University of Santo Tomas

The Graduate School

NATURAL SCIENCES CLUSTER
M.Sc. major in Microbiology

Academic Year 2021 – 2022

An Outcomes-Based Learning Program

MT – 806 ADVANCED MICROBIAL GENETICS
Course Code Course Title

Part 1 Course Information

3 Asst. Prof. Aimee Caye G. Chang, Ph.D.

Course Credit Course Facilitator
Specialization UST Graduate School
Course Category Office
Tuesdays / 6:00 – 9:00 (02) 3406 1611 local 8297
Class Schedule Contact Number
(Day/Time)
UST BlackBoard/Zoom agchang@ust.edu.ph
Venue E-mail
Prerequisite (Specify All) By appointment
Consultation Period (Schedule/Venue)

Course Description
Rationale Genetics in inherent in all life forms, microorganisms included. Molecular biology and
genetic engineering – from chemicals to genotype, then to phenotype - have their roots
in microbial genetics. Microbial genetics, in fact, is currently of immense importance as
a tool in applied sciences, e.g., in biotechnology, human health, agriculture, resource
conservation, environmental management, among others.

Focus The course focuses on heredity in microbial systems and its application in applied
biology. Included is the nature of the genetic element (DNA & RNA), the central
dogma, the mechanics of vertical and horizontal gene transfers, and mutation and its
repair in focused microorganisms. The course also highlights microbial genomics and
its application in taxonomy, molecular phylogeny, and evolution.

Outcome To equip students in microbiology and related disciplines with fundamental

understanding of the genetical phenomena commonly encountered in microorganisms
used in research. The students are also expected to learn about the recent trends and
developments in the field of microbial genomics.

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 University of Santo Tomas
The Graduate School
NATURAL SCIENCES CLUSTER
M.Sc. major in Microbiology

Part 2. Outcomes-Based Macro-curriculum Framework for Seminar on Teacher

Education Across Levels

Intended Learning Outcomes (ILOs)

M Institutional (IILOs) Program (PILOs) Course (CILOs)
I
S
S When you successfully complete
USTGS Graduate Attributes When you successfully complete
I Advanced Microbial Genetics,
A USTGS Graduate is expected to be a: M.Sc. Major in Microbiology,
O you will be able to:
you will be able to:
N

1. Competent Professional Exhibit high level of adeptness and

Relate to vast amount of new
who, inspired by the ideals of St. Antoninus of genetical information in popular
C expertise in sourcing, interpreting,
Florence, promotes excellence in the and technical media for use as a
and conveying both basic and applied
O production, advancement, and transmission resource during meaningful
microbiological knowledge before a
M of specialized knowledge and skills in the participation in scientific fora and
broad range of audience.
P sciences, the arts, and community services. in generation of quality papers.
E 2. Scholarly Researcher and Critical
T Thinker
Demonstrate critical analysis of
Conduct scientific inquiries into
E who, kindled by St. Thomas Aquinas’ ardor the genetical modification of target
current microbiological knowledge in
for truth, aspires to become fronts of microorganisms especially those
N duality with specific problems for the
intellectual creativity and, in his quest for with potential in the resolution of
C quality research, is proficient and critical in
generation of new principles evolved
regional, national and global
E thru the rigors of the scientific
assessing and communicating information in problems in food security, human
method.
various fields that impact the professions, the health, and environment upkeep.
church, the nation, and the global community.

3. Professional Christian Leader Manifest the mark of a professional as

Interact at equal level with peers in
who, touched by St. Dominic de Guzman a scientist in the discipline, able to
the discipline to undertake various
C Apostolic’ fire and warmed by Mary’s engage with commitment in personal
broad and holistic studies in
motherly care, articulates ethics and truth, and collaborative life-centered
O microbial genetics requiring vital
high level of maturity in resolving issues and advocacies in the promotion of
M promoting social justice and compassion for societal interest anchored on truth and
multidisciplinary inputs and high-
P impact outputs.
the poor, and care for the environment. ethical and moral values.
A
S
S Observe open-mindedness on
4. Globally Engaged Citizen Keep abreast of and be sensitive to opposing views on resource
I who, with ardent advocacy for life, promotes
changes in various aspects of humane methods yet to be subjected to
O a deeper understanding of tolerance and
relationships in the context of local more experimentations and
N justice as well as linguistic, religious, and
and global microbiological milieu. interpretations in the light of still
cultural diversities as a result of precise
large number of microorganisms
evaluation of modern problems and inquiries.
worldwide with unknown
genetical oddities.

