Edouard de Castro et al. (2001) International C. elegans Meeting "Identification of genes involved in oxidative stress response and aging in Caenorhabditis elegans"

Sarah Hegi de Castro, Thomas E Johnson, Edouard de Castro

[International C. elegans Meeting, 2001]

Aging is a multifactorial phenomenon; yet, the accumulation of oxidative damage to macromolecules appears to play a crucial role. There is an intimate relationship between longevity and the ability to prevent/repair chronic damage to macromolecules. The efficiency of anti-damages mechanisms can be revealed by the ability to endure environmentally imposed stress (Such 'external' stress can be considered as an exacerbation of the chronic endogenous accumulation of damages). All environmental or genetic interventions that increased longevity also increased resistance to environmental stress. It appears that the capacity to control the accumulation of damages to macromolecules modulates both longevity and environmental stress resistance. In order to get insight into the mechanisms of resistance to oxidative stress and its relation with aging, we have isolated C. elegans mutants showing an increased resistance to the oxidative stress inducing compound Juglone (5-hydroxy- 1,4- naphthoquinone). Juglone, is a redox active quinone causing reduction of O 2 to . O 2 - , and thus exerting an oxygen-dependent toxicity. We analyzed six independent mutant lines. Four of these lines show a concomitant life-span extension (up to 36% increase in mean life-span), substantiating the strong relation between oxidative stress and aging. None of these mutants are Daf-c at 27degc, suggesting that their life-span extension is not due to mutations in the daf -2 - daf -16 pathway. We are currently using Transposon Insertion Display to identify the mutated genes (transposon tagging).

Andreas Kampkoetter et al. (2001) International C. elegans Meeting "The Onchocerca volvulus glutathione S-transferase 3 (Ov-GST-3) confers an increased resistance to oxidative stress in transgenic Caenorhabditis elegans"

Andreas Kampkoetter, Britta Leiers, Sarah Hegi de Castro, Lars-Oliver Klotz, Kimberly Henkle-Duehrsen, Chris Link, Helmut Sies

[International C. elegans Meeting, 2001]

Onchocerca volvulus is a parasitic nematode which is infectious for humans, resulting in the disease called River Blindness or Onchocerciasis. Onchocerciasis is the worlds second cause of blindness, due to an infection. A total of 18 million people are infected with this parasite, 120 million live at risk, and roughly half a million are completely blind due to this disease. The adult parasites live for many years in nodules under the skin of the human host and produce large numbers of offspring called microfilariae. These microfilariae migrate in the subcutaneous tissue, can be swallowed by a blood sucking black fly and mature to juveniles. During another blood meal of the mosquito, the larval parasites can enter the human host to continue the life cycle. Like all aerobic organisms O. volvulus must defend itself against cellular oxidative stress generated by metabolism and incomplete respiration. Therefore, protective enzymatic and non-enzymatic antioxidants exist that prevent, repair or eliminate oxidative damage. Detoxification enzymes, like the glutathione S-transferases (GSTs), minimize the concentration of oxidatively damaged cellular components, particularly oxidized DNA, proteins and lipids. Nevertheless, the parasite is able to persist for a long time in the human host even though it is heavily attacked by the immune system of the human host. This attack includes the release of a variety of reactive oxygen species from stimulated host phagocytic cells which cause an external oxidative stress. This means that O. volvulus must have evolved additional mechanisms to protect itself against the immune response of the human host to ensure its own survival. A glutathione S-transferase of O. volvulus ( Ov -GST-3), shown to be upregulated in response to oxidative stress, is suspected to be involved in the defense against the host's immune system. To have the chance to investigate the function of this molecule in more detail, transgenic C. elegans (AK1) containing the Ov -GST-3 gene under the control of a C. elegans promotor (let-858) were generated. The comparison of AK1 worms and control worms on plates with artificially produced oxidative stress revealed significant higher survival rates of the transgenic line. The extent of lipid peroxidation, one type of damage caused by oxidative stress, is also reduced in the transgenic worms as determined by the measurement of the level of malondialdehyde (MDA). These findings clearly demonstrate that the overexpression of Ov -GST-3 confers an increased resistance to oxidative stress in the transgenic AK1 worms.

Zarkower D et al. (1994) Worm Breeder's Gazette "mab-3 YAC Rescue"

De Bono M, Hodgkin JA, Zarkower D

[Worm Breeder's Gazette, 1994]

mab-3 YAC rescue David Zarkower, Mario de Bono, and Jonathan Hodgkin MRC Laboratory of Molecular Biology, Cambridge, England

Eberhardt AG et al. (2008) Vet Parasitol "The Strongyloides (Nematoda) of sheep and the predominant Strongyloides of cattle form at least two different, genetically isolated populations."

