Research Article
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Year 2020, Volume: 9 Issue: 1, 15 - 22, 30.06.2020

Mehtap Bayır , Gökhan Arslan , Pinar Oğuzhan Yıldız

https://doi.org/10.33714/masteb.660220
Cited By: 2

Abstract

References

  • Amores, A., Force, A., Yan, Y. L., Joly, L., Amemiya, C., Fritz, A., Ho, R. K., Langeland, J., Prince, V. & Wang, Y. L. (1998). Zebrafish hox clusters and vertebrate genome evolution. Science, 282(5394): 1711-1714. https://doi.org/10.1126/science.282.5394.1711
  • Arslan, H. (2015). Pestisit sinerjisinin; gökkuşağı alabalıklarında (Oncorhynchus mykiss) yüzme performansı, biyokimyasal hematolojik, histopatolojik ve genotoksik etkilerinin araştırılması. Ph.D. Thesis. Atatürk University, Erzurum, Turkey.
  • Basu, S., Binder, R. J., Suto, R., Anderson, K. M. & Srivastava, P. K. (2000). Necrotic but not apoptotic cell death releases heat shock proteins, which deliver a partial maturation signal to dendritic cells and activate the NF-kappa B pathway. International Immunology, 12(11): 1539-1546. https://doi.org/10.1093/intimm/12.11.1539
  • Braasch, I. & Postlethwait, J. H. (2012). Polyploidy in fish and the teleost genome duplication (pp. 341-383). In: Soltis, P. S., Soltis, D. E. (eds.), Polyploidy and Genome Evolution. Springer. 420p. https://doi.org/10.1007/978-3-642-31442-1_17
  • Collins, F. S., Patrinos, A., Jordan, E., Chakravarti, A., Gesteland, R. & Walters, L. (1998). New goals for the U.S. human genome project: 1998-2003. Science, 282(5389): 682-689. https://doi.org/10.1126/science.282.5389.682
  • Çapan, E. C. (2019). Plati balığı (Xiphophorus maculatus)’nda katalaz enzim geninin biyoenformatiği ve doku spesifik dağılımı. Master Thesis. Atatürk University, Erzurum, Turkey.
  • Hori, H. (2001). A glance at the past of medaka fish biology (pp. 1-16). In: Naruse, K., Tanaka, M., Takeda, H. (eds.), Medaka: A model for organogenesis, human disease, and evolution. Tokyo: Springer. 387p. https://doi.org/10.1007/978-4-431-92691-7_1
  • Ishikawa, Y. (2000). Medakafish as a model system for vertebrate developmental genetics. BioEssays, 22(5): 487-495. https://doi.org/10.1002/(SICI)1521-1878(200005)22:5%3C487::AID-BIES11%3E3.0.CO;2-8
  • Iwama, G. K., Vijayan, M. M., Forsyth, R. B. & Ackerman, P .A. (1999). Heat shock proteins and physiological stress in fish. American Zoologist, 39(6): 901-909.
  • Jacquet, C., Thermes, V., de Luze, A., Puiseux-Dao, S., Bernard, C., Joly, J. S., Bourrat, F. & Edery, M. (2004). Effects of microcystin-LR on development of medaka fish embryos (Oryzias latipes). Toxicon, 43(2): 141-147. https://doi.org/10.1016/j.toxicon.2003.11.010
  • Kan, B., London, I. M. & Levin, D. H. (1988). Role of reversing factor in the inhibition of protein synthesis initiation by oxidized glutathione. Journal of Biological Chemistry, 263(30): 15652- 15656.
  • Kell, A. J. E., Yamins, D. .L. K., Shook, E. N., Norman-Haignere, S. V. & McDermott, J. H. (2018). A task-optimized neural network replicates human auditory behavior, predicts brain responses, and reveals a cortical processing hierarchy. Neuron, 98(3): 630-644.e16. https://doi.org/10.1016/j.neuron.2018.03.044
  • McLean, L., Young, I. S., Doherty, M. K., Robertson, D. H. L., Cossins, A. R., Gracey, A. Y., Beynon, R. J. & Whitfield, P. D. (2007). Global cooling: Cold acclimation and the expression of soluble proteins in carp skeletal muscle. Proteomics, 7(15): 2667-2681. https://doi.org/10.1002/pmic.200601004
  • Meyer, A. & Schartl, M. (1999). Gene and genome duplications in vertebrates: The one-to-four (-to-eight in fish) rule and the evolution of novel gene functions. Current Opinion in Cell Biology, 11(6): 699-704. https://doi.org/10.1016/s0955-0674(99)00039-3
  • Naruse, K., Fukamachi, S., Mitani, H., Kondo, M., Matsuoka, T., Kondo, S., Hanamura, N., Morita, Y., Hasegawa, K., Nishigaki, R., Shimada, A., Wada, H., Kusakabe, T., Suzuki, N., Kinoshita, M., Kanamori, A., Terado, T., Kimura, H., Nonaka, M. & Shima, A. (2000). A detailed linkage map of medaka, Oryzias latipes: Comparative genomics and genome evolution. Genetics, 154(4): 1773–1784.
  • Postlethwait, J. H., Woods, I. G., Ngo-Hazelett, P., Yan, Y. L., Kelly, P. D., Chu, F., Huang, H., Hill-Force, A., Talbot, W. S. (2000). Zebrafish comparative genomics and the origins of vertebrate chromosomes. Genome Research, 10(12): 1890-1902. https://doi.org/10.1101/gr.164800
  • Shima, A. & Mitani, H. (2004). Medaka as a research organism: past, present and future. Mechanisms of Development, 121(7-8): 599–604. https://doi.org/10.1016/j.mod.2004.03.011
  • Stryer, L. (1995). Biochemistry (4th Ed.). New York: W.H. Freeman and Company. 1064 p.
  • Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994). CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22(22): 4673-4680. https://doi.org/10.1093/nar/22.22.4673
  • Yamamoto, T. (1953). Artificial sex-reversal in the genotypic males of the medaka, Oryzias latipes. Journal of Experimental Zoology, 123(3): 517-594. https://doi.org/10.1002/jez.1401230309

