研究生: |
江偉立 Kong, Wye Lup |
---|---|
論文名稱: |
使用核酸比率作為真核生物生長速度指標的開發研究 Development of Nucleic Acid Ratios as Eukaryote Growth Rate Indices |
指導教授: |
町田龍二
Machida, Ryuji |
口試委員: |
蔡怡陞
Tsai, Isheng 王慧瑜 Wang, Hui-Yu 林秀瑾 Lin, Hsiu-Chin 單偉彌 Denis, Vianney 町田龍二 Machida, Ryuji |
口試日期: | 2022/09/30 |
學位類別: |
博士 Doctor |
系所名稱: |
生命科學系 Department of Life Science |
論文出版年: | 2022 |
畢業學年度: | 111 |
語文別: | 英文 |
論文頁數: | 109 |
英文關鍵詞: | Growth rate indices, Ribosomal ratio, mRNA ratio, real-time qPCR, RNA-Seq, Daphnia magna |
研究方法: | 實驗設計法 |
DOI URL: | http://doi.org/10.6345/NTNU202205215 |
論文種類: | 學術論文 |
相關次數: | 點閱:81 下載:7 |
分享至: |
查詢本校圖書館目錄 查詢臺灣博碩士論文知識加值系統 勘誤回報 |
Quantification of growth is one of the essential steps to understand the flow of elements and energy in food webs. However, in situ estimation of the growth rate, in general, is challenging, especially for zooplankton. In the past, many biochemical indices were developed to estimate animal growth rates by measuring the ratio of certain biochemicals, such as DNA and RNA. Those indices reduce the effort of time series measurement in the field. However, many researchers claimed that the current available biochemical indices are still imperfect and require improvements. Due to proteins encode by mitochondrial genes responsible for energy generation, while nuclear genes encode the rest of the biological processes, including growth, I hypothesized that the ratio between various groups of nuclear and mitochondrial gene RNA abundance capable of growth rate estimation. In this thesis, we explored a total of five nucleic acid ratios as the potential growth rate indices. Daphnia magna were mainly used as the model species to investigate these nucleic acid ratios.
In chapter 2, I introduced the first nucleic acid ratio, the (1) nuclear and mitochondrial ribosomal ratio (Nuc:Mito-rRNA). Using ribosomal RNA read abundances as the proxy for ribosomes quantities, I measured the ratio between nuclear-encoded cytosolic ribosome and mitochondrial ribosome, and determine the correlation between the ratio and the growth rate. The results of this study showed a significant positive correlation between the proposed ribosomal ratio and somatic growth rate. This demonstrated the potential of the Nuc:Mito-rRNA ratio as a growth rate index.
Despite the result from chapter 2 showed significant correlation between the ratio and growth rate, there are many genes that translates through nuclear ribosome do not contribute to growth can resulted in unwanted noise. Hence, in chapter 3 I introduced another four mRNA growth rate indices with different level of specificity in term of gene functions, which are (2) nuclear and mitochondrial total mRNA ratio (Nuc:Mito-TmRNA), (3) nuclear and mitochondrial ribosomal protein mRNA ratio (Nuc:Mito-RPmRNA), (4) gene ontology (GO) term and total mitochondrial mRNA ratio, and (5) nuclear and mitochondrial specific gene mRNA ratio. I investigated these ratios on D. magna RNA-Seq data. These ratios were also tested on RNA-Seq datasets of Saccharomyces cerevisia retrieved from the NCBI Sequence Read Archive to serve as a verification dataset. Using RNA-Seq data, I discovered that both Nuc:Mito-TmRNA and Nuc:Mito-RPmRNA showed significant correlations with the growth rate for both species. I identified that several GO terms and total mitochondrial mRNA ratio showed significant correlations with the growth rate of S. cerevisiae. Lastly, I also identified mRNA ratios of several specific nuclear and mitochondrial gene pairs that showed significant correlations with growth rates.
I foresee future implications of those proposed growth rate indices in metatranscriptome analyses to estimate the growth rate of communities and species. Finally in chapter 4, I discussed this aspect by providing some examples of potential implications of the growth rate indices proposed.