Mayer WE, Eberhardt AG, Streit A, Bonfoh B

[Vet Parasitol, 2008]

Strongyloides sp. (Nematoda) are very wide spread small intestinal parasites of vertebrates that can form a facultative free-living generation. Most authors considered all Strongyloides of farm ruminants to belong to the same species, namely Strongyloides papillosus (Wedl, 1856). Here we show that, at least in southern Germany, the predominant Strongyloides found in cattle and the Strongyloides found in sheep belong to separate, genetically isolated populations. While we did find mixed infections in cattle, one form clearly dominated. This variety, in turn, was never found in sheep, indicating that the two forms have different host preferences. We also present molecular tools for distinguishing the two varieties, and an analysis of their phylogenetic relationship with the human parasite Strongyloides stercoralis and the major laboratory model species Strongyloides ratti. Based on our findings we propose that Strongyloides from sheep and the predominant Strongyloides from cattle should be considered separate species as it had already been proposed by [Brumpt, E., 1921. Recherches sur le determinisme des sexes et de l''evolution des Anguillules parasites (Strongyloides). Comptes rendu hebdomadaires des seances et memoires de la Societe de Biologie et de ses filiales 85, 149-152], but was largely ignored by later authors. For nomenclature, we follow [Brumpt, E., 1921. Recherches sur le determinisme des sexes et de l''evolution des Anguillules parasites (Strongyloides). Comptes rendu hebdomadaires des seances et memoires de la Societe de Biologie et de ses filiales 85, 149-152] and use the name S. papillosus for the Strongyloides of sheep and the name Strongyloides vituli for the predominant Strongyloides of cattle.

De Stasio E et al. (1994) Worm Breeder's Gazette "Mutagenesis of C. elegans Using N-ethyl-N-nitrosourea."

De Stasio E, Stanislaus D, Lephoto C

[Worm Breeder's Gazette, 1994]

Mutagenesis of C. elegans using N-ethyl-N-nitrosourea Elizabeth De Stasio, Dinesh Stanislaus and Catherine Lephoto. Department of Biology, Lawrence University, Appleton, Wl 54911

Sokolowski MB (2002) Nature "Neurobiology: social eating for stress."

Sokolowski MB

[Nature, 2002]

Behavioral ecologists have shown that many animals form social groups in conditions. Neurobiological evidence for this behaviour has now been discovered in the nematode worm, Caenorhabditis elegans. On pages 899 and 925 of this issue, de Bono et al. and Coates and de Bono present striking results on the genetic, molecular and neural mechanisms underlying nematode social feeding. These discoveries provide tantalizing insights into the effects of stress in social groupings.

Platzer K et al. (2018) Am J Hum Genet "De Novo Variants in MAPK8IP3 Cause Intellectual Disability with Variable Brain Anomalies."

Stegmann APA, Bonati MT, Panis B, Smith-Hicks C, Lemke JR, Pepler A, Wilson C, Iascone M, McWalter K, Brasington C, Allen W, Di Donato N, Platzer K, Ramos L, Edwards SL, Jamra R, Gamble CN, Mandel H, Stobe P, Mahida S, Marquardt T, Demmer LA, Miller KG, Falik-Zaccai T, Pinz H, Hellenbroich Y, Sticht H, Kok F, Cho MT, Stumpel CTRM, Shinde DN, Angione KM

[Am J Hum Genet, 2018]

Using exome sequencing, we have identified de novo variants in MAPK8IP3 in 13 unrelated individuals presenting with an overlapping phenotype of mild to severe intellectual disability. The de novo variants comprise six missense variants, three of which are recurrent, and three truncating variants. Brain anomalies such as perisylvian polymicrogyria, cerebral or cerebellar atrophy, and hypoplasia of the corpus callosum were consistent among individuals harboring recurrent de novo missense variants. MAPK8IP3 has been shown to be involved in the retrograde axonal-transport machinery, but many of its specific functions are yet to be elucidated. Using the CRISPR-Cas9 system to target six conserved amino acid positions in Caenorhabditis elegans, we found that two of the six investigated human alterations led to a significantly elevated density of axonal lysosomes, and five variants were associated with adverse locomotion. Reverse-engineering normalized the observed adverse effects back to wild-type levels. Combining genetic, phenotypic, and functional findings, as well as the significant enrichment of de novo variants in MAPK8IP3 within our total cohort of 27,232 individuals who underwent exome sequencing, we implicate de novo variants in MAPK8IP3 as a cause of a neurodevelopmental disorder with intellectual disability and variable brain anomalies.

Ma B (2015) J Am Soc Mass Spectrom "Novor: real-time peptide de novo sequencing software."

Ma B

[J Am Soc Mass Spectrom, 2015]

De novo sequencing software has been widely used in proteomics to sequence new peptides from tandem mass spectrometry data. This study presents a new software tool, Novor, to greatly improve both the speed and accuracy of today's peptide de novo sequencing analyses. To improve the accuracy, Novor's scoring functions are based on two large decision trees built from a peptide spectral library with more than 300,000 spectra with machine learning. Important knowledge about peptide fragmentation is extracted automatically from the library and incorporated into the scoring functions. The decision tree model also enables efficient score calculation and contributes to the speed improvement. To further improve the speed, a two-stage algorithmic approach, namely dynamic programming and refinement, is used. The software program was also carefully optimized. On the testing datasets, Novor sequenced 7%-37% more correct residues than the state-of-the-art de novo sequencing tool, PEAKS, while being an order of magnitude faster. Novor can de novo sequence more than 300 MS/MS spectra per second on a laptop computer. The speed surpasses the acquisition speed of today's mass spectrometer and, therefore, opens a new possibility to de novo sequence in real time while the spectrometer is acquiring the spectral data. Graphical Abstract .

Walser M et al. (2017) PLoS Genet "-Integrin de-phosphorylation by the Density-Enhanced Phosphatase DEP-1 attenuates EGFR signaling in C. elegans."

Hajnal A, Frohli E, Walser M, Nanni P, Umbricht CA

[PLoS Genet, 2017]

Density-Enhanced Phosphatase-1 (DEP-1) de-phosphorylates various growth factor receptors and adhesion proteins to regulate cell proliferation, adhesion and migration. Moreover, dep-1/scc1 mutations have been detected in various types of human cancers, indicating a broad tumor suppressor activity. During C. elegans development, DEP-1 mediates binary cell fate decisions by negatively regulating EGFR signaling. Using a substrate-trapping DEP-1 mutant in a proteomics approach, we have identified the C. elegans -integrin subunit PAT-3 as a specific DEP-1 substrate. DEP-1 selectively de-phosphorylates tyrosine 792 in the membrane-proximal NPXY motif to promote integrin activation via talin recruitment. The non-phosphorylatable -integrin mutant pat-3(Y792F) partially suppresses the hyperactive EGFR signaling phenotype caused by loss of dep-1 function. Thus, DEP-1 attenuates EGFR signaling in part by de-phosphorylating Y792 in the -integrin cytoplasmic tail, besides the direct de-phosphorylation of the EGFR. Furthermore, in vivo FRAP analysis indicates that the -integrin/talin complex attenuates EGFR signaling by restricting receptor mobility on the basolateral plasma membrane. We propose that DEP-1 regulates EGFR signaling via two parallel mechanisms, by direct receptor de-phosphorylation and by restricting receptor mobility through -integrin activation.

Yuen KW et al. (2011) Curr Biol "Rapid de novo centromere formation occurs independently of heterochromatin protein 1 in C. elegans embryos."

Nabeshima K, Oegema K, Desai A, Yuen KW

[Curr Biol, 2011]

DNA injected into the Caenorhabditis elegans germline forms extrachromosomal arrays that segregate during cell division [1, 2]. The mechanisms underlying array formation and segregation are not known. Here, we show that extrachromosomal arrays form de novo centromeres at high frequency, providing unique access to a process that occurs with extremely low frequency in other systems [3-8]. De novo centromerized arrays recruit centromeric chromatin and kinetochore proteins and autonomously segregate on the spindle. Live imaging following DNA injection revealed that arrays form after oocyte fertilization via homologous recombination and nonhomologous end-joining. Individual arrays gradually transition from passive inheritance to active segregation during the early embryonic divisions. The heterochromatin protein 1 (HP1) family proteins HPL-1 and HPL-2 are dispensable for de novo centromerization even though arrays become strongly enriched for the heterochromatin-associated H3K9me3 modification over time. Partial inhibition of HP1 family proteins accelerates the acquisition of segregation competence. In addition to reporting the first direct visualization of new centromere formation in living cells, these findings reveal that naked DNA rapidly builds de novo centromeres in C. elegans embryos in an HP1-independent manner and suggest that, rather than being a prerequisite, HP1-dependent heterochromatin antagonizes de novo centromerization.