Characterization, Identification and Phylogeny of the Creatine Kinase (ckma) Gene in Medaka (Oryzias latipes)

Year 2020, Volume: 9 Issue: 1, 15 - 22, 30.06.2020

Mehtap Bayır , Gökhan Arslan , Pinar Oğuzhan Yıldız

https://doi.org/10.33714/masteb.660220
Cited By: 2

Abstract

Creatine kinase (ckma) has been characterized and described in
the medaka (Oryzias latipes), an aquatic model organism and the gene
structure has been designed using the exons, introns, produced amino acids of
the gene, TATA box, poly A tail and 5’ UTR and 3’ UTR regions of the ckma
gene. In another step, firstly, the chromosome region of the ckma gene
was determined in medaka and then the other genes which placed in the same
region were determined. Then the locations of these genes were determined in
zebrafish and human which are the orthologs of medaka. Finally, the conserved
gene synteny was designed manually, using these data. However, genetic identity
and similarity ratio between medaka and its orthologs were calculated. In this
study, characterization and identification, phylogenetic relationship,
conserved gene synteny of ckma gene in medaka (O. latipes) which
is an important model organism were analyzed by using bioinformatics tools
(NCBI database, Ensembl genomic database, Expasy, Reverse Complementary and
some programs such as MEGA6 program, BLOSUM62 matrix program and BioEdit
software). All these data will be used in future studies on molecular stress
response in fish and they were presented to the scientific world with this
study.