Demonstrate in-depth knowledge and

5. Committed Scholar functional understanding of Able to apply knowledge of
C who, nurtured by the dogmas of the Christian
microbiological concepts and specific aspects of microbial
O faith and values, is dedicated to pursuit of
principles and their application in genetics in various academic
truth through the promotion of an intellectual
M culture that values academic rigor and
microbiology-related problems in (basic) and societal (applied)
M industrial, medical and research- biological endeavors
freedom of scientific investigation.
oriented professions.
I
T
M 6. Lifelong Learner
who, empowered by St. Antoninus of Show that microorganisms are
E Demonstrate infinite desire to learn
Florence’s zeal for learning, is committed to intricately linked either positively,
N the advancement of a higher culture through a
and master new competence and
negatively, or neutrally to all
T skills, with the end-in-view to their
continuous search of intellectual inquiries and aspects of basic and applied human
application in the science and
new knowledge as well as faithfulness to endeavors.
technology of the discipline.
Catholic intellectual traditions.

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 University of Santo Tomas
The Graduate School
NATURAL SCIENCES CLUSTER
M.Sc. major in Microbiology

Part 3. Teaching and Learning Matrix

Intended Learning Assessment

Course Contents Learning Activities
Outcomes (ILOs) Tasks
ILO 1: LECTURE #1 1. Lecture PPT Class Activity /
a. to summarize the major The Prokaryotic Genome 2. Supplementary Concepts Review
discoveries related to microbial 1.Mendel and the beginning of material/s:
genetics genetics DNA IN BACTERIAL Discussion Board:
b. to differentiate the different 2.Discovery of DNA CELLS Journal about
3.PCR and the Omics Era https://www.labxchang Lecture#1
types of genetic elements
4.Chromosomes and other genetic e.org/library/items/lb:L
elements abXchange:079d5ae3:lx_i Virtual Simulation
5. Prokaryotic genome mage:1
organization
ILO 2: LECTURE #2 1. Lecture PPT Class Activity /
a. to compare and contrast Flow of Genetic Information 2. Supplementary Concepts Review
replication, transcription and 1.Structure of nucleic acids and material/s:
translation proteins (self- review) THE CENTRAL Discussion Board:
b. to describe the process in 2.DNA synthesis: Replication DOGMA Journal about
3.RNA synthesis: Transcription https://www.jove.com Lecture#2
protein secretion
4.Protein synthesis: Translation /science-
5.Protein processing, secretion and education/10798/the- Online Test
targeting central-dogma
ILO 3: LECTURE #3 1. Lecture PPT Class Activity /
a. to discuss the molecular basis DNA Damage and Repair 2. Supplementary Concepts Review
of mutations and the various 1.Mutations and mutants material/s:
repair mechanisms 2.Determining mutation rates TYPES OF Discussion Board:
b. to compute survival and 3.Mutagenesis, reversion & MUTATIONS Journal about
suppression https://www.jove.com Lecture#3
mutation rates
4.DNA damage repair systems /science-
education/11483/muta Essay
tions
PRELIMINARY EXAMINATIONS
ILO 4: LECTURE #4 1. Lecture PPT Class Activity /
a. to distinguish between Regulation of Gene Expression 2. Supplementary Concepts Review
negative and positive control of 1. DNA-binding proteins and material/s:
gene regulation transcriptional regulation OPERONS Discussion Board:
b. to predict the bacterial 2.RNA-based regulation https://www.jove.com Journal about
3.Regulation of enzymes and other /science- Lecture#4
responses to different regulatory
proteins education/11610/opero
mechanisms
4.Signal transduction, Other ns Virtual Simulation
regulatory mechanisms PROKARYOTIC
TRANSCRIPTIONAL
ACTIVATORS AND
REPRESSORS
https://www.jove.com
/science-
education/11609/proka
ryotic-transcriptional-
activators-and-
repressors