Adams, K. L., & Palmer, J. D. (2003). Evolution of mitochondrial gene content: Gene loss and transfer to the nucleus. Molecular Phylogenetics and Evolution, 29(3), 380–395. doi:10.1016/S1055-7903(03)00194-5
Alvarez, M., Schrey, A. W., & Richards, C. L. (2015). Ten years of transcriptomics in wild populations: What have we learned about their ecology and evolution? Molecular Ecology, 24(4), 710–725. doi:10.1111/mec.13055
Anders, S., Pyl, P. T., & Huber, W. (2015). HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics, 31(2), 166–169. doi:10.1093/bioinformatics/btu638
Andrews, S. (2010). FASTQC. A quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc
Anger, K., & Hirche, H. J. (1990). Nucleic acids and growth of larval and early juvenile spider crab, Hyas araneus. Marine Biology, 105(3), 403-411. doi:10.1007/BF01316311
Audesirk, T. E. (1979). A field study of growth and reproduction in Aplysia californica. Biological Bulletin, 157(3): 407-421. doi:10.2307/1541026
Ben-Shem, A., Garreau de Loubresse, N., Melnikov, S., Jenner, L., Yusupova, G., & Yusupov, M. (2011). The structure of the eukaryotic ribosome at 3.0 Å resolution. Science, 334(6062), 1524-1529. doi:10.1126/science.1212642
Boeuf, G., & Payan, R. (2001). How should salinity influence fish growth? Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology, 130(4), 411-423. doi:10.1016/S1532-0456(01)00268-X
Bonawitz, N. D., Chatenay-Lapointe, M., Pan, Y., & Shadel, G. S. (2007). Reduced TOR signaling extends chronological life span via increased respiration and upregulation of mitochondrial gene expression. Cell metabolism, 5(4), 265-277. doi:10.1016/j.cmet.2007.02.009
Bose, S., French, S., Evans, F. J., Joubert, F., & Balaban, R. S. (2003). Metabolic network control of oxidative phosphorylation: multiple roles of inorganic phosphate. Journal of Biological Chemistry, 278(40), 39155-39165. doi:10.1074/jbc.M306409200
Bradley, M. C., Perrin, N., & Calow, P. (1991). Energy allocation in the cladoceran Daphnia magna Straus, under starvation and refeeding. Oecologia, 86(3), 414-418. doi:10.1007/BF00317610
Brauer, C. J., Unmack, P. J., & Beheregaray, L. B. (2017). Comparative ecological transcriptomics and the contribution of gene expression to the evolutionary potential of a threatened fish. Molecular Ecology, 26(24), 6841–6856. doi:10.1111/mec.14432
Brown, J. H., Gillooly, J. F., Allen, A. P., Savage, V. M., & West, G. B. (2004). Toward a metabolic theory of ecology. Ecology, 85(7), 1771–1789. doi:10.1890/03-9000
Buckley, L. J. (1984). RNA-DNA ratio: an index of larval fish growth in the sea. Marine Biology, 80(3), 291-298. doi:10.1007/BF00392824
Bulow, F. J. (1970). RNA–DNA ratios as indicators of recent growth rates of a fish. Journal of the Fisheries Board of Canada, 27(12), 2343-2349. doi:10.1139/f70-262
Caron, D. A., Alexander, H., Allen, A. E., Archibald, J. M., Armbrust, E. V., Bachy, C., Bell, C. J., Bharti, A., Dyhrman, S. T., & Guida, S. M. (2017). Probing the evolution, ecology and physiology of marine protists using transcriptomics. Nature Reviews Microbiology, 15(1), 6–20. doi:10.1038/nrmicro.2016.160
