Full Text Journal Articles by
Author Ryan Doonan

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Highly improved cloning efficiency for plasmid-based CRISPR knock-in in C. elegans.

Ella DeMott, Daniel J Dickinson, Ryan Doonan,

Plasmid-based CRISPR knock-in is a streamlined, scalable, and versatile approach for generating fluorescent protein tags in <i>C. elegans</i> (Dickinson <i>et al</i>. 2015; Schwartz and Jorgensen 2016). However, compared to more recent protocols that utilize commercially available Cas9/RNP products and linear DNA repair templates (Dokshin <i>et al</i>. 2018; Ghanta and Mello ... Read more >>

MicroPubl Biol (microPublication biology)
[2021, 2021:]

Cited: 0 times

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Improved CRISPR/Cas9 knock-in efficiency via the self-excising cassette (SEC) selection method in C. elegans.

George Huang, Bailey de Jesus, Alex Koh, Sara Blanco, Aubrie Rettmann, Ella DeMott, Melynda Sylvester, Cassie Ren, Carrie Meng, Skye Waterland, Anita Rhodes, Persephone Alicea, Abbey Flynn, Daniel J Dickinson, Ryan Doonan,

Streamlined, selection-based CRISPR knock-in protocols for <i>C. elegans</i> were first introduced six years ago (Dickinson <i>et al</i>. 2015; Schwartz and Jorgensen 2016). Though these selection-based approaches are powerful, one drawback has been the requirement to inject large numbers of P0 worms (~30-60 per gene target). We have found that a ... Read more >>

MicroPubl Biol (microPublication biology)
[2021, 2021:]

Cited: 3 times

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An expanded auxin-inducible degron toolkit for Caenorhabditis elegans.

Guinevere E Ashley, Tam Duong, Max T Levenson, Michael A Q Martinez, Londen C Johnson, Jonathan D Hibshman, Hannah N Saeger, Nicholas J Palmisano, Ryan Doonan, Raquel Martinez-Mendez, Brittany R Davidson, Wan Zhang, James Matthew Ragle, Taylor N Medwig-Kinney, Sydney S Sirota, Bob Goldstein, David Q Matus, Daniel J Dickinson, David J Reiner, Jordan D Ward,

The auxin-inducible degron (AID) system has emerged as a powerful tool to conditionally deplete proteins in a range of organisms and cell types. Here, we describe a toolkit to augment the use of the AID system in Caenorhabditis elegans. We have generated a set of single-copy, tissue-specific (germline, intestine, neuron, ... Read more >>

Genetics (Genetics)
[2021, 217(3):]

Cited: 7 times

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Expanding theCaenorhabditis elegansauxin-inducible degron system toolkit with internal expression and degradation controls and improved modular constructs for CRISPR/Cas9-mediated genome editing

Guinevere Ashley, Tam Duong, Max Levenson, Michael Martinez, Jonathan Hibshman, Hannah Saeger, Ryan Doonan, Nicholas Palmisano, Raquel Martinez-Mendez, Brittany Davidson, Wan Zhang, James Matthew Ragle, Taylor Medwig-Kinney, Sydney Sirota, Bob Goldstein, David Matus, Daniel Dickinson, David Reiner, Jordan Ward,

The auxin-inducible degron (AID) system has emerged as a powerful tool to conditionally deplete proteins in a range of organisms and cell-types. Here, we describe a toolkit to augment the use of the AID system in Caenorhabditis elegans . We have generated a set of single-copy, tissue-specific (germline, intestine, neuron, ... Read more >>

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DamID in C. elegans reveals longevity-associated targets of DAF-16/FoxO.

Eugene Schuster, Joshua J McElwee, Jennifer M A Tullet, Ryan Doonan, Filip Matthijssens, John S Reece-Hoyes, Ian A Hope, Jacques R Vanfleteren, Janet M Thornton, David Gems,

Insulin/IGF-1 signaling controls metabolism, stress resistance and aging in Caenorhabditis elegans by regulating the activity of the DAF-16/FoxO transcription factor (TF). However, the function of DAF-16 and the topology of the transcriptional network that it crowns remain unclear. Using chromatin profiling by DNA adenine methyltransferase identification (DamID), we identified 907 ... Read more >>

Mol Syst Biol (Molecular systems biology)
[2010, 6:399]

Cited: 75 times

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Antioxidant defense and aging in C. elegans: is the oxidative damage theory of aging wrong?

David Gems, Ryan Doonan,

The oxidative damage theory of aging once seemed almost proven. Yet recently the buzzards have been assembling in the blue skies above it. New challenges to the theory from work using nematode worms seem set to bring them down to peck at its bones. But is the theory really dead, ... Read more >>

Cell Cycle (Cell cycle (Georgetown, Tex.))
[2009, 8(11):1681-1687]

Cited: 144 times

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HLH-3 is a C. elegans Achaete/Scute protein required for differentiation of the hermaphrodite-specific motor neurons.

Ryan Doonan, Julia Hatzold, Saleel Raut, Barbara Conradt, Aixa Alfonso,

Basic helix-loop-helix (bHLH) proteins of the Achaete/Scute (Ac/Sc) family are required for neurogenesis in both Drosophila and vertebrates. These transcription factors are commonly referred to as 'proneural' factors, as they promote neural fate in many contexts. Although Ac/Sc proteins have been studied in Hydra, jellyfish, many insects, and several vertebrates, ... Read more >>

Mech Dev (Mechanisms of development)
[2008, 125(9-10):883-893]

Cited: 16 times

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Against the oxidative damage theory of aging: superoxide dismutases protect against oxidative stress but have little or no effect on life span in Caenorhabditis elegans.

Ryan Doonan, Joshua J McElwee, Filip Matthijssens, Glenda A Walker, Koen Houthoofd, Patricia Back, Andrea Matscheski, Jacques R Vanfleteren, David Gems,

The superoxide radical (O(2)(-)) has long been considered a major cause of aging. O(2)(-) in cytosolic, extracellular, and mitochondrial pools is detoxified by dedicated superoxide dismutase (SOD) isoforms. We tested the impact of each SOD isoform in Caenorhabditis elegans by manipulating its five sod genes and saw no major effects ... Read more >>

Genes Dev (Genes & development)
[2008, 22(23):3236-3241]

Cited: 255 times

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