Waksman Student Scholars Program Poster

1. RESEARCH POSTER PRESENTATION DESIGN © 2012
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The purpose of this experiment was to analyze the DNA sequence of the duckweed plant Landoltia
punctata and compare these sequences to those found in other plants. In order to find a coding for a
protein, one must inoculate and amplify the bacteria samples with duckweed DNA using Polymerase
Chain Reaction (PCR) and finding good inserts. Then, they would do a plasmid miniprep to get rid of
bacterial DNA and use Restriction Digest (RDG) to prepare DNA for analysis. Finally, the DNA would
get sequenced and analyzed for the coding of a protein. Using the National Center for Biotechnology
Information (NCBI), it determined the coding of the protein Mitogen-Activated Protein Kinase (MAPK)
from my sample 65WK2.14. MAPK’s function is to regulate cellular responses to a diverse array of
stimuli, resulting in cell functions such as proliferation, gene expression, differentiation, mitosis,
cell survival, and apoptosis in an organism. This protein contains multiple conserved domains such as
PKc_like superfamily, Pkinase, and PLN00009 with the three dimensional structure of this protein has
8 alpha helices and 11 antiparallel beta-strands. The three dimensional structure of a protein that is
similar, “Chain B, Crystal Structure of the Human Cdkl1 Kinase Domain”, found in humans, Homo
sapiens. Therefore, it can be concluded that this indicates this protein provides an evolutionary
advantage to organisms and it can be found in different kingdoms.
ABSTRACT'
The different species of duckweed were selected to be decoded was for growth ability and the wide
ranges of uses. Duckweed is considered an ideal plant because it grows on water, tolerates various
nutrient levels, high growth rate, grows year round, and easy to harvest. Its flexibility makes this
plant become one of the most efficient and cheapest plants to farm compared to corn, wheat, or
potatoes. These studies in duckweed led to the creation of a duckweed cropping system. The
applications of duckweed are also beneficial to humans and also to the environment. In an
experiment in North Carolina, USA, scientist successfully used duckweed to treat the swine
wastewater. This has been studied as a greener alternative for farmers than to use spray-field
irrigation, which has caused serious environmental concerns for nutrient contamination and
greenhouse gas emissions. Another application is that using duckweed to feed animals, poultry, and
fish. Duckweed has shown to be an alternative efficient starch source for fuel ethanol production.
       I hope that these experiments will encourage other scientists to find new environmental and agricultural uses of this plant to expand the field of duckweed so we would get a healthier, greener
environment.
METHODS'
ANALYSIS'
CONCLUSION' The protein that was sequenced determined to be Mitogen-Activated Protein Kinase (MAPK). It was
84% identical to the “mitogen-activated protein kinase 9-like isoform X2” in Date Palms (Phoenix
dactylifera). MAPK’s function is to regulate cellular responses to a diverse array of stimuli, leading to
cell functions including proliferation, gene expression, differentiation, mitosis, cell survival, and
apoptosis in an organism. In other words, it makes cells react to stress from their environment.
This protein contains multiple conserved domains such as PKc_like superfamily, Pkinase, and PLN00009. These domains cover protein kinases. There is a three dimensional structure of a protein
that is similar to, “Chain B, Crystal Structure of the Human Cdkl1 Kinase Domain”, found in humans
(Homo sapiens). This indicates this protein provides an evolutionary advantage to organisms of
different kingdoms. The three dimensional structure of this protein has 8 alpha helices and 11
antiparallel beta-strands.
Based on this information that my BLAST analysis results indicate my sequences does not match organisms from different kingdoms yet my protein has a similar structure to humans, I would
experiment further on comparing the variations of the sequence for protein kinase in organisms of
different kingdoms to my protein. An example would be comparing duckweed to birds and bacteria.
REFERENCES'Cheng, Jay J., and Anne M. Stomp. Growing Duckweed to Recover Nutrients from Wastewater and
for Production of Fuel Ethanol and Animal Feed. Publication. N.p.: n.p., n.d. Print.
"National Center for Biotechnology Information." National Center for Biotechnology Information. U.S. National Library of Medicine, n.d. Web. 09 Jan. 2015.
"Rutgers University." Rutgers University. N.p., n.d. Web. 12 Jan. 2015.
"Waksman Student Scholars Program." Waksman Student Scholars Program. N.p., n.d. Web. 12 Jan. 2015.
Wikipedia. Wikimedia Foundation, n.d. Web. 10 Jan. 2015.
ACKNOWLEDGMENTS'AND'CONTACTS'
I owe many thanks to my teacher at Dougherty Valley High School, Ms. Katherine Huang, for her
support and guidance throughout the experiment in the school year. I would also thank to Manik
Khurana and Nick Coppola as part of my lab members. I am grateful for Rutgers University for giving
me the opportunity to conduct this research.
Wesley&Kwong,&Ms.&Katherine&Huang,&Dougherty&Valley&High&School&RUTGARS&UNIVERSITY,&LAWRENCE&LIVERMORE&NATIONAL&LABS&MitogenGAcHvated&Protein&Kinase&(MAPK)&
BACKGROUND'AND'INTRODUCTION'
1. Innoculate bacteria samples
2. Amplify Duckweed DNA insert with PCR
3. Run Agarose Gel with PCR samples to find inserts of good size
4. Plasmid Miniprep (Get rid of bacterial DNA)
5. Use restriction digest on plasmid to prepare DNA for analysis
6. Run Agarose Gel for restriction digest to find insert size
7. Sequence DNA
8. Edit DNA sequence and analyze DNA for coding of a protein
9. Submit sequence for publishing
RESULTS'
PCR Results: The Polymerase Chain Reaction is used to amplify the cDNA insert in the bacteria. The
DNA which had duckweed and bacterial DNA was determined to be 350 base pairs in the second
solution (65WK2.14) using the Agarose Gel. The first sample, 65WK1.14, did not have any DNA. This
was because I didn’t insert the solution into the gel deep enough, resulting in no DNA.
RDG Results: After getting rid of the bacterial DNA, the pure duckweed DNA was determined to be
300 base pairs using the Agarose Gel in the second solution. Since there was no DNA in the PCR for
the first solution, there was no DNA here.
The PCR (left) results was that the DNA sequence size was 350 bp and the RDG (right) was 300 bp.
The M stands for the ladder. It is used to determine the size.
BLASTn: This analysis compares the nucleotide query sequence against the National Center for
Biotechnology Infomation (NCBI) nucleotide sequence database. The result was that the edited
sequence was significantly similar to sequences found in any other organism but not found in
different kingdoms.
BLASTx: This analysis compares the nucleotide query sequence translated in all three reading frames against
the NCBI protein sequence database. The result was similar to the BLASTn: there were significantly similar sequences but they were only in a single kingdom.
ORF Analysis: This analysis changes the nucleotide query sequence into the protein sequence database. Based on the results of BLASTx, it was determined that the sequence started on A126 to
C920 on Frame 3.
BLASTx vs. BLASTp: By comparing the two different analysis, there are two proteins found in both database with similar E-values. However, the alignments of the BLASTx and BLASTp were different.
This is the 3-D structure of Mitogen-activated protein kinase (MAPK). The picture on the left is the
backbone of the protein. The picture on the right displays the alpha helices and beta-strands.