Cooper, C. E., & Brown, G. C. (2008). The inhibition of mitochondrial cytochrome oxidase by the gases carbon monoxide, nitric oxide, hydrogen cyanide and hydrogen sulfide: chemical mechanism and physiological significance. Journal of bioenergetics and biomembranes, 40(5), 533-539. doi:10.1007/s10863-008-9166-6
Chang, J. H., & Tong, L. (2012). Mitochondrial poly(A) polymerase and polyadenylation. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 1819(9–10), 992–997. doi:10.1016/j.bbagrm.2011.10.012
Chen, Q., & Haddad, G. G. (2004). Role of trehalose phosphate synthase and trehalose during hypoxia: from flies to mammals. Journal of Experimental Biology, 207(18), 3125-3129. doi:10.1242/jeb.01133
Cherry, J. M., Hong, E. L., Amundsen, C., Balakrishnan, R., Binkley, G., Chan, E. T., Christie, K. R., Costanzo, M. C., Dwight, S. S., & Engel, S. R. (2012). Saccharomyces Genome Database: The genomics resource of budding yeast. Nucleic Acids Research, 40(D1), D700–D705. doi:10.1093/nar/gkr1029
Chıcharo, L. M., Chıcharo, M. A., Alves, F., Amaral, A., Pereira, A., & Regala, J. (2001). Diel variation of the RNA/DNA ratios in Crassostrea angulata (Lamarck) and Ruditapes decussatus (Linnaeus 1758) (Mollusca: Bivalvia). Journal of Experimental Marine Biology and Ecology, 259(1), 121-129. doi:10.1016/S0022-0981(01)00229-5
Clark, K., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., & Sayers, E. W. (2016). GenBank. Nucleic acids research, 44(D1), D67–D72. doi:10.1093/nar/gkv1276
Cloern, J. E., Grenz, C., & Vidergar‐Lucas, L. (1995). An empirical model of the phytoplankton chlorophyll: Carbon ratio‐the conversion factor between productivity and growth rate. Limnology and Oceanography, 40(7), 1313–1321. doi:10.4319/lo.1995.40.7.1313
Colbourne, J. K., Singan, V. R., & Gilbert, D. G. (2005). wFleaBase: The Daphnia genome database. BMC Bioinformatics, 6(1), 1–5. doi:10.1186/1471-2105-6-45
Conover, R. J., & Poulet, S. A. (1986). Physiological methods for determining copepod production. Syllogeus, 58, 85-99.
Crick, F. (1970). Central dogma of molecular biology. Nature, 227(5258), 561–563. doi:10.1038/227561a0
Damon, C., Lehembre, F., Oger-Desfeux, C., Luis, P., Ranger, J., Fraissinet-Tachet, L., & Marmeisse, R. (2012). Metatranscriptomics reveals the diversity of genes expressed by eukaryotes in forest soils. PLoS One, 7(1), e28967. doi:10.1371/journal.pone.0028967
Dortch, Q., Roberts, T. L., Clayton Jr, J. R., & Ahmed, S. I. (1983). RNA/DNA ratios and DNA concentrations as indicators of growth rate and biomass in planktonic marine organisms. Marine ecology progress series. Oldendorf, 13(1), 61-71.
Elser, J. J., Acharya, K., Kyle, M., Cotner, J., Makino, W., Markow, T., ... & Sterner, R. W. (2003). Growth rate–stoichiometry couplings in diverse biota. Ecology Letters, 6(10), 936-943. doi:10.1046/j.1461-0248.2003.00518.x
Elser, J. J., Dobberfuhl, D. R., MacKay, N. A., & Schampel, J. H. (1996). Organism size, life history, and N: P stoichiometry. BioScience, 46(9), 674-684. doi:10.2307/1312897
Euent, S., Menzel, R., & Steinberg, C. E. (2008). Gender-specific lifespan modulation in Daphnia magna by a dissolved humic substances preparation. Annals of Environmental Science, 2, 7-10.
