Rosenberg R (1978) Worm Breeder's Gazette

Rosenberg R

[Worm Breeder's Gazette, 1978]

All eyes are on the newest fashion trend, the Dumpy Look . Pace setting designer I.M. Worm s androgynous wardrobe is all the rage in Paris. Bianca Jagger quips, Tres, tres - Women s Wear Daily writes, Elegans personified - Patti Smith thinks, The punks won t buy it and Craig Russell says, It fits right in with my act . A product of Mutant Isolation, Inc.

Kravtsov, V. et al. (2013) International Worm Meeting "The effects of aging on dendritic plasticity and PVD-FLP branch coexistence."

Podbilewicz, B., Oren-Suissa, M., Kravtsov, V.

[International Worm Meeting, 2013]

Self-avoidance, tiling and coexistence are the main mechanisms that enable the best dendritic coverage. C. elegans undergoes aging-associated changes that ultimately lead to decreased functionality of the organism, including its neurological functions. Recent research has shown that the nervous system of C. elegans undergoes changes and alterations during aging including dendritic morphology (Tank et al., 2011). We study dendritic plasticity, aging and spatial dendritic organization of two highly arborized mechanoreceptors in C. elegans, PVD and FLP (Oren-Suissa et al., 2010). PVD dendrites of L4s and young adults show regenerative ability following dendrotomy (laser induced severing of dendrites). Our working hypothesis is that in older ages this ability to regenerate is compromised. Previous studies and our preliminary results indicate that PVD and FLP do not overlap in larval stages (Smith et al., 2010). In addition, dendrites within each bilateral PVD do not overlap through a self-avoidance mechanism (Smith et al., 2012). We found that (1) the coverage fields of the PVD and FLP overlap in adult worms, which indicates coexistence and not tiling. This overlap increases as the worm ages. (2) PVDs show aberrant arborization at the age of 9 days of adulthood. (3) Dramatic increase in self-avoidance defects as animals age. In humans many neurodegenerative diseases as well as generalized cognitive decline are associated with age, aberrant arborization or both (e.g. autism and Alzheimer's disease). However our understanding of how these disorders are triggered and aggravated is scarce. Our research provides an insight into the aging and regeneration process of individual neurons. Oren-Suissa, M., et al. (2010). Science 328, 1285-1288. Smith, C.J. et al. (2010). Developmental Biology 345, 18-33. Smith, C.J., et al. (2012). Nature Neuroscience 15, 731-737. Tank, E.M.H. et al. (2011). Journal of Neuroscience 31, 9279-9288.

Cassada RC et al. (1980) Worm Breeder's Gazette "initial characterization of ts embryonic defective (emb) mutants (Goettingen set)."

Culotti MR, Cassada RC, Von Ehrenstein G, Isnenghi E

[Worm Breeder's Gazette, 1980]

[See Figure 1] Already published allelism: Wood et al., 1980: b117=b189; b246 = let- 2.Miwa et al., 1980: hc57 = hc62; hc61 = hc67. Our global complementation results: g1 = g4; g16 = g65 = hc61 = hc67; g36 = hc65; g23 = g34 = hc70 = b117 = b189; g37 = b246 = let-2; b84 = hc66; g14 = g43; g57 = b1O. From frequency of multiple alleles we estimate 200-400 genes essential for embryogenesis. Mapping is in progress. We are also doing tsp's, R + H Tests, and cellular defects ( Isnenghi, Cassada, Radnia, Schierenberg, K. Smith, v. Ehrenstein).

Jeong J et al. (2019) Nanotoxicology "Developing adverse outcome pathways on silver nanoparticle-induced reproductive toxicity via oxidative stress in the nematode Caenorhabditis elegans using a Bayesian network model."

Choi I, Song T, Choi J, Chatterjee N, Jeong J, Cha YK

[Nanotoxicology, 2019]

An adverse outcome pathway (AOP) is a framework that organizes the mechanistic or predictive relationships between molecular initiating events (MIEs), key events (KEs), and adverse outcomes (AOs). Previously, we intensively investigated the molecular mechanism that underlies toxicity caused by AgNPs in the nematode Caenorhabditis elegans. Using transcriptomics, functional genetics, and various molecular/biochemical tools, we identified oxidative stress as the major mechanism underlying toxicity and reproduction failure as the outcome. With this information, here we conducted a case study of building an AOP to link oxidative stress with reproductive toxicity. To validate this AOP, we filled the gaps by conducting further experiments on its elements, such as NADPH oxidase, ROS formation, PMK-1 P38 MAPK activation, HIF-1 activation, mitochondrial damage, DNA damage, and apoptosis. The establishment of a causal link between the MIE and AO is critical for the construction of an AOP. Therefore, causal relationships between each KE and AO were verified by using functional genetic mutants of each KE. By combining these experimental data with our previously published results, we established causal relationships between the MIE, KEs, and AO using a Bayesian network (BN) model, culminating in an AOP entitled 'NADPH oxidase and P38 MAPK activation leading to reproductive failure in C. elegans ( https://aopwiki.org/aops/207)' . Overall, our approach shows that an AOP can be developed using existing data and further experiments can be conducted to fill the gaps between the MIE, KEs, and the AO. This study also shows that BN modeling has the potential to identify causal relationships in an AOP.

