My PhD dissertation is now available for free online at http://pqdtopen.proquest.com/pubnum/10164019.html
I'm also making my laboratory notebooks from grad school available. They don't cover everything I did, they're pretty messy, and I'm not sure they will be useful or interesting to anyone, but here they are.
Here is the abstract to my dissertation:
Plant natural products are useful for many different applications,
including medicines, flavors and fragrances, and industrial uses. Two
important aspects of plant natural products research are the
identification of compounds in their source plants, and the
characterization of the processes involved in their biosynthesis. To aid
in the identification of plant natural products, we developed the
Spektraris family of databases. These databases include highperformance
liquid chromatography mass spectrometry data, and 13C and 1H
nuclear magnetic resonance data, which are searchable through an online
interface. The utility of Spektraris was validated by using it to
identify compounds in plant extracts and as part of a workflow to
elucidate the structure of a previously undescribed compound.
Mints have a long history of use as model systems for studying the
processes of terpene natural products biosynthesis in specialized plant
tissues. The mint family (Lamiaceae), synthesizes and stores volatile
terpenes in glandular trichomes. Using a comparative transcriptomic
approach, we identified differences in gene expression of monoterpene
biosynthetic genes among mint species with different oil profiles. We
also assembled the genome of a mint species, Mentha longifolia. The genome assembly will be valuable for future mint research.
To further investigate biosynthetic processes in mint, I developed a
detailed mathematical model of the metabolism of peppermint glandular
trichomes. The model incorporates multiple sources of data, including
transcriptome data, metabolite data, enzymatic data from the peppermint
literature, and previously developed models of plant metabolism. The
creation of a new metabolic modeling software package, called YASMEnv,
facilitated construction of the model. Model-based simulated reaction
knockouts using flux balance analysis revealed that fermentation may be
important for ATP regeneration in secretory phase glandular trichomes.
Follow up experiments confirmed high levels of alcohol dehydrogenase
activity in secretory phase isolated trichomes. Simulations also
supported an essential role for ferredoxin and ferredoxin-NADP
reductase. Transcriptome analysis revealed the presence of an isoform of
ferredoxin in trichomes distinct from the one expressed in root. The
presence of a distinct ferredoxin isoform in trichomes supports the
hypothesis that selection pressure for efficient natural products
biosynthesis may also act on the enzymes of primary metabolism.