Freese, H. M., & Martin-Creuzburg, D. (2013). Food quality of mixed bacteria–algae diets for Daphnia magna. Hydrobiologia, 715(1), 63-76. doi:10.1007/s10750-012-1375-7
Giebelhausen, B., & Lampert, W. (2001). Temperature reaction norms of Daphnia magna: the effect of food concentration. Freshwater Biology, 46(3), 281-289. doi:10.1046/j.1365-2427.2001.00630.x
Gillooly, J. F., Brown, J. H., West, G. B., Savage, V. M., & Charnov, E. L. (2001). Effects of size and temperature on metabolic rate. Science, 293(5538), 2248-2251. doi:10.1126/science.1061967
Granados, M., Altshuler, I., Plourde, S., & Fussmann, G. F. (2017). Size and variation in individual growth rates among food web modules. Ecosphere, 8(7), e01862. doi:10.1002/ecs2.1862
Gregory, T. R., Nicol, J. A., Tamm, H., Kullman, B., Kullman, K., Leitch, I. J., Murray, B. G., Kapraun, D. F., Greilhuber, J., & Bennett, M. D. (2007). Eukaryotic genome size databases. Nucleic Acids Research, 35(suppl_1), D332–D338. doi:10.1093/nar/gkl828
Gurvich, Y., Leshkowitz, D., & Barkai, N. (2017). Dual role of starvation signaling in promoting growth and recovery. PLoS Biology, 15(12), e2002039. doi:10.1371/journal.pbio.2002039
Gusmão, L. F. M., & McKinnon, A. D. (2011). Nucleic acid indices of egg production in the tropical copepod Acartia sinjiensis. Journal of experimental marine biology and ecology, 396(2), 122-137. doi:10.1016/j.jembe.2010.10.008
Haines, T. A. (1973). An evaluation of RNA–DNA ratio as a measure of long-term growth in fish populations. Journal of the Fisheries Board of Canada, 30(2), 195-199. doi:10.1139/f73-035
Heugens, E. H., Tokkie, L. T., Kraak, M. H., Hendriks, A. J., Van Straalen, N. M., & Admiraal, W. (2006). Population growth of Daphnia magna under multiple stress conditions: joint effects of temperature, food, and cadmium. Environmental Toxicology and Chemistry: An International Journal, 25(5), 1399-1407. doi:10.1897/05-294R.1
Hsu, D. K., Guo, Y., Peifley, A. K., & Winkles, A. J. (1997). Differential control of murine aldose reductase and fibroblast growth factor (FGF)-regulated-1 gene expression in NIH 3T3 cells by FGF-1 treatment and hyperosmotic stress. Biochemical Journal, 328(2), 593-598. doi:10.1042/bj3280593
Jurgens, K. (1994). Impact of Daphnia on planktonic. Marine Microbial Food Webs, 8(1-2), 295-324.
Johnston, J. E. (1939). The Avogadro Number. Journal of Chemical Education, 16(7), 333. doi:10.1021/ed016p333
Kaiser, M. J., Attrill, M. J., Jennings, S., Thomas, D. N., & Barnes, D. K. (2011). Marine ecology: processes, systems, and impacts. Oxford University Press.
Karakiri, M., Berghahn, R., & van der Veer. H. W. (1991). Variations in settlement and growth of 0-group plaice (Pleuronectes platessa L.) in the Dutch Wadden Sea as determined by otolith microstructure analysis. Netherlands Journal of Sea Research, 27(3-4), 345-351. doi:10.1016/0077-7579(91)90037-2
Kawabata, K., & Urabe, J. (1998). Length–weight relationships of eight freshwater planktonic crustacean species in Japan. Freshwater Biology, 39(2), 199–205. doi:10.1046/j.1365-2427.1998.00267.x