Walker MW et al. (2005) J Biomol Screen "Use of Caenorhabditis elegans G{alpha}q chimeras to detect G-protein-coupled receptor signals."

Smith KE, Branchek TA, Walker MW, Jones KA, Gerald C, Tamm J, Zhong H, Vaysse P

[J Biomol Screen, 2005]

G-protein-coupled receptors (GPCRs) activate heterotrimeric G-proteins (G(i)-, G(s)-, G(q)-, or G(12)-like) to generate specific intracellular responses, depending on the receptor/G-protein coupling. The aim was to enable a majority of GPCRs to generate a predetermined output by signaling through a single G-protein-supported pathway. The authors focused on calcium responses as the output, then engineered Galpha(q) to promote promiscuous receptor interactions. Starting with a human Galpha(q) containing 5 Galpha(z) residues in the C-terminal receptor recognition domain (hGalpha(q/z5)), they evaluated agonist-stimulated calcium responses for 33 diverse GPCRs (G(i)-, G(s)-, and G(q)-coupled) and found 20 of 33 responders. In parallel, they tested Caenorhabditis elegans Galpha(q) containing 5 or 9 C-terminal Galpha(z) residues (cGalpha(q/z5), cGalpha(q/z9)). Signal detection was enhanced with cGalpha(q/z5) and cGalpha(q/z9) (yielding 25/33 and 26/33 responders, respectively). In a separate study of Galpha(s)-coupled receptors, the authors compared hGalpha(q/s5) versus hGalpha(q/s9), cGalpha(q/s9), andcGalphaq/s21 and observed optimal function with cGalpha(q/s9). Cotransfection of an engineered Galpha(q) "cocktail" (cGalpha(q/z5) plus cGalpha(q/s9)) provided a powerful and efficient screening platform. When the chimeras included N-terminal myristoylation sites (to promote membrane localization), calcium responses were sustained or improved, depending on the receptor. This approach toward a "universal functional assay" is particularly useful for orphan GPCRs whose signaling pathways are unknown.

Pourkarimi, Ehsan et al. (2015) International Worm Meeting "Epigenetic program of DNA replication."

Whitehouse, Iestyn, Pourkarimi, Ehsan, Bellush, James

[International Worm Meeting, 2015]

In eukaryotes, multiple replication origins initiate DNA synthesis bidirectionally. Half of the genome is duplicated discontinuously on the lagging strand in the form of Okazaki Fragments (OFs). Previously we have purified and sequenced OFs from S. cerevisiae, and have demonstrated their utility in mapping genome wide DNA replication patterns (1,2). Despite many years of research, the precise location efficiency and abundance of replication origins in metazoa remains elusive. Here we capture and sequence OFs from C. elegans and generate a genome wide map of DNA replication.We use a DNA ligation compromised genetic background and purify single stranded OFs from developing embryos. Aligning sequence reads of OFs to the C. elegans genome reveals a characteristic strand bias at specific sites that are approximately 50-100 Kb apart. The complementary enrichment of Okazaki fragments to either the Watson or Crick strands is the hallmark of a replication origin. Additionally we have found that origins of replication in C. elegans are correlated with transcriptionally active regions of chromatin. Using the histone modification data set of modENCODE we found a strong association between replication start sites and acetylation of Histone H3 lysine 27 (H3K27ac). Acetylation of H3K27 is a chromatin mark characteristic of gene enhancer elements. Finally, we show that a partial depletion of CBP/P300 the sole histone H3 acetyltransferase (HAT) responsible for H3K27 acetylation has a profound effect on DNA replication. Our data indicate that the DNA replication program is likely plastic and is matched with the transcriptional program. Ultimately our data show, both DNA replication and gene transcription are likely regulated by similar epigenetic processes. 1. Intrinsic coupling of lagging-strand synthesis to chromatin assemblyDuncan J. Smith& Iestyn Whitehouse. Nature, 20122. Quantitative, genome-wide analysis of eukaryotic replication initiation and termination.McGuffee SR, Smith DJ, Whitehouse I. Mol Cell, 2013.

Gross, E. et al. (2013) International Worm Meeting "The neuroglobin GLB-5 regulates C. elegans responses to hypoxic exposure."

Soltesz, Z., Gross, E., Zelmanovich, V., de-Bono, M.

