The topology of Hox gene networks during the development of the crustacean Parhyale hawaiensis
Generating a multicellular animal from a single-celled zygote requires the coordinated spatiotemporal expression of thousands of genes. Members of the Hox family of transcription factors, expressed in different domains along the anterior-posterior axis of Bilaterian embryos, are well known for their role in determining regional identity (Figure 1).
The Hox proteins, however, only regulate the process as transcription factors; it is the hundreds of downstream genes they mobilize that physically construct the embryo. This downstream network that builds each unique region is largely a black box.
The goal of my thesis research is to comprehensively identify genes regulated by Hox proteins in Parhyale hawaiensis and to begin to dissect their role in appendage morphogenesis and evolution.
To do this, I hand dissected Parhyale embryos (Figure 2) to generate 32 RNA-seq Illumina expression profiles. RNAseq profiles were constructed from 5 different appendage types at 6 embryonic stages throughout appendage morphogenesis. I compared these appendage expression profiles to identify 92 candidate genes that appear to be differentially expressed between different appendage types. I will verify the expression patterns of these candidate genes by in situ. Genes with interesting expression patterns will be knocked out by CRISPR-Cas9.
These experiments will correlate a massive number of genes with the structures that they build. This is critical to our understanding of how genetic circuits create physical form during development and how changes in these circuits generate new physical forms over the course of evolution.
I was born and raised in the south Bay Area, near Starfleet headquarters, until I was 12 years old, when my parents moved to the backwater Class H desert planet of Cornville, Arizona. Although neither of my parents had attended Starfleet, I had always wanted to explore strange worlds, to seek out new life and new civilizations, and to boldly go where no one had gone before, so decided to become a Starfleet cadet. I transferred to the tiny M-class planet of Yavapai College, and trained in the biological sciences under the tutelage of Captain Chris Breitmeyer and First Officer Jan Albright. For my birthday, they gave me the famous evodevo manual, Endless Forms Most Beautiful, by Sean Carroll. I was entranced by the idea that animals were constructed from networks of genetic circuits. In theory, the genetic architecture of development could be tweaked to create designer animals, such as reproductively-hindered, K-selected tribbles. Of course, the experimental foundations had to be established before this could become reality. Therefore, upon earning my Associate of Science from Starfleet, I transferred to the M-class planet the University of Arizona, where I majored in Molecular and Cellular Biology.
My first mission was with Captain Lisa Nagy, of the USS Ilyanassa obsoleta. My mission was to determine whether the Hox gene post2, an orthologue of AbdB, played a role in the development and evolution of the mollusk shell, a morphological novelty. For my heroism at the University of Arizona, I was promoted to Lieutenant of Science, and transferred to my dream assignment on the major M-class planet, the University of California, Berkeley.
I am now Lieutenant of Hox Operations for two of the greatest Starfleet Officers of evodevo, Captain Nipam Patel of the mighty USS Parhyale hawaiensis, decorated for his glorious battle against countless developmentally important genes in non-model arthropods; and Captain Mike Eisen, a pioneer of the latest transcriptomics-class starship USS Drosophila melanogaster and fearless crusader of Open Access science publishing. My current mission is to characterize the Hox gene interactome and appendage diversity in the crustacean Parhyale hawiensis.