Travel Report: Heather Coatsworth, Biological Sciences, Colombia
From October to mid December 2014, I conducted research for my Master’s thesis at CIDEIM (Centro Internacional de Entrenamiento e Investigaciones Medicas) in Cali, Colombia. While at CIDEIM I hoped to learn both laboratory and field skills from the Vector Biology and Control team, who work with a variety of insects responsible for carrying disease agents. I also hoped to share my acquired knowledge in the field of Bioinformatics, including sequence mapping and alignment, differential expression analyses, clustering and pathway expression.
Specifically my research was aimed at using a combination of bioinformatic and molecular biology techniques to investigate and characterize genes associated with the refractory and susceptible phenotypes of Colombian strains of Aedes aegypti, the mosquito primarily responsible for the spread of dengue and yellow fever. My specific objectives for my training and research at CIDEIM were:
i. Begin to develop an understanding of the roles select genes play in phenotypic expression via RNA interference (RNAi) gene knockdown (KD) procedures via:
- Creation of double stranded RNA (dsRNA)
- Intrathoracic injection of dsRNA into susceptible or refractory mosquitoes
- Exposure of the KD insects to infection with dengue virus serotype 2 (DENv-2)
- Mosquito dissection for gene expression studies
- Analysis of phenotype
ii. Extend field research skills through the study of the feral refractory Aedes aegypti mosquito populations currently existent in Cali, Colombia and surrounding areas via:
- Mosquito specific insect collection techniques
- Maintenance of mosquito laboratory populations
- Ecological mosquito tracking and recording techniques
iii. Share acquired bioinformatics knowledge with the Vector Biology group and all other members of CIDEIM through seminars on Bioinformatic analyses of RNA seq data, focusing on:
- Outlining current common practices, procedures and guidelines
- Providing a step by step guide to analyzing large quantities of sequencing data
- Obtaining and demonstrating how to properly use and apply bioinformatics related software
- Suggesting possible statistical and graphical down-stream analyses tools
Through the two month duration of my stay I was able to complete most of these objectives; however, due to unforeseen problems with the mosquito colonies at CIDEIM, I was unable to complete my own KD experiments, although I was able to participate in other students KD experiments. I was also unable to field collect mosquitoes myself, although I was walked through common field collection areas and techniques. Despite some setbacks, the unique positon of the mosquito colonies allowed me to accomplish an experiment investigating possible physiological refractory barriers which I had not initially set out to complete, as well as aid other labs in their analysis of a variety of sequence and genome data.
I substantially increased my laboratory skills surrounding mosquito rearing, and maintenance, including: artificially blood feeding mosquitoes, mixing cell growth medium, growing C6/36 cells, infecting C6/36 cells with dengue virus, infecting mosquitoes with dengue virus, titrating viral levels, preparing and reading immunofluorescence assays, vector competence tests, intrathoracic injections, generational selection protocols as well as dissecting out mosquito midguts and salivary glands. In addition to these mosquito specific techniques, I also carried out a wide variety of molecular biology procedures such as RNA and DNA extraction, cDNA synthesis, dsRNA synthesis, PCR, and qPCR.
I know that the laboratory and presentation skills as well as my research results obtained from Colombia will further my studies here at Simon Fraser. They will enable me to carry out more intricate and detailed tasks in a more independent and time efficient manner, as well as providing me with a network of support both locally and now, internationally.
Although I learned a great deal from my research at CIDEIM, I also experienced an immeasurable amount of personal gain from the Colombian culture, people, nature and overall life mentality, and I am extremely grateful to CIDEIM, SFU and Dr. Carl Lowenberger for giving me this wonderful opportunity.
Tags: Student Voices