Molecular Project Final Lab Report

I attached the rubrics and also provided all the necessary documents to write the complete report. I also attached my draft report, I left some notes on the draft if there are any necessary changes and additional parts that I missed out (there are some feedbacks from the professor as well). Only need help on (Introduction, purpose, hypothesis, methods, results, discussion, and conclusion) = that’s about 4 pages addition to my draft, I will finish the images for the result since it’s a bit hard to explain.Thank you so much

Draft
reportpage
Nguyen 2
*Introduction
Methods
①
Extracting DNA from Sample 6
Instant
grits
+
company
+
brand
t
store
DNA extraction process from an unknown sample involves several steps to attain the result. I
began the experiment by wiping and disinfecting the working station with disinfectant
wipe/spray. Wearing gloves is crucial in any lab setting to avoid hazard, chemicals, toxicity and
contamination. Lab materials were placed on a clean paper towel to eliminate potential
estimate
in
volume
instead t f gu estimate amount of
contamination. First, I measured about 0.3 grams of (sample) in a weighing boat and transferred
into a collecting tube. I grinded the samples in the collecting tube using a sterile pestle (it works
almost like a mortar and pestle). During the process, the amount of sand was added to the sample
tube depending on the complexity of the given sample, and continuously grinded until a fine
texture. About 250 µl of sterilized grade water was also transferred into the sample tube mixture
using a small pipette to further the grinding process and to maintain it until the mixture seems
slurry. After several minutes of continuously grinding the mixture until a fine texture, the
product was set on the rack and sat for few minutes until the contents settles at the bottom of the
macro liters
tube. After few minutes, I transferred 300mm
Oof the content into Instagene matrix tube. The
matrix is made of this tiny beads that can remove compounds that destroys or interfere DNA
amplification. The tiny beads lie at the bottom of the tube, lightly tab the bottom of the tube to
help make sure my matrix is well mixed with the extract. I lightly mixed the product by flipping
# H
( DNA extract from home)
it up and down for a few times before placing it into the heating light for 5 minutes. After 5
minutes passed, I removed the content from the heating light, set it on the rack, left the lid open
–
sand
*
missing
details
#
# 13
–
method section
( filtration unit
procedure
# B
–
17
Nguyen 3
Ggt
)
and cooled for 3 minutes. Then, I transferred some of that amount into the new collecting tube
17
( DNA extraction
at home
add paragraph in
using a pipette and label the tube.
-9A
procedure)
about filtration
PCR – Polymerase Chain Reaction Setup
polymerase chain reaction
The following experiment requires setting up reaction of PCR, the initial denaturation step is
–
unit
carried out at the start of PCR to break the double-stranded DNA template into 2 single strands
so the primers can attach and initiate extensions to target region. During the first amplification
step, complete DNA denaturation ensure effective amplification of the target sequence at first
{
rewords
amplification cycle. The initial denaturation step is typically conducted at 94-98or 1 minute a
cycle. Along with initial DNA denaturation step, temperature and time should be optimized
depending on the existence of then DNA, buffer components and DNA polymerase.
Subsequently after the initial denaturation step, PCT cycles began with another denaturation
phase lasting 0.5-2 minutes at 94
The following step is the primer annealing optimization
step, where the temperature of the reaction is lowered enable the primers to bind to the target
DNA. The incubation time is about 2 minutes at 94 for 20 sec. 56 for 30 secs and 72 for 1
additional
details
minute. Next step in PCR is the extension of the 3’end of primers, complementary to the
how she set up
template strand. Generally, begin with a temperature of 3-5
following the step of the final
extension evaluation involving the incubated PCR mixture at 72 for final 5-10 minutes., The
the PCR
( refers to
documents)
result of the PCR was recorded in the data (table 1).

Casting the Agarose Gel via Electrophoresis ( professor
did this
section
,
:
get casting )
The 1x TAE buffer required a 2% Agarose gel. Before setting up a gel electrophoresis, x
we first
make the gel.x
I measured about 70mL of 1x TAE buffer and make a 2% Agarose gel by mixing
1.4 grams of agarose with the TAE buffer. x
I transferred about 5 microliters of SYBR safe stain
into the agarose solution, and let it sit. Once the gel is solidified and the PCT product to ready,x
I
F.
