Outline

Overview

Microorganisms are vital to life on Earth. By examining the role of microbes in healthy ecosystems, and high profile recent cases in emerging infections, students will gain perspective on the critical role that microbes play in health and disease. This unit is structured along three themes: 1. Microbes in the anthropocene: you will evaluate the role of microbes in healthy and disturbed ecosystems and how epidemiology and surveillance can track disease outbreaks; 2. Emergence of microbes: you will explore how and why infectious diseases emerge and re-emerge; 3. Current challenges and new approaches: you will evaluate the role of microbes in chronic diseases and diseases of unknown cause, and how new drugs and treatments are developed and used. This advanced unit includes six tutorial sessions on current challenges and new approaches that support self-directed learning with discussions on contemporary microbiology topics. The integrated practical component teaches advanced practical skills in culture, microscopy and molecular biology in the PC2 laboratory context. Workshops and professional tutorials relate the material to the real world. This unit sits at the forefront of modern medical microbiology and will equip you for a career in microbiology in areas including fundamental research, industry, biotechnology, hospital services, policy and teaching, among others.

Unit details and rules

Academic unit	Life and Environmental Sciences Academic Operations
Credit points	6
Prerequisites ?	A mark of 70 or above in (MIMI2X02 or MEDS2004 or MICR2X22 or BMED2404)
Corequisites ?	None
Prohibitions ?	MICR3011 or MICR3021 or MICR3911
Assumed knowledge ?	Fundamental concepts of microorganisms, biomolecules and ecosystems
Available to study abroad and exchange students	Yes

Teaching staff

Coordinator	Ziggy Marzinelli, e.marzinelli@sydney.edu.au
Laboratory supervisor(s)	Leona Campbell, leona.campbell@sydney.edu.au
Lecturer(s)	Helen Agus, helen.agus@sydney.edu.au
	Timothy Newsome, timothy.newsome@sydney.edu.au
	David Guest, david.guest@sydney.edu.au
	Christopher Harmer, christopher.harmer@sydney.edu.au
	Dee Carter, dee.carter@sydney.edu.au
	Ziggy Marzinelli, e.marzinelli@sydney.edu.au

Type	Description	Weight	Due	Length
Final exam (Record+)	Final exam Final exam assessing all course content.	40%	Formal exam period	1.5 hours
Outcomes assessed:
Small test	In-class quiz Assessment of theory/lectures of the first module of the course.	14%	Week 06	50 min
Outcomes assessed:
Presentation	Group presentation Group presentation on a paper in the context of the One Health concept.	6%	Week 07 Due date: 05 Apr 2022 at 14:00	10 minutes
Outcomes assessed:
Assignment	Lab archives Up-to-date lab book through lab archives based on wet laboratory practicals	10%	Week 10 Due date: 06 May 2022 at 23:59	Ongoing
Outcomes assessed:
Tutorial quiz	Bioinformatics quiz 1 Quiz to assess knowledge of first 2 bioinformatics tutorials.	6%	Week 11 Due date: 10 May 2022 at 14:00	30 minutes
Outcomes assessed:
Assignment	Report Report based on the findings of the laboratory (wet) practicals	10%	Week 12 Due date: 20 May 2022 at 23:59	Ongoing
Outcomes assessed:
Tutorial quiz	Bioinformatics quiz 2 Assessment based on bioinformatics tutorials 3-4.	14%	Week 13 Due date: 24 May 2022 at 14:00	120 min
Outcomes assessed:
= hurdle task ? = group assignment ? = Type B final exam ?

Assessment summary

Details of all assessments, such as rubrics, submission mode/dates, etc., available in Canvas.

In-class quiz (hurdle task): Assessment of the theory / lecture content of module 1 of the course through a combination of multiple choice and short answer questions. Students must meet the required standard in this assessment to pass the unit.

Student presentation: Assessment of critical understanding, interpretation and presentation of the scientific literature on genotyping; oral communication skills and group work.

Lab activities: Ongoing assessment of record-keeping in lab book throughout the laboratory practical component of the course which must be submitted when all laboratory practicals are completed (10%) through LabArchives and a submitted report based on the aims, methodologies, results and interpretation of the lab activities (10%).

Bioinformatic quizzes (hurdle task): Two in-class quizzes (6%, 14%) testing your understanding of the content of the four bioinformatics tutorials. Students must meet the required standard in this assessment to pass the unit.

Final exam (hurdle task): End-of-semester exam assessing all components of the unit. The exam will cover all material in the unit from both lectures and practical classes. The exam will have a mixture of multiple choice questions and short answer questions. Students must meet the required standard in this assessment to pass the unit.

Final exam: This assessment is compulsory and failure to attend, attempt, or submit will result in the award of an AF grade.

If a second replacement exam is required, this exam may be delivered via an alternative assessment method, such as a viva voce (oral exam). The alternative assessment will meet the same learning outcomes as the original exam. The format of the alternative assessment will be determined by the unit coordinator.

Assessment criteria

The University awards common result grades, set out in the Coursework Policy 2014 (Schedule 1).

As a general guide, a high distinction indicates work of an exceptional standard, a distinction a very high standard, a credit a good standard, and a pass an acceptable standard.

Result name	Mark range	Description
High distinction	85 - 100	Awarded when you demonstrate the learning outcomes for the unit at an exceptional standard.
Distinction	75 - 84	Awarded when you demonstrate the learning outcomes for the unit at a very high standard.
Credit	65 - 74	Awarded when you demonstrate the learning outcomes for the unit at a good standard.
Pass	50 - 64	Awarded when you demonstrate the learning outcomes for the unit at an acceptable standard.
Fail	0 - 49	When you don’t meet the learning outcomes of the unit to a satisfactory standard.

For more information see guide to grades.

Late submission

In accordance with University policy, these penalties apply when written work is submitted after 11:59pm on the due date:

Deduction of 5% of the maximum mark for each calendar day after the due date.
After ten calendar days late, a mark of zero will be awarded.

Academic integrity

The Current Student website provides information on academic integrity and the resources available to all students. The University expects students and staff to act ethically and honestly and will treat all allegations of academic integrity breaches seriously.

We use similarity detection software to detect potential instances of plagiarism or other forms of academic integrity breach. If such matches indicate evidence of plagiarism or other forms of academic integrity breaches, your teacher is required to report your work for further investigation.

Use of generative artificial intelligence (AI) and automated writing tools

You may only use generative AI and automated writing tools in assessment tasks if you are permitted to by your unit coordinator. If you do use these tools, you must acknowledge this in your work, either in a footnote or an acknowledgement section. The assessment instructions or unit outline will give guidance of the types of tools that are permitted and how the tools should be used.

Your final submitted work must be your own, original work. You must acknowledge any use of generative AI tools that have been used in the assessment, and any material that forms part of your submission must be appropriately referenced. For guidance on how to acknowledge the use of AI, please refer to the AI in Education Canvas site.

The unapproved use of these tools or unacknowledged use will be considered a breach of the Academic Integrity Policy and penalties may apply.

Studiosity is permitted unless otherwise indicated by the unit coordinator. The use of this service must be acknowledged in your submission as detailed on the Learning Hub’s Canvas page.

Outside assessment tasks, generative AI tools may be used to support your learning. The AI in Education Canvas site contains a number of productive ways that students are using AI to improve their learning.

Learning support

Simple extensions

If you encounter a problem submitting your work on time, you may be able to apply for an extension of five calendar days through a simple extension.  The application process will be different depending on the type of assessment and extensions cannot be granted for some assessment types like exams.

Special consideration

If exceptional circumstances mean you can’t complete an assessment, you need consideration for a longer period of time, or if you have essential commitments which impact your performance in an assessment, you may be eligible for special consideration or special arrangements.

Special consideration applications will not be affected by a simple extension application.

Using AI responsibly

Co-created with students, AI in Education includes lots of helpful examples of how students use generative AI tools to support their learning. It explains how generative AI works, the different tools available and how to use them responsibly and productively.

Weekly schedule

WK	Topic	Learning activity
Multiple weeks	Working in PC2 labs, key microbiology lab techniques, clinical investigation of microbial infections and molecular techniques for analyses of disease outbreaks.	Science laboratory (21 hr)
Multiple weeks	Bioinformatics	Tutorial (15 hr)
Week 07	Group presentation on a research paper on microbiology	Presentation (3 hr)
Weekly	The role microorganisms play on human and environmental health. Encompasses bacteria, fungi, protists and viruses free-living and/or associated with eukaryotic hosts on land and in the ocean.	Lecture (26 hr)

Study commitment

Typically, there is a minimum expectation of 1.5-2 hours of student effort per week per credit point for units of study offered over a full semester. For a 6 credit point unit, this equates to roughly 120-150 hours of student effort in total.

Learning outcomes

Learning outcomes are what students know, understand and are able to do on completion of a unit of study. They are aligned with the University's graduate qualities and are assessed as part of the curriculum.

Outcomes
Graduate qualities

At the completion of this unit, you should be able to:

LO1. Assess, analyse and evaluate the role of microbes in our environment, how they can act to provide healthy ecosystems, water, food, animals and people, and how this can be disrupted, resulting in disruption leading to disease outcomes.
LO2. Evaluate and develop an advanced understanding of how microbes might emerge or re-emerge to impact on global health, using specific illustra�ve examples.
LO3. Evaluate and develop an advanced understanding of the ways in which important microbes pose ongoing challenges to human and planetary health, and new approaches to meet these challenges.
LO4. Interpret complex microbiology laboratory findings, analyse data and assess and validate methodologies.
LO5. Demonstrate and develop an advanced, high-level practical dexterity in the biosafety context and knowledge and skills relevant to the microbiology profession.
LO6. Critically evaluate and synthesise the research literature and other sources to create and communicate independent ideas and knowledge relating to microbes in current real-world challenges.

Graduate qualities

The graduate qualities are the qualities and skills that all University of Sydney graduates must demonstrate on successful completion of an award course. As a future Sydney graduate, the set of qualities have been designed to equip you for the contemporary world.

GQ1	Depth of disciplinary expertise Deep disciplinary expertise is the ability to integrate and rigorously apply knowledge, understanding and skills of a recognised discipline defