ZFIN ID: ZDB-PERS-960905-4
Clark, Karl
Email: kjclark@mac.com
URL:
Affiliation: Clark Lab
Address: Mayo Clinic Cancer Center Dept. Biochemistry and Molecular Biology 200 1st St S Guggenheim 1321A Rochester, MN 55905 USA
Country: United States
Phone: 507-538-5311
Fax:
ORCID ID: 0000-0002-9637-0967


BIOGRAPHY AND RESEARCH INTERESTS
My lab, the Behavioral and Functional Genetics Laboratory at Mayo Clinic, is built upon my interest and long history of technology development and genome engineering. I collaborate with a large array of scientists with whom I work to develop new methods of gene editing, and my lab focuses on deployment in zebrafish. We apply these molecular and genetic tools to dissect and discover the interactions between genes and the environment that affect both short and long-term changes in physiology and behavior. We have developed zebrafish assays and genetic tools to identify modifiers of hypothalamic-pituitary-adrenal (interrenal) stress responses looking at both rapid (non-genomic) and delayed (genomic) responses to stressors. Our expertise in both gene editing and behavioral genetics have made us an ideal partner to work with the Center for Individualized Medicine’s Translational Omics Program to functionally test patient variants using diverse biological assays and models to assess potential for pathogenicity in a wide variety of rare disorders. In the next five to ten years, we will move beyond diagnostics by taking advantage of gene editing tools and animal models to develop new therapeutics for rare disease.


PUBLICATIONS
Lee, H.B., Shams, S., Dang Thi, V.H., Boyum, G.E., Modhurima, R., Hall, E.M., Green, I.K., Cervantes, E.M., Miguez, F.E., Clark, K.J. (2024) Key HPI axis receptors facilitate light adaptive behavior in larval zebrafish. Scientific Reports. 14:77597759
Ding, Y., Lang, D., Yan, J., Bu, H., Li, H., Jiao, K., Yang, J., Ni, H., Morotti, S., Le, T., Clark, K.J., Port, J., Ekker, S.C., Cao, H., Zhang, Y., Wang, J., Grandi, E., Li, Z., Shi, Y., Li, Y., Glukhov, A.V., Xu, X. (2022) A phenotype-based forward genetic screen identifies Dnajb6 as a sick sinus syndrome gene. eLIFE. 11:
Sabharwal, A., Campbell, J.M., Schwab, T.L., WareJoncas, Z., Wishman, M.D., Ata, H., Liu, W., Ichino, N., Hunter, D.E., Bergren, J.D., Urban, M.D., Urban, R.M., Holmberg, S.R., Kar, B., Cook, A., Ding, Y., Xu, X., Clark, K.J., Ekker, S.C. (2022) A Primer Genetic Toolkit for Exploring Mitochondrial Biology and Disease Using Zebrafish. Genes. 13(8):
Liu, F., Kambakam, S., Almeida, M.P., Ming, Z., Welker, J.M., Wierson, W.A., Schultz-Rogers, L.E., Ekker, S.C., Clark, K.J., Essner, J.J., McGrail, M. (2022) Cre/lox regulated conditional rescue and inactivation with zebrafish UFlip alleles generated by CRISPR-Cas9 targeted integration. eLIFE. 11:
Sabharwal, A., Kar, B., Restrepo-Castillo, S., Holmberg, S.R., Mathew, N.D., Kendall, B.L., Cotter, R.P., WareJoncas, Z., Seiler, C., Nakamaru-Ogiso, E., Clark, K.J., Ekker, S.C. (2021) The FusX TALE Base Editor (FusXTBE) for Rapid Mitochondrial DNA Programming of Human Cells In Vitro and Zebrafish Disease Models In Vivo. The CRISPR journal. 4(6):799-821
Welker, J.M., Wierson, W.A., Almeida, M.P., Mann, C.M., Torrie, M.E., Ming, Z., Ekker, S.C., Clark, K.J., Dobbs, D.L., Essner, J.J., McGrail, M. (2021) GeneWeld: Efficient Targeted Integration Directed by Short Homology in Zebrafish. Bio-protocol. 11:e4100
Almeida, M.P., Welker, J.M., Siddiqui, S., Luiken, J., Ekker, S.C., Clark, K.J., Essner, J.J., McGrail, M. (2021) Endogenous zebrafish proneural Cre drivers generated by CRISPR/Cas9 short homology directed targeted integration. Scientific Reports. 11:1732
