ZFIN Person: Clark, Karl

ZFIN ID: ZDB-PERS-960905-4

ZFIN ID: ZDB-PERS-960905-4

Clark, Karl

Email:	clark.karl@mayo.edu
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:

BIOGRAPHY AND RESEARCH INTERESTS

My research interests are focused on applying 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. In particular, I am interested in the bridge between genes and environment that is gated by the stress response- with a focus on addiction.

PUBLICATIONS

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:

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

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

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

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

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

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

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

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

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

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

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

Ekker, S., Clark, K., ZFIN Staff (2012) Curation of zfishbook links. ZFIN Direct Data Submission.

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

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., Boczek, N.J., and Ekker, S.C. (2011) Stressing zebrafish for behavioral genetics. Reviews in the Neurosciences. 22(1):49-62

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

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
Hyland, K.A., Olson, E.R., Clark, K.J., Aronovich, E.L., Hackett, P.B., Blazer, B.R., Tolar, J.*, and McIvor, R.S.* (2011) Sleeping Beauty-mediated correction of Fanconi anemia type C. Journal of Gene Medicine 13: 462-469.

Carlson, D.F., Garbe, J.R., Wenfang, T., Martin, M.J., Dobrinsky, J.R., Hackett, P.B., Clark, K.J. and Fahrenkrug, S.C. (2011) Strategies for selection marker-free swine transgenesis using the Sleeping Beauty transposon system. Transgenic Research.

Garbe, J.R., Elsik, C.G., Antoniou, E., Reecy, J.M., Clark, K.J., Venkatraman, A., Kim, J-W., Schnabel, R.D., Dickens, C.M., Wolfinger, R.D., Fahrenkrug, S.C. and Taylor, J.F. (2010) Development and application of bovine and porcine oligonucleotide arrays with protein based annotation. J Biomed and Biotechnol 2010:453638

Clark, K.J., Leaver, M.J., Foster, L.K., Carlson, D.F., and Fahrenkrug, S.C. (2009) Passport, a native Tc1/mariner transposon from a flatfish, is functionally active in vertebrate cells. Nucleic Acids Research 37(4):1239-47. Epub 2009 Jan 9. PMC2651795

Ni, J., Clark, K.J., Fahrenkrug, S.C., and Ekker, S.C. (2008). Transposon tools hopping in vertebrates. Brief Funct Genomic Proteomic 7:444-53. PMC2722259

Clark, K.J.*, Carlson, D.F.*, and Fahrenkrug, S.C. (2007) Pigs taking wing with transposons and recombinases. Genome Biology 8(Suppl 1):S13. PMC2106845

Clark, K.J., Carlson, D.F., Foster, L.K., Kong, B.W., Foster, D.N., and Fahrenkrug, S.C. (2007). Enzymatic engineering of the porcine genome with transposons and recombinases. BMC Biotechnol 7:42. PMC1939997

Geurts, A.M, Wilbur, A., Carlson, C.M., Lobitz, P.D., Clark, K.J., Hackett, P.B., McIvor, R.S., and Largaespada, D.A. (2006) Conditional gene expression in the mouse using a Sleeping Beauty gene-trap transposon. BMC Biotechnol 6:30. PMC1557845

Wadman, S.A., Clark, K.J. and Hackett, P.B. (2005) Fishing for answers with transposons. Mar. Biotech 7:135-141.

Ohlfest, J.R., Frandsen, J.L., Fritz, S., Lobitz, P.D., Perkinson, S.G., Clark, K.J., Nelsestuen, G., Key, N.S., McIvor, R.S., Hackett, P.B., and Largaespada, D.A. (2005) Phenotypic correction and long-term expression of factor VIII in hemophilic mice by immunotolerization and nonviral gene transfer using the Sleeping Beauty transposon system. Blood 105:2691-2698.

Geurts, A.M., Yang, Y., Clark, K.J., Liu, G., Cui, Z., Dupuy, A.J., Bell, J.B., Largaespada, D.A., and Hackett, P.B. (2003) Gene transfer into genomes of human cells by the sleeping beauty transposon system. Mol Ther 8:108-17.

*Authors Contributed Equally.