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AUA DNA BARCODING
PROJECT: SPRING 2022
Faraaz Khan
Mansi Khariwal
Amisha Nimawat
Netra Patel
Priyanka Priyadarshini
WHAT IS DNA
BARCODING?
Species diversity across the world is limitless, with discoveries
occurring in perpetuity. The world is not traversable by a handful of
individuals belonging to the relevant disciplines, so a more
collaborative approach—involving students, professionals, and other
eager individuals—has been initiated to classify and gather in a
database the variety of creation the world has to offer. “Classifying
and gathering” is achieved by DNA Barcoding.
20XX 2
LEARNING OBJECTIVES
LO. 1 Collect 10 samples of different species within 1 m^2
area at Walling Nature Reserve and to identify the species
based on their phenotype and label them accordingly.
LO.2 To process the plant sample using biochemical
methods like PCR to extract plant DNA
LO.3 To perform the Gel electrophoresis and record the
DNA sequence using bioinformatics
LO.4 To compare the data with previous studies and to
observe the effect of external factors like climate change on
Antigua’s biodiversity and to preserve the same
3
COLLECTION
Obtain distinctly different
specimens from one precise
location within Wallings Nature
Reserve in Antigua
SEQUENCING
Send amplified samples to
GeneWIz (from Azenta Life
Sciences) for appropriate gene
sequencing
PREPARATION
Prepare the obtained samples, via
lysing and “grinding”, to precipitate
and carefully extract DNA for further
analysis
BIOINFORMATICS
Using platforms DNA Subway and
BOLD, contribute sequenced specimens
to an integrated, worldwide repository
available worldwide
PROCESSING & ANALYSIS
After storage, the samples were
amplified through PCR using
appropriate primers and the results
were visualized via gel
electrophoresis
ARGS2022 4
WALLINGS NATURE RESERVE
ARGS2022 5
• Rugged trails outline a diverse Antiguan rainforest
• Possesses vast unique—yet familiar—flora/fauna
• Ripe for analysis of variety of speciation
Preparation and procedures done
after the sample collection
6
DNA extraction, PCR, analysing the PCR products on
Gel electrophoresis
7
SEQUENCING
SPECIES
GATHERED
CHIONANTHUS COMPACTUS
known also as “Fringetrees”
LOCATION
Native to the Caribbean,
Colombia, Venezuela
GENUS
• Consists of 150+ species
• Present as shrubs as well as
medium-sized trees ranging
from 3-25m
• Bark used to make tea
consumed to reduce fever
and relieve dyspepsia,
among other medicinal uses
A1-ARGS2022 PITCH DECK 9
SCUTIA MYRTINA
COMMONLY KNOWN AS “CAT THORN”
Distribution includes almost all of Africa, as
well as parts of Asia (i.e. India)
FEATURES
• ​Fragrant, small, white flowers
from October to January
• Edible fruits that attract birds
ADDITIONAL PROPERTIES
• Bark of tree used to treat fever
• Infusion of plant is used to treat
malaria
A3-ARGS2022 10
OLYRA LATIFOLIA
commonly known AS
“CARRYCILLO”
Found in the Americas – Range includes
the West Indies, Mexico and Central and
South America—as well as sub-Saharan
Africa
FEATURES
• Grows up to 5m tall
• Leaves are found as
ovate or oblong in shape
• a species of bamboo
PURPOSE
• Stems used as drinking straws
• Bobbins for “spinning”
A5-ARGS2022 © BY ALEX POPOVKIN, BAHIA, BRAZIL - OLYRA LATIFOLIA L., CC BY 2.0,
HTTPS://COMMONS.WIKIMEDIA.ORG/W/INDEX.PHP?CURID=34686716
11
QUADRELLA AUGUSTIFOLIA
LOCATION
FEATURES
UTILITY
Restricted to North America, Central
America, South America, & West Indies
• ​stellate to lepidote peltate indumenta
• flowers with valvate calyces and dehiscent
fruits bearing green and white embryos
• limited medicinal or environmental
properties
A7-ARGS2022 12
RANDIA TRUNCATA
LOCATION
• Primarily Yucatan Peninsula of Mexico
• Terrestrial habitat
FEATURES
• Pollen in permanent tetrads, diecious flowers,
clustered leaves and stipules
• Fruits have discoid seed embedded in sweet pulp
that turns dark when dried
ARGS2022 13
PHYLOGENY TREE
20XX 14
SOURCES OF ERROR
- Collect more samples
- Try to avoid sample contamination by proper preservation
techniques
- Avoiding experimental and instrumental errors
15
PLANS FOR THE FUTURE
- Involving more people in the project
- Choosing a bigger sample area
- Collecting more samples
- Collecting species from variable eco-systems
16
CONCLUSION
ARGS2022
Wallings Nature Reserve provides perhaps the most
varied sampling of all the species that have made Antigua
home. Rapidly accelerating climate change dares to
threaten the vast—and possibly untapped—diversity the
rainforest boasts. Strong efforts need to be initiated and
maintained to ensure that future utility of the Reserve’s
holdings remain even a possibility.
