include eanIR158 and jyIR3 covering 15-19 Mb of chromosome V. We appreciate their help.