Mitochondrial Complex I (CI) is composed of 44 distinct subunits that are assembled with eight Fe- S clusters and a single flavin mononucleotide. Mitochondria is highly enriched in the flight muscles of Drosophila melanogaster, however the assembly mechanism of Drosophila CI has not been described. We report that the mechanism of CI biogenesis in Drosophila flight muscles proceeds via the formation of ~315- , ~550-, and ~815 kDa CI assembly intermediates. Additionally, we define specific roles for several CI subunits in the assembly process. In particular, we show that dNDUFS5 is required for converting the ~700 kDa transient CI assembly intermediate into the ~815 kDa assembly intermediate, by stabilizing or promoting the incorporation of dNDUFA10 into the complex. Our findings highlight the potential values of Drosophila as a suitable model organism and resource to study the CI biogenesis in vivo, and to address questions relevant to CI biogenesis in humans. CI biogenesis is regulated by transient interactors known as CI assembly factors (CIAFs). To date, about half of CI disorders are attributed to the mutations in the CI subunits and the known CIAFs. The cause for the other half remains to be discovered, warranting the investigation for additional regulators of CI biogenesis such as novel CIAFs. To identify novel regulators, we cataloged interactors of a core subunit, NDUFS3, knocked each one down by RNAi in the Drosophila flight muscle, and analyzed its effect in the stability of CI by blue-native PAGE. We identified the Drosophila Fragile X Mental Retardation protein (dFMRP) to destabilize the holoenzyme of CI and cause it to misassemble. Therefore, we report dFMRP as a novel regulator of CI biogenesis, and demonstrate the utilization of Drosophila as an effective model system to uncover the mysteries of CI biogenesis.

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During development DNA-binding transcription factors are deployed downstream of patterning events to enable specific gene regulatory programs that define diverse cell identities. Within a given eukaryotic cell only a subset of potential binding targets in the genome, called cis-regulatory modules, are available due to the distribution of nucleosomes which restrict access to the underlying DNA. The accessible landscape of cells is highly dynamic over time and across different cell types, although how this process is regulated and influences the function of transcription factors in patterning of complex tissues is not well understood. In this thesis I focused on dissecting the cell type-specific chromatin accessibility landscapes that distinguishes different cell populations within the Drosophila dorsal appendages. The patterning of this system is extremely well characterized allowing for a detailed understanding of how transcription factors at the top of cell fate hierarchies influence, or respond to, the chromatin landscape during development. In Chapter 2 I describe the differences in chromatin accessibility along the proximal-distal axis of the wing imaginal disc which gives rise to distinct populations of the thoracic body wall and appendage in the second thoracic segment (T2). I found that a major driver of chromatin differences in these populations is the repressive input of the conserved insect wing marker Nubbin, whose function in the appendage is associated with decreasing accessibility of select chromatin regions relative to their conformation in body wall cells. In Chapter 3 I characterized the serially homologous body wall and appendage cells in the adjacent third thoracic body segment (T3), which diverge extensively in morphology from the T2 state due to influence of a single gene, Ultrabithorax (Ubx). Ubx is a member of the Hox gene family which functions to provide cells with spatial identity along the anterior-posterior axis. I show this function for Ubx in specifying T3 cells coincides with widespread changes to chromatin accessibility which contribute to a segment and cell type-specific regulatory program.

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Recent evidence has shown that fruit fly adults and larvae are heavily attracted to food sites occupied by larvae. This attraction is especially strong in mated females that are looking for a suitable site for egg laying. In the first set of experiments, we compared the value assigned to social information provided by larvae at a site to the nutritional information that a female has access to by sampling a food. Lowering food quality did decrease egg-laying preference for a food, but females still showed a much stronger preference for occupied foods. We theorized that the social egg-laying preference may be due to an advantage of developing near older larvae. However, eggs that developed near larvae showed lower survival to adulthood, slower development time, and lower adult body mass. Females were also not able to reduce their social egg-laying preference, even when foods were already heavily occupied by larvae. Finally, we found that larvae were not better able to identify a high quality food site than an adult female, and thus the smell of used food was not a reliable cue to the quality of a site. These results provide evidence that the preference for females to lay eggs near larvae is very robust but the exact benefit it provides for the female and her offspring is unknown. We then ran a series of experiments to test larval social information use to see if they value it as heavily as adult females. Our experiments consisted of focal larvae being put on lower quality food and trying to find a higher quality food nearby that was either occupied or unoccupied by a single model larva. Larvae did not reliably use this social information. Overall, it is unclear whether the larvae are using social information to help them find higher quality foods. / Thesis / Master of Science (MSc)

The reliability of biomarker discovery by means of proteomics has been called into question. It was speculated that "background noise" variation resulting from differences in preparation and handling of samples and proteome dynamics may mask subtle, yet important, differences due to the biological condition. Little is understood about complex proteomes and their variability. A critical aspect of proteomic biomarker research that is largely unexplored is the comparative reproducibility of certain methods such as two-dimensional gel electrophoresis and liquid chromatography/mass spectrometry. In particular, with liquid chromatography/mass spectrometry, it is not known whether variability in peptide quantitation is dependent on any of their several properties such as size, abundance, or hydrophobicity. Such determinations may be critical in properly assessing the value of proteomics data. The fruit fly Drosophila melanogaster was used as a well-controlled multicellular animal model to study the relationship between the background variation and expected changes induced by environmental or genetic factors. The data, gathered by two different proteomics methods, were used to compare and evaluate the reproducibility of the methods. It is reported that there was on average 15 to 18% variability in quantitative measurements of protein abundance using 2-dimensional gel electrophoresis or liquid chromatography/mass spectrometry. Using liquid chromatography/mass spectrometry, peptides with a smaller mass-to-charge ratio were shown to be measured less reproducibly than peptides with a larger ratio. Statistically significant proteomic differences between fly populations could be demonstrated between males and females. In dynamic experiments, less than 0.5% of proteins measured were shown to change after 24 hour starvation of the flies. However, no significant difference in peptide composition could be found for flies fed on a second diet consisting of the standard diet augmented with 10% ethanol. These results suggest that proteomic variability while evident allowed for biomarker discovery using either method for this model system.

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