Ichino, N., Serres, M.R., Urban, R.M., Urban, M.D., Treichel, A.J., Schaefbauer, K.J., Greif, L.E., Varshney, G.K., Skuster, K.J., McNulty, M.S., Daby, C.L., Wang, Y., Liao, H.K., El-Rass, S., Ding, Y., Liu, W., Anderson, J.L., Wishman, M.D., Sabharwal, A., Schimmenti, L.A., Sivasubbu, S., Balciunas, D., Hammerschmidt, M., Farber, S.A., Wen, X.Y., Xu, X., McGrail, M., Essner, J.J., Burgess, S.M., Clark, K.J., Ekker, S.C. (2020) Building the vertebrate codex using the gene breaking protein trap library. eLIFE. 9:
Wierson, W.A., Welker, J.M., Almeida, M.P., Mann, C.M., Webster, D.A., Torrie, M.E., Weiss, T.J., Kambakam, S., Vollbrecht, M.K., Lan, M., McKeighan, K.C., Levey, J., Ming, Z., Wehmeier, A., Mikelson, C.S., Haltom, J.A., Kwan, K.M., Chien, C.B., Balciunas, D., Ekker, S.C., Clark, K.J., Webber, B.R., Moriarity, B.S., Solin, S.L., Carlson, D.F., Dobbs, D.L., McGrail, M., Essner, J. (2020) Efficient targeted integration directed by short homology in zebrafish and mammalian cells. eLIFE. 9:
Wierson, W.A., Simone, B.W., WareJoncas, Z., Mann, C., Welker, J.M., Kar, B., Emch, M.J., Friedberg, I., Gendron, W.A.C., Barry, M.A., Clark, K.J., Dobbs, D.L., McGrail, M.A., Ekker, S.C., Essner, J.J. (2019) Expanding the CRISPR Toolbox with ErCas12a in Zebrafish and Human Cells. The CRISPR journal. 2(6):417-433
Nelson, C.M., Lennon, V.A., Lee, H., Krug, R.G., Kamalova, A., Madigan, N.N., Clark, K.J., Windebank, A.J., Henley, J.R. (2019) Glucocorticoids Target Ependymal Glia and Inhibit Repair of the Injured Spinal Cord. Frontiers in cell and developmental biology. 7:56
Lee, H.B., Schwab, T.L., Sigafoos, A.N., Gauerke, J.L., Krug, R.G., Serres, M.R., Jacobs, D.C., Cotter, R.P., Das, B., Petersen, M.O., Daby, C.L., Urban, R.M., Berry, B.C., Clark, K.J. (2018) Novel Zebrafish Behavioral Assay to Identify Modifiers of the Rapid, Nongenomic Stress Response. Genes, brain, and behavior. 18(2):e12549
Ata, H., Ekstrom, T.L., Martínez-Gálvez, G., Mann, C.M., Dvornikov, A.V., Schaefbauer, K.J., Ma, A.C., Dobbs, D., Clark, K.J., Ekker, S.C. (2018) Robust Activation of Microhomology-mediated End Joining for Precision Gene Editing Applications. PLoS Genetics. 14:e1007652
Krug, R.G., Lee, H.B., El Khoury, L.Y., Sigafoos, A.N., Petersen, M.O., Clark, K.J. (2018) The endocannabinoid gene faah2a modulates stress-associated behavior in zebrafish. PLoS One. 13:e0190897
Kim, J., Clark, K., Barton, C., Tanguay, R., Moulton, H. (2018) A Novel Zebrafish Model for Assessing In Vivo Delivery of Morpholino Oligomers. Methods in molecular biology (Clifton, N.J.). 1828:293-306
Brady, C., Denora, M., Shannon, I., Clark, K.J., Rich, A. (2017) Intestinal Transit Time and Cortisol-Mediated Stress in Zebrafish. Zebrafish. 14(5):404-410
El-Rass, S., Eisa-Beygi, S., Khong, E., Brand-Arzamendi, K., Mauro, A., Zhang, H., Clark, K.J., Ekker, S.C., Wen, X.Y. (2017) Disruption of pdgfra alters endocardial and myocardial fusion during zebrafish cardiac assembly.. Biology Open. 6(3):348-357
Gerlai, R., Poshusta, T.L., Rampersad, M., Fernandes, Y., Greenwood, T.M., Cousin, M.A., Klee, E.W., Clark, K.J. (2017) Forward Genetic Screening Using Behavioral Tests in Zebrafish: A Proof of Concept Analysis of Mutants. Behavior Genetics. 47(1):125-139
Leveque, R.E., Clark, K.J., Ekker, S.C. (2016) Mayo Clinic Zebrafish Facility Overview. Zebrafish. 13 Suppl 1:S44-6
Lee, H.B., Schwab, T.L., Koleilat, A., Ata, H., Daby, C.L., Cervera, R.L., McNulty, M.S., Bostwick, H.S., Clark, K.J. (2016) Allele-Specific Quantitative PCR for Accurate, Rapid, and Cost-Effective Genotyping. Human gene therapy. 27:425-35