[International Worm Meeting, 2013]

Fine-tuned O2 metabolism is essential for most animals, requiring animals to monitor and adapt to changes in O2 levels. We previously identified a polymorphic neuroglobin, GLB-5, that acts in O2-sensing neurons and enables C. elegans to respond to small changes in O2 concentration (Persson et al, 2009). Here we show that GLB-5 is essential for fast behavioural recovery after exposure to hypoxia. Whereas glb-5(Haw) animals recovered from hypoxia within minutes, glb-5(Bri) recovered slowly, over four hours. By combining genetics, biochemistry, and Calcium imaging we provide evidence that glb-5 enables fast recovery of O2-sensing neurons after prolonged hypoxic exposure. We designed mutagenesis screens to explore how GLB-5 regulates recovery from hypoxia. One mutant we identified disrupts a conserved chaperone that regulates the activity of the O2 sensing neurons. The chaperone regulates the spatial organization of soluble guanylate cyclases in these neurons, altering the way they interact with the neuroglobin to control the O2 response properties of these neurons. Persson A, Gross E, Laurent P, Busch KE, Bretes H, de Bono M (2009) Natural variation in a neural globin tunes oxygen sensing in wild Caenorhabditis elegans. Nature 458: 1030-1033.

Bo S et al. (2019) J Theor Biol "Potential relations between post-spliced introns and mature mRNAs in the Caenorhabditis elegans genome."

Zhao X, Li H, Bao T, Zhang Q, Lu Z, Bo S

[J Theor Biol, 2019]

There are potential interactions between introns and their corresponding coding sequences (CDSs) in ribosomal protein genes that have been proposed by our group and the interactions are achieved by sequence matches between the two kinds of sequences. Here, the optimal matching relations between mature mRNAs and their corresponding introns in Caenorhabditis elegans (C.elegans) were investigated by improved Smith-Waterman local alignment software. Our results showed that the remarkably matched regions appear in the untranslated regions (UTRs) of mRNAs, especially in the 3' UTR. The optimal matched segments (OMSs) are highly organized segments. In addition, the optimal matching relations were analysed between mature mRNAs and other introns. The matching strengths in the UTRs are clearly lower than those in their corresponding introns. Our studies indicate that there are potential interactions between mature mRNAs and their corresponding introns and the post-spliced introns should have other novel functions in the gene expression process.

Cohn DH et al. (2003) Am J Hum Genet "Mental retardation and abnormal skeletal development (Dyggve-Melchior-Clausen dysplasia) due to mutations in a novel, evolutionarily conserved gene."

Ehtesham N, Shanske A, Cohn DH, Krakow D, Powell BR, Rimoin DL, Unger S, Reinker K

[Am J Hum Genet, 2003]

Dyggve-Melchior-Clausen dysplasia (DMC) and Smith-McCort dysplasia (SMC) are similar, rare autosomal recessive osteochondrodysplasias. The radiographic features and cartilage histology in DMC and SMC are identical. However, patients with DMC exhibit significant developmental delay and mental retardation, the major features that distinguish the two conditions. Linkage studies localized the SMC and DMC disease genes to chromosome 18q12-21.1, providing evidence suggesting that they are allelic disorders. Sequence analysis of the coding exons of the FLJ90130 gene, a highly evolutionarily conserved gene within the recombination interval defined in the linkage study, identified mutations in SMC and DMC patients. The affected individuals in two consanguinous DMC families were homozygous for a stop codon mutation and a frameshift mutation, respectively, demonstrating that DMC represents the FLJ90130-null phenotype. The data confirm the hypothesis that SMC and DMC are allelic disorders and identify a gene necessary for normal skeletal development and brain function.

Lee DG et al. (1997) International C. elegans Meeting "THE EXPRESSION PATTERN OF CALETICULIN, A HIGH AFFINITY CALCIUM BINDING PROTEIN"

Ahnn JH, Lee DG

[International C. elegans Meeting, 1997]

In C. elegans, a homologue of mammalian calreticulins was cloned and sequenced (M. Smith, DNA seq. 2: 235-40). This gene is composed of three exons and two introns and encodes a protein of 395 amino acid residues including an N-terminal signal sequence. The C-terminus contains an ER retention signal HDEL preceded by a polyacidic region similar to the mammalian calreticulins. Especially, the sequence displays 61% homology to mouse calreticulin, increasing up to 82% in the proline-rich region. This gene was designated as crt-1 and mapped to the left end of chromosome V of the physical map. To observe the expression pattern of calreticulin in some tissues of C. elegans, we are currently constructing a genomic clone fused with GFP reporter, which will be injected into an animal to obtain transgenic lines. At the same time, a cDNA clone obtained by PCR will be used for over expression in E. coli to produce antibodies.