ILO 5: LECTURE #5 1. Lecture PPT Class Activity /

a. to differentiate the horizontal Gene Exchanges in Bacteria and 2. Supplementary Concepts Review
and vertical gene transfers Archaea material/s:
between Archaea and Bacteria 1.Genetic recombination Discussion Board:
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 University of Santo Tomas
The Graduate School
NATURAL SCIENCES CLUSTER
M.Sc. major in Microbiology

b. to illustrate genetic exchanges 2.Transformation in Bacteria MECHANISMS OF Journal about

in Bacteria 3.Transduction in Bacteria DNA TRANSFER IN Lecture#5
4.Conjugation in Bacteria BACTERIA
5.Horizontal gene transfer in https://www.labxchan Online Test
Archaea ge.org/library/items/lb
6. Restriction enzymes and :LabXchange:9348a636:h
molecular cloning tml:1
MOLECULAR
CLONING
https://www.jove.com
/v/5074/molecular-
cloning
ILO 6: LECTURE #6 1. Lecture PPT Class Activity /
a. to evaluate the benefits and Gene Cloning and Genetic 2. Supplementary Concepts Review
risks of genetic engineering Engineering with Basic material/s:
Bioinformatics OVERVIEW OF Discussion Board:
and other genome-based
1. Tools for manipulating DNA GENETIC Journal about
technologies
2. GMOs and genetic engineering ENGINEERING Lecture#6
b. to construct a phylogenetic 3. Synthetic biology and genome https://www.jove.com
tree based on similarities of editing /v/5552/an-overview- Submit a
gene sequences 4. Constructing phylogenetic trees of-genetic-engineering phylogenetic tree
5. Bioinformatics / NGS tools SYNTHETIC using an online
BIOLOGY tool/software
https://www.jove.com
/science-
education/12037/synth
etic-biology
GENOMICS AND
BIOINFORMATICS
https://www.jove.com
/science-
education/11122/geno
mics
FINALS EXAMINATIONS
Capstone Requirement 1: Infographic Poster
Capstone Requirement 2: Critique on Microbial Genetics Paper

Part 4 Course Resources

Basic Reading • Madigan MT, Martinko JM, Parker J, 2018. Brock’s Biology of
Microorganisms 15th edition. Prentice Hall International, Inc., USA.
• Alberts, B., A. Johnson, J. Lewis and D. Morgan, M. Raff , K. Roberts and P.
Walter. 2014. Molecular Biology of the Cell. 6th ed. Garland Science. 1464 pp.
• Chaudhari, K. 2013. Microbial Genetics. Teri Press.
• Maloy,S.R., J.E. Cronan and D. Freifelder. 1994. Microbial Genetics.
Jones & Bartlett. 484 pp.
• Streips, U.N. and R.E. Yasbin. 2004. Modern Microbial Genetics, 2nd Ed.
John Wiley & Sons. 672 pp.
• Tortora, G.J. Microbiology.2010. An Introduction, 10th ed. San Francisco:
Pearson

Extended Readings • Kolter, R. and S. Maloy. 2012. Microbes and Evolution. The World that
Darwin Never Saw. ASM Press.

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 University of Santo Tomas
The Graduate School
NATURAL SCIENCES CLUSTER
M.Sc. major in Microbiology

• Synder, L., J.E. Peters, T.M. Henkin and W. Champness. 2013. Molecular
Genetics of Bacteria. 4th ed. ASM Press. 728 pp.
• White, D., J. Drummond and C. Fuqua. 2011. The Physiology and
Biochemistry of Prokaryotes. 4th ed. Oxford Univ. Press. 656 pp.
• Handelsman, J. 2004. Metagenomics: Application of Genomics to Uncultured
Microorganisms. Microbiol Mol. Biol. Rev. 68(4) 669-685.
• Rhodes, H. and K. Sawyer (Rapporteurs). 2015. Public Engagement on
Genetically Modified Organisms: When Science and Citizens Connect: A
Workshop Summary. National Academies Press. 59 pp.