Nguyen 4
added 6 microliters of DNA loading dye into the PCR product. DNA is negatively charged and it
moves from negative side off the gel box to the positive side. Then next, I prepared DNA ladder
by adding DNA loading dye to 1 Kb plus DNA ladder. Once it is loaded, I made sure the
negative on the negative side and positive is on the positive side and the gel was allowed to run
at 100 volts in the electric current for approximately 20 minutes, while the results displayed in
the illuminator using UV radiations and the results are recorded (table 1).
Result
tribes’T!!!
about the result first
the
provide data
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Table 1: Experiments repeated with similar food samples
Nguyen 5
If
crop
picture 9
( refer
Figure 1: PCR product of gene visualize under UV light
screen image after electrophoresis in agarose gel
*Discussion
to
label
the
gel
)
instructions
Nguyen 6
Reference
APAI change
{
include
citations
on
paper
Levin, R.E. The Application of Real-Time PCR to Food and Agricultural Systems. A Review.
Food Biotech 18, 97–133 (2004) 

Markuolatos, P., et al., Qualitative and Quantitative Detection of Protein and Genetic Traits in
Genetically Modified Food, Food Rev Int. 20, 275–296 (2004) 
Rugg, Jeff. “There’s a difference between GEO and GMO.” Sioux City Journal.
https://siouxcityjournal.com/advertorial/siouxland_homes/there-s-a-difference-betweengeo-and-gmo/article_b044ec4f-ec27-5634-9c00-e1b206272f9d.html. Accessed 19 March
2019.
.
.
.
BIOL 2103
Molecular Final Report Guidelines
Molecular Project Final Lab Report – Required Components
The molecular genetics project final report is worth 15% of your total course grade. Incorporating the feedback from
your draft report will help you earn a higher grade on this report.
Review the Academic Honesty Policy and the additional document posted in BBL. In addition, be sure your report does not
contain:
x Sentences that are copied and pasted directly from internet or another text.
x High similarities between students’ lab reports.
x Data or reports from previous semesters, whether your own work or the work of another student.
x Any other action that is intentionally deceitful and covers contents that are significant parts of your report.
x Please note that your lab report must be done independently.
x Please review the documents posted in BBL, and discussed in class, regarding the proper format and technique for a
scientific lab report.
x Please review and address all comments given on your draft version. Failure to address comments will result in a lower
grade on your final report.
x Submit your final Molecular Genetics Report via Turnitin in Blackboard Learn. Turnitin will check for plagiarism and
similarity with files available on the Internet.
Your final report should contain the following components:
✓x
Title (1 points) the title should be descriptive and depict concepts covered in the paper
x Introduction – Background (10 points) Overview of the topics. Some examples include:
o What is GEO and how it is produced?
o What are the purpose and benefits of generating GEO?
o What common GEOs are there and how abundant is it?
o How can we test for the presence of GEO in food?
o Background or explanation of the methods used.
o You are REQUIRED to have references for background, and they must be cited with in-text citations.
x Purpose (4 points)
o What are the research questions we are addressing?
x Hypothesis (5 points)
o Give a specific hypothesis and the rationale behind it. The hypothesis must be in the correct format.
x Methods (10 points)
o You should have the method for BLAST search, extracting DNA, setting up PCR reactions, running PCR
reactions, and agarose gel electrophoresis. They can be used as subtitles for each paragraph.
o You have to indicate the identities of all food items (not just your own) as tested by your group in the
method. Be sure to include the following information regarding your food items: brand name, store name,
marketed as GE or not, description.
o Include items from your draft report
o Use the revision of your draft method as the model to write the rest of the methods
o Be concise while allowing enough detail to repeat
BIOL 2103
Molecular Final Report Guidelines
x Results (20 points) Results must have two sections:
o Text that describes each of the figures or table. (10 points): This text is separate from the figure legends.
The purpose of the text is to describe the results in paragraphs with references to the tables and figures.
They need to be specific, descriptive and matter of fact. Do not include discussions on why something did
not work. If something did not work, describe as “a
bp band was absent for…” instead of “it did not
work”. The results section should START WITH TEXT, NOT A FIGURE or TABLE.
o Figures and tables (10 points): 1) Figures with gel pictures with a title and a legend, 2) a table that
summarizes the gel results with positive and negative results for tubulin and 35S with a title and a legend,
and 3) a figure with sequence and the blast result with a figure title and legend.
o You should have gel images/figures for the two DNA extractions done practice round and the round
where you brought foods. You should have a figure from your BLAST search.
o For samples were tested twice, please indicate whether the results from two trials were consistent or not.
