Beruflich Dokumente
Kultur Dokumente
University
College of Medical
Laboratory Science
Valenzuela City
Philippines
RESEARCH PROPOSAL CAPSULE
Bautista Justine Marie Dela Rosa
Besacruz Lyn Ann Chayene Mateo
Estose Jane Dafnel Clyde Divinagracia
Fortunato Noreen Rama
Lactao Katrina Marie Pelias
Molina Cristhene Joy Precious Viloria
Salazar Joedith Mose
Sandigan Merry Kris Diano
Last Name First Name Middle Name
Field of
Bachelor in Medical Laboratory Science
Specialization
Research Approach Quantitative
Research Design Descriptive Cross-sectional
Research Technique Molecular
Research Domain
This study limits on 4th Year regulars of Medical Technology students
Research
school year 2018-2019 of Our Lady of Fatima University. Its main purpose is
Attributes
to test every student for Alzheimer's disease. It included a gene from a
Delineated Factors student which will be tested for the early-onset of the said disease.
Bagyinsky E., Youn Y., An S., Kim S. (2014) The genetics of Alzheimer’s disease
ISI Journals
Reviewed Cai Y., An S., Kim S. (2015) Mutations in presenilin 2 and its implications in Alzheimer’s disease
(Follow the APA and other dementia-associated disorders
Style)
Darawi MN, Ai-Vyrn C, Ramasamy K, Hua PP, Pin TM, Kamaruzzaman SB, Majeed AB (2013)
Allele-specific polymerase chain reaction for the detection of Alzheimer's disease-related single
nucleotide polymorphisms.
Page 1 of 16
Dawskin E., Small D. (2014) Insights into Physiology function of the beta-amyloid precursor
protein: beyond Alzheimer’s disease
Ehtisham M., Nissar S. (2016) Polymerase Chain Reaction (PCR): Back to Basics
Garibyan L., Avashia N. (2014) Research Techniques made simple: Polymerase chain reaction (pcr)
Guo T., Noble W., Hanger D. (2017) Roles of tau protein in health and disease
Maheaswari R., Kshirsagar J., Lavanya N. (2016) Polymerase chain reaction: a molecular
diagnostic tool in Periodontology https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4847456/
Nhan H., Chiang K., Koo E. (2015) The multifaceted nature of amyloid precursor protein and its
proteolytic fragments: friends and foes
University of Texas Medical Branch at Galveston. (2016). New insight into how Alzheimer's
disease begins. www.sciencedaily.com/releases/2016/11/161118131600.htm
Perneczky R., Guo LH., KAgerbauer SM., Werle L., Kurz A., et. Al., (2013) Soluble amyloid
precursor protein beta as a blood-based biomarker of Alzheimer's disease
Tellechera P., Pujol N., Esteve-Belloch P., Escheveste B., Garcia-Eulate M.R. (2015) Early- and
late-onset Alzheimer disease: Are they the same entity?
Verma K., Dalal J., Sharma S. (2014) Scientific concepts of Polymerase chain reaction
Page 2 of 16
Alzheimer's disease is a type of dementia that causes problems with memory, thinking,
and behavior. This disorder is not a normal part of aging, although the greatest known risk factor is
increasing age, and the majority of people with the AD are 65 and older.
Most cases of early-onset of the AD are caused by a gene mutation that can be passed
from parent to child. Researchers have found that the three main genes that are involved in this
Proposal disorder are amyloid precursor protein (APP), presenilin (PSEN1), and presenilin 2 (PSEN2).
Abstract
This study will focus only on one gene, which is the Amyloid Precursor Protein, for it is
the most common protein that causes Alzheimer’s disease. Researchers are aiming that at the end of
this study they will know the percentage of the respondents, 4th year regular Medical Technology
Students of OLFU Valenzuela, who will be tested positive acquiring the APP gene.
1. Introduction
Page 3 of 16
to provide a general guide. (Jon Johnson, et. Al, 2017). Mutations in three genes – the
amyloid precursor protein, presenilin 1, and presenilin 2 lead to Early Onset Alzheimer
disease. PSEN1 is the most commonly involved gene, with 221 mutations reported as
pathogenic in the Alzforum database. The second most commonly involved gene is APP,
with 32 pathogenic mutations described, while 19 different PSEN2 pathogenic mutations
have been reported. APP encodes the amyloid-β precursor protein, the processing of which
by the β-secretase and the γ-secretase complex leads to the production of the amyloid β
(Aβ) peptide, a key event in AD pathogeny. The aggregation of the Aβ peptide in the brain's
parenchyma indeed triggers a cascade of events leading to the AD. (Lanoiselée HM, Nicolas
G, Wallon D, et al. 2017)
2.1.2 Dementia
Since APP is a protein, it gets used, broken down and recycled. This can be
processed by a number of enzymes that can act as a-secretases that can cleave or chop to
produce small fragments of proteins. One of these enzymes is the B-secretases which is
type 1 transmembrane aspartyl proteases or the B-site APP-cleaving enzyme 1 (BACE 1)
which cleaves APP at position 11 through the cleavage significance of the enzyme is unclear.
Page 4 of 16
Proteolytic processing of APP can lead to the pathological production by B-secretase of AB.
(Dawkins et.al, 2014) The proteolytic fragment derived from the APP are the soluble APP
peptides (sAPPa, sAPPB), C- and N-terminal fragments, p3, and APP intracellular domain
fragments. (Nhan et. al, 2015) The SAPPb In the blood may serve as a marker of the AD.
(Dawkins et.al, 2014) In the brain, senile plaques and neurofibrillary tangles play a role in
which the amyloid-B peptide abnormal aggregation initiates events that result in
pathological changes, cognitive decline and neurodegeneration these conceptualize that
soluble AB oligomers are present before AB peptides and are toxic species aggregated and
deposited as amyloid plaques in the brain. (Nhan et. al, 2015)
Polymerase Chain Reaction, or simply PCR, was introduced by Mullis way back
1983 and won the Noble Prize in Chemistry for his discovery became one of the most
important revolutionary techniques in molecular biology (Maheaswari et al., 2016). PCR is
an enzymatic process in which specific regions of DNA are duplicated repeatedly to yield
millions of copies of a sequence in a matter of few hours (Verma et al., 2014) as what Mullis
has said that it lets you pick the piece of DNA you're interested in and have as much of it as
you want.
PCR has many uses, it can be used for diagnosing many human diseases such
as infectious diseases, cancers especially leukemia and lymphomas. It also permits
identifications or microorganisms like bacteria and viruses that can be a help in diagnosing
infectious diseases (Rahman et al., 2013). This technique can be performed using source
DNA from a variety of tissues and organisms, including peripheral blood, skin, hair, saliva,
and microbes. Only trace amounts of DNA are needed for PCR to generate enough copies
to be analyzed using conventional laboratory methods. For this reason, PCR is a sensitive
assay (Garibyan et al., 2013). The core principle of PCR is the use of an enzyme called DNA
polymerase to make a copy of a DNA strand then the steps of PCR are consisting of
denaturation, annealing and the extension step. (Verma et al., 2014) The last step of this
process is the visualization which has different methods, one is staining using ethidium
bromide and the other is through gel electrophoresis on polyacrylamide or agarose. Using
of electrophoresis Is the most common method used (Garibyan et al., 2014)
Page 5 of 16
The pre-experimental phase starts with a collection of blood samples from the
respondents, 4th-year regular medical technology students of OLFU Valenzuela campus
enrolled in the school year 2018-2019, through venipuncture using syringe method and
transfers to EDTA-rinsed microcentrifuge tube. Blood samples will be processed fresh and
served as the subjects’ DNA isolation reference. Using a hypotonic buffer, lymphocytes will
be separated from whole blood by lysing the RBC. DNA extraction kit will also be used to
extract the DNA from the blood samples.
The integrity of genomic DNA will be tested by resolving DNA extracts in agarose
gel by electrophoresis followed by visualization using ethidium bromide as the stain.
Afterward, researchers will proceed with DNA amplification using the Early-onset
Alzheimer’s Disease Primer. The products of this amplification will be subjected to
electrophoresis on agarose gel and stained and images will be obtained in gel
documentation.
All data that will be gathered from the experimentation will be used to solve for the
percentage of the respondents that acquired the APP gene.
3. Research Methodology
Sample collection and all the experimentations regarding extraction, amplification, and
interpretation of the DNA will be held at the Research Laboratory of Our Lady of Fatima
University located at Marulas, Valenzuela City.
Page 6 of 16
3.4.1 Research Materials
A method that is most widely used for analyzing, visualizing, and determining
the presence and size of the PCR product. It also separates the DNA products by its size
and charge (Garibyan et al. 2013). It has proven to be an efficient and effective way of
separating nucleic acids. Agarose's high gel strength allows for the handling of low
percentage gels for the separation of large DNA fragments. Molecular sieving is
determined by the size of pores generated by the bundles of agarose7 in the gel matrix.
