SavedAdd your journal

Journals / Biyolojik Çeşitlilik ve Koruma / 2025 / Volume: 18 Issue: 3

Evaluating yield of DNA extraction methods across different tissues of moon jellyfish Aurelia aurita (Linnaeus, 1758)

Ay denizanası Aurelia aurita'nın (Linnaeus, 1758) farklı dokularında DNA izolasyon yöntemlerinin verimliliklerinin değerlendirilmesi

Sümeyra Zeynep Çalıcı(İSTANBUL ÜNİVERSİTESİ, SU BİLİMLERİ FAKÜLTESİ, AKUATİK BİYOTEKNOLOJİ VE GENOMİK BÖLÜMÜ)0009-0006-0348-1884
Buse Bayrak(İSTANBUL ÜNİVERSİTESİ, SU BİLİMLERİ FAKÜLTESİ, SU BİLİMLERİ VE MÜHENDİSLİĞİ BÖLÜMÜ)0009-0000-6916-5776
Hatice Buse Yavuz(İSTANBUL ÜNİVERSİTESİ, SU BİLİMLERİ FAKÜLTESİ, SU BİLİMLERİ VE MÜHENDİSLİĞİ BÖLÜMÜ)0009-0008-1919-3910
Nida Kelel(İSTANBUL ÜNİVERSİTESİ, SU BİLİMLERİ FAKÜLTESİ, SU BİLİMLERİ VE MÜHENDİSLİĞİ BÖLÜMÜ)0009-0002-5540-9981
Zeynep Aslıhan Avşaroğlu(İSTANBUL ÜNİVERSİTESİ, SU BİLİMLERİ FAKÜLTESİ, SU BİLİMLERİ VE MÜHENDİSLİĞİ BÖLÜMÜ)0009-0004-9084-2515
Merve Nur Aydemir(İSTANBUL ÜNİVERSİTESİ, SU BİLİMLERİ FAKÜLTESİ, AKUATİK BİYOTEKNOLOJİ VE GENOMİK BÖLÜMÜ, GENOM ANABİLİM DALI)0000-0001-6328-626X
Pages
—
Publication Date
2025-12-15
🏛️Bibliographic metadata and full text access for this article are provided via DergiPark.
DergiPark Record ↗
✨

AI Summary & Key Takeaways

AI Insight
⚡ TL;DR(Too Long; Didn't Read)

The salting-out method, when applied to gonadal tissue with moderate Proteinase K incubation, is recommended for efficient and reliable DNA isolation from Aurelia aurita.

📌 3 Key Takeaways

🎯
Objective & Hypothesis:Purpose: This study aimed to optimize DNA extraction from the moon jellyfish Aurelia aurita, a gelatinous marine invertebrate, by comparing different methodologies and evaluating the influence of tissue type and Proteinase K treatment duration on DNA yield.
📊
Key Findings & Data:Method: A total of 48 different combinations were tested using three extraction methods (salting-out, kit-based, and Trizol-based) across four tissue types (gonads, tentacles, epidermis, and gastrodermis).
💡
Conclusion & Impact:The salting-out method, when applied to gonadal tissue with moderate Proteinase K incubation, is recommended for efficient and reliable DNA isolation from Aurelia aurita.
🔬Design:Research Article
📍Scope:Comprehensive Sample
⚙️Variables:DNA isolation · DNA extraction · Aurelia aurita

Abstract

Purpose: This study aimed to optimize DNA extraction from the moon jellyfish Aurelia aurita, a gelatinous marine invertebrate, by comparing different methodologies and evaluating the influence of tissue type and Proteinase K treatment duration on DNA yield. Method: A total of 48 different combinations were tested using three extraction methods (salting-out, kit-based, and Trizol-based) across four tissue types (gonads, tentacles, epidermis, and gastrodermis). Each method was applied with varying Proteinase K incubation times (0, 1, 3, and 24 hours) to assess their impact on DNA yield and integrity. Findings: Gonadal tissues consistently provided the highest DNA concentrations, likely due to their relatively high cellular density and structural robustness. Among the methods, the salting-out protocol yielded superior results, particularly with 1–3 hours of Proteinase K incubation. In contrast, highly hydrated tissues such as epidermis and gastrodermis led to underestimated yields due to distorted wet weight measurements. Conclusion: Tissue selection, enzymatic treatment time, and extraction methodology critically affect DNA recovery from jellyfish. The salting-out method, when applied to gonadal tissue with moderate Proteinase K incubation, is recommended for efficient and reliable DNA isolation from Aurelia aurita.