Use language like “the two trial with Oreo cookies gave inconsistent results from two trials, with a faint
126bp S35 band in the first trial but no S35 band in the second trial”.
o In the results, simply state the results whether a band was present, etc. Leave the interpretation and
discussion for below.
x Discussion (15 points)
o Interpret your results
o Specify and distinguish between the three types of results and provide explanation for each of them,
including not enough DNA was extracted, GE negative, or GE positive.
o Did your controls work? What could be the explanation?
o You have to discuss the result of the NCBI blast which reveals the identity of the transgene in your GE
crops.
o You are required to find one additional credible resource that is related to the GE crops from our
selection. The information from the resource should support your discussion. You can incorporate the
paragraph you have written from the credible sources/ SEEI assignment into your discussion. The
information from the resource should support your discussion.
x Conclusion (20 points)
o Was your initial hypothesis supported or refuted?
o Hypotheses to explain any discrepancies
o Where would you take the experiment from here?
o Required- address this bolded prompt as part of your conclusions: Based on EVERYTHING we have
done in the labs, including the wet experiments, bioinformatics and searching for creditable
information on the internet, present your position on whether you support genetically
engineered/modified food and explain your position. Furthermore, how, if at all, will the content you
learned in this laboratory project affect your daily life? For example, will you make any changes in your
food shopping or food consumption? You are expected to incorporate all aspects of your learning (as
outlined above) in your responses.
x References (5 points)
o This should be a legitimate source and primary article, not wikipedia or other such website.
o Correct APA format
x Revisions (10 points)
o This section should contain a paragraph explaining what changes you made to your report (can be for the
entire report, not just the sections from the draft) based on the feedback you received from your
professor. You should be explicit in detailing the feedback you incorporated, and how (if?) it improved
your final report.
x Other ways you can gain or lose points
o Failure to include the checklist
o Plagiarism; Participation: did you do your own work?
o Clarity: is the paper organized and easy to follow?
o Good writing grammar, etc.
o Interpretation of results
o Extra credit (+5) for writing center visit attach receipt from center to last page of report. I do not accept
this receipt by email. Include it with your report (at the end) if you want the extra credit.
DNA Extraction at home
1. Fill out a provided 50 ml conical tube with water up to the 20 ml mark and place the tube
inside your freezer. This will be used to keep your DNA cold during transport back to
campus.
2. One the day/time of DNA extraction, slowly bring to boiling up to 500 ml of water (to be
used as a water bath). You can do this is a glass pitcher, large coffee mug, or a small pot.
3. Use a weigh boat to transfer selected food sample up to the 0.5 ml mark of the collecting
tube (estimated weigh 0.30 – 0.35 grams). I will show an example during class if you do not
have a kitchen scale.
4. Transfer small amount of sand (VWR – Part number MK706206) inside the collecting tube if
it is required. Foods that begin in very fine texture do not need sand. For other samples,
add approximately half of the provided sand to your tube.
5. Grind and mix the content in collecting tube continuously with a plastic pestle (Fischer
scientific – Part number 14-222-357) until you get fine particles
6. Transfer 0.5mL of the molecular grade water (VWR – Part number 95043-414) into the
collecting tube and continue to grind for few minutes until you get a smooth consistency.
7. Add additional 0.5mL of the molecular grade water with the plastic pipette into the
contents.
8. Grind and mix the content for few minutes and place the collecting tube onto a Styrofoam
rack (upside-down cup bottom) for 3 – 5 minutes for gravity separation
9. Use the same plastic pipette and transfer up to 300uL of the upper portion to the 1.5mL
microcentrifuge tube with InstaGene matrix (BioRad – Part number 7326030). If you see a
thin layer on top, this is the lipids (and you would actually have three layers). Avoid picking
up the lipids.
10. Gently tap the tip of the tube with the matrix beads and mix the content 20 times
11. Place the boiling water away from the heat source and incubate your tube with InstGene
Matrix and food extract in the interior portion of Styrofoam and float it onto the water bath
for 5 – 7 minutes.
