3010BBS Molecular and Applied Microbiology ... - Griffith University

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COURSE OUTLINE


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Academic Organisation: School of Biomolecular and Physical Sciences
Faculty: Science, Environment, Engineering and Technology
Credit point value: 10
Student Contribution Band: Band 2
Course level: Undergraduate
Campus/Location/Learning Mode: Logan / On Campus / In Person
Nathan / On Campus / In Person
Convenor/s: Prof Bharat Patel (Logan)
Prof Bharat Patel (Nathan)
Enrolment Restrictions: Restricted: Approval from Head of School
This document was last updated: 28 July 2008
BRIEF COURSE DESCRIPTION
This course provides detailed studies of rapidly expanding areas of microbiology and everyday
applications of microorganisms. It studies the molecular organisation of the genomes of prokaryotic
microorganisms. The use of modern molecular biology tools in the study of microbial genomes and their
potential power in biotechnology will be highlighted. The application of these tools has provided new
information in areas such as microbial diversity and the evolution of life. In light of this, the extremes of life
on Earth and the prospect of life elsewhere will be discussed. The course also looks at microbial
biotechnology, applications of microorganisms in industry and the environment, and negative aspects of
microbes in industry such as product contamination.
Incompatible: SB13BMM Molecular and Applied Microbiology AND SS13BMM Molecular and Applied
Microbiology AND SS13050 Bacteriology
Prior Assumed: BBS2004 Molecular Genetics OR SB12BMG Molecular Genetics OR SS12BMG Molecular
Genetics
Prior Assumed: BBS2005 Microbiology OR BBS2005L Microbiology OR SB12BMI Microbiology OR
SS12BMI Microbiology


1

SECTION A – TEACHING, LEARNING AND ASSESSMENT
COURSE AIMS
This is a defining course for the Bachelor of Science Microbiology major and Bachelor of Biotechnology
programs. The course focuses on three main areas, that specifically deal with microorganisms: genomics,
bioinformatics and biotechnology. It is designed to provide in-depth studies of the molecular biology of
prokaryotic microorganisms as applied to genes, genome organisation and evolution, molecular
physiology, and methods for studying genomes and bioinformatics. In addition, the important and varied
role of microorganisms in industrial and biotechnological processes will be studied. The course follows on
from the core second year Microbiology and / or Microbial Physiology courses and prepares students for
the option of further postgraduate studies in Microbiology or Biotechnology and / or employment in
industry. It further emphases the importance of microorganisms in our understanding of life and the
environment.
LEARNING OUTCOMES
The course provides an advanced coverage of the many facets of microbiology and how it impacts on our
everyday lives. After completion of this course, students will have an understanding of the following:
1. Characteristics, organisation and function of microbial genomes
2. Techniques for sequencing microbial genomes and the analysis of sequence data by computers
3. Use of genomics in microbial systematics and the comparison of organisms
4. Evolutionary changes in organisms and the prospect of life elsewhere
5. Growth, survival and evolution of microbes through interactions with their environment
6. How microbes are used to improve the environment and produce commercially valuable products in
biotechnology processes
7. Computers and bioinformatics
8. How to critically analyse scientific literature and be able to present this information in the form of a
written assignment
CONTENT, ORGANISATION AND TEACHING STRATEGIES
The course will be taught in modules consisting of lectures and computer labs. The lecture periods will be
used to provide the course detail. Computer labs will provide further explanation and understanding of the
content using web based bioinformatics resources.
Lectures will be presented in-person at Nathan campus and video-conferenced to Logan campus.
Computer-based labs will only be held at the Nathan Campus.
Contact Summary

Lectures will be presented as three-hour sessions once a week. Students are expected to attend all of
these sessions. Interactive computer-based bioinformatics workshops are scheduled as two-hour sessions
and form an integral part of the course.
CONTENT SUMMARY
Section 1. Lecture Schedule and modules:

Course content will be presented in six modules with each module separated into numerous topics.
Depending on the depth of material, the modules can run for one, two or three weeks. The following table
represents a summary of the course content, the weeks in which the modules will run in, and the
assessment items associate with the modules and when the assessment items are to be submitted.