Özet

Özet Amaç: Bu çalışma, jelatinimsi yapısı nedeniyle DNA izolasyonu zor olan denizanası Aurelia aurita’dan elde edilecek DNA verimini optimize etmeyi; doku türü, enzimatik inkübasyon süresi ve farklı izolasyon yöntemlerinin etkilerini karşılaştırarak değerlendirmeyi amaçlamıştır. Yöntem: Toplamda üç farklı DNA izolasyon yöntemi (salting-out, kit bazlı ve Trizol bazlı) dört farklı doku türü (gonad, tentakül, epidermis ve gastrodermis) üzerinde uygulanmış, her biri Proteinaz K ile 0, 1, 3 ve 24 saat inkübasyona tabi tutulmuştur. Böylece 48 farklı kombinasyon analiz edilmiştir. Bulgular: En yüksek DNA konsantrasyonları gonad dokularında elde edilmiş olup bu durum, dokunun yüksek hücresel yoğunluğu ve yapısal bütünlüğü ile ilişkilendirilmiştir. Özellikle 1–3 saatlik Proteinaz K uygulamasıyla birlikte salting-out yöntemi, diğer iki yönteme kıyasla daha yüksek verim sağlamıştır. Aşırı nemli olan epidermis ve gastrodermis dokularında ise yaş ağırlık ölçümünde sapmalar oluşmuş ve bu durum biyolojik girdiye göre DNA veriminin olduğundan düşük hesaplanmasına neden olmuştur. Sonuç: Jelatinöz denizel omurgasızlardan DNA izolasyonunda doku seçimi, enzimatik inkübasyon süresi ve kullanılan metodoloji büyük önem taşımaktadır. Aurelia aurita örneklerinde, özellikle gonad dokusuna 1–3 saatlik Proteinaz K uygulaması ile salting-out yöntemi kullanımı, verimli ve güvenilir bir DNA izolasyonu için önerilmektedir.

🔖

Cite This Article

Çalıcı, S. Z., Bayrak, B., Yavuz, H. B., Kelel, N., Avşaroğlu, Z. A., Aydemir, M. N. (2025). Evaluating yield of DNA extraction methods across different tissues of moon jellyfish Aurelia aurita (Linnaeus, 1758). Biyolojik Çeşitlilik ve Koruma, Volume: 18 Issue: 3. https://doi.org/10.46309/biodicon.2025.1697734

📄 Full Text PDF Viewer

📄

PDF görüntüleyici hazırlanıyor...

References (37)