Kemp, P. F., Lee, S., & LaRoche, J. (1993). Estimating the growth rate of slowly growing marine bacteria from RNA content. Applied and environmental microbiology, 59(8), 2594-2601. doi:10.1128/aem.59.8.2594-2601.1993
Kong, W.-L., Miki, T., Lin, Y.-Y., Makino, W., Urabe, J., Gu, S.-H., & Machida, R. J. (2019). Nuclear and mitochondrial ribosomal ratio as an index of animal growth rate. Limnology and Oceanography: Methods, 17(11), 575–584. doi:10.1046/j.1365-2427.1998.00267.x
Lampert, W., & Trubetskova, I. (1996). Juvenile growth rate as a measure of fitness in Daphnia. Functional Ecology, 631–635. doi:10.2307/2390173
Lenz, P. H., Lieberman, B., Cieslak, M. C., Roncalli, V., & Hartline, D. K. (2021). Transcriptomics and metatranscriptomics in zooplankton: Wave of the future? Journal of Plankton Research, 43(1), 3–9. doi:10.1093/plankt/fbaa058
Leray, M., Ho, S.-L., Lin, I.-J., & Machida, R. J. (2018). MIDORI server: A webserver for taxonomic assignment of unknown metazoan mitochondrial-encoded sequences using a curated database. Bioinformatics, 34(21), 3753–3754. doi:10.1093/bioinformatics/bty454
Libiad, M., Yadav, P. K., Vitvitsky, V., Martinov, M., & Banerjee, R. (2014). Organization of the Human Mitochondrial Hydrogen Sulfide Oxidation Pathway. Journal of Biological Chemistry, 289(45), 30901-30910. doi:10.1074/jbc.M114.602664
Lin, K. Y., Sastri, A. R., Gong, G. C., & Hsieh, C. H. (2013). Copepod community growth rates in relation to body size, temperature, and food availability in the East China Sea: a test of metabolic theory of ecology. Biogeosciences, 10(3), 1877-1892. doi:10.5194/bg-10-1877-2013
Logan, J. A., Wollkind, D. J., Hoyt, S. C., & Tanigoshi, L. K. (1976). An analytic model for description of temperature dependent rate phenomena in arthropods. Environmental Entomology, 5(6), 1133–1140. doi:10.1093/ee/5.6.1133
Lopez, J. V., Yuhki, N., Masuda, R., Modi, W., & O’Brien, S. J. (1994). Numt, a recent transfer and tandem amplification of mitochondrial DNA to the nuclear genome of the domestic cat. Journal of Molecular Evolution, 39(2), 174–190. doi:10.1007/BF00163806
Lopez, M. L. D., Lin, Y.-Y., Sato, M., Hsieh, C.-H., Shiah, F.-K., & Machida, R. J. (2021). Using metatranscriptomics to estimate the diversity and composition of zooplankton communities. Molecular Ecology Resources, 22(2), 638-652. doi:10.1111/1755-0998.13506
Machida, R. J., Kurihara, H., Nakajima, R., Sakamaki, T., Lin, Y.-Y., & Furusawa, K. (2021). Comparative analysis of zooplankton diversities and compositions estimated from complement DNA and genomic DNA amplicons, metatranscriptomics, and morphological identifications. ICES Journal of Marine Science, 78(9), 3428-3443. doi:10.1093/icesjms/fsab084
Machida, R. J., Leray, M., Ho, S.-L., & Knowlton, N. (2017). Metazoan mitochondrial gene sequence reference datasets for taxonomic assignment of environmental samples. Scientific Data, 4(1), 1–7. doi:10.1093/bioinformatics/bty454
Mair, P., & Wilcox, R. (2018). WRS2: Wilcox robust estimation and testing. Retrieved from https://cran.r-project.org/web/packages/WRS2/
Margulis, L., & Bermudes, D. (1985). Symbiosis as a mechanism of evolution: Status of cell symbiosis theory. Symbiosis, 1, 101-124.
Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal, 17(1), 10–12. doi:10.14806/ej.17.1.200
Martínez-Jerónimo, F. (2012). Description of the individual growth of Daphnia magna (Crustacea: Cladocera) through the von Bertalanffy growth equation. Effect of photoperiod and temperature. Limnology, 13(1), 65-71. doi:10.1007/s10201-011-0356-2
McCarthy, I., Moksness, E., & Pavlov, D. A. (1998). The effects of temperature on growth rate and growth efficiency of juvenile common wolffish. Aquaculture International, 6(3), 207–218. doi:10.1023/A:1009202710566
McMahon, J. W., & Rigler, F. H., (1965). Feeding rate of Daphnia magna Straus in different foods labeled with radioactive phosphorus 1. Limnology and Oceanography, 10(1), 105-113. doi:10.4319/lo.1965.10.1.0105
Melser, S., Lavie, J., & Bénard, G. (2015). Mitochondrial degradation and energy metabolism. Biochimica et Biophysica Acta (BBA)-Molecular Cell Research, 1853(10) 2812-2821. doi:10.1016/j.bbamcr.2015.05.010
Mukherjee, A., & Reddy, M. S. (2020). Metatranscriptomics: an approach for retrieving novel eukaryotic genes from polluted and related environments. 3 Biotech, 10(2), 1-19. doi:10.1007/s13205-020-2057-1
Nakao, A., Yoshihama, M., & Kenmochi, N. (2004). RPG: the ribosomal protein gene database. Nucleic Acids Research, 32(suppl_1), D168–D170. doi:10.1093/nar/gkh004
Nejstgaard, J. C., Frischer, M. E., Raule, C. L., Gruebel, R., Kohlberg, K. E., & Verity, P. G. (2003). Molecular detection of algal prey in copepod guts and fecal pellets. Limnology and Oceanography: Methods, 1(1), 29-38. doi:10.4319/lom.2003.1.29
Orcutt, J. D., & Porter, K. G. (1984). The synergistic effects of temperature and food concentration of life history parameters of Daphnia. Oecologia, 63(3), 300-306. doi:10.1007/BF00390657
Ota, A. Y., & Landry, M. R. (1984). Nucleic acids as growth rate indicators for early developmental stages of Calanus pacificus Brodsky. Journal of Experimental Marine Biology and Ecology, 80(2), 147–160. doi:10.1016/0022-0981(84)90009-1
Petrash, J.M. (2004) All in the family: aldose reductase and closely related aldo-keto reductases. Cellular and Molecular Life Sciences, 61, 737–749. doi:10.1007/s00018-003-3402-3
Pianka, E. R. (1970). On r-and K-selection. The American Naturalist, 104(940), 592-597. doi:10.1086/282697
Pietri, R., Román-Morales, E., & López-Garriga, J. (2011). Hydrogen sulfide and hemeproteins: knowledge and mysteries. Antioxidants & redox signaling, 15(2), 393-404. doi:10.1089/ars.2010.3698
Putman, A., Vanvlasselaer, E., Panis, B., & Van Dijck, P. (2015). Strong differences in trehalose levels between sexual and asexual eggs of the water flea Daphnia magna. Cryopreservation of Daphnia magna genotypes, 57.
Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., & Glöckner, F. O. (2012). The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research, 41(D1), D590-D596. doi:10.1093/nar/gks1219
R Core Team (2020). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/
Ramana, K. V., Friedrich, B., Tammali, R., West, M. B., Bhatnagar, A., & Srivastava, S. K. (2005). Requirement of aldose reductase for the hyperglycemic activation of protein kinase C and formation of diacylglycerol in vascular smooth muscle cells. Diabetes, 54(3), 818-829. doi:10.2337/diabetes.54.3.818
Rambold, A. S., Kostelecky, B., Elia, N., & Lippincott-Schwartz. J. (2011). Tubular network formation protects mitochondria from autophagosomal degradation during nutrient starvation. Proceedings of the National Academy of Sciences, 108(25) 10190-10195. doi:10.1073/pnas.1107402108
Reef, R., Ball, M. C., Feller, I. C., & Lovelock, C. E. (2010). Relationships among RNA: DNA ratio, growth and elemental stoichiometry in mangrove trees. Functional Ecology, 24(5), 1064-1072. doi:10.1111/j.1365-2435.2010.01722
Sahebekhtiari, N., Fernandez-Guerra, P., Nochi, Z., Carlsen, J., Bross, P., & Palmfeldt, J. (2019). Deficiency of the mitochondrial sulfide regulator ETHE1 disturbs cell growth, glutathione level and causes proteome alterations outside mitochondria. Biochimica et Biophysica Acta (BBA)-Molecular Basis of Disease, 1865(1), 126-135. doi:10.1016/j.bbadis.2018.10.035
Sato, Y., Miya, M., Fukunaga, T., Sado, T., & Iwasaki, W. (2018). MitoFish and MiFish pipeline: A mitochondrial genome database of fish with an analysis pipeline for environmental DNA metabarcoding. Molecular Biology and Evolution, 35(6), 1553–1555. doi:10.1093/molbev/msy074
Schmelzle, T., & Hall, M. N. (2000). TOR, a central controller of cell growth. Cell, 103(2) 253-262. doi:10.1016/S0092-8674(00)00117-3
Shinn, E. A. (1966). Coral growth-rate, an environmental indicator. Journal of Paleontology, 40(2), 233-240.