Topic
Module
Content
Weeks

Assessment
Dates
1. Domain
Archaea
Cell structure, habitats, physiology, molecular
biology & biotechnology Evolution and
1, 2 Not applicable

2

Topic
Module
Content
Weeks

Assessment
Dates
Extreme
Environments &
Astrobiology
molecular adaptation and strategies of
extreme environment microbes;
extraterrestrial life.
2 Bioinformatics:
An introduction
Databases, functional genomics, protein
structure-function relationships (Computer
labs- General Bioinformatics methods related
to the topic)
3, 4 Not applicable
3 Bioinformatics:
Molecular
Evolution
Concepts of Evolution, ribosomal RNA &
phylogeny (Computer labs- phylogeny tools)
5 - 7 Bioinformatics 1:
rRNA alignments
& secondary
structures due
week 8
4. Bioinformatics:
Microbial
genomes
Gene transfer mechanisms and microbial
diversity, prokaryotic & eukaryotic genomes,
sequencing and studying genomes,
comparative genomics of pathogenic
microbes (Computer labs- Comparative
genomics & Systems Biology)
8, 9 Bioinformatics 2:
KEGG / Metabolic
pathways due
week 11
5. Environmental
Biotechnology
Bioremediation, Bioleaching, Microbial-
enhanced oil recovery (MEOR), Wastewater
treatment
10, 11 Not applicable
6. Industrial
microbiology
Foods, supplements & beverages,
pharmaceuticals,
Commercial enzymes
12 Environmental /
Industrial
Microbiology Quiz
in week 13
Professor Bharat Patel will teach Topics 1 to 4 (weeks 1 to 9) Dr Tony Greene topics 5 & 6 (weeks 10 to
12). Lectures will be held on Fridays from 9.00 to 12.00 (N61_-2.06, Law) and computer labs will be held
on Wednesdays from 12:00-14:00 in N13_2.04 (Environment 2).
Section 2. Assignment Topics
:
Bioinformatics Assignment 1- rRNA alignments & secondary structures:
The details are available at the
URL
http://trishul.sci.gu.edu.au/courses/ss13bmm/assignment1.pdf

Bioinformatics
Assignment 2- KEGG / Metabolic pathways: The details are available at the URL
http://trishul.sci.gu.edu.au/courses/ss13bmm/assignment2.html

ASSESSMENT
Summary of Assessment

The table below summaries the assessment items for the course. The two bioinformatics assessment items are
worth 15% each, the quiz is worth and the final 1.5 hour end-of-semester exam is worth a further 55%. The two
Bioinformatics assignments are due by COB of the Friday of the week they are due in.

Item

Assessment Task
Length
Weigh
Total
Marks
Relevant
Learning
Outcomes
Due Day and Time
1. Bioinformatics 1:
rRNA alignments &
secondary structures
Requires
specific
answers
15% 100 7 Week 8
2. Bioinformatis 2:
KEGG / Metabolic
pathways
Requires
specific
answers
15% 100 1, 2, 3 Week 11
3. Quiz 30 mins 15% 100 4, 5, 6 Week 13
4. End-of-semester
examination
1.5 hours 55% 100 1 - 6 Examination period

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Note: The assignments should be submitted no later than 5pm of the Friday of the week they are due in.
Failure to submit the assignment by the specified time as specified above will result in zero marks unless there
is documentary evidence of medical or other extenuating circumstances. Without a prior authorised extension,
late submission of assignments will result in a loss of 10% of marks per day.
Assessment Details:

Please note the following:
1. All assessment items for the course are compulsory
and a pass in each of the assessment items is
required to pass the course.
2. Failure to submit the assignment
by the specified time as specified in “Summary of Assessment” above
will result in zero marks unless there is documentary evidence of medical or other extenuating
circumstances. Without a prior authorised extension, late submission of assignments will result in a loss of
10% of marks per day.
3. Students are required to attend the quizzes at either Nathan or Logan
. If students do not wish to attend
the quiz at the campus where they are enrolled, then they should advise the convenor. Quiz attendance is
compulsory; failure to attend or complete the quiz at the specified time will result in a zero mark for the
quiz unless documentary evidence of medical or other extenuating circumstances is provided to the
Convenor within one week of the date of the quiz. Where satisfactory documentation is provided, an
alternative sitting of the quiz can be offered.
4. Results of the assignments and quizzes will be posted at
http://trishul.sci.gu.edu.au/courses/ss13bmm/

Assessment Tasks 1 & 2- Bioinformatics Assignments (15% each):