Journals Proceedings of the National Academy of Sciences

Nature
Science
Journal of Molecular Biology
Cell
Molecular Cell
Nature Reviews Molecular Cell Biology
Trends in Genetics
Microbiology
Genome Biology
Journal of Bacteriology
Microbiology and Molecular Biology Reviews

Web References www.nature.com/scitable/ebooks/...Microbial-Genetics-16570311/contents

microbiology.muohio.edu/~steven/mbi161/genetics161.html
www.biomedcentral.com/bmcmicrobiol/sections/microbial...

Part 5 . Learner Assessment

(to be negotiated with students)

Course Requirements Percentage

Attendance 5%
Participation 10%
Individual 5%
Group Activities 5%
Assessments 55%
• ILO 1: Individual Activity Output / Group Report 5%
• ILO 2: Online Test / Group Report 5%
• ILO 3: Essay / Group Report 5%
• Capstone 1: Infographic Poster 10%
• ILO 4: Individual Activity Output / Group Report 5%
• ILO 5: Online Test / Group Report 5%
5%
• ILO 6: Phylogenetic Tree / Group Report
15%
• Capstone 2: Critique on Microbial Genetics Paper
Examination 30%
Preliminary 15%
Final 15%

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 University of Santo Tomas
The Graduate School
NATURAL SCIENCES CLUSTER
M.Sc. major in Microbiology

Part 6. Course Policies

1. Regular attendance is expected. In case of failure to attend the class session due to unavoidable
circumstance, you are responsible for making up any work missed.
2. Report to class on time and stay during the entire class session.
3. Active participation is expected in every session.
4. In-class activities must be accomplished in class.
5. Extended out of class activities must be computerized.
6. Observe strictly the schedule for submission of all out of class activities.
7. Feel free to come and consult with the professor regarding problems in assigned work.
8. Observe proper classroom decorum.
9. Intellectual and academic honesty is expected of everyone. Acknowledge all source of
information. Avoid any form of plagiarism.
10. Other policies may be decided and negotiated by students.
11. Observe strictly the schedule for submission of all out of class activities.
12. Consult with the professor regarding problems in assigned task.
13. Intellectual and academic honesty is expected of everyone. Acknowledge all source of
information used in your papers.
14. Policies in the student handbook applies.

Prepared by: Approved by:

Asst. Prof. Aimee Caye G. Chang, PhD ________________________

Faculty Dean

Date: August 6, 2021 Date:

Part 7. Course Calendar

Session/ Target Topics /Activities Outputs

Week Dates
August 17, COURSE ORIENTATION N/A
01 2021

August 24, Lecture #1: Individual Activity Output from

02 2021 The Prokaryotic Genome Virtual Simulation

August 31, Discussion: Journal about Lecture #1 Group Reporting:

03 2021 Group 1

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 University of Santo Tomas
The Graduate School
NATURAL SCIENCES CLUSTER
M.Sc. major in Microbiology

September 7, Lecture #2: Online Test

04 2021 Flow of Genetic Information

September Discussion: Journal about Lecture #2 Group Reporting:

05 14, 2021 Group 2

September Lecture #3: Essay

06 21, 2021 DNA Damage and Repair

September Discussion: Journal about Lecture #3 Group Reporting:

07 28, 2021 Group 3

October 5, Capstone 1 Presentation and Grading of

08 2021 Infographic Poster

October 12,
09 2021 PRELIMINARY EXAMINATIONS

October 19, Lecture #4: Individual Activity Output from

10 2021 Regulation of Gene Expression Virtual Simulation

October 26, Discussion: Journal about Lecture #4 Group Reporting:

11 2021 Group 1

November 2, HOLIDAY: All Souls’ Day

12 2021

November 9, Lecture #5: Online Test

13 2021 Gene Exchanges in Bacteria and Archaea

November 16, Discussion: Journal about Lecture #5 Group Reporting:

14 2021 Group 2

November 23, Lecture #6: Phylogenetic Tree (generated

15 2021 Gene Cloning and Genetic Engineering from using an online
with Basic Bioinformatics tool/software)
November 30, Discussion: Journal about Lecture #6 Group Reporting:
16 2021 Group 3

December 7, Capstone 2 Presentation and Grading of

17 2021 Critique Paper

December 14,
18 2021 FINAL EXAMINATIONS

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