MICRO 3000 - Infection & Immunity IIIA

North Terrace Campus - Semester 1 - 2023

This advanced course examines the molecular basis of host-pathogen interactions for bacterial, viral and parasite infections of significant global and medical importance. This includes how these interactions contribute to the pathogenesis (i.e. mechanisms of disease) and subsequent transmission of the pathogens to new hosts, their dependence on access to nutrients and evasion of host clearance mechanisms. Key strategies used by pathogens to survive in the host, along with the importance of vaccines, antimicrobial drugs, the microbiome and tools used to research and identify pathogens will also be discussed. The lecture program is complemented by tutorials, which extend skills in exploring and critically assessing the scientific literature, and practicals which develop advanced experimental skills for the study of pathogenic mechanisms.

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Course Details

Course Code	MICRO 3000
Course	Infection & Immunity IIIA
Coordinating Unit	School of Biological Sciences
Term	Semester 1
Level	Undergraduate
Location/s	North Terrace Campus
Units	6
Contact	Up to 8 hrs per week
Available for Study Abroad and Exchange	N
Prerequisites	MICRO 2500 or MICRO 2504 or equivalent
Incompatible	MICRO 3007, MICRO 3102
Assessment	Written assignments; Scientific Communication Assignment; Tests

Course Staff

Course Coordinator: Professor Michael Beard

Course Timetable

The full timetable of all activities for this course can be accessed from Course Planner.

Course Learning Outcomes

1	To gain an understanding of the molecular mechanisms that underpin the pathogenesis and control of bacterial, virus, and parasite infections, and the interaction of microbial pathogens with the immune system.
2	To gain a body of experimental skills and techniques frequently used in molecular microbiology research which are fundamental to understanding how research in these disciplines is conducted.
3	To develop essential skills in experimental design, techniques and execution which are highly relevant to solving problem in microbial pathogenesis and many other areas of scientific research.
4	To develop organisational and time management skills and the capacity for multi-tasking.
5	To foster the ability to work in small teams and to communicate and coordinate outcomes with a larger group of colleagues.
6	To become exposed to experimental processes that develop over many weeks, building up a framework of experience with techniques and concepts that could not readily be obtained in the course of a semester within a single research laboratory.
7	To be adequately educated and mentored through close contact with academic staff.

University Graduate Attributes

This course will provide students with an opportunity to develop the Graduate Attribute(s) specified below:

University Graduate Attribute	Course Learning Outcome(s)
Attribute 1: Deep discipline knowledge and intellectual breadth Graduates have comprehensive knowledge and understanding of their subject area, the ability to engage with different traditions of thought, and the ability to apply their knowledge in practice including in multi-disciplinary or multi-professional contexts.	1, 2, 3, 6, 7
Attribute 2: Creative and critical thinking, and problem solving Graduates are effective problems-solvers, able to apply critical, creative and evidence-based thinking to conceive innovative responses to future challenges.	1,2,3,6
Attribute 3: Teamwork and communication skills Graduates convey ideas and information effectively to a range of audiences for a variety of purposes and contribute in a positive and collaborative manner to achieving common goals.	1,2,3,4,5,6,7
Attribute 4: Professionalism and leadership readiness Graduates engage in professional behaviour and have the potential to be entrepreneurial and take leadership roles in their chosen occupations or careers and communities.	1,2,3,4,5,6
Attribute 5: Intercultural and ethical competency Graduates are responsible and effective global citizens whose personal values and practices are consistent with their roles as responsible members of society.	2,3,4,5,6,7
Attribute 8: Self-awareness and emotional intelligence Graduates are self-aware and reflective; they are flexible and resilient and have the capacity to accept and give constructive feedback; they act with integrity and take responsibility for their actions.	4,5,6,7

Learning Resources

Required Resources

Textbook

The recommended text book is:

"Bacterial Pathogenesis. A Molecular Approach" Third edition. Wilson, B.A., Salyers, A.A., Whitt, D.D., and Winkler, M.E. ASM Press.

Additional resourses

Please refer to MyUni for additional reading and video material

Practical laboratory

An essential component of the physical fabric is a large modern and well-equipped teaching laboratory, designed and maintained for advanced practical experiments. This laboratory can be at most only be marginally removed from research standard and should be in close proximity to Biological Sciences. This close juxtaposition of research and undergraduate education is entirely in keeping with the aspirations of a research-intensive university where active research informs and stimulates in the classroom.

A combined course and practical manual will be supplied during orientation/week 1.

