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AUA DNA
BARCODING
PROJECT
Nicole Gousy, Vithura Kunarathnam, Nick
Pargoff, and Adam Willey
What is DNA Barcoding?
● DNA barcodes allow non-experts to objectively identify different species
regardless of what the specimen has been exposed to or where it came
from
● A species’ DNA is uniquely different to them
● DNA barcoding turns DNA into an easily translatable, unique pattern of
bars, such as seen in a consumer product’s universal product code (UPC)
Goals
● DNA Barcoding has never been performed on the flora living
on the island of Antigua
● This project hopes to initiate conservation efforts for this
island, as well as surrounding Caribbean islands
● To be able to connect Antiguan flora to Barcoding projects
around the globe
Acquiring the Data
● Location: Lookout Trail, Galleon Beach
Plant-crushing method (aka DNA
extraction and PCR)
1. Get
plant
2. Extract
DNA
3. Run a gel
electrophoresis
4. Sequence
DNA
5. Upload DNA sequences
to DNA subway and Blast
websites
Data analysis and input
● Upload DNA into DNA subway, a DNA
sequence annotator and analysis
website
● Upload the resulting sequence to Bold-
Systems SPD website, an integrated
workbench supporting the assembly,
analysis and publication of DNA
barcode data by students.
● Enter Barcode data into BLAST website
to identify regions of similarity between
documented sequences and the
unknown sequence and calculates the
statistical significance
Findings
● Several of our collected samples produced a positive
identification of known species when entered into the
BLAST nucleotide analysis software
● When positive identifications came up, the unknown
species was identified, documented and further
researched
Cool plant Specimen
Jasminum fluminense (Vell.)
“Common Jasmine”
medicinal plant used by Shangaan
people in villages under Jongilanga tribal
council, South Africa as a STI medication
[7]
Talinum paniculatum (Jacq.
Gaertn.) “Fameflower"
a source of pharmaceutical efficacy
similar to ginseng, and a widely
distributed and planted edible
vegetable [1, 5]
Rivina humilis L.
“Bloodberry”
the berries are safe to consume,
rich in nutrient content and exhibit
efficient biological activity [4]
Conclusions
● Several of the species we collected were
able to be sequenced, identified and
recorded in the Barcode Database
● The efforts of this research will lead to
further evaluation of the floral species
present on the island
● In addition to further experimentation,
island conservation efforts will increase
due to increased knowledge on what
species of plants live on the island
If we were to repeat this experiment
● We would want to ensure we received
enough of the plant sample to ensure a
successful DNA extraction
● We would want to repeat the PCR process
and electrophoresis process to ensure the
best DNA samples of each species get sent
for analyzation
● We would want to further analyze the
surveyed location for increased awareness
of what potentially could be found
Vachellia farnesiana
Thank you!
We would also like to extend a sincere “thank you” to
Dr. Joseph Cross and Dr. Karen James for their
mentorship and guidance in the lab and for suffering
up and down the trails looking for plants with us
References
1. Ramos, M. P. O. et al., (2010), Antinociceptive and edematogenic activity and chemical constituents of Talinum paniculatum
Wild, Journal of Chemical and Pharmaceutical Research, 2(6), 265-274
2. Biosecurity Queensland Government Weeds of Australia. “Weeds of Australia - Biosecurity Queensland Edition Fact Sheet.”
Tradescantia Zebrina, keyserver.lucidcentral.org/weeds/data/media/Html/rivina_humilis.htm.
3. Center for Invasive Species and Ecosystem Health. “Brazilian Jasmine (Jasminum Fluminense ).” Multiflora Rose, Rosa
Multiflora Rosales: Rosaceae, 23 Mar. 2009, www.invasive.org/browse/detail.cfm?imgnum=5392237.
4. Khan, Mohammad Imtiyaj, et al. “Betalains Rich Rivina Humilis L. Berry Extract as Natural Colorant in Product (Fruit Spread
and RTS Beverage) Development.” Journal of Food Science and Technology, vol. 52, no. 3, 2013, pp. 1808–1813.,
doi:10.1007/s13197-013-1175-8.
5. Liu, Xia, et al. “Chloroplast Genome of the Folk Medicine and Vegetable Plant Talinum Paniculatum (Jacq.) Gaertn.: Gene
Organization, Comparative and Phylogenetic Analysis.” Molecules, vol. 23, no. 4, 2018, p. 857.,
doi:10.3390/molecules23040857.
6. Manager. “Talinum Paniculatum (Jacq.) Gaertn.” Nature, www.asia-medicinalplants.info/talinum-paniculatum-jacq-gaertn/.
7. Tshikalange, Thilivhali Emmanuel, et al. “An Ethnobotanical Study Of Medicinal Plants Used In Villages Under Jongilanga
Tribal Council, Mpumalanga, South Africa.” African Journal of Traditional, Complementary and Alternative Medicines, vol. 13,
no. 6, 2016, pp. 83–89., doi:10.21010/ajtcam.v13i6.13.
8. WoFP. “Vachellia Farnesiana (Mimosa Bush).” World of Flowering Plants, World of Flowering Plants, 27 Oct. 2018,
worldoffloweringplants.com/vachellia-farnesiana-mimosa-bush-needle-bush/.
9. Zicha, Ondrej. “BioLib: Biological Library.” Gerbillus Campestris (North African Gerbil) | BioLib.cz,
www.biolib.cz/en/taxon/id199881/.

