2011 Research Project Descriptions

De novo Assembly of Loblolly Pine (Pinus taeda) Transcripts obtained from RNA-Seq

Student Name: 
Charles Zhang
UCD Department: 
Department of Plant Sciences
UCD Mentor: 
David Neal

Forest trees provide a host of benefits to both humans and the biosphere. In order to better understand them, it is helpful to sequence their genetic information. In this project, RNA-Seq was performed on the needle transcriptome of four loblolly pine (Pinus taeda) individuals. The data was then assembled using Velvet and Oases de novo assemblers. The assembled transcripts were then analyzed using a combination of BLAST and Gene Ontology. The data from RNA-Seq was assembled using two different sets of parameters, and the results of these runs were compared. Sequencing the transcriptome is often the first step in a large enome-sequencing project. The results gained here will improve the overall understanding of the diversity of genes within the transcriptome as well as provide a foundation for assembling the much larger genome. 

Movement of dissolved reactive phosphorous from soils to bodies of water in relation to eutrophication

Student Name: 
Kristen Chinn
UCD Mentor: 
Emily Carlson

Dissolved reactive phosphorous (DRP), or soluble reactive phosphorous (SRP), is a nutrient that can flow from agricultural land to bodies of water, causing eutrophication, which poses a threat to the health and efficiency of waterways. In order to prevent eutrophication from harming bodies of water, it is crucial to understand the movement of these nutrients, which was the main objective of this research.

Levels of DRP/SRP were analyzed by studying the sorption and desorption capacities of soils from different areas using the Bridgham et al (2001) method. This study found that sorption and desorption capacities varied between soil samples taken at different locations, indicating the level of effectiveness of different areas at retaining high amounts of phosphorous while releasing very low levels.

The information from this study can be used to evaluate potential areas for restoration based on the soil’s sorption and desorption abilities. In restoring wetland buffers, it is possible to benefit the environment by protecting water quality, using agricultural land more efficiently, managing waterways, and reducing or preventing eutrophication.