Von Stetina, S. E. et al. (2019) International Worm Meeting "Testing local CRISPR gene drives using C. elegans."

Min, J., Normandin, A, Von Stetina, S. E., Esvelt, K.

[International Worm Meeting, 2019]

CRISPR-mediated genetic engineering has the potential to help humanity in a multitude of ways, such as improved gene therapies, the ability to easily mimic disease-causing mutations in model organisms, and the potential to use CRISPR-driven gene drives to reduce vector-borne diseases. Gene drives function by inserting all necessary CRISPR machinery, plus the payload, into genome of the organism. When a CRISPR-carrying organism mates with a wild-type, super-Mendelian inheritance is observed, as all the progeny become homozygous CRISPR-carrying organisms. However, with nothing to stop CRISPR-activity, the potential exists for every organism within a species to become edited, a very undesirable outcome. The Sculpting Evolution group is dedicated to solving this problem by inventing and testing self-limiting gene drives, as well as immunizing reversal drives. We have dubbed one form of self-exhausting drive a daisy drive1, as the elements required to drive are separated into modules (example: parts A, B, C) that depend on each other for complete drive. Part C drives B which drives A, but nothing drives C. This means that when C is diluted out, B is no longer driven. When B is diluted out, C is no longer driven and the gene drive stops. Our mathematical models predict that the introduced drives quickly spread throughout a local population, but in the absence of additional modified animals the population will revert back to wild-type. We are developing daisy drives in C. elegans to test if the biology matches the mathematical models. Nematodes are the only metazoan where a billion organisms over multiple generations could be tested in a reasonable amount of time, and thus determine if our theory can become reality. Our preliminary results suggest that germline expressed SpCas9 has insufficient activity to sustain a drive at C. elegansrearing temperatures. We have redesigned our daisy drive constructs to use the Cas12a/Cpf1 nuclease from Lachnospiraceae bacterium ND2006 (LbCas12a), which is reported to be active at lower temperatures than SpCas9 or AsCas12a2,3. We are currently generating strains that express germline LbCas12a and the daisy drive elements, using fluorescent proteins to mark the daisy elements. I will present negative data regarding Cas9 activity and gene drive in worms, our current data on LbCas12a activity and an update on generating functional daisy drives in worms. Our future ambitions are to use community-guided science to identify problems where daisy drives could be helpful (i.e. culling mosquito-borne diseases or rat infestations), and with the community's help come up with viable solutions using our tested ideas. 1. Noble et al, 2016, bioRxiv 2. Malzahn et al, 2019, BMC Biol. 3. Liu et al, 2019, NAR

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

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

[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.

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.

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.

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.

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."

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

[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.

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

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

[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.

Wong C et al. (2003) Curr Biol "Dispatch. Centrosome biology: a SAS-sy centriole in the cell cycle."

Wong C, Stearns T

[Curr Biol, 2003]

A novel protein in Caenorhabditis elegans, SAS-4, is a component of centrioles and is required for centriole duplication. Depletion of SAS-4 results in stunted centrioles and a smaller centrosome, suggesting a link to organelle size control.