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.

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