Welker, J.M., Wierson, W.A., Wang, Y., Poshusta, T.L., McNulty, M.S., Tisdale, E.E., Solin, S.L., Ekker, S.C., Clark, K.J., McGrail, M., Essner, J.J. (2016) GoldyTALEN Vectors with Improved Efficiency for Golden Gate TALEN Assembly. Human gene therapy. 27:423-4
Ma, A.C., McNulty, M.S., Tanya, P.L., Jarryd, C.M., Martínez-Gálvez, G., Argue, D.P., Lee, H.B., Urban, M.D., Bullard, C.E., Blackburn, P.R., Man, T.K., Clark, K.J., Ekker, S.C. (2016) FusX: A rapid one-step TALE assembly system for genome science. Human gene therapy. 27(6):451-63
Ata, H., Clark, K.J., Ekker, S.C. (2016) The zebrafish genome editing toolkit. Methods in cell biology. 135:149-70
Ma, A.C., Lee, H.B., Clark, K.J., and Ekker, S.C. (2013) High Efficiency In Vivo Genome Engineering with a Simplified 15-RVD GoldyTALEN Design. PLoS One. 8(5):e65259
Patowary, A., Purkanti, R., Singh, M., Chauhan, R., Singh, A.R., Swarnkar, M., Singh, N., Pandey, V., Torroja, C., Clark, M.D., Kocher, J.P., Clark, K.J., Stemple, D.L., Klee, E.W., Ekker, S.C., Scaria, V., and Sivasubbu, S. (2013) A sequence-based variation map of zebrafish. Zebrafish. 10(1):15-20
Blackburn, P.R., Campbell, J.M., Clark, K.J., and Ekker, S.C. (2013) The CRISPR System-Keeping Zebrafish Gene Targeting Fresh. Zebrafish. 10(1):116-8
Ding, Y., Liu, W., Deng, Y., Jomok, B., Yang, J., Huang, W., Clark, K.J., Zhong, T., Lin, X., Ekker, S.C., and Xu, X. (2013) Trapping Cardiac Recessive Mutants via Expression-based Insertional Mutagenesis Screening. Circulation research. 112(4):606-617
Bedell, V.M., Wang, Y., Campbell, J.M., Poshusta, T.L., Starker, C.G., Krug, R.G., Tan, W., Penheiter, S.G., Ma, A.C., Leung, A.Y., Fahrenkrug, S.C., Carlson, D.F., Voytas, D.F., Clark, K.J., Essner, J.J., and Ekker, S.C. (2012) In vivo genome editing using a high-efficiency TALEN system. Nature. 491(7422):114-118
Hoeppner, L.H., Phoenix, K.N., Clark, K.J., Bhattacharya, R., Gong, X., Sciuto, T.E., Vohra, P., Suresh, S., Bhattacharya, S., Dvorak, A.M., Ekker, S.C., Dvorak, H.F., Claffey, K.P., and Mukhopadhyay, D. (2012) Revealing the role of phospholipase Cβ3 in the regulation of VEGF-induced vascular permeability. Blood. 120(11):2167-2173
Klee, E.W., Schneider, H., Clark, K.J., Cousin, M.A., Ebbert, J.O., Hooten, W.M., Karpyak, V.M., Warner, D.O., and Ekker, S.C. (2012) Zebrafish: a model for the study of addiction genetics. Human genetics. 131(6):977-1008
Xu, J., Gao, J., Li, J., Xue, L., Clark, K.J., Ekker, S.C., and Du, S.J. (2012) Functional analysis of slow Myosin heavy chain 1 and myomesin-3 in sarcomere organization in zebrafish embryonic slow muscles. Journal of genetics and genomics = Yi chuan xue bao. 39(2):69-80
Liao, H.K., Wang, Y., Watt, K.E., Wen, Q., Breitback, J., Kemmet, C.K., Clark, K.J., Ekker, S.C., Essner, J.J., and McGrail, M. (2012) Tol2 gene trap integrations in the zebrafish amyloid precursor protein genes appa and aplp2 reveal accumulation of secreted APP at the embryonic veins. Developmental Dynamics : an official publication of the American Association of Anatomists. 241(2):415-425
Bedell, V.M., Person, A.D., Larson, J.D., McLoon, A., Balciunas, D., Clark, K.J., Neff, K.I., Nelson, K.E., Bill, B.R., Schimmenti, L.A., Beiraghi, S., and Ekker, S.C. (2012) The lineage-specific gene ponzr1 is essential for zebrafish pronephric and pharyngeal arch development. Development (Cambridge, England). 139(4):793-804
Clark, K.J., Argue, D.P., Petzold, A.M., Ekker, S.C. (2012) zfishbook: connecting you to a world of zebrafish revertible mutants.. Nucleic acids research. 40(Database issue):D907-11
Ekker, S., Clark, K., ZFIN Staff (2012) Curation of zfishbook links. ZFIN Direct Data Submission.
