Anatoli Pouzyrev et al. (2001) International C. elegans Meeting "Enrichment of cDNA Libraries for Clones Representing Rare mRNAs."

Anatoli Pouzyrev, Donald Riddle

[International C. elegans Meeting, 2001]

Identification of recombinant clones corresponding to rare mRNAs requires large-scale screening of cDNA libraries. We have developed a method to remove abundant sequences from cDNA libraries based on the second-order kinetics of DNA reassociation. It is simpler and more direct than existing methods. First, we cloned the same set of cDNAs (unnormalized cDNAs) into two vectors - lambda gt11 and lambda ZapII. Second, the cDNA inserts of recombinant lambda gt11 molecules were amplified by PCR and used for preparation of an abundant cDNA pool. The preparation of this pool involved denaturation of the double-stranded cDNA inserts, partial reassociation, and selection of the double-stranded fraction. Single-stranded unnormalized cDNAs were prepared from the lambda Zap II library and mixed with an excess of the abundant cDNA pool. After denaturation and partial reassociation, the single-stranded fraction was selected for preparation of the rare cDNA library. We have characterized rare cDNA libraries from dauer larvae and adults. Abundant sequences (e.g., Hsp90 and Cytochrome C oxidase subunit I) generally became undetectable, whereas rare clones increased in concentration up to 197-fold. Sequence analysis of 40 clones from the two subtracted libraries showed that 19 corresponded to genes that previously lacked ESTs. This method should improve the tools for gene discovery in any organism, especially vertebrate systems in which accurate gene predictions from genomic sequences are difficult. It should also have applications in microarray technology, since EST-based microarrays currently lack sequences expressed at low levels. In addition, use of subtracted libraries for hybridization with microarrays should greatly improve the sensitivity of that technology.

Suzan J Holt et al. (2003) International Worm Meeting "A dauer approach to survival: Modulate internal oxygen exposure and manufacture metabolites de novo."

Donald L Riddle, Suzan J Holt

[International Worm Meeting, 2003]

A lowered metabolic rate and availability of stored lipids are thought to contribute to the longevity of dauer larvae, which can remain non-feeding for months. At least 5% external oxygen is required for lipid utilization in starving Caenorhabditis (1). The small size of a C. elegans dauer larva, 20 m in diameter, might indicate that oxygen passage by cuticular diffusion is sufficient for maintenance of aerobic physiology. Nevertheless, recent evidence from gene expression profiles suggests that anaerobic metabolism is augmented in dauer larvae. Serial analysis of gene expression (SAGE) has revealed that the dauer larva, though developmentally arrested, has a surprisingly complex transcriptome (2). We compared transcript abundance between the dauer and mixed-stage profiles for 59 genes with confirmed or predicted involvement in carbohydrate metabolism. The most prominent transcript was for phosphoenolpyruvate carboxykinase (PEPCK). The pyruvate kinase:PEPCK SAGE tag ratio for either profile supports a glycolytic shunt such as that found in parasitic helminths which are characterized by succinate fermentation and anaerobic ATP formation. However, the transcript patterns for key enzymes in the glyoxylate cycle, gluconeogenesis, and for glycogen phosphorylase reflected higher potential involvement for PEPCK in carbohydrate synthesis in mixed stages compared to the dauer. Transcripts for additional proteins with predicted functions in oxygen-independent routes for energy generation were dauer-enriched. The morphology of dauer larvae together with apparent upregulation of anaerobic pathways indicates that the dauer interior could be hypoxic. These data may help explain the hypoxia resistance (Hyp) of N2 dauer larvae and may have implications regarding the adult Hyp phenotype of certain daf-2 mutants (3). The lowering of the aerobic metabolic rate, as well as oxygen level, may lower the rate of oxidative damage accumulation and contribute to dauer longevity, as long as the -oxidation of lipids is not seriously compromised. In addition, fermentation byproducts, used as alternative nutrient sources, could serve to slow the depletion of lipid stores and extend the survival period.1. Cooper and Van Gundy. 1970. J. Nematol. 2:305; 2. Jones, Riddle, Pouzyrev, Velculescu, Hillier, Eddy, Stricklin, Baillie, Waterston, and Marra. 2001. Genome Res. 11:1346; 3. Scott, Avidan, and Crowder. 2002. Science 296:2388.