(Lee et al. 2012)
3.4.1.2 PCR
A device commonly seen at the laboratory and has the main function of mixing
small vials of liquids such as reagents, experimental sample, and diluents. It works with
a piece of a rubber moving into a circular motion by means of rapid oscillation. Just like
other laboratory mixer machines, it has controls and its speed is adjustable.
3.4.1.4 Centrifuge
Laminar flow cabinets (hoods) are physical containment devices that act as
primary barriers either to protect the material within the hood from different sources
of contamination, or to protect the laboratory worker and laboratory environment from
Page 7 of 16
exposure to infectious or other hazardous materials that are present within the hood
during routine procedures (Coecke et al., 2005).
A dry bath is a type of laboratory equipment that is used to heat samples. Dry
baths are often used in molecular biology, microbiology, biochemistry and genetic
applications. The capacity of these baths is measured in blocks. Depending on the size
of the block, the user can place a certain amount of tubes into each block. The most
common sizes for blocks are 1, 2 and 4 block models.
There are two main types of dry baths including digital dry bath and analog dry
baths. Digital dry baths incorporate a microchip into the model which allows the
temperature of the bath to be controlled through the digital interface while analog dry
baths do not use microchip technology. (Universal medical)
3.4.2.1 Chloroform
3.4.2.2 Phenol
Poorly soluble in water and, at room temperature, forms only a 6.7% aqueous
solution. Consequently, phenol is frequently prepared with contrast dyes and either
sterile water, saline or glycerin.
3.4.2.3 Proteinase K
Page 8 of 16
3.4.2.4 Isoamyl alcohol
Colorless liquid with a mild, choking alcohol odor. Less dense than water,
soluble in water. Hence floats on water. Produces an irritating vapor. (USCG, 1999)
3.4.2.5 RNAse
Page 9 of 16
including Western Blotting and ELISA procedures as well as protein assays which are
sensitive to the presence of detergents in the lysis buffer.
3.4.2.9 Primer
PCR primers often require optimization for the best results. This optimization
can require significant time in evaluating varying concentrations for DNA polymerase,
2′-deoxynucleotide triphosphates (dNTPs), magnesium, KCl, Tris buffer, bovine serum
albumin, and the designed and purchased PCR primers. The annealing temperatures
of the primers also need to be evaluated experimentally for the best results. In this
experiment, the annealing temperatures will be evaluated using gradient real-time
PCR (Higuchi et al. 1993), but the concentrations of the other reagents will be fixed
as in the purchased proprietary 2X reagent mixture containing dNTPs, 50 U/μL
antibodies-mediated hot-start iTaq DNA polymerase, 6 mM MgCl2, SYBR Green I,
enhancers, stabilizers, and 20 nM fluorescein. A 25 μL reaction volume will be used
for all reactions.
In this study, data will be collected based on the information and results of the
samples that will be collected from the respondents. The extraction of DNA will be done
using a method adapted from Ghatak et al. (See Appendix A). Lymphocytes from whole
blood will be separated by lysing the red blood cells (RBCs) using a hypotonic buffer with
minimal lysing effect on lymphocytes. Three volumes of RBC lysis buffer will be added to
the blood sample and mix by vortexing and inverting thoroughly for 5 min and centrifuged
at 20,00 g for 10 min. The supernatant will be mostly discarded, leaving behind 1ml to
prevent loss of cells. To the pellet, 3 vol RBC lysis buffer will be added, and vortexing,
inverting, and centrifuging steps will be repeated two to three times until a clear
supernatant and a clean white pellet was obtained. After the final wash, the supernatant
will be discarded completely, and the pellet was resuspended in 500 l PBS, followed by
addition of 400 l cell lysis buffer (10 mM Tris-HCl, 10 mM EDTA,50 mM NaCl, 10% SDS, pH
7.5) and 10 l proteinase K (10 mg/ml stock; Himedia). The sample will be vortexed to
dissolve the pellet completely and incubate for 2 h at 56°C in a water bath for lysis. An equal
Page 10 of 16
volume of phenol will be subsequently added to the tube and mix well by inverting for 1
min. The tube will be centrifuged at 10,000 g (at 4°C) for 10 min, and the aqueous upper
layer will be transferred to a fresh tube containing equal volumes (1:1) of phenol and
chloroform: isoamyl alcohol (24:1). The tube will be mixed by inverting for 1 min and
centrifuge for 10 min at 10,000 g (at 4°C). The supernatant will then be transferred to a
fresh tube, and 10 l of 10 mg/ml RNase A will be added. The sample will be incubated at
37°C for 30 min before an equal volume of chloroform: isoamyl alcohol (24:1) will be added
and mix by inverting the tube for 1 min and centrifuging at 10,000 g (at 4°C) for 10 min. The
supernatant will be transferred to a fresh tube, and twice the volume of absolute alcohol
(Merck) was added and inverted gently a few times and chilled at 20°C, followed by
centrifugation at 10,000 g at (4°C) for 20 min. The supernatant will be discarded, 250 l 70%
ethanol was added, and the pellet will be tapped gently, followed by centrifugation at
10,000 rpm for 10 min and decanting the supernatant gently. The pellet will be air-dried in
a laminar airflow, and the dried pellet will be resuspended in 50 l nuclease-free water or 1
TE buffer and freeze at 20°C or 80°C for storage.
