Discipline: Computer Sciences and Information Management
Subcategory: Computer Science & Information Systems
Kaayla Tippins - Jarvis Christian College
Co-Author(s): Nyosha Moore, University of Arkansas at Pine Bluff, Pine Bluff, AR ; Abigail S. Newsome, Ph.D., Mississippi Valley State University, Itta Bena, MS
Can the utilization of the Polymerase Chain Reaction and DNA Barcoding method identify unknown fish species?
Food fraud from species substitution is an emerging risk given the increasingly global food supply chain and potential food safety issues. Economic food fraud is committed when food is deliberately placed on the market, for financial gain, with the intention of deceiving the consumer. DNA barcoding has received substantial attention as an accurate and comprehensively applicable device for animal species identifications.
The names of each fish used in the experiment were unrevealed to researchers prior to the time of starting experiments; the objective is to use the DNA barcoding technique to confirm the type of fish species identified. Fish tissue samples were collected from 2 different fish specimen, Fish #5 and Fish #Gar. DNA was extracted from each fish tissue using a standard DNA protocol. Once DNA was extracted, amplification of COI genes was performed through the process of polymerase chain reaction at 94°C for both 2 minutes then 30 seconds, 55°C 2 minutes, 72°C 1 minute and repeated 35 times before machine was cooled at 72°C for 10 minutes and stored at 4°C in a thermal cycler. After the COI gene was amplified from each tissue sample, the resultant PCR products were analyzed using electrophoresis and stained with ethidium bromide to allow the results to be seen using UV light. The resultant PCR samples were sent to be sequenced using a Dye Terminator Cycle Sequencer. Using the Barcode of Life Database (BOLD), the sequence results were used to form contigs and a barcode for each fish sample, #5 fish and #GAR. After retrieving the results from being sequenced, the COI gene of each sample was determined to be 652bp and 652bp, Fish #5 and Fish #Gar respectively. Sequence results of the samples, 1SEQ_ASN and 2SEQ_ASN, were considered to be high quality and sufficient to analyze using the BOLD-SDP Database. Results indicated that 1SEQ_ASN (#5 fish) was a Bighead Carp (Hypophthalmichthys nobilis). After analyzing 2SEQ_ASN (#Gar fish), it was determined that this fish was a Gar (Lepisosteus platostomus).
Funder Acknowledgement(s): Nyosha Moore, University of Arkansas at Pine Bluff, Pine Bluff, AR ; Abigail S. Newsome, Ph.D., Director of Bioinformatics, Mississippi Valley State University, Itta Bena, MS
Faculty Advisor: Abigail S. Newsome, Ph.D., Director of Bioinformatics, Mississippi Valley State University, Itta Bena, MS, firstname.lastname@example.org
Role: Prior to this experiment, each fish was unknown and given to conduct experiments for identification. Within this experiment, I preformed DNA extraction, polymerase chain reaction using thermal cycler, gel electrophoresis, and used the Barcode of Life Database (BOLD) sequenced results to form contigs and a barcode to identify. After each researcher completed the identification process on BOLD, each fish and taxonomic levels were confirmed by the mentor for correct naming of each fish.