Keywords

Medaka Genomic organization Model organism Bioinformatics

References

  • Amores, A., Force, A., Yan, Y. L., Joly, L., Amemiya, C., Fritz, A., Ho, R. K., Langeland, J., Prince, V. & Wang, Y. L. (1998). Zebrafish hox clusters and vertebrate genome evolution. Science, 282(5394): 1711-1714. https://doi.org/10.1126/science.282.5394.1711
  • Arslan, H. (2015). Pestisit sinerjisinin; gökkuşağı alabalıklarında (Oncorhynchus mykiss) yüzme performansı, biyokimyasal hematolojik, histopatolojik ve genotoksik etkilerinin araştırılması. Ph.D. Thesis. Atatürk University, Erzurum, Turkey.
  • Basu, S., Binder, R. J., Suto, R., Anderson, K. M. & Srivastava, P. K. (2000). Necrotic but not apoptotic cell death releases heat shock proteins, which deliver a partial maturation signal to dendritic cells and activate the NF-kappa B pathway. International Immunology, 12(11): 1539-1546. https://doi.org/10.1093/intimm/12.11.1539
  • Braasch, I. & Postlethwait, J. H. (2012). Polyploidy in fish and the teleost genome duplication (pp. 341-383). In: Soltis, P. S., Soltis, D. E. (eds.), Polyploidy and Genome Evolution. Springer. 420p. https://doi.org/10.1007/978-3-642-31442-1_17
  • Collins, F. S., Patrinos, A., Jordan, E., Chakravarti, A., Gesteland, R. & Walters, L. (1998). New goals for the U.S. human genome project: 1998-2003. Science, 282(5389): 682-689. https://doi.org/10.1126/science.282.5389.682
  • Çapan, E. C. (2019). Plati balığı (Xiphophorus maculatus)’nda katalaz enzim geninin biyoenformatiği ve doku spesifik dağılımı. Master Thesis. Atatürk University, Erzurum, Turkey.
  • Hori, H. (2001). A glance at the past of medaka fish biology (pp. 1-16). In: Naruse, K., Tanaka, M., Takeda, H. (eds.), Medaka: A model for organogenesis, human disease, and evolution. Tokyo: Springer. 387p. https://doi.org/10.1007/978-4-431-92691-7_1
  • Ishikawa, Y. (2000). Medakafish as a model system for vertebrate developmental genetics. BioEssays, 22(5): 487-495. https://doi.org/10.1002/(SICI)1521-1878(200005)22:5%3C487::AID-BIES11%3E3.0.CO;2-8
  • Iwama, G. K., Vijayan, M. M., Forsyth, R. B. & Ackerman, P .A. (1999). Heat shock proteins and physiological stress in fish. American Zoologist, 39(6): 901-909.
  • Jacquet, C., Thermes, V., de Luze, A., Puiseux-Dao, S., Bernard, C., Joly, J. S., Bourrat, F. & Edery, M. (2004). Effects of microcystin-LR on development of medaka fish embryos (Oryzias latipes). Toxicon, 43(2): 141-147. https://doi.org/10.1016/j.toxicon.2003.11.010
  • Kan, B., London, I. M. & Levin, D. H. (1988). Role of reversing factor in the inhibition of protein synthesis initiation by oxidized glutathione. Journal of Biological Chemistry, 263(30): 15652- 15656.
  • Kell, A. J. E., Yamins, D. .L. K., Shook, E. N., Norman-Haignere, S. V. & McDermott, J. H. (2018). A task-optimized neural network replicates human auditory behavior, predicts brain responses, and reveals a cortical processing hierarchy. Neuron, 98(3): 630-644.e16. https://doi.org/10.1016/j.neuron.2018.03.044
  • McLean, L., Young, I. S., Doherty, M. K., Robertson, D. H. L., Cossins, A. R., Gracey, A. Y., Beynon, R. J. & Whitfield, P. D. (2007). Global cooling: Cold acclimation and the expression of soluble proteins in carp skeletal muscle. Proteomics, 7(15): 2667-2681. https://doi.org/10.1002/pmic.200601004
  • Meyer, A. & Schartl, M. (1999). Gene and genome duplications in vertebrates: The one-to-four (-to-eight in fish) rule and the evolution of novel gene functions. Current Opinion in Cell Biology, 11(6): 699-704. https://doi.org/10.1016/s0955-0674(99)00039-3
  • Naruse, K., Fukamachi, S., Mitani, H., Kondo, M., Matsuoka, T., Kondo, S., Hanamura, N., Morita, Y., Hasegawa, K., Nishigaki, R., Shimada, A., Wada, H., Kusakabe, T., Suzuki, N., Kinoshita, M., Kanamori, A., Terado, T., Kimura, H., Nonaka, M. & Shima, A. (2000). A detailed linkage map of medaka, Oryzias latipes: Comparative genomics and genome evolution. Genetics, 154(4): 1773–1784.
  • Postlethwait, J. H., Woods, I. G., Ngo-Hazelett, P., Yan, Y. L., Kelly, P. D., Chu, F., Huang, H., Hill-Force, A., Talbot, W. S. (2000). Zebrafish comparative genomics and the origins of vertebrate chromosomes. Genome Research, 10(12): 1890-1902. https://doi.org/10.1101/gr.164800
  • Shima, A. & Mitani, H. (2004). Medaka as a research organism: past, present and future. Mechanisms of Development, 121(7-8): 599–604. https://doi.org/10.1016/j.mod.2004.03.011
  • Stryer, L. (1995). Biochemistry (4th Ed.). New York: W.H. Freeman and Company. 1064 p.
  • Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994). CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Research, 22(22): 4673-4680. https://doi.org/10.1093/nar/22.22.4673
  • Yamamoto, T. (1953). Artificial sex-reversal in the genotypic males of the medaka, Oryzias latipes. Journal of Experimental Zoology, 123(3): 517-594. https://doi.org/10.1002/jez.1401230309
There are 20 citations in total.

Details

Primary Language English
Subjects Hydrobiology
Journal Section Research Article
Authors

Mehtap Bayır 0000-0002-7794-1058

Gökhan Arslan 0000-0002-8634-8598

Pinar Oğuzhan Yıldız 0000-0002-9892-7925

Publication Date June 30, 2020
Submission Date December 17, 2019
Acceptance Date February 3, 2020
Published in Issue Year 2020 Volume: 9 Issue: 1

Cite

APA Bayır, M., Arslan, G., & Oğuzhan Yıldız, P. (2020). Characterization, Identification and Phylogeny of the Creatine Kinase (ckma) Gene in Medaka (Oryzias latipes). Marine Science and Technology Bulletin, 9(1), 15-22. https://doi.org/10.33714/masteb.660220
AMA Bayır M, Arslan G, Oğuzhan Yıldız P. Characterization, Identification and Phylogeny of the Creatine Kinase (ckma) Gene in Medaka (Oryzias latipes). Mar. Sci. Tech. Bull. June 2020;9(1):15-22. doi:10.33714/masteb.660220
Chicago Bayır, Mehtap, Gökhan Arslan, and Pinar Oğuzhan Yıldız. “Characterization, Identification and Phylogeny of the Creatine Kinase (ckma) Gene in Medaka (Oryzias Latipes)”. Marine Science and Technology Bulletin 9, no. 1 (June 2020): 15-22. https://doi.org/10.33714/masteb.660220.
EndNote Bayır M, Arslan G, Oğuzhan Yıldız P (June 1, 2020) Characterization, Identification and Phylogeny of the Creatine Kinase (ckma) Gene in Medaka (Oryzias latipes). Marine Science and Technology Bulletin 9 1 15–22.
IEEE M. Bayır, G. Arslan, and P. Oğuzhan Yıldız, “Characterization, Identification and Phylogeny of the Creatine Kinase (ckma) Gene in Medaka (Oryzias latipes)”, Mar. Sci. Tech. Bull., vol. 9, no. 1, pp. 15–22, 2020, doi: 10.33714/masteb.660220.
ISNAD Bayır, Mehtap et al. “Characterization, Identification and Phylogeny of the Creatine Kinase (ckma) Gene in Medaka (Oryzias Latipes)”. Marine Science and Technology Bulletin 9/1 (June 2020), 15-22. https://doi.org/10.33714/masteb.660220.
JAMA Bayır M, Arslan G, Oğuzhan Yıldız P. Characterization, Identification and Phylogeny of the Creatine Kinase (ckma) Gene in Medaka (Oryzias latipes). Mar. Sci. Tech. Bull. 2020;9:15–22.
MLA Bayır, Mehtap et al. “Characterization, Identification and Phylogeny of the Creatine Kinase (ckma) Gene in Medaka (Oryzias Latipes)”. Marine Science and Technology Bulletin, vol. 9, no. 1, 2020, pp. 15-22, doi:10.33714/masteb.660220.
Vancouver Bayır M, Arslan G, Oğuzhan Yıldız P. Characterization, Identification and Phylogeny of the Creatine Kinase (ckma) Gene in Medaka (Oryzias latipes). Mar. Sci. Tech. Bull. 2020;9(1):15-22.

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