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Group 2 AUA DNA barcoding project

  • 1. AUA DNA BARCODING PROJECT Nicole Gousy, Vithura Kunarathnam, Nick Pargoff, and Adam Willey
  • 2. What is DNA Barcoding? ● DNA barcodes allow non-experts to objectively identify different species regardless of what the specimen has been exposed to or where it came from ● A species’ DNA is uniquely different to them ● DNA barcoding turns DNA into an easily translatable, unique pattern of bars, such as seen in a consumer product’s universal product code (UPC)
  • 3. Goals ● DNA Barcoding has never been performed on the flora living on the island of Antigua ● This project hopes to initiate conservation efforts for this island, as well as surrounding Caribbean islands ● To be able to connect Antiguan flora to Barcoding projects around the globe
  • 4. Acquiring the Data ● Location: Lookout Trail, Galleon Beach
  • 5. Plant-crushing method (aka DNA extraction and PCR) 1. Get plant 2. Extract DNA 3. Run a gel electrophoresis 4. Sequence DNA 5. Upload DNA sequences to DNA subway and Blast websites
  • 6. Data analysis and input ● Upload DNA into DNA subway, a DNA sequence annotator and analysis website ● Upload the resulting sequence to Bold- Systems SPD website, an integrated workbench supporting the assembly, analysis and publication of DNA barcode data by students. ● Enter Barcode data into BLAST website to identify regions of similarity between documented sequences and the unknown sequence and calculates the statistical significance
  • 7. Findings ● Several of our collected samples produced a positive identification of known species when entered into the BLAST nucleotide analysis software ● When positive identifications came up, the unknown species was identified, documented and further researched
  • 8. Cool plant Specimen Jasminum fluminense (Vell.) “Common Jasmine” medicinal plant used by Shangaan people in villages under Jongilanga tribal council, South Africa as a STI medication [7] Talinum paniculatum (Jacq. Gaertn.) “Fameflower" a source of pharmaceutical efficacy similar to ginseng, and a widely distributed and planted edible vegetable [1, 5] Rivina humilis L. “Bloodberry” the berries are safe to consume, rich in nutrient content and exhibit efficient biological activity [4]
  • 9. Conclusions ● Several of the species we collected were able to be sequenced, identified and recorded in the Barcode Database ● The efforts of this research will lead to further evaluation of the floral species present on the island ● In addition to further experimentation, island conservation efforts will increase due to increased knowledge on what species of plants live on the island
  • 10. If we were to repeat this experiment ● We would want to ensure we received enough of the plant sample to ensure a successful DNA extraction ● We would want to repeat the PCR process and electrophoresis process to ensure the best DNA samples of each species get sent for analyzation ● We would want to further analyze the surveyed location for increased awareness of what potentially could be found Vachellia farnesiana
  • 11. Thank you! We would also like to extend a sincere “thank you” to Dr. Joseph Cross and Dr. Karen James for their mentorship and guidance in the lab and for suffering up and down the trails looking for plants with us
  • 12. References 1. Ramos, M. P. O. et al., (2010), Antinociceptive and edematogenic activity and chemical constituents of Talinum paniculatum Wild, Journal of Chemical and Pharmaceutical Research, 2(6), 265-274 2. Biosecurity Queensland Government Weeds of Australia. “Weeds of Australia - Biosecurity Queensland Edition Fact Sheet.” Tradescantia Zebrina, keyserver.lucidcentral.org/weeds/data/media/Html/rivina_humilis.htm. 3. Center for Invasive Species and Ecosystem Health. “Brazilian Jasmine (Jasminum Fluminense ).” Multiflora Rose, Rosa Multiflora Rosales: Rosaceae, 23 Mar. 2009, www.invasive.org/browse/detail.cfm?imgnum=5392237. 4. Khan, Mohammad Imtiyaj, et al. “Betalains Rich Rivina Humilis L. Berry Extract as Natural Colorant in Product (Fruit Spread and RTS Beverage) Development.” Journal of Food Science and Technology, vol. 52, no. 3, 2013, pp. 1808–1813., doi:10.1007/s13197-013-1175-8. 5. Liu, Xia, et al. “Chloroplast Genome of the Folk Medicine and Vegetable Plant Talinum Paniculatum (Jacq.) Gaertn.: Gene Organization, Comparative and Phylogenetic Analysis.” Molecules, vol. 23, no. 4, 2018, p. 857., doi:10.3390/molecules23040857. 6. Manager. “Talinum Paniculatum (Jacq.) Gaertn.” Nature, www.asia-medicinalplants.info/talinum-paniculatum-jacq-gaertn/. 7. Tshikalange, Thilivhali Emmanuel, et al. “An Ethnobotanical Study Of Medicinal Plants Used In Villages Under Jongilanga Tribal Council, Mpumalanga, South Africa.” African Journal of Traditional, Complementary and Alternative Medicines, vol. 13, no. 6, 2016, pp. 83–89., doi:10.21010/ajtcam.v13i6.13. 8. WoFP. “Vachellia Farnesiana (Mimosa Bush).” World of Flowering Plants, World of Flowering Plants, 27 Oct. 2018, worldoffloweringplants.com/vachellia-farnesiana-mimosa-bush-needle-bush/. 9. Zicha, Ondrej. “BioLib: Biological Library.” Gerbillus Campestris (North African Gerbil) | BioLib.cz, www.biolib.cz/en/taxon/id199881/.