Date of Award
Honors College Thesis
Timothy McLean, Ph.D.
Karenia brevis is a species of dinoflagellates that is responsible for “red tides” (more formally known as harmful algal blooms) found in the Gulf of Mexico. The blooms have adverse effects on humans and marine animals. Karenia brevis produces toxins that, in humans, can cause upper and lower respiratory problems as well as nausea and vomiting. For marine mammals, birds, fish, and other marine organisms, exposure to brevetoxins can result in morbidity and even death.
Even with the technology and resources we have today, scientist do not fully understand the mechanisms behind toxin production and bloom initiation. Because cellular processes may play a major role in Karenia brevis blooms, attempts have been made to understand K. brevis at the molecular level, but studies are still ongoing due to lack of understanding gene organization and expression. Thus, our goal was to help guide the reconstruction or sequencing of the genome. The purpose of my research was to find if there are multiple copies of certain gene sequences, and what variability exists between and within the genes. I attempted determine the copy number of a suspected multi-copy gene and if any sequence variability existed within the gene and the intergenic regions. Focus was placed on the gene for proliferating cell nuclear antigen (PCNA) whose known function is to aid in DNA replication and repair, because the PCNA is present in multiple copies and (Zhang et al. 2006) and the EST collection of K. brevis contained several PCNA single nucleotide polymorphisms (Lidie et al, 2005; McLean, unpublished data).
Techniques involved were DNA extraction, PCR (polymerase chain reaction) primer design, PCR amplification of genic and intergenic regions of the chromosomes, and PCR purification and ligation. Research stopped at this point due to time constraints. Southern blotting (to quantify the number of copies) was to be performed and then the PCRs products sent to another lab to be sequenced. Simple bioinformatic gene sequence analysis would have determine if there were base changes that could result in changes in amino acids. Intergenic sequence analysis would have determined if each copy of a gene was capable of being expressed or regulated. Results of further research could advance understanding of the genetics of K. brevis and dinoflagellates in general. Additionally, results could shape further predictions on mutation rates and variability in the dinoflagellate genome.
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Gregg, Colleen A., "Intergenic Regions and Repeating Gene Sequences in the Dinoflagellate Karenia brevis" (2013). Honors Theses. 163.