Recommended Resources

Recommemded reading will be posted on MyUni.

Online Learning

Teaching materials and course documentation will be posted on the MyUni website (http://myuni.adelaide.edu.au/).

Learning & Teaching Modes

This course will be delivered in the following means:

Internal

3 x 1 hour lectures per week,
1 x 2 hour tutorial per fortnight (total of 5 sessions)
3 x 5 hours practical per fortnight

Practical sessions of 5 hours on
Wednesday and Thursday afternoons in odd weeks and 5 hours in even weeks.
Practicals include: wet lab sessions and dry lab bioinformatics sessions.

Workload

The information below is provided as a guide to assist students in engaging appropriately with the course requirements.

A student enrolled in a 6 unit course, such as this, should expect to spend, on
average 24 hours per week on the studies required. This includes both the
formal contact time required to the course (e.g., lectures and practicals), as
well as non-contact time (e.g., reading and revision).

Learning Activities Summary

Week	Type of learning activity	Topic
1	Lecture	Bacteria-host interactions and innate defences
	Practical	Molecular analysis of bacterial virulence factors
	Tutorial
2	Lecture	Bacteria-host interactions and innate defences Gut pathogens Intracellular bacterial pathogens
	Practical	Molecular analysis of bacterial virulence factors
	Tutorial	Critical thinking and analysis of primary research papers related to lecture material
3	Lecture	Intracellular bacterial pathogens Bacteria and subversion of host cell biology
	Practical	Molecular analysis of bacterial virulence factors
	Tutorial
4	Lecture	Cell surface polysacchardies Gene regulation and the host environment
	Practical	Molecular analysis of bacterial virulence factors
	Tutorial	Critical thinking and analysis of primary research papers related to lecture material
5	Lecture	Antibiotics
	Practical	Molecular analysis of bacterial virulence factors
	Tutorial
6	Lecture	Vaccines
	Practical	Introduction to Bioinformatics
	Tutorial	Critical thinking and analysis of primary research papers related to lecture material
Mid-Semester Break
7	Lecture	Microbiota
	Tutorial
	Practical	Molecular analysis of bacterial virulence factors In silico analysis of gene sequences and sequence manipulation
8	Lecture	Stress responses
	Tutorial	Critical thinking and analysis of primary research papers related to lecture material, , including problem solving questions
	Practical	Molecular analysis of bacterial virulence factors In silico analysis of gene sequences and sequence manipulation
9	Lecture	Mucosal, skin, and respiratory tract pathogens
	Tutorial
	Practical	Molecular analysis of bacterial virulence factors In silico analysis of gene sequences and sequence manipulation
10	Lecture	Respiratory tract pathogens Gene expression in vivo
	Tutorial	Critical thinking and analysis of primary research papers related to lecture materia, including problem solving questions
	Practical	Molecular analysis of bacterial virulence factors In silico analysis of gene sequences and sequence manipulation
11	Lecture	Respiratory tract pathogens Membrane proteins
	Tutorial
	Practical	Molecular analysis of bacterial virulence factors In silico analysis of gene sequences and sequence manipulation
12	Lecture	Parasites: Viruses and Malaria
	Tutorial
	Practical	Molecular analysis of bacterial virulence factors In silico analysis of gene sequences and sequence manipulation
13*

*Optional teaching week

The University's policy on Assessment for Coursework Programs is based on the following four principles:

Assessment must encourage and reinforce learning.
Assessment must enable robust and fair judgements about student performance.
Assessment practices must be fair and equitable to students and give them the opportunity to demonstrate what they have learned.
Assessment must maintain academic standards.

Assessment Summary

The marks for I&IA are distributed as follows:

Assessment Task	Type of Assessment	Percentage of total assessemnt for grading purposes	Hurdle Yes/No	Outcomes being assessed/achieved
Experimental Summary #1 (500 words)	Summative	5%	No	1-7
Experimental Summary #2 (1200 words)	Summative	15%	No	1-7
Bioinformatics Assignments	Summative	20%	No	1-7
Tutorials	Summative	10%	No	1,3,4,7
Final Exam	Summative	50%	No	1,3,7

Assessment Detail

Exams (50% of course grade).

One exam will be given to test the capacity to comprehend and integrate knowledge
from a broad range of topics relevant to the disciplines of bacterial microbiology.

1/3rd of the marks will be on questions of a “problem solving nature” which be posted
on MyUni 7-10 days before the exam. This provides students time and resources
to research the problem and prepare a solution.

2/3rd of the marks will be by short answer or similar questions.

Tutorials (10% of course grade)

Small groups of students will analyse and reflect on key primary research papers
relevant to the lecture course, and will be guided by set of questions. These
questions are used to drive participation in the tutorial

The tutorials assess knowledge of scientific concepts, techniques and technologies,
cognitive skills, and critical thinking.

Assessment will be performance and participation and determined via the use of a scoring
rubrick. See Course manual for details.

Practicals (40% of course)

Assessment will be by a combination of activities that include one or more of the following:

1) Practical theory question
assignment, A series of questions are used to promote reading of the practical
manual and the theory behind the methods and reagents used. Online via MyUni.
Feed back given before completion of other reports.

2) Daybook.
This is used to record all experimental work and results. It is used to write the experimental reports.

3) Wet lab practical experimental reports.
Write-up of a simple experiments: assessment of recording, analysis, interpretation and
written presentation of experimental data.
This first assessment provides feedback on essential skills required for
good laboratory practice and for later assessments.

4) Bioinformatics dry exercises and experiments

Divided into 2 to 3 sections with
evenly spread, separate submission dates. Assesses ability to handle software,
nature of the DNA sequences, identify and analyse sequence motifs, relationship
to protein sequence, in silico cloning exercise. Feedback given for each
report. Due half of semester that does not have wet prac..

Submission

Submission Guidelines

It is your responsibility to ensure that your work is submitted on time. All assessments (except daybook) are to be submitted electronically (the study questions are located on MyUni). In the case of the Experimental Summaries and Bioinformatics assessments, you will use the provided templates and submit your completed work via the relevant
submission links MyUni. Note that The Experimental summaries will be submitted via a “Turnitin submission link” to check for plagiarism (see page XXVIII) and if evidence of plagiarism is detected, you may be penalised up to and including a zero mark for the assessment in question.

Late submission of assessments

If an extension is not applied for, or not granted then a penalty for late
submission will apply. A penalty of 10% of the value of the assignment for each calendar day that is late (i.e. weekends count as 2 days), up to a maximum of 50% of the available marks will
be applied. This means that an assignment that is 5 days or more late without an approved extension can only receive a maximum of 50% of the mark.

Course Grading

Grades for your performance in this course will be awarded in accordance with the following scheme:

M10 (Coursework Mark Scheme)
Grade	Mark	Description
FNS		Fail No Submission
F	1-49	Fail
P	50-64	Pass
C	65-74	Credit
D	75-84	Distinction
HD	85-100	High Distinction
CN		Continuing
NFE		No Formal Examination
RP		Result Pending

Further details of the grades/results can be obtained from Examinations.

Grade Descriptors are available which provide a general guide to the standard of work that is expected at each grade level. More information at Assessment for Coursework Programs.

Final results for this course will be made available through Access Adelaide.

Student Feedback

The University places a high priority on approaches to learning and teaching that enhance the student experience. Feedback is sought from students in a variety of ways including on-going engagement with staff, the use of online discussion boards and the use of Student Experience of Learning and Teaching (SELT) surveys as well as GOS surveys and Program reviews.

SELTs are an important source of information to inform individual teaching practice, decisions about teaching duties, and course and program curriculum design. They enable the University to assess how effectively its learning environments and teaching practices facilitate student engagement and learning outcomes. Under the current SELT Policy (http://www.adelaide.edu.au/policies/101/) course SELTs are mandated and must be conducted at the conclusion of each term/semester/trimester for every course offering. Feedback on issues raised through course SELT surveys is made available to enrolled students through various resources (e.g. MyUni). In addition aggregated course SELT data is available.
Student Support
Policies & Guidelines
This section contains links to relevant assessment-related policies and guidelines - all university policies.
Fraud Awareness

Students are reminded that in order to maintain the academic integrity of all programs and courses, the university has a zero-tolerance approach to students offering money or significant value goods or services to any staff member who is involved in their teaching or assessment. Students offering lecturers or tutors or professional staff anything more than a small token of appreciation is totally unacceptable, in any circumstances. Staff members are obliged to report all such incidents to their supervisor/manager, who will refer them for action under the university's student’s disciplinary procedures.

The University of Adelaide is committed to regular reviews of the courses and programs it offers to students. The University of Adelaide therefore reserves the right to discontinue or vary programs and courses without notice. Please read the important information contained in the disclaimer.

Authorised by:	Deputy Vice-Chancellor and Vice-President (Academic)
Maintained by:	Course Outlines Administrator