Smith, F. E. (1963). Population dynamics in Daphnia magna and a new model for population growth. Ecology, 44(4), 651-663.
Speekmann, C. L., Nunez, B. S., & Buskey, E. J. (2007). Measuring RNA: DNA ratios in individual Acartia tonsa (Copepoda). Marine biology, 151(2), 759-766. doi:10.1007/s00227-006-0520-0
Stapanian, M. A., Lewis, T. E., Palmer, C. J., & Amos, M. M. (2016). Assessing accuracy and precision for field and laboratory data: a perspective in ecosystem restoration. Restoration Ecology, 24(1), 18-26. doi:10.1111/rec.12284
Sutcliffe Jr., W. H. (1965). Growth estimates from ribonucleic acid content on some small organisms. Limnology and Oceanography, 10(suppl), R253–R258. https://doi.org/10.4319/lo.1965.10.suppl2.r253
Tang, B., Wang, S., Wang, S. G., Wang, H. J., Zhang, J. Y., & Cui, S. Y. (2018). Invertebrate trehalose-6-phosphate synthase gene: genetic architecture, biochemistry, physiological function, and potential applications. Frontiers in Physiology, 9, 30. doi:10.3389/fphys.2018.00030
Taylor, S. C., Nadeau, K., Abbasi, M., Lachance, C., Nguyen, M., & Fenrich, J. (2019). The ultimate qPCR experiment: Producing publication quality, reproducible data the first time. Trends in Biotechnology, 37(7), 761–774. https://doi.org/10.1016/j.tibtech.2018.12.002
Thomas Jr, C. A. (1971). The genetic organization of chromosomes. Annual Review of Genetics, 5, 237-256. doi:10.1146/annurev.ge.05.120171.001321
Tiranti, V., D’Adamo, P., Briem, E., Ferrari, G., Mineri, R., Lamantea, E., ... & Zeviani, M. (2004). Ethylmalonic encephalopathy is caused by mutations in ETHE1, a gene encoding a mitochondrial matrix protein. The American Journal of Human Genetics, 74(2), 239-252. doi:10.1086/381653
Tkaczyk, A., Bownik, A., Dudka, J., Kowal, K., & Ślaska, B. (2021). Daphnia magna model in the toxicity assessment of pharmaceuticals: A review. Science of The Total Environment, 763, 143038. doi:10.1016/j.scitotenv.2020.143038
Tovar, J., Fischer, A., & Clark, C. G. (1999). The mitosome, a novel organelle related to mitochondria in the mitochondrial parasite Entamoeba histolytica. Molecular Microbiology, 32(5), 1013–1021. doi:10.1046/j.1365-2958.1999.01414.x
Trapnell, C., Pachter, L., & Salzberg, S. L. (2009). TopHat: Discovering splice junctions with RNA-Seq. Bioinformatics, 25(9), 1105–1111. doi:10.1093/bioinformatics/btp120
UniProt.org (2021). UniProt: The universal protein knowledgebase in 2021. Nucleic Acids Research, 49(D1), D480–D489. https://doi.org/10.1093/nar/gkaa1100
Untergasser, A., Cutcutache, I., Koressaar, T., Ye, J., Faircloth, B. C., Remm, M., & Rozen, S. G. (2012). Primer3—New capabilities and interfaces. Nucleic Acids Research, 40(15), e115–e115. doi:10.1093/nar/gks596
Urabe, J., Clasen, J., & Sterner, R. W. (1997). Phosphorus limitation of Daphnia growth: Is it real? Limnology and Oceanography, 42(6), 1436–1443. doi:10.4319/lo.1997.42.6.1436
Untergasser, A., Cutcutache, I., Koressaar, T., Ye, J., Faircloth, B. C., Remm, M., & Rozen, S. G. (2012). Primer3—new capabilities and interfaces. Nucleic Acids Research, 40(15), e115-e115. doi:10.1093/nar/gks596.