Quartey MO et al. (2021) Sci Rep "The A(1-38) peptide is a negative regulator of the A(1-42) peptide implicated in Alzheimer disease progression."

Pennington PR, Heistad RM, Nyarko JNK, Barnes JR, Bolanos MAC, Parsons MP, Knudsen KJ, De Carvalho CE, Leary SC, Mousseau DD, Buttigieg J, Maley JM, Quartey MO

[Sci Rep, 2021]

The pool of -Amyloid (A) length variants detected in preclinical and clinical Alzheimer disease (AD) samples suggests a diversity of roles for A peptides. We examined how a naturally occurring variant, e.g. A(1-38), interacts with the AD-related variant, A(1-42), and the predominant physiological variant, A(1-40). Atomic force microscopy, Thioflavin T fluorescence, circular dichroism, dynamic light scattering, and surface plasmon resonance reveal that A(1-38) interacts differently with A(1-40) and A(1-42) and, in general, A(1-38) interferes with the conversion of A(1-42) to a -sheet-rich aggregate. Functionally, A(1-38) reverses the negative impact of A(1-42) on long-term potentiation in acute hippocampal slices and on membrane conductance in primary neurons, and mitigates an A(1-42) phenotype in Caenorhabditis elegans. A(1-38) also reverses any loss of MTT conversion induced by A(1-40) and A(1-42) in HT-22 hippocampal neurons and APOE 4-positive human fibroblasts, although the combination of A(1-38) and A(1-42) inhibits MTT conversion in APOE 4-negative fibroblasts. A greater ratio of soluble A(1-42)/A(1-38) [and A(1-42)/A(1-40)] in autopsied brain extracts correlates with an earlier age-at-death in males (but not females) with a diagnosis of AD. These results suggest that A(1-38) is capable of physically counteracting, potentially in a sex-dependent manner, the neuropathological effects of the AD-relevant A(1-42).

Danielle Thierry-Mieg et al. (2003) Worm Breeder's Gazette "www.wormgenes.org , a new gene centered database"

Vahan Simonyan, Michel Potdevin, Mark Sienkiewicz, Yuji KOHARA, Jean Thierry-Mieg, Danielle Thierry-Mieg, Tadasu SHIN-I

[Worm Breeder's Gazette, 2003]

Wormgenes is a new resource for C.elegans offering a detailed summary about each gene and a powerful query system.

Tangrodchanapong T et al. (2020) Front Pharmacol "Frondoside A Attenuates Amyloid- Proteotoxicity in Transgenic Caenorhabditis elegans by Suppressing Its Formation."

Tangrodchanapong T, Sobhon P, Meemon K

[Front Pharmacol, 2020]

Oligomeric assembly of Amyloid- (A) is the main toxic species that contribute to early cognitive impairment in Alzheimer's patients. Therefore, drugs that reduce the formation of A oligomers could halt the disease progression. In this study, by using transgenic <i>Caenorhabditis elegans</i> model of Alzheimer's disease, we investigated the effects of frondoside A, a well-known sea cucumber <i>Cucumaria frondosa</i> saponin with anti-cancer activity, on A aggregation and proteotoxicity. The results showed that frondoside A at a low concentration of 1 M significantly delayed the worm paralysis caused by A aggregation as compared with control group. In addition, the number of A plaque deposits in transgenic worm tissues was significantly decreased. Frondoside A was more effective in these activities than ginsenoside-Rg3, a comparable ginseng saponin. Immunoblot analysis revealed that the level of small oligomers as well as various high molecular weights of A species in the transgenic <i>C. elegans</i> were significantly reduced upon treatment with frondoside A, whereas the level of A monomers was not altered. This suggested that frondoside A may primarily reduce the level of small oligomeric forms, the most toxic species of A. Frondoside A also protected the worms from oxidative stress and rescued chemotaxis dysfunction in a transgenic strain whose neurons express A. Taken together, these data suggested that low dose of frondoside A could protect against A-induced toxicity by primarily suppressing the formation of A oligomers. Thus, the molecular mechanism of how frondoside A exerts its anti-A aggregation should be studied and elucidated in the future.