  1. Putnam, N., Srivastava, M., Hellsten, U., Dirks, B., Chapman, J., … & Salamov, A. (2007). Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science, 317. https://doi.org/10.1126/science.1139158
  2. Park, E., Hwang, D.S., Lee, J.-S., Song, J.-I., Seo, T.-K., & Won, Y.-J. (2012). Estimation of divergence times in cnidarian evolution based on mitochondrial protein-coding genes and the fossil record. Molecular Phylogenetics and Evolution, 62(1), 329–345. https://doi.org/10.1016/j.ympev.2011.10.008
  3. Purcell, J. E., Uye, S., & Lo, W. (2007). Anthropogenic causes of jellyfish blooms and their direct consequences for humans: A review. Marine Ecology Progress Series, 350, 153–174. https://doi.org/10.3354/meps07093
  4. Condon, R. H., Steinberg, D. K., del Giorgio, P. A., Bouvier, T. C., Bronk, D. A., … & Graham, W. M. (2011). Jellyfish blooms result in a major microbial respiratory sink of carbon in marine systems. Proceedings of the National Academy of Sciences, 108(25), 10225–10230. https://doi.org/10.1073/pnas.1015782108
  5. Brekhman, V., Malik, A., Haas, B., (2015). Transcriptome profiling of the dynamic life cycle of the scyphozoan jellyfish Aurelia aurita. BMC Genomics, 16(74). https://doi.org/10.1186/s12864-015-1320-z
  6. Purcell, J. E. (2007). Environmental effects on asexual reproduction rates of the scyphozoan Aurelia labiata. Marine Ecology Progress Series, 348, 183–196. https://doi.org/10.3354/meps07056
  7. Miller, M.-E. C., & Graham, W. M. (2012). Environmental evidence that seasonal hypoxia enhances survival and success of jellyfish polyps in the northern Gulf of Mexico. Journal of Experimental Marine Biology and Ecology, 432–433, 113–120. https://doi.org/10.1016/j.jembe.2012.07.015
  8. Fuchs, B., Wang, W., Graspeuntner, S., Li, Y., Insua, S., Herbst, E.,. & Khalturin, K. (2014). Regulation of polyp-to-jellyfish transition in Aurelia aurita. Current Biology, 24(3), 263–268. https://doi.org/10.1016/j.cub.2013.12.003
  9. Lucas, C. H., & Dawson, M. N. (2014). What are jellyfishes and thaliaceans and why do they bloom? In Jellyfish Blooms (pp. 9–44). Springer. https://doi.org/10.1007/978-94-007-7015-7_2
  10. Brotz, L., Cheung, W. W. L., Kleisner, K., Pakhomov, E., … & Pauly, D. (2012). Increasing jellyfish populations: Trends in large marine ecosystems. Hydrobiologia, 690(1), 3–20. https://doi.org/10.1007/s10750-012-1039-7
  11. Goldstein, J., & Steiner, U. K. (2019). Ecological drivers of jellyfish blooms: The complex life history of a ‘well‐known’ medusa (Aurelia aurita). Journal of Animal Ecology, 89(3), 697–707. https://doi.org/10.1111/1365-2656.13147
  12. Purcell, J. E. (2011). Jellyfish and ctenophore blooms coincide with human proliferations and environmental perturbations. Annual Review of Marine Science, 4(1), 209–235. https://doi.org/10.1146/annurev-marine-120709-142751
  13. Richardson, A. J., Bakun, A., Hays, G. C., & Gibbons, M. J. (2009). The jellyfish joyride: Causes, consequences and management responses to a more gelatinous future. Trends in Ecology & Evolution, 24(6), 312–322. https://doi.org/10.1016/j.tree.2009.01.010
  14. Brown, D. D., & Cai, L. (2007). Amphibian metamorphosis. Developmental Biology, 306(1), 20–33. https://doi.org/10.1016/j.ydbio.2007.03.021
  15. McBrayer, Z., Ono, H., Shimell, M., Parvy, J., Beckstead, R. B., Warren, J. T.,. & O’Connor, M. B. (2007). Prothoracicotropic hormone regulates developmental timing and body size in Drosophila. Developmental Cell, 13(6), 857–871. https://doi.org/10.1016/j.devcel.2007.11.003
  16. Laudet, V. (2011). The origins and evolution of vertebrate metamorphosis. Current Biology, 21(18), R726–R737. https://doi.org/10.1016/j.cub.2011.07.030
  17. Miglioli, A., Canesi, L., Gomes, I. D. L., Schubert, M., & Dumollard, R. (2021). Nuclear receptors and development of marine invertebrates. Genes, 12(1), 52. https://doi.org/10.3390/genes12010083
  18. Fujita, S., Kuranaga, & E., Nakajima, Y. (2021). Regeneration potential of jellyfish: Cellular mechanisms and molecular insights. Genes, 12(5), 758. https://doi.org/10.3390/genes12050758
  19. Cunningham, K., Anderson, D. J., & Weissbourd, B. (2024). Jellyfish for the study of nervous system evolution and function. Current Opinion in Neurobiology, 88, 102903. https://doi.org/10.1016/j.conb.2024.102903
  20. Kurchaba, N., Cassone, B. J., Northam, C., Ardelli, B. F., & LeMoine, C. M. R. (2020). Effects of MP polyethylene microparticles on microbiome and inflammatory response of larval zebrafish. Toxics, 8(3), 55. https://doi.org/10.3390/toxics8030055
  21. Yang, B., Liu, B., & Chen, Z. (2020). DNA Extraction with TRIzol Reagent Using a Silica Column. Analytical Sciences, 37(7), 1033–1037. https://doi.org/10.2116/analsci.20p361
  22. Sugrue, V. J., Prescott, M., Glendining, K. A., Bond, D. M., Horvath, S., Anderson, G. M.,. & Hore, T. A. (2025). The androgen clock is an epigenetic predictor of long-term male hormone exposure. Proceedings of the National Academy of Sciences, 122(3), e2420087121. https://doi.org/10.1073/pnas.2420087121
  23. Martínez, G., Shaw, E. M., Carrillo, M., & Zanuy, S. (1998). Protein Salting-Out Method Applied to Genomic DNA Isolation from Fish Whole Blood. BioTechniques, 24(2), 238–239. https://doi.org/10.2144/98242bm14
  24. Desjardins, P., & Conklin, D. (2010). NanoDrop Microvolume Quantitation of nucleic acids. Journal of Visualized Experiments, 1. https://doi.org/10.3791/2565
  25. Sthle, L., & Wold, S. (1989). Analysis of variance (ANOVA). Chemometrics and Intelligent Laboratory Systems, 6(4), 259–272. https://doi.org/10.1016/0169-7439(89)80095-4
  26. Sevindik, E., Coşkun, F., Selvi, S., & Alkaç, S. A. (2013). Comparative analysis of the genomic DNA isolation methods on some Silene L. (Caryophyllaceae). Biological Diversity and Conservation, 6(3), 67-71.
  27. Dawson, M. N., & Jacobs, D. K. (2001). Molecular evidence for cryptic species of Aurelia aurita (Cnidaria, Scyphozoa). Biological Bulletin, 200(1), 92–96. https://doi.org/10.2307/1543089
  28. Morrissey, S. J., Jerry, D. R., & Kingsford, M. J. (2022). Genetic Detection and a Method to Study the Ecology of Deadly Cubozoan Jellyfish. Diversity, 14(12), 1139. https://doi.org/10.3390/d14121139
  29. Ortman, B. D., Bucklin, A., Pagès, F., & Youngbluth, M. (2010). DNA barcoding the Medusozoa using mtCOI. Hydrobiologia, 645, 3–16. https://doi.org/10.1016/j.dsr2.2010.09.017
  30. Shao, Z., Chen, Q., Wu, S., Zhang, M., & Xu, P. (2021). Mitochondrial genome of the moon jelly Aurelia aurita (Cnidaria, Scyphozoa): A linear DNA molecule lacking tRNA genes. Frontiers in Marine Science, 8, 640527. https://doi.org/10.3389/fmars.2021.640527
  31. Minamoto, T., Miya, M., Sado, T., Seino, S., Doi, H., Kondoh, M.,. & Takahara, T. (2017). High-throughput sequencing of environmental DNA from jellyfish. PLoS One, 12(3), e0173073. https://doi.org/10.1371/journal.pone.017307
  32. Takahashi S, Sakata MK, Minamoto T, & Masuda R. (2020) Comparing the efficiency of open and enclosed filtration systems in environmental DNA quantification for fish and jellyfish. PLoS One. 15(4), e0231718. https://doi.org/10.1371/journal.pone.0231718
  33. Ogata, M., Masuda, R., & Harino, H. (2021). Environmental DNA preserved in marine sediment for detecting jellyfish blooms after a tsunami. Scientific Reports, 11, 16830. https://doi.org/10.1038/s41598-021-94286-2
  34. Fuchs, B., Wang, W., Graspeuntner, S., Li, Y., Insua, S., Herbst, E.,. & Khalturin, K. (2014). Regulation of polyp-to-jellyfish transition in Aurelia aurita. Current Biology, 24(3), 263–268. https://doi.org/10.1016/j.cub.2013.12.003
  35. McBrayer, Z., Ono, H., Shimell, M., Parvy, J., Beckstead, R. B., Warren, J. T.,. & O’Connor, M. B. (2007). Prothoracicotropic hormone regulates developmental timing and body size in Drosophila. Developmental Cell, 13(6), 857–871. https://doi.org/10.1016/j.devcel.2007.11.003
  36. Sugrue, V. J., Prescott, M., Glendining, K. A., Bond, D. M., Horvath, S., Anderson, G. M.,. & Hore, T. A. (2025). The androgen clock is an epigenetic predictor of long-term male hormone exposure. Proceedings of the National Academy of Sciences, 122(3), e2420087121. https://doi.org/10.1073/pnas.2420087121
  37. Minamoto, T., Miya, M., Sado, T., Seino, S., Doi, H., Kondoh, M.,. & Takahara, T. (2017). High-throughput sequencing of environmental DNA from jellyfish. PLoS One, 12(3), e0173073. https://doi.org/10.1371/journal.pone.017307