12. Take out the floating Styrofoam out of the water bath and place the microcentrifuge tube
on the Styrofoam rack for about 5 – 7 minutes to cool down the contents. It is imperative
that this step is not rushed. The samples MUST be cooled for the filtration in the next step
to work.
Note: During this time, the content in the tube will be separated into two phases, a
semisolid lower portion and an aqueous upper portion
13. Transfer the aqueous upper portion using a new plastic pipette into the filtration unit (Note:
avoid transferring any of the semisolid lower portion to the filtration unit)
14. Keep the filtration unit inside a new 1.5 ml microcentrifuge tube and obtain up to 6 drops of
filtrate by gravity filtration
15. Optional: Insert the provided bulb on the top of filtration unit if you are not able to obtain
filtrate through gravity filtration and force the DNA extract inside the 1.5 ml microcentrifuge
tube.
16. Label your tube using a sharpie with the sample number and group number and keep the
content inside a 50 ml conical tube with the frozen water and place the tube back in the
freezer. See the example below. Place the cap hinge on the left, and label your tube
precisely as shown in the image. This will allow me to correctly run your PCRs.
17. Bring the frozen 50ml conical tube with the extracted DNA to STB lobby area on the
appointed day/time. I will set up and run the PCR reactions after the last time slot, so you
must not miss your drop-off time.
Cap hinge
G#
S#
1
Unit One Testing for the Presence of Genetically Engineered Food (Continued)
Exercise 2. A hypothesis based inquiry to explore the presence of genetically engineered food
At this point, you have isolated DNA from your sample and dropped them up for analysis on campus,
where your instructor set up PCR reactions and ran agarose gel electrophoresis. Please watch a quick clip
(in the module) of our actions in the lab. In this exercise, as a group, you will come up with a hypothesis
on different brands of grits or corn meal purchased from grocery stores.
This semester, we decided to investigate into a variety of corn products, because genetically engineered
corn is the most abundant genetically engineered crop used in processed food. Just how much of our
corn-containing processed food contains genetically engineered variety? That is for us to find out. Here
is what we know:
1. We picked eight different products with corn as the main ingredient. Two are controls because
we know whether they contain genetically engineered corns. The other six are unknown
experimental groups.
2. Each group received the two controls and 2-3 experimental groups. The same food is tested by
people in different groups.
3. We provide you with the information on the types of food, stores, unit price, etc. See below.
Sample Name
1. Grits Quick 5-Minutes
Brand
Quaker (24 oz)
Price
$2.33
Store
HEB
2. Red Mill Corn Grits
3. Quick Grits
Bob’s (24 oz)
Minute 3 Brand (24 OZ)
$3.99
$1.80
Whole Foods Y (USDA Organic)
N
HEB
4. Quick Grits
Jim Dandy (16 oz)
5. Classic Fry Breading Mix Louisiana Fish Fry Products, LTD (10 oz)
$0.94
$1.32
HEB
HEB
N
N
6. Instant Grits
7. Yellow Corn Meal
Hill Country Fare (11.85 oz)
Quaker (24 oz)
$2.34
$1.61
HEB
HEB
N
N
8. Red Mill Corn Grits
Bon’s (24 oz)
$4.99
HEB
N (Manufactured in facility
that also uses tree nuts,
soy, wheat and milk)
Labeled Organic (Y / N)
N
Labeled GMO (Y / N)
Y (Produced with Genetic
Engineering)
N
Y (Produced with Genetic
Engineering)
N
Y (Produced with Genetic
Engineering)
N
Y (Produced with Genetic
Engineering)
N (Manufactured in facility that
also uses tree nuts, soy, wheat
and milk)
https://www.ncbi.nlm.nih.gov/nucleotide/NC_001497.2?
report=genbank&log$=nuclalign&blast_rank=1&RID=RC8B219E014
https://blast.ncbi.nlm.nih.gov/Blast.cgi#alnHdr_1391336607
https://www.ncbi.nlm.nih.gov/nucleotide/KX640115.1?
report=genbank&log$=nuclalign&blast_rank=3&RID=RC9NMVJ301R
}
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gcaagacccttcctctatat
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websites
I
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sequence
BLAST search
Unit Two Bioinformatics and Credible Information Search
Purpose
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E
1. B
E
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2.
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M
GE
Exercise Bioinformatics search on the transgene commonly found in genetically
engineered crops
Background
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