Hodgkin JA (1998) International Journal of Developmental Biology "Seven types of pleiotropy."

Hodgkin JA

[International Journal of Developmental Biology, 1998]

Pleiotropy , a situation in which a single gene influences multiple phenotypic tra its, can arise in a variety of ways. This paper discusses possible underlying mechanisms and proposes a classification of the various phenomena involved.

Tuck S (2011) Curr Biol "Extracellular vesicles: budding regulated by a phosphatidylethanolamine translocase."

Tuck S

[Curr Biol, 2011]

Recent work on a Caenorhabditis elegans transmembrane ATPase reveals a central role for the aminophospholipid phosphatidylethanolamine in the production of a class of extracellular vesicles.

Viney ME et al. (2004) Naturwissenschaften "Is dauer pheromone of Caenorhabditis elegans really a pheromone?"

Viney ME, Franks NR

[Naturwissenschaften, 2004]

Animals respond to signals and cues in their environment. The difference between a signal (e.g. a pheromone) and a cue (e.g. a waste product) is that the information content of a signal is subject to natural selection, whereas that of a cue is not. The model free-living nematode Caenorhabditis elegans forms an alternative developmental morph (the dauer larva) in response to a so-called 'dauer pheromone', produced by all worms. We suggest that the production of 'dauer pheromone' has no fitness advantage for an individual worm and therefore we propose that 'dauer pheromone' is not a signal, but a cue. Thus, it should not be called a pheromone.

Schaeffer JM et al. (1990) J Antibiot (Tokyo) "Cochlioquinone A, a nematocidal agent which competes for specific [3H]ivermectin binding sites."

Williamson JM, Schaeffer JM, Bergstrom AR, Liesch JM, Goetz MA, Frazier EG

[J Antibiot (Tokyo), 1990]

Cochlioquinone A, isolated from the fungus Helminthosporium sativum, was found to have nematocidal activity. Cochlioquinone A is a competitive inhibitor of specific [3H]ivermectin binding suggesting that cochlioquinone A and ivermectin interact with the same membrane receptor.

Desta IT et al. (2016) J Lab Autom "Detecting and Trapping of a Single C. elegans Worm in a Microfluidic Chip for Automated Microplate Dispensing."

Giakoumidis N, Mustafa N, AlGharibeh N, Orozaliev A, Al-Sharif A, Song YA, Desta IT, Gunsalus KC

[J Lab Autom, 2016]

Microfluidic devices offer new technical possibilities for a precise manipulation of Caenorhabditis elegans due to the comparable length scale. C. elegans is a small, free-living nematode worm that is a popular model system for genetic, genomic, and high-throughput experimental studies of animal development and neurobiology. In this paper, we demonstrate a microfluidic system in polydimethylsiloxane (PDMS) for dispensing of a single C. elegans worm into a 96-well plate. It consists of two PDMS layers, a flow and a control layer. Using five microfluidic pneumatic valves in the control layer, a single worm is trapped upon optical detection with a pair of optical fibers integrated perpendicular to the constriction channel and then dispensed into a microplate well with a dispensing tip attached to a robotic handling system. Due to its simple design and facile fabrication, we expect that our microfluidic chip can be expanded to a multiplexed dispensation system of C. elegans worms for high-throughput drug screening.