The first page of the assignment should include your surname, name, student ID and the course code. The
assignment should be based on your own independent research of the topic and summarised in your own
words. Avoid regurgitating information taken directly from books, journals or websites. Remember that non-
peer reviewed websites may contain incorrect or unproven information. I strongly suggest that you seek
assistance from the library in using EndNote database referencing software if you are unfamiliar with it. The
software allows you to search library databases such as the NCIB PubMed and download references and
abstracts from these searches onto to your own computer. The references can be than be inserted into your
Word assignment document while you are writing. After completion of your written work, the bibliography can
be formatted into a relevant citation style of your choice.
Assessment Task- Quiz (final marks = 15%):

A multiple-choice quiz of 30 minutes duration will be held in week 13. You will need to pass this assessment
item to pass the course.
Assessment Task 3: End-of-semester Exam (final marks = 55%):

The exam will consist of a range of question types including multiple choice questions and short answer
questions. The exam format will be discussed in week 12 or 13.
Rationale for assessment:

The Bioinformatics assignment
s will be used to assess the student’s ability to research, analyse and retrieve
information from the web resources. The assignments will assist students in undertaking hands on exercises in
modern biology and expose them to the use of extensive bioinformatics resources including molecular
databases, and online / off line data mining and analysis tools.
The quizzes
will test the understanding of the course matter in specific modules and will be in the form of
multiple choice questions. They will cover material in preceding lectures and the exact content covered will be
advised in the class prior to the quiz.
The end of semester exam
is aimed at testing the overall concepts and understanding of the course detail for
all modules. It will be a combination of multiple choice questions and short answer questions. It will be
undertaken during the end of semester exam period.
GRADUATE SKILLS
The course contributes to the development of graduate skills that students should acquire throughout their
program. These skills are listed below.


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Graduate Skills

Taught
Practised
Assessed
Effective communication (written)



Effective communication (oral)



Effective communication (interpersonal)



Information literacy



Problem solving



Critical evaluation



Work autonomously



Work in teams



Creativity and innovation



Ethical behaviour in social / professional / work environments



Responsible, effective citizenship



TEACHING TEAM
Course Convenor

Convenor Details
Nathan & Logan
Campus Convenor Professor Bharat Patel
Email b.patel@griffith.edu.au
Office Location Science 2, 2.36
Phone 3735 7695
Fax 3735 7773
Consultation times Please contact via email or phone to arrange an appointment
Additional teaching team members

Dr Tony Greene, Email:
t.greene@griffith.edu.au
. Details of any additional members to the teaching team
will be provided in the lectures, via email or on the noticeboard of the
learning@griffith
website.
COURSE COMMUNICATIONS
The course convenor will communicate and make any announcements in the lectures and workshops.
Announcements and information will also be placed on the noticeboard of the Learning@griffith website
and students should consult it regularly in between scheduled classes. As students are expected to attend
the scheduled classes, explanations and clarification of any issues can be made then. Students can also
contact the convenor via email or phone or make an appointment at a suitable time for an individual
consultation.
TEXTS AND SUPPORTING MATERIALS
Reading Material
: Lecture summary is available at the URL
http://trishul.sci.gu.edu.au/courses/ss13bmm/

and at the Learning@Griffith website. Remember that the material provided at the websites is only a
summary of the lectures. For further reading, students should refer to the University library or electronic
databases and journals. Students should also refer to wither of the following two text books:
(a) Madigan, Martinko and Parker, Brock Biology of Microorganisms, Prentice Hall International, 2006,
11th edition

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(b) Prescott, Harley and Klein, Microbiology. McGraw-Hill, 2005 6
th
edition
Computer-based Bioinformatics
: Several websites will be shown and discussed during the lectures and
during the computer labs. Important links have been provided as part of the lecture summary at the URL
http://trishul.sci.gu.edu.au/courses/ss13bmm/

SECTION B – ADDITIONAL COURSE INFORMATION
Enrolment in this course is granted on the basis that a grade of P (Pass) or better has been achieved in
any Pre-requisite or Prior Assumed requirement in this course as listed in this outline. Failure to meet this
requirement may result in you having difficulty with the course and not being able to complete it
successfully. Any additional support or special assistance cannot be expected nor requested if the
prerequisite and/or prior assumed requirements have not been met.
Students should refer to the URL
http://trishul.sci.gu.edu.au/courses/ss13bmm/
and Learning@Griffith
website for further information about this course.


6


SECTION C – KEY UNIVERSITY INFORMATION
ACADEMIC MISCONDUCT
Students must conduct their studies at the University honestly, ethically and in accordance with accepted
standards of academic conduct. Any form of academic conduct that is contrary to these standards is
academic misconduct and is unacceptable.
Some students engage deliberately in academic misconduct, with intent to deceive. This conscious, pre-
mediated form of cheating is one of the worst forms of fraudulent academic behaviour, for which the
University has zero tolerance and for which penalties, including exclusion from the University, will be
applied.
However the University recognises many students commit academic misconduct without intent to deceive.
These students may be required to undertake additional educational activities to remediate their behaviour.
Specifically it is academic misconduct for a student to:
• Cheat in examinations and tests by communicating, or attempting to communicate, with a fellow
individual who is neither an invigilator or member of staff; by copying, or attempting to copy from a
fellow candidate; attempting to introduce or consult during the examination, any unauthorised
printed or written material, or electronic calculating or information storage device; or mobile
phones or other communication device, or impersonates another.

• Fabricate results by claiming to have carried out tests, experiments or observations that have not
taken place or by presenting results not supported by the evidence with the object of obtaining an
unfair advantage.

• Misrepresent themselves by presenting an untrue statement or not disclosing where there is a
duty to disclose in order to create a false appearance or identity.

• Plagiarise by representing the work of another as their own original work, without appropriate
acknowledgement of the author or the source. This category of cheating includes the following:
1. collusion, where a piece of work prepared by a group is represented as if it were the student's
own;
1. acquiring or commissioning a piece of work, which is not his/her own and representing it as if it
were, by
 purchasing a paper from a commercial service, including internet sites, whether pre-written
or specially prepared for the student concerned
 submitting a paper written by another person, either by a fellow student or a person who is
not a member of the University;
2. duplication of the same or almost identical work for more than one assessment item;
3. copying ideas, concepts, research data, images, sounds or text;
4. paraphrasing a paper from a source text, whether in manuscript, printed or electronic form, without
appropriate acknowledgement;
5. cutting or pasting statements from multiple sources or piecing together work of others and
representing them as original work;
6. submitting, as one own work, all or part of another student's work, even with the student's
knowledge or consent.

A student who willingly assists another student to plagiarise (for example by willingly giving them their
own work to copy from) is also breaching academic integrity, and may be subject to disciplinary action.
Visit the University’s Institutional Framework for Promoting Academic Integrity Among Students for further
details.
PLAGIARISM DETECTION SOFTWARE
The University uses plagiarism detection software. Students should be aware that your Course Convenor
may use this software to check submitted assignments. If this is the case your Course Convenor will
provide more detailed information about how the detection software will be used for individual assessment
items.

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HEALTH AND SAFETY
Griffith University is committed to providing a safe work and study environment, however all students, staff and visitors
have an obligation to ensure the safety of themselves and those whose safety may be affected by their actions. Staff
in control of learning activities will ensure as far as reasonably practical, that those activities are safe and that all safety
obligations are being met. Students are required to comply with all safety instructions and are requested to report
safety concerns to the University.
General health and safety information can be obtained from
http://www.griffith.edu.au/hrm/health_and_safety/

Information about Laboratory safety can be obtained from
http://www.griffith.edu.au/ots/secure/health/content_labsafety.html

KEY STUDENT-RELATED POLICIES
All University policy documents are accessible to students via the University’s Policy Library website at:
www.griffith.edu.au/policylibrary
. Links to key policy documents are included below for easy reference:
Academic Calendar

Academic Standing, Progression and Exclusion Policy

Assessment Policy

Examinations Timetabling Policy and Procedures

Guideline on Student E-Mail

Health and Safety Policy

Institutional Framework for Promoting Academic Integrity Among Students

Policy on Student Grievances and Appeals

Student Administration Policy

Student Charter

UNIVERSITY SUPPORT RESOURCES
The University provides many facilities and support services to assist students in their studies. Links to
information about University support resources available to students are included below for easy
reference:
Learning Centres
- the University provides access to common use computing facilities for educational
purposes. For details visit
www.griffith.edu.au/cuse

Learning@Griffith
- there is a dedicated website for this course via the Learning@Griffith student portal.
Student Services
facilitate student access to and success at their academic studies. Student Services
includes: Careers and Employment Service; Chaplaincy; Counselling Service; Health Service; Student
Equity Services (incorporating the Disabilities Service); and the Welfare Office.
Learning Services
within the Division of Information Services provides learning support in three skill areas:
computing skills; library skills; and academic skills. The study skills resources on the website include self-
help tasks focusing on critical thinking, exam skills, note taking, preparing presentations, referencing,
writing, proof reading, and time management.