Clark, K.J., Voytas, D.F., and Ekker, S.C. (2011) A TALE of Two Nucleases: Gene Targeting for the Masses. Zebrafish. 8(3):147-149
Clark, K.J., Balciunas, D., Pogoda, H.M., Ding, Y., Westcot, S.E., Bedell, V.M., Greenwood, T.M., Urban, M.D., Skuster, K.J., Petzold, A.M., Ni, J., Nielsen, A.L., Patowary, A., Scaria, V., Sivasubbu, S., Xu, X., Hammerschmidt, M., and Ekker, S.C. (2011) In vivo protein trapping produces a functional expression codex of the vertebrate proteome. Nature Methods. 8(6):506-512
Clark, K.J., Urban, M.D., Skuster, K.J., and Ekker, S.C. (2011) Transgenic zebrafish using transposable elements. Methods in cell biology. 104:137-149
Clark, K.J., Boczek, N.J., and Ekker, S.C. (2011) Stressing zebrafish for behavioral genetics. Reviews in the Neurosciences. 22(1):49-62
Wang, Y., Kaiser, M.S., Larson, J.D., Nasevicius, A., Clark, K.J., Wadman, S.A., Roberg-Perez, S.E., Ekker, S.C., Hackett, P.B., McGrail, M., and Essner, J.J. (2010) Moesin1 and Ve-cadherin are required in endothelial cells during in vivo tubulogenesis. Development (Cambridge, England). 137(18):3119-3128
Petzold, A.M., Bedell, V.M., Boczek, N.J., Essner, J.J., Balciunas, D., Clark, K.J., and Ekker, S.C. (2010) SCORE imaging: specimen in a corrected optical rotational enclosure. Zebrafish. 7(2):149-154
Petzold, A.M., Balciunas, D., Sivasubbu, S., Clark, K.J., Bedell, V.M., Westcot, S.E., Myers, S.R., Moulder, G.L., Thomas, M.J., and Ekker, S.C. (2009) Nicotine response genetics in the zebrafish. Proceedings of the National Academy of Sciences of the United States of America. 106(44):18662-18667
Kalén, M., Wallgard, E., Asker, N., Nasevicius, A., Athley, E., Billgren, E., Larson, J.D., Wadman, S.A., Norseng, E., Clark, K.J., He, L., Karlsson-Lindahl, L., Häger, A.K., Weber, H., Augustin, H., Samuelsson, T., Kemmet, C.K., Utesch, C.M., Essner, J.J., Hackett, P.B., and Hellström, M. (2009) Combination of reverse and chemical genetic screens reveals angiogenesis inhibitors and targets. Chemistry & Biology. 16(4):432-441
Bill, B.R., Petzold, A.M., Clark, K.J., Schimmenti, L.A., and Ekker, S.C. (2009) A primer for morpholino use in zebrafish. Zebrafish. 6(1):69-77
Larson, J.D., Wadman, S.A., Chen, E., Kerley, L., Clark, K.J., Eide, M., Lippert, S., Nasevicius, A., Ekker, S.C., Hackett, P.B., and Essner, J.J. (2004) Expression of VE-cadherin in zebrafish embryos: A new tool to evaluate vascular development. Developmental Dynamics : an official publication of the American Association of Anatomists. 231(1):204-213
Clark, K.J., Geurts, A.M., Bell, J.B., and Hackett, P.B. (2004) Transposon vectors for gene-trap insertional mutagenesis in vertebrates. Genesis (New York, N.Y. : 2000). 39(4):225-233
Dupuy, A.J., Clark, K., Carlson, C.M., Fritz, S., Davidson, A.E., Markley, K.M., Finley, K., Fletcher, C.F., Ekker, S.C., Hackett, P.B., Horn, S., and Largaespada, D.A. (2002) Mammalian germ-line transgenesis by transposition. Proceedings of the National Academy of Sciences of the United States of America. 99(7):4495-4499
Cui, Z., Clark, K.J., Kaufman, C.D., and Hackett, P.B. (2001) Inhibition of skiA and skiB gene expression ventralizes zebrafish embryos. Genesis (New York, N.Y. : 2000). 30(3):149-153
Fahrenkrug, S.C., Dahlquist, M.O., Clark, K.J., and Hackett, P.B. (1999) Dynamic and tissue-specific expression of elF4E during zebrafish embryogenesis. Differentiation; research in biological diversity. 65(4):191-201
Fahrenkrug, S.C., Clark, K., Dahlquist, M.O., and Hackett, P.B. (1999) Dicistronic gene expression in developing zebrafish. Marine biotechnology (New York, N.Y.). 1(6):552-561

NON-ZEBRAFISH PUBLICATIONS
A complete listing of my publications can be found on my NCBI Bibliography (https://www.ncbi.nlm.nih.gov/sites/myncbi/karl.clark.1/bibliography/42584231/public/?sort=date&direction=descending)