The following dissertation comprises five publishable units and a discussion. The first two units examine epithelial dynamics (cell loss, cell proliferation, endoreplication) in the guts of mosquitos, in the light of their role as vectors of major human diseases. Chapter 1 is an opinion piece which posits that epithelial dynamics impact multiple aspects of mosquitoes’ life history (longevity, fecundity, etc.) and potential to transmit disease. Chapter 2 is an original research paper describing epithelial dynamics in multiple mosquito species in the context of maturation, infection and blood-feeding. The next chapters are transcriptomic papers examining fundamental aspects of mosquito physiology. Chapter 3 is an original research paper analyzing an anatomical RNAseq dataset with profiles for the head, thorax, abdomen, gut, Malpighian tubules, and ovaries of the female Aedes aegypti mosquito. Chapter 4 is an original research paper examining the transcriptional responses of Ae. aegypti and Anopheles gambiae to systemic infection with Gram-negative, Gram-positive, and fungal pathogens. Major conclusions from this chapter include (a) that Ae. aegypti and An. gambiae each mount a core transcriptional response to all types of infection (b) that the nature of this response is highly conserved between species (c) that neither species appears to mount a Gram type-specific response to infection (in contrast to the canonical model of immune regulation) but that both mount distinct responses to bacteria versus fungi. Chapter 5 is a review article which integrates literature about host-microbe interactions in Aedes mosquitoes, with new insights from Chapters 3 and 4.