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526 results on '"Castoe, Todd A."'

1. Specimen collection is essential for modern science.

Author

Nachman, Michael, Beckman, Elizabeth, Bowie, Rauri, Cicero, Carla, Conroy, Chris, Hayes, Tyrone, Koo, Michelle, Lacey, Eileen, Martin, Christopher, McGuire, Jimmy, Patton, James, Spencer, Carol, Wake, Marvalee, Wang, Ian, Achmadi, Anang, Álvarez-Castañeda, Sergio, Andersen, Michael, Arroyave, Jairo, Austin, Christopher, Barker, F, Barrow, Lisa, Barrowclough, George, Bates, John, Bauer, Aaron, Bell, Kayce, Bell, Rayna, Bronson, Allison, Brown, Rafe, Burbrink, Frank, Burns, Kevin, Cadena, Carlos, Cannatella, David, Castoe, Todd, Chakrabarty, Prosanta, Colella, Jocelyn, Cook, Joseph, Cracraft, Joel, Davis, Drew, Davis Rabosky, Alison, DElía, Guillermo, Dumbacher, John, Dunnum, Jonathan, Edwards, Scott, Esselstyn, Jacob, Faivovich, Julián, Fjeldså, Jon, Flores-Villela, Oscar, Ford, Kassandra, Fuchs, Jérôme, Fujita, Matthew, Good, Jeffrey, Greenbaum, Eli, Greene, Harry, Hackett, Shannon, Hamidy, Amir, Hanken, James, Haryoko, Tri, Hawkins, Melissa, Heaney, Lawrence, Hillis, David, Hollingsworth, Bradford, Hornsby, Angela, Hosner, Peter, Irham, Mohammad, Jansa, Sharon, Jiménez, Rosa, Joseph, Leo, Kirchman, Jeremy, LaDuc, Travis, Leaché, Adam, Lessa, Enrique, López-Fernández, Hernán, Mason, Nicholas, McCormack, John, McMahan, Caleb, Moyle, Robert, Ojeda, Ricardo, Olson, Link, Kin Onn, Chan, Parenti, Lynne, Parra-Olea, Gabriela, Patterson, Bruce, Pauly, Gregory, Pavan, Silvia, Peterson, A, Poe, Steven, Rabosky, Daniel, Raxworthy, Christopher, Reddy, Sushma, Rico-Guevara, Alejandro, Riyanto, Awal, Rocha, Luiz, Ron, Santiago, Rovito, Sean, Rowe, Kevin, Rowley, Jodi, Ruane, Sara, Salazar-Valenzuela, David, Shultz, Allison, and Sidlauskas, Brian

Subjects
Animals, Museums, Specimen Handling, Natural History
Abstract

Natural history museums are vital repositories of specimens, samples and data that inform about the natural world; this Formal Comment revisits a Perspective that advocated for the adoption of compassionate collection practices, querying whether it will ever be possible to completely do away with whole animal specimen collection.

Published
2023

2. Assessing Target Specificity of the Small Molecule Inhibitor MARIMASTAT to Snake Venom Toxins: A Novel Application of Thermal Proteome Profiling

Author

Smith, Cara F., Modahl, Cassandra M., Ceja Galindo, David, Larson, Keira Y., Maroney, Sean P., Bahrabadi, Lilyrose, Brandehoff, Nicklaus P., Perry, Blair W., McCabe, Maxwell C., Petras, Daniel, Lomonte, Bruno, Calvete, Juan J., Castoe, Todd A., Mackessy, Stephen P., Hansen, Kirk C., and Saviola, Anthony J.

Published
2024
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8. Diverse Gene Regulatory Mechanisms Alter Rattlesnake Venom Gene Expression at Fine Evolutionary Scales.

Author

Gopalan, Siddharth S, Perry, Blair W, Francioli, Yannick Z, Schield, Drew R, Guss, Hannah D, Bernstein, Justin M, Ballard, Kaas, Smith, Cara F, Saviola, Anthony J, Adams, Richard H, Mackessy, Stephen P, and Castoe, Todd A

Subjects
GENE regulatory networks, GENE expression, GENE families, TRANSCRIPTION factors, GENETIC regulation, VENOM
Abstract

Understanding and predicting the relationships between genotype and phenotype is often challenging, largely due to the complex nature of eukaryotic gene regulation. A step towards this goal is to map how phenotypic diversity evolves through genomic changes that modify gene regulatory interactions. Using the Prairie Rattlesnake (Crotalus viridis) and related species, we integrate mRNA-seq, proteomic, ATAC-seq and whole-genome resequencing data to understand how specific evolutionary modifications to gene regulatory network components produce differences in venom gene expression. Through comparisons within and between species, we find a remarkably high degree of gene expression and regulatory network variation across even a shallow level of evolutionary divergence. We use these data to test hypotheses about the roles of specific trans-factors and cis-regulatory elements, how these roles may vary across venom genes and gene families, and how variation in regulatory systems drive diversity in venom phenotypes. Our results illustrate that differences in chromatin and genotype at regulatory elements play major roles in modulating expression. However, we also find that enhancer deletions, differences in transcription factor expression, and variation in activity of the insulator protein CTCF also likely impact venom phenotypes. Our findings provide insight into the diversity and gene-specificity of gene regulatory features and highlight the value of comparative studies to link gene regulatory network variation to phenotypic variation. [ABSTRACT FROM AUTHOR]

Published
2024
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10. Solenodon genome reveals convergent evolution of venom in eulipotyphlan mammals

Author

Casewell, Nicholas R., Petras, Daniel, Card, Daren C., Suranse, Vivek, Mychajliw, Alexis M., Richards, David, Koludarov, Ivan, Albulescu, Laura-Oana, Slagboom, Julien, Hempel, Benjamin-Florian, Ngum, Neville M., Kennerley, Rosalind J., Brocca, Jorge L., Whiteley, Gareth, Harrison, Robert A., Bolton, Fiona M. S., Debono, Jordan, Vonk, Freek J., Alföldi, Jessica, Johnson, Jeremy, Karlsson, Elinor K., Lindblad-Toh, Kerstin, Mellor, Ian R., Süssmuth, Roderich D., Fry, Bryan G., Kuruppu, Sanjaya, Hodgson, Wayne C., Kool, Jeroen, Castoe, Todd A., Barnes, Ian, Sunagar, Kartik, Undheim, Eivind A. B., and Turveyb, Samuel T.

Published
2019

15. ASSESSING TARGET SPECIFICITY OF THE SMALL MOLECULE INHIBITOR MARIMASTAT TO SNAKE VENOM TOXINS: A NOVEL APPLICATION OF THERMAL PROTEOME PROFILING

Author

Smith, Cara F., primary, Modahl, Cassandra M., additional, Ceja-Galindo, David, additional, Larson, Keira Y., additional, Maroney, Sean P., additional, Bahrabadi, Lilyrose, additional, Brandehoff, Nicklaus P., additional, Perry, Blair W., additional, McCabe, Maxwell C., additional, Petras, Daniel, additional, Lomonte, Bruno, additional, Calvete, Juan J., additional, Castoe, Todd A., additional, Mackessy, Stephen P., additional, Hansen, Kirk C., additional, and Saviola, Anthony J., additional

Published
2023
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20. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs

Author

Green, Richard E, Braun, Edward L, Armstrong, Joel, Earl, Dent, Nguyen, Ngan, Hickey, Glenn, Vandewege, Michael W, St John, John A, Capella-Gutiérrez, Salvador, Castoe, Todd A, Kern, Colin, Fujita, Matthew K, Opazo, Juan C, Jurka, Jerzy, Kojima, Kenji K, Caballero, Juan, Hubley, Robert M, Smit, Arian F, Platt, Roy N, Lavoie, Christine A, Ramakodi, Meganathan P, Finger, John W, Suh, Alexander, Isberg, Sally R, Miles, Lee, Chong, Amanda Y, Jaratlerdsiri, Weerachai, Gongora, Jaime, Moran, Christopher, Iriarte, Andrés, McCormack, John, Burgess, Shane C, Edwards, Scott V, Lyons, Eric, Williams, Christina, Breen, Matthew, Howard, Jason T, Gresham, Cathy R, Peterson, Daniel G, Schmitz, Jürgen, Pollock, David D, Haussler, David, Triplett, Eric W, Zhang, Guojie, Irie, Naoki, Jarvis, Erich D, Brochu, Christopher A, Schmidt, Carl J, McCarthy, Fiona M, Faircloth, Brant C, Hoffmann, Federico G, Glenn, Travis C, Gabaldón, Toni, Paten, Benedict, and Ray, David A

Subjects
Genetics, Human Genome, Alligators and Crocodiles, Animals, Biological Evolution, Birds, Conserved Sequence, DNA Transposable Elements, Dinosaurs, Evolution, Molecular, Genetic Variation, Genome, Molecular Sequence Annotation, Molecular Sequence Data, Phylogeny, Reptiles, Sequence Alignment, Sequence Analysis, DNA, Transcriptome, General Science & Technology
Abstract

To provide context for the diversification of archosaurs-the group that includes crocodilians, dinosaurs, and birds-we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs.

Published
2014

21. Snakes on a plain: biotic and abiotic factors determine venom compositional variation in a wide-ranging generalist rattlesnake

Author

Smith, Cara F., primary, Nikolakis, Zachary L., additional, Ivey, Kathleen, additional, Perry, Blair W., additional, Schield, Drew R., additional, Balchan, Neil R., additional, Parker, Joshua, additional, Hansen, Kirk C., additional, Saviola, Anthony J., additional, Castoe, Todd A., additional, and Mackessy, Stephen P., additional

Published
2023
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23. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage

Author

Bradley Shaffer, H, Minx, Patrick, Warren, Daniel E, Shedlock, Andrew M, Thomson, Robert C, Valenzuela, Nicole, Abramyan, John, Amemiya, Chris T, Badenhorst, Daleen, Biggar, Kyle K, Borchert, Glen M, Botka, Christopher W, Bowden, Rachel M, Braun, Edward L, Bronikowski, Anne M, Bruneau, Benoit G, Buck, Leslie T, Capel, Blanche, Castoe, Todd A, Czerwinski, Mike, Delehaunty, Kim D, Edwards, Scott V, Fronick, Catrina C, Fujita, Matthew K, Fulton, Lucinda, Graves, Tina A, Green, Richard E, Haerty, Wilfried, Hariharan, Ramkumar, Hernandez, Omar, Hillier, LaDeana W, Holloway, Alisha K, Janes, Daniel, Janzen, Fredric J, Kandoth, Cyriac, Kong, Lesheng, de Koning, AP, Li, Yang, Literman, Robert, McGaugh, Suzanne E, Mork, Lindsey, O'Laughlin, Michelle, Paitz, Ryan T, Pollock, David D, Ponting, Chris P, Radhakrishnan, Srihari, Raney, Brian J, Richman, Joy M, St John, John, Schwartz, Tonia, Sethuraman, Arun, Spinks, Phillip Q, Storey, Kenneth B, Thane, Nay, Vinar, Tomas, Zimmerman, Laura M, Warren, Wesley C, Mardis, Elaine R, and Wilson, Richard K

Abstract

Abstract Background We describe the genome of the western painted turtle, Chrysemys picta bellii, one of the most widespread, abundant, and well-studied turtles. We place the genome into a comparative evolutionary context, and focus on genomic features associated with tooth loss, immune function, longevity, sex differentiation and determination, and the species' physiological capacities to withstand extreme anoxia and tissue freezing. Results Our phylogenetic analyses confirm that turtles are the sister group to living archosaurs, and demonstrate an extraordinarily slow rate of sequence evolution in the painted turtle. The ability of the painted turtle to withstand complete anoxia and partial freezing appears to be associated with common vertebrate gene networks, and we identify candidate genes for future functional analyses. Tooth loss shares a common pattern of pseudogenization and degradation of tooth-specific genes with birds, although the rate of accumulation of mutations is much slower in the painted turtle. Genes associated with sex differentiation generally reflect phylogeny rather than convergence in sex determination functionality. Among gene families that demonstrate exceptional expansions or show signatures of strong natural selection, immune function and musculoskeletal patterning genes are consistently over-represented. Conclusions Our comparative genomic analyses indicate that common vertebrate regulatory networks, some of which have analogs in human diseases, are often involved in the western painted turtle's extraordinary physiological capacities. As these regulatory pathways are analyzed at the functional level, the painted turtle may offer important insights into the management of a number of human health disorders.

Published
2013

32. Squamate Reptile Genomics and Evolution

Author

Shaney, Kyle J., Card, Daren C., Schield, Drew R., Ruggiero, Robert P., Pollock, David D., Mackessy, Stephen P., Castoe, Todd A., Gopalakrishnakone, P., Editor-in-chief, and Calvete, Juan J., editor

Published
2016
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33. Signals of differential introgression in the genome of natural hybrids of Caribbean anoles.

Author

Farleigh, Keaka, Ascanio, Alfredo, Farleigh, Mackenzie E., Schield, Drew R., Card, Daren C., Leal, Manuel, Castoe, Todd A., Jezkova, Tereza, and Rodríguez‐Robles, Javier A.

Subjects
ANOLES, NOTCH genes, INTROGRESSION (Genetics), GENOMES, MITOCHONDRIAL DNA, SPECIES hybridization, CELL differentiation
Abstract

Hybridization facilitates recombination between divergent genetic lineages and can be shaped by both neutral and selective processes. Upon hybridization, loci with no net fitness effects introgress randomly from parental species into the genomes of hybrid individuals. Conversely, alleles from one parental species at some loci may provide a selective advantage to hybrids, resulting in patterns of introgression that do not conform to random expectations. We investigated genomic patterns of differential introgression in natural hybrids of two species of Caribbean anoles, Anolis pulchellus and A. krugi in Puerto Rico. Hybrids exhibit A. pulchellus phenotypes but possess A. krugi mitochondrial DNA, originated from multiple, independent hybridization events, and appear to have replaced pure A. pulchellus across a large area in western Puerto Rico. Combining genome‐wide SNP datasets with bioinformatic methods to identify signals of differential introgression in hybrids, we demonstrate that the genomes of hybrids are dominated by pulchellus‐derived alleles and show only 10%–20% A. krugi ancestry. The majority of A. krugi loci in hybrids exhibit a signal of non‐random differential introgression and include loci linked to genes involved in development and immune function. Three of these genes (delta like canonical notch ligand 1, jagged1 and notch receptor 1) affect cell differentiation and growth and interact with mitochondrial function. Our results suggest that differential non‐random introgression for a subset of loci may be driven by selection favouring the inheritance of compatible mitochondrial and nuclear‐encoded genes in hybrids. [ABSTRACT FROM AUTHOR]

Published
2023
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37. Additional file 4 of Snakes on a plain: biotic and abiotic factors determine venom compositional variation in a wide-ranging generalist rattlesnake

Author

Smith, Cara F., Nikolakis, Zachary L., Ivey, Kathleen, Perry, Blair W., Schield, Drew R., Balchan, Neil R., Parker, Joshua, Hansen, Kirk C., Saviola, Anthony J., Castoe, Todd A., and Mackessy, Stephen P.

Abstract

Additional file 4: Table S4. Environmental Modeling. Percent contributions of WorldClim environmental layers to ENM predictions.

Published
2023
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38. Additional file 6 of Snakes on a plain: biotic and abiotic factors determine venom compositional variation in a wide-ranging generalist rattlesnake

Author

Smith, Cara F., Nikolakis, Zachary L., Ivey, Kathleen, Perry, Blair W., Schield, Drew R., Balchan, Neil R., Parker, Joshua, Hansen, Kirk C., Saviola, Anthony J., Castoe, Todd A., and Mackessy, Stephen P.

Abstract

Additional file 6: Table S6. Diet Data Collection Information. Museum collections investigated, collection location, and number of specimens examined.

Published
2023
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39. Additional file 5 of Snakes on a plain: biotic and abiotic factors determine venom compositional variation in a wide-ranging generalist rattlesnake

Author

Smith, Cara F., Nikolakis, Zachary L., Ivey, Kathleen, Perry, Blair W., Schield, Drew R., Balchan, Neil R., Parker, Joshua, Hansen, Kirk C., Saviola, Anthony J., Castoe, Todd A., and Mackessy, Stephen P.

Abstract

Additional file 5: Table S5. Genomic Information. Species ID, project ID, locality, tree label, SRA accession, and reference study for genomic data.

Published
2023
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40. Single-Cell Heterogeneity in Snake Venom Expression Is Hardwired by Co-Option of Regulators from Progressively Activated Pathways.

Author

Westfall, Aundrea K, Gopalan, Siddharth S, Perry, Blair W, Adams, Richard H, Saviola, Anthony J, Mackessy, Stephen P, and Castoe, Todd A

Subjects
GENE expression, VENOM, SNAKE venom, GENE regulatory networks, UNFOLDED protein response, GENE families, HETEROGENEITY
Abstract

The ubiquitous cellular heterogeneity underlying many organism-level phenotypes raises questions about what factors drive this heterogeneity and how these complex heterogeneous systems evolve. Here, we use single-cell expression data from a Prairie rattlesnake (Crotalus viridis) venom gland to evaluate hypotheses for signaling networks underlying snake venom regulation and the degree to which different venom gene families have evolutionarily recruited distinct regulatory architectures. Our findings suggest that snake venom regulatory systems have evolutionarily co-opted trans -regulatory factors from extracellular signal-regulated kinase and unfolded protein response pathways that specifically coordinate expression of distinct venom toxins in a phased sequence across a single population of secretory cells. This pattern of co-option results in extensive cell-to-cell variation in venom gene expression, even between tandemly duplicated paralogs, suggesting this regulatory architecture has evolved to circumvent cellular constraints. While the exact nature of such constraints remains an open question, we propose that such regulatory heterogeneity may circumvent steric constraints on chromatin, cellular physiological constraints (e.g. endoplasmic reticulum stress or negative protein–protein interactions), or a combination of these. Regardless of the precise nature of these constraints, this example suggests that, in some cases, dynamic cellular constraints may impose previously unappreciated secondary constraints on the evolution of gene regulatory networks that favors heterogeneous expression. [ABSTRACT FROM AUTHOR]

Published
2023
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41. Evidence for divergent patterns of local selection driving venom variation in Mojave Rattlesnakes (Crotalus scutulatus)

Author

Strickland, Jason L., Smith, Cara F., Mason, Andrew J., Schield, Drew R., Borja, Miguel, Castañeda-Gaytán, Gamaliel, Spencer, Carol L., Smith, Lydia L., Trápaga, Ann, Bouzid, Nassima M., Campillo-García, Gustavo, Flores-Villela, Oscar A., Antonio-Rangel, Daniel, Mackessy, Stephen P., Castoe, Todd A., Rokyta, Darin R., and Parkinson, Christopher L.

Published
2018
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43. Evidence that genomic incompatibilities and other multilocus processes impact hybrid fitness in a rattlesnake hybrid zone

Author

Nikolakis, Zachary L., primary, Schield, Drew R., additional, Westfall, Aundrea K., additional, Perry, Blair W., additional, Ivey, Kathleen N., additional, Orton, Richard W., additional, Hales, Nicole R., additional, Adams, Richard H., additional, Meik, Jesse M., additional, Parker, Joshua M., additional, Smith, Cara F., additional, Gompert, Zachariah, additional, Mackessy, Stephen P., additional, and Castoe, Todd A., additional

Published
2022
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48. Snake venom gene expression is coordinated by novel regulatory architecture and the integration of multiple co-opted vertebrate pathways

Author

Perry, Blair W., primary, Gopalan, Siddharth S., additional, Pasquesi, Giulia I.M., additional, Schield, Drew R., additional, Westfall, Aundrea K., additional, Smith, Cara F., additional, Koludarov, Ivan, additional, Chippindale, Paul T., additional, Pellegrino, Mark W., additional, Chuong, Edward B., additional, Mackessy, Stephen P., additional, and Castoe, Todd A., additional

Published
2022
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49. The Burmese python genome reveals the molecular basis for extreme adaptation in snakes

Author

Castoe, Todd A., de Koning, A. P. Jason, Hall, Kathryn T., Card, Daren C., Schield, Drew R., Fujita, Matthew K., Ruggiero, Robert P., Degner, Jack F., Daza, Juan M., Gu, Wanjun, Reyes-Velasco, Jacobo, Shaney, Kyle J., Castoe, Jill M., Fox, Samuel E., Poole, Alex W., Polanco, Daniel, Dobry, Jason, Vandewege, Michael W., Li, Qing, Schott, Ryan K., Kapusta, Aurélie, Minx, Patrick, Feschotte, Cédric, Uetz, Peter, Ray, David A., Hoffmann, Federico G., Bogden, Robert, Smith, Eric N., Chang, Belinda S. W., Vonk, Freek J., Casewell, Nicholas R., Henkel, Christiaan V., Richardson, Michael K., Mackessy, Stephen P., Bronikowsi, Anne M., Yandell, Mark, Warren, Wesley C., Secor, Stephen M., and Pollock, David D.

Published
2013

50. The king cobra genome reveals dynamic gene evolution and adaptation in the snake venom system

Author

Vonk, Freek J., Casewell, Nicholas R., Henkel, Christiaan V., Heimberg, Alysha M., Jansen, Hans J., McCleary, Ryan J. R., Kerkkamp, Harald M. E., Vos, Rutger A., Guerreiro, Isabel, Calvete, Juan J., Wüster, Wolfgang, Woods, Anthony E., Logan, Jessica M., Harrison, Robert A., Castoe, Todd A., de Koning, A. P. Jason, Pollock, David D., Yandell, Mark, Calderon, Diego, Renjifo, Camila, Currier, Rachel B., Salgado, David, Pla, Davinia, Sanz, Libia, Hyder, Asad S., Ribeiro, José M. C., Arntzen, Jan W., van den Thillart, Guido E. E. J. M., Boetzer, Marten, Pirovano, Walter, Dirks, Ron P., Spaink, Herman P., Duboule, Denis, McGlinn, Edwina, Kini, Manjunatha, and Richardson, Michael K.

Published
2013

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