Van Dam, T. J., Zwartkruis, F. J., Bos, J. L., & Snel, B. (2011). Evolution of the TOR pathway. Journal of Molecular Evolution, 73(3), 209-220. doi:10.1007/s00239-011-9469-9
Vorobev, A., Dupouy, M., Carradec, Q., Delmont, T. O., Annamalé, A., Wincker, P., & Pelletier, E. (2020). Transcriptome reconstruction and functional analysis of eukaryotic marine plankton communities via high-throughput metagenomics and metatranscriptomics. Genome research, 30(4), 647-659. doi:10.1101/gr.253070.119
Von Bertalanffy, L. (1938). A quantitative theory of organic growth (inquiries on growth laws. II). Human biology, 10(2), 181-213.
Vrede, T., Persson, J., & Aronsen, G. (2002). The influence of food quality (P: C ratio) on RNA: DNA ratio and somatic growth rate of Daphnia. Limnology and Oceanography, 47(2), 487-494. doi:10.4319/lo.2002.47.2.0487
Wagner, M., Durbin, E., & Buckley, L. (1998). RNA:DNA ratios as indicators of nutritional condition in the copepod Calanus finmarchicus. Marine Ecology Progress Series, 162, 173–181. doi:10.3354/meps162173
Warner, J. R. (1999). The economics of ribosome biosynthesis in yeast. Trends in Biochemical Sciences, 24(11), 437–440. doi:10.1016/S0968-0004(99)01460-7
Wenner, A. M., Fusaro, C., & Oaten, A. (1974). Size at onset of sexual maturity and growth rate in crustacean populations. Canadian Journal of Zoology, 52(9) 1095-1106. doi:10.1139/z74-147
Whelan, J. A., Russell, N. B., & Whelan, W. A. (2003). A method for the absolute quantification of cDNA using real-time PCR. Journal of Immunological Methods, 278(1-2) 261-269. doi:10.1016/S0022-1759(03)00223-0
Wickham, H. (2011). Ggplot2. Wiley Interdisciplinary Reviews: Computational Statistics, 3(2), 180–185. doi:10.1002/wics.147
Witherspoon, M., Sandu, D., Lu, C., Wang, K., Edwards, R., Yeung, A., ... & Lipkin, S. (2019). ETHE1 overexpression promotes SIRT1 and PGC1α mediated aerobic glycolysis, oxidative phosphorylation, mitochondrial biogenesis and colorectal cancer. Oncotarget, 10(40), 4004. doi:10.18632/oncotarget.26958
Yang, G., Wu, L., Bryan, S., Khaper, N., Mani, S., & Wang, R. (2010). Cystathionine gamma-lyase deficiency and overproliferation of smooth muscle cells. Cardiovascular research, 86(3), 487-495. doi:10.1093/cvr/cvp420
Yebra, L., Kobari, T., Sastri, A. R., Gusmão, F., & Hernández-León, S. (2017). Advances in biochemical indices of zooplankton production. Advances in Marine Biology, 76, 157–240. doi:10.1016/bs.amb.2016.09.001
Yönten, V., & Aktaş, N. (2014). Exploring the optimum conditions for maximizing the microbial growth of Candida intermedia by response surface methodology. Preparative Biochemistry and Biotechnology, 44(1), 26-39. doi:10.1080/10826068.2013.782044
Zhang, W., Liu, Z., Tang, S., Li, D., Jiang, Q., & Zhang, T. (2020). Transcriptional response provides insights into the effect of chronic polystyrene nanoplastic exposure on Daphnia pulex. Chemosphere, 238, 124563. doi:10.1016/j.chemosphere.2019.124563