Degree Type


Date of Award


Degree Name

Doctor of Philosophy


Biochemistry, Biophysics and Molecular Biology

First Advisor

Basil Nikolau


The goal of my research is to provide metabolic profiling and transcriptome profiling data from which the hydrocarbon biosynthesis pathway can be dissected via the isolation and characterization of genes involved in hydrocarbon biosynthesis in four organisms.

Conditions for the hyper- and hypo-accumulation of hydrocarbons in four organisms were established. The physiological conditions that induce the hyper- and hypo-accumulation of hydrocarbons conditions were used to simultaneously collect RNA for transcriptome sequencing analysis. Simultaneously, the hydrocarbons were analyzed in the four biological systems, specifically to identify the positions of double bonds in alkenes, which provide biochemical evidence about how hydrocarbons are biosynthesized. The comparative transcriptome profiling of cells that hyper- and hypo-accumulate hydrocarbon in all four biological systems is being used to identify genes that are differentially expressed between these two conditions. My research has finished the entire pipeline for maize. Maize silk with differential hydrocarbon accumulation at different developmental stages were utilized and transcriptomes of these silks for candidate genes involved in hydrocarbon biosynthesis were mined. This comparative transcriptome profiling approach is also being applied to pea epidermis, and the two algae, B. braunii and E. huxleyi.

These accomplishments have set the stage for comparative transcriptome profiling to identify candidate genes involved in the hydrocarbon biosynthetic pathway(s) in these four biological systems. In addition, sequence similarity networks can be built from these four biological systems by pairwise blast. The within system networks can then be clustered to identify highly inter-connected modules using the Markov Chain Clustering method. Then, modules without any genes increasing their expression in the direction of hydrocarbon accumulation and genes without increasing expression in the direction of hydrocarbon accumulation will be filtered out. By this cross-system analysis, the candidate genes involved in hydrocarbon biosynthetic pathway(s) shared by maize silk, pea epidermis, B. braunii and E. huxleyi can be discovered. In addition, the systems that have been set up and characterized in this body of work can also be used to identify the hydrocarbon biosynthetic pathways specific to each of the individual biological systems.

Addressing these research goals will add to the current understanding of how hydrocarbons are biosynthesized in different biological systems. This fundamental understanding has the potential of impacting the development alternative advanced biofuels that can be used in place of petroleum-sourced fuels. It is widely recognized that the current use of fossil-carbon as an energy source is unsustainable because of depleting supplies and the accumulation of carbon dioxide in the environment. Because biologically-sourced hydrocarbons have chemical structures that are nearly identical to petroleum, they ultimately could have an application in the development of advanced biofuels.

Copyright Owner

Wenmin Qin



File Format


File Size

300 pages

SupplementalTablesforChapter2.xlsx (38 kB)
Supplemental Tables for Chapter 2

supplementtablesforchapter3.xlsx (34 kB)
Supplemental Tables for Chapter 3

Included in

Biochemistry Commons