The extracted DNA for blood will be amplified by PCR using the primer of the APP
gene. PCR will be carried out in 25 l total reaction volumes, each containing 100 ng template
DNA, 0.2 pM of each primer, 2.5 l 10 PCR buffer (final 1 PCR buffer), 1.5 mM MgCl2, 200
mM dNTPs, and 1-unit Taq DNA polymerase. The reaction mixture will be heated to 94°C
for 5 min, followed by 40 cycles, each consisting of 1 min denaturation at 94°C, 1 min
annealing at 63°C, 1.5 min extension at 72°C, and a final 10-min extension at 72°C. The PCR
amplification products (10 l) will be subjected to electrophoresis on 1.2% agarose gel in 1
Tris-acetate- EDTA buffer at 80 V for 30 min and will be stained with ethidium bromide, and
images will be obtained in gel documentation systems.
Page 11 of 16
Data gathered during the experimentation will be studied and presented and will be
treated with Probability Analysis accordingly.
The data that will be gathered, the DNA results of the respondents, will be subjected to the
computation of their individual probability of acquiring Early-onset of Alzheimer’s Disease using
Bayes’ theorem, a formula that describes how to compute the probabilities of hypotheses when
given evidence.
This study aims to investigate the Probability of Medical Technology student to acquire
Early-Onset of Alzheimer’s disease. Specifically, this study answers the following questions:
Research Research Question 1: What is the Percentage of 4th Year Regular OLFU Medical Technology
Questions Students S.Y.: 2018-2019 to Acquire Early-onset of Alzheimer’s Disease if:
This study hopes to establish an understanding to detect the possibility of the students to
acquire an early-onset Alzheimer’s disease.Detection of early-onset Alzheimer’s disease would
allow immediate intervention and hinder the possibility of neurodegeneration before it leads to
brain cell death and cognitive decline arise.
An early diagnosis opens the door to future care and treatment in detecting the disease. It
Significance of
could prevent the physician to prescribe medications that may worsen the cognitive function that
the Proposed
Research would greatly increase the chances for better treatment options and for better management of
comorbidity. In relation to this, it is beneficial to positively detected students to maintain their
mental function, control behavior, and slow the progress of the disease.
This study would be useful as awareness for those people who weren’t knowledgeable about
the genetic test and for the said disease. To the future researchers, this can be used as a tool and
as their basis in conducting their study with the same topic.
Page 12 of 16
PRE-EXPERIMENTAL PHASE
PRE-EXPERIMENTAL PHASE
Page 13 of 16
CURRICULUM VITAE
Page 14 of 16
Justine Marie Dela Rosa Bautista
19 years old, living in #1144 Camba Extension Tondo, Manila
City. Born on May 09, 1998 in Manila. Took her primary and secondary
education at Holy Child Catholic School. Currently studying at Our Lady
of Fatima University Valenzuela Campus as a BS Medical Laboratory
Science student.
Page 15 of 16
Katrina Marie Pelias Lactao
19 years old, living in #32 Road B Project 7, Veterans Village,
Quezon City. Born on July 27, 1998, in Metro Manila. Took her
primary education in Esteban Abada Elementary School and
secondary education in Ernesto Rondon High School. Currently
studying at Our Lady of Fatima University as a BS Medical Laboratory
Science student.
P
Nathaniel B. Ranon Jr., RMT
Prof. Jose Jurel M. Nuevo, RMT, MSMT, Ph.D.
Res 1 Laboratory Instructor Chair, Panel of Evaluators
Dean of the College of Med. Lab. Science
Page 16 of 16