17
THANK YOU
ARGS2022 PITCH DECK 18
REFERENCES
ARGS2022 19
https://sernecportal.org/portal/taxa/index.php?taxon=192511
https://powo.science.kew.org/taxon/urn:lsid:ipni.org:names:316519-2
https://www.tropicos.org/name/100362718
https://dnasubway.cyverse.org/
http://v3.boldsystems.org/index.php/Login/page?destination=SDP_Management_StudentsConsole
https://www.ncbi.nlm.nih.gov/nuccore/?term

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A. AUA DNA Barcoding Project - AUA Research Group - Spring 2022.pptx

  • 1. AUA DNA BARCODING PROJECT: SPRING 2022 Faraaz Khan Mansi Khariwal Amisha Nimawat Netra Patel Priyanka Priyadarshini
  • 2. WHAT IS DNA BARCODING? Species diversity across the world is limitless, with discoveries occurring in perpetuity. The world is not traversable by a handful of individuals belonging to the relevant disciplines, so a more collaborative approach—involving students, professionals, and other eager individuals—has been initiated to classify and gather in a database the variety of creation the world has to offer. “Classifying and gathering” is achieved by DNA Barcoding. 20XX 2
  • 3. LEARNING OBJECTIVES LO. 1 Collect 10 samples of different species within 1 m^2 area at Walling Nature Reserve and to identify the species based on their phenotype and label them accordingly. LO.2 To process the plant sample using biochemical methods like PCR to extract plant DNA LO.3 To perform the Gel electrophoresis and record the DNA sequence using bioinformatics LO.4 To compare the data with previous studies and to observe the effect of external factors like climate change on Antigua’s biodiversity and to preserve the same 3
  • 4. COLLECTION Obtain distinctly different specimens from one precise location within Wallings Nature Reserve in Antigua SEQUENCING Send amplified samples to GeneWIz (from Azenta Life Sciences) for appropriate gene sequencing PREPARATION Prepare the obtained samples, via lysing and “grinding”, to precipitate and carefully extract DNA for further analysis BIOINFORMATICS Using platforms DNA Subway and BOLD, contribute sequenced specimens to an integrated, worldwide repository available worldwide PROCESSING & ANALYSIS After storage, the samples were amplified through PCR using appropriate primers and the results were visualized via gel electrophoresis ARGS2022 4
  • 5. WALLINGS NATURE RESERVE ARGS2022 5 • Rugged trails outline a diverse Antiguan rainforest • Possesses vast unique—yet familiar—flora/fauna • Ripe for analysis of variety of speciation
  • 6. Preparation and procedures done after the sample collection 6 DNA extraction, PCR, analysing the PCR products on Gel electrophoresis
  • 9. CHIONANTHUS COMPACTUS known also as “Fringetrees” LOCATION Native to the Caribbean, Colombia, Venezuela GENUS • Consists of 150+ species • Present as shrubs as well as medium-sized trees ranging from 3-25m • Bark used to make tea consumed to reduce fever and relieve dyspepsia, among other medicinal uses A1-ARGS2022 PITCH DECK 9
  • 10. SCUTIA MYRTINA COMMONLY KNOWN AS “CAT THORN” Distribution includes almost all of Africa, as well as parts of Asia (i.e. India) FEATURES • ​Fragrant, small, white flowers from October to January • Edible fruits that attract birds ADDITIONAL PROPERTIES • Bark of tree used to treat fever • Infusion of plant is used to treat malaria A3-ARGS2022 10
  • 11. OLYRA LATIFOLIA commonly known AS “CARRYCILLO” Found in the Americas – Range includes the West Indies, Mexico and Central and South America—as well as sub-Saharan Africa FEATURES • Grows up to 5m tall • Leaves are found as ovate or oblong in shape • a species of bamboo PURPOSE • Stems used as drinking straws • Bobbins for “spinning” A5-ARGS2022 © BY ALEX POPOVKIN, BAHIA, BRAZIL - OLYRA LATIFOLIA L., CC BY 2.0, HTTPS://COMMONS.WIKIMEDIA.ORG/W/INDEX.PHP?CURID=34686716 11
  • 12. QUADRELLA AUGUSTIFOLIA LOCATION FEATURES UTILITY Restricted to North America, Central America, South America, & West Indies • ​stellate to lepidote peltate indumenta • flowers with valvate calyces and dehiscent fruits bearing green and white embryos • limited medicinal or environmental properties A7-ARGS2022 12
  • 13. RANDIA TRUNCATA LOCATION • Primarily Yucatan Peninsula of Mexico • Terrestrial habitat FEATURES • Pollen in permanent tetrads, diecious flowers, clustered leaves and stipules • Fruits have discoid seed embedded in sweet pulp that turns dark when dried ARGS2022 13
  • 15. SOURCES OF ERROR - Collect more samples - Try to avoid sample contamination by proper preservation techniques - Avoiding experimental and instrumental errors 15
  • 16. PLANS FOR THE FUTURE - Involving more people in the project - Choosing a bigger sample area - Collecting more samples - Collecting species from variable eco-systems 16
  • 17. CONCLUSION ARGS2022 Wallings Nature Reserve provides perhaps the most varied sampling of all the species that have made Antigua home. Rapidly accelerating climate change dares to threaten the vast—and possibly untapped—diversity the rainforest boasts. Strong efforts need to be initiated and maintained to ensure that future utility of the Reserve’s holdings remain even a possibility. 17