MT6319

Molecular Biology & Diagnostics (Lecture)

Orientation Portfolio
(First Term, AY 2023-2024)

Course Facilitators
Clemente • Dumaoal • Gigante • Malana • Mercado
The Course Facilitators
and
Course Information
Benjie M. Clemente, RMT, MLS(ASCPi)cm, MPH
Email: bmclemente@ust.edu.ph

Academic Qualifications
• PhD in Medical Technology (on-going) - University of Santo Tomas
Master in Public Health – Urdaneta City University
Bachelor of Medical Laboratory Science – Saint Louis University

Professional Experience/ Qualifications

• Faculty Member, Department of Medical Technology, Faculty of Pharmacy, University of
Santo Tomas
Faculty Member, Central Luzon Doctors’ Hospital – Educational Institution PICTURE
Medical Technologist – Calamba Medical Center
Junior Medical Technologist – Jecson Medical Center

Courses Taught
• Clinical Chemistry, Hematology, Community Health in Medical Technology,
Histopathologic Techniques and Cytogenetics, Principles of Medical Technology
Practice
Oliver Shane R. Dumaoal, RMT, MSMT, CBO, IFBA PC
Email address: ordumaoal@ust.edu.ph
Academic Qualifications
• PhD in Medical Technology (on-going) - University of Santo Tomas
• Philippine Advanced Biosafety Officers Training Course, UP Manila National Institutes of Health
• Master of Science in Medical Technology - University of Santo Tomas
• Bachelor of Science in Medical Technology - Lyceum of the Philippines University - Batangas
Professional Experience/ Qualifications
• Faculty Member, Department of Medical Technology, Faculty of Pharmacy, University of Santo
Tomas
• Vice President, Biorisk Association of the Philippines
• Subject matter expert, UP Manila National Training Center for Biosafety and Biosecurity
• Board Director, Philippine Association of Schools of Medical Technology and Public Health
• Regional Director and Chapters Chair, Philippine Association of Medical Technologists
• Laboratory Administrator, Lyceum of the Philippines University – Batangas
• Assistant Professor, Lyceum of the Philippines University – Batangas
• Biosafety Officer, Batangas Medical Center Molecular Diagnostics Laboratory
• Chief Medical Technologist, Healthcare Specialists, Inc.
Courses Taught
• Molecular Biology
• Mycology and Virology
• Thesis Writing
• Seminar 1
Mr. Ian Paulo C. Gigante, MPH
Email address: glmartini@ust.edu.ph

Academic Qualifications
• Master of Public Health, University of Philippines, Manila, 2021
• Licensed Professional Teacher
• BS Medical Technology, University of Santo Tomas, 2012 , Magna cum Laude
Professional Experience/ Qualifications
• Full-Time Faculty, UST (2019– present)
• Full-Time Faculty, Virgen Milagrosa University (2016-2019)
• Medical Technologist 1 – Senior Santo Nino Hospital and Capitol Medical Center
2013-2015
• Certificate Training in Microbiology RITM - 2012 PICTURE
Courses Taught
• MT 6310: Biochemistry for Medical Technology
• MT 6315: Cytogenetics
• MT 635: Analytical Chemistry
• MT 6319: Molecular Biology
• MT 6321: Histopathology and Cytology
• MT 6322: Mycology-Virology
• MT 6326: Immunoserology
• MT 6328: Analysis of Urine and Other Body Fluids
Joemari T. Malana, RMT, MSMT
Email address: jtmalana@ust.edu.ph
Academic Qualifications
• BS Medical Technology, Cagayan State University-Andrews (2012)
• MS Medical Technology, The Philippine Women’s University (2017)
• PhD major in Medical Technology, University of Santo Tomas (ongoing)
Professional Experience/ Qualifications
• Medical Technology Clinical Internship Coordinator, Faculty of Pharmacy, University of
Santo Tomas (August 2021-present)
• Faculty Member, Department of Medical Technology, Faculty of Pharmacy, University
of Santo Tomas (January 2019-present)
• Assistant Quality Management Representative, Faculty of Pharmacy, University of Santo
Tomas (August 2019-2021)
• Quality Assurance and Training Officer, Makati Medical Center - Medi Linx Laboratory,
Inc (2017-2019)
• Junior MT(2013-2014), Senior MT for Molecular Pathology (2014-2017) and Department
Training Officer (2016-2017), Department of Pathology and Laboratories, Makati
Medical Center
• HIV Testing Certified Medical Technologist by DOH NRL-SACCL
• Drug Testing Certified Medical Technologist by DOH EAMC-NRL
Courses Taught
• Laboratory Management, Clinical Parasitology, Molecular Biology and Diagnostics,
Principles of Medical Technology Practice
Clive Ivan S. Mercado, RMT, MSMT
Email address: csmercado@ust.edu.ph

Academic Qualifications
• Bachelor of Medical Laboratory Science, St. Scholastica’s College Tacloban
• Master of Science in Medical Technology, Philippine Women’s University
• 9th Placer, March 2015 Medical Technology Licensure Examination

Professional Experience/ Qualifications

• Assistant Professor 1 – St. Scholastica’s College College-Tacloban (2016 to 2020)
• Department Chairperson – Medical Laboratory Science Department, SSCT (2019-2020)
• Molecular Analyst – Eastern Visayas COVID Testing Center (2020) PICTURE
• Instructor IV– University of Santo Tomas (2021 - present)

Courses Taught
• Clinical Chemistry 1 • Hematology 1
• Clinical Chemistry 2 • Hematology 2
• Molecular Biology • Histopathology
• Mycology and Virology • AUBF
 Course Information
Course Code MT6319

Course Title Molecular Biology & Diagnostics

Pre-requisites All First and Second Year courses

Course Placement Third Year 1st term

Mode of Delivery FTF

 Course Information
Number of Units 2 units lecture, 2 units laboratory
Total Number of School
18 weeks
Days
Number of Hours / Week
2 hours lecture, 6 hours laboratory/week
(Lecture, Laboratory)

This course is a pre-requisite to: MT6324

 Course Description
This course gives a comprehensive overview of the fundamental principles of
molecular biology and explores the use of molecular techniques in the diagnosis of
diseases. It provides a detailed look at the molecular basis and function of
deoxyribonucleic acid, ribonucleic acid, and protein in the biosynthetic pathways of the
central dogma, their molecular mechanisms in causing disease and the methodology
employed in the clinical laboratory for the diagnosis of disease. This will include but
will not be limited to inherited disorders, cancer and infectious disease. It also includes
discussions and simulations of the different techniques in molecular biology such as
nucleic acid and protein extractions, amplification techniques like polymerase chain
reaction (PCR), gel electrophoresis, macromolecule blotting and probing, microarrays
and among others.
 Course Intended Learning Outcomes
1. Demonstrate mastery of knowledge and skills on molecular biology and diagnostics.
2. Create a system that will facilitate teamwork with other health care professionals in
applying concepts of molecular biology in diagnosing diseases.
3. Correlate laboratory results with clinical cases seen in professional practice.
4. Evaluate the needs and challenges in the current practice of molecular diagnostics in
the field of Medical Technology and apply appropriate actions.
5. Advocate health information literacy.
 Course Policies
(General and Course-Specific Policies)
 Policy on Attendance
▪ Students are required to attend at least 80% of scheduled
classes, which is equivalent to maximum allowable absences of 7
meetings for the Lecture and 7 meetings for the Laboratory.
▪ Three (3) counts of tardiness of at least 15 minutes shall be counted
as one absence.
▪ Absences in excess of specified number of allowable absences for
either Lecture or Laboratory will mean an encoded grade of FA or
failure due to absences.
▪ For other Policies and Guidelines on Attendance, please refer to PPS
1010 p.46 of the Student Handbook.
 Policy on Academic Assessment Evaluation
▪ All gradable assessments are incorporated as part of the Course Plan.
▪ There will be 3 shifting periods (1st, 2nd, and 3rd) per term.
▪ There will be one (1) shifting examination scheduled per shifting period.

▪ Summative and Formative Assessments can be given to students as

deemed necessary for achieving the learning outcomes for the course.
▪ Formative assessments are not graded.
▪ Summative assessments are graded and must be part of a grade component
for the course.
 Policy on Academic Assessment Evaluation
▪ All shifting examinations will be deployed face-to-face and will be
scheduled by the Dean’s Office within a given examination week.
▪ Questions for shifting examination will be designed using the prescribed
Table of Specification (TOS).
▪ A copy of the TOS will not be given to the student but will be submitted for
documentation.
▪ Time allotment will also be determined by the faculty members following a
beta-testing for the examination.
 Specific Course Policies
▪ Shifting examination is DEPARTMENTAL and will be limited to a maximum of 70 items prepared by the
respective course facilitators following the TOS provided. Quizzes on the other hand will be limited to a
maximum of 30 items. All gradable assessments will be done ONSITE.
▪ Approximately 2-4 quizzes will be given per shift. The time allotted will depend on the number of items.
▪ The manner of the graded examinations can either be multiple choice, true or false, identification, matching
type, essay, and other similar forms at the discretion of the cluster and course facilitators. The manner of
delivery for such graded examinations are at the discretion of the course facilitators
▪ Laboratory sheets will be accomplished individually and submitted as 1 bundle per group. All submitted sheets
per shifting period are ONLY considered as 1 gradable assessment
▪ Official Scantron sheets from the Faculty will be used in shifting exams and must be properly filled up during
the scheduled examination. A ZERO score will be given if scantrons sheets are not recognized due to improper
filling up of answers.
 Specific Course Policies
▪ There will be NO manual checking of scantrons sheets.
▪ In cases of absence (excused), students must coordinate with the course facilitator for the scheduled make-up shifting
exams/practical exams. Incomplete grades may be encoded temporarily in the portal if make-up has not been complied
with and the grade must already be encoded. Adjustments will just be made in the encoding of the final grade. An
incomplete final grade that was encoded will be a permanent record of the student.
▪ All deadlines for submissions of OLA (Lecture) and Activity sheets (Laboratory) MUST be strictly followed. A ZERO
grade for late submission will be given due to non-compliance.
▪ Students who will be caught cheating in any form during the unit, shifting, or practical examinations shall automatically
be given a grade of zero (0) for the particular examination and shall be endorsed to the SWD coordinator of the
Faculty of Pharmacy for appropriate action and to the Counselors for proper guidance.
▪ All Test Questions shall be reviewed and validated by all Course Facilitators.
▪ NO PPE’s NO laboratory activities policy will be strictly implemented in the laboratory class.
▪ No adjustment and correction in GRADE will be entertained after the computation has been consulted with students
and has been finalized.
 Grading System
and Interventions
 Grading System
Course Requirement First Shifting Second Shifting Third Shifting
Lecture Components (%) Components (%) Components (%)

Unit Tests 30 30 30

Other Learning
20 20 20
Activities

Shifting Examinations 50 50 50

Total 100 100 100

 Grading System
Shifting Period Breakdown Lecture – Laboratory
First 30 % 60% Lec – 40% Lab
Second 35% 60% Lec – 40% Lab
Third 35% 60% Lec – 40% Lab

Passing Grade
Raw Score 70%
Transmuted Grade 75
Final Grade 3.00
 Course Interventions
• Faculty Members shall take into consideration the possible student’s concerns which
are as follows:
• Health and wellness (medical condition, mental health, etc.)
• Family concerns
• Learning resources
• Learning environment
• Faculty Members shall conduct regular CONSULTATION with students.
• Consultation must be made during scheduled consultation.
• Special consultation scheduling may be made upon request to course facilitators.
 Student Concerns
▪ Students may discuss their concerns with the following:
▪ Course facilitators assigned to the course
▪ Guidance counsellors
▪ Department Chair
▪ Dean

▪ Student may also seek assistance from the FPSC Student Council in
writing their concerns or through the Student Welfare and
Development Board (SWDB).
 Weekly Class Expectation
Week Activities

Unit 1. Introduction to Molecular Biology and Diagnostics

1. What is Molecular Biology and Diagnostics?
2. History of Molecular Biology
1 3. Applications of Molecular Diagnostic
 Weekly Class Expectation
Week Activities
Unit 2. Nucleic Acids: DNA and RNA
1. DNA
1.1 DNA structure
1.2 Nucleotides
1.3 Nucleic Acid
2. RNA
2 2.1 Types/structures of RNA
2.2 Ribosomal RNA
2.3 Messenger RNA
2.4 Small Nuclear RNA
2.5 Transfer RNA
2.6 Other RNAs
 Weekly Class Expectation
Week Activities
Unit 3. Central Dogma
DNA REPLICATION
1. Polymerases
2. Patterns & Fidelity
3. DNA Mutation and Damage
3 4. Damage Repair
5. Recombination in sexually reproducing organisms
6. Recombination in asexual reproduction
7. Conjugation
8. Transduction
9. Transformation
 Weekly Class Expectation
Week Activities
GENE EXPRESSION: TRANSCRIPTION OF THE GENETIC CODE
1. RNA Synthesis
2. Transcription Initiation
3. Transcription Elongation
4. Transcription Termination
5. RNA polymerases
6. Other RNA-metabolizing enzymes
7. Ribonucleases

4-5 8. RNA Helicases

9. Regulation of transcription
10. Regulation of Messenger RNA Synthesis at Initiation
11. Post-Transcriptional Regulation
12. Post-Translational Regulation
GENE EXPRESSION: TRANSLATION OF THE GENETIC CODE
1. Amino Acids structure and properties
2. Protein Structure
3. Genetic Code
4. Protein Synthesis
 Weekly Class Expectation
Week Activities
Unit 4. Genomes, Variants and Polymorphisms
1. Human Genome
2. Non-human Genome
3. Variations in the Human Genome
3.1 Single nucleotide variants
3.2 Copy number variations
3.3 Fusions
3.4 Short tandem repeats
3.5 Transposable elements and their genetic fossils
6 4. Nomenclature
5. Epigenetics
5.1 Histone Modification
5.2 Nucleic Acid Methylation
6. Classification of epigenetic factors
7. Noncoding RNAs
7.1 MicroRNAs
7.2 Small Interfering RNAs
7.3 Other Small RNAs
7.4 Long Noncoding RNAs
 Weekly Class Expectation
Week Activities

Unit 5. Molecular Diagnosis of Chromosomal Disorder

1. Chromosome
2. Molecular cytogenetics
3. Comparative Genomic Hybridization
7-8 4. Chromosomal Disorders
4.1 Numerical Abnormalities
4.2 Sex Chromosome Abnormalities
4.3 Structural Chromosome Abnormalities
 Weekly Class Expectation
Week Activities

Unit 5. Molecular Diagnosis of Chromosomal Disorder

1. Chromosome
2. Molecular cytogenetics
3. Comparative Genomic Hybridization
9-10 4. Chromosomal Disorders
4.1 Numerical Abnormalities
4.2 Sex Chromosome Abnormalities
4.3 Structural Chromosome Abnormalities
 Weekly Class Expectation
Week Activities

Unit 6. Molecular Diagnosis of Mutation and Inherited Diseases

1. Variations That Cause Human Disease
2. Choice of techniques
11 3. Single Gene Disorders
4. Polygenic Disorders and Gene Clustering
5. Mitochondrial Disorders
6. Diseases Caused by Mutations in Mitochondrial Dynamics Machinery
 Weekly Class Expectation
Week Activities

Unit 7. Molecular Diagnosis of Infectious Diseases

1. Detection of Bacteria Pathogens
2. Detection of Fungal Pathogens
12 3. Detection of Viruses
4. Emerging Technologies for Microbial Species Identification
 Weekly Class Expectation
Week Activities

Unit 8. Techniques in Sequencing

1. Chain Termination DNA Sequencing Technique
2. Pyrosequencing
3. Genome Sequencing
13 4. Clone Fingerprinting Techniques
5. New Generation Sequencing Strategies
6. Third Generation Sequencer
7. NGS Data Analysis
 Weekly Class Expectation
Week Activities

Unit 9. Genome and Transcriptome Analysis

1. Genome-Wide Sampling Sequencing for Genetic Polymorphisms
2. Genome-Wide Association Studies
14 3. Transcriptome Sequencing
4. RNA Structurome
5. Metabolomics: Linking the Genome to the Metabolome
 Weekly Class Expectation
Week Activities

Unit 10. Ethical, Legal, and Social Implications of Molecular Diagnosis

1. Ethical, Legal, and Social Implications of Human Genetics Research
15 2. ELSI in the Human Genome Project
 References
Official Textbook: Chang-Hui, S. (2019). Diagnostic Molecular Biology. Elsevier Inc.

Laboratory Manual: Pineda-Cortel MR, Manahan, E., Tesalona, S., Ranido, M., & Vargas, A. (2020). Worktext in Molecular Biology and Diagnostics. C&E Publishing, Inc.

Journals: American Journal of Clinical Pathology Journal of Infectious Disease

The New England Journal of Medicine Cancer

Web-based Sources/Instructional Media: LABSTER

https://accessmedicine.mhmedical.com/
https://www.cdc.gov/labtraining/training-courses/basic-molecular-biology/basic-science.html
https://www.ncbi.nlm.nih.gov/
https://www.omim.org/

References:
1. Agrawal, K., Bouchal, J., Das, V., Drábek, J., et al (2021) Laboratory Techniques in Cellular and Molecular Medicine. Palacký University Olomouc
2. Chandar, N., Viselli, S. (2019) Cell and Molecular Biology (2nd edition). Philadelphia Wolters Kluwer
3. Clark, D., Pazdernik, N. and McGehee, M. (2018) Principles and Applications of Molecular Diagnostics Elsevier Inc.
4. McPherson, R.A. & Pincus, M.R. (2019). Henry's clinical diagnosis and management by laboratory methods (23rd edition). Elsevier.
5. Raghavendra, P. and Pullaiah, T. (2018) Advances in Cell and Molecular Diagnostics Elsevier Inc.
6. Rifai, N., Horvath, A.R., Wittwer, C.T., & Park, J. (2018). Principles and Applications of Molecular Diagnostics. Elsevier Inc.
7. Rifai, Nader (2018). Tietz Textbook of Clinical Chemistry and Molecular Diagnostics - E-Book Sixth edition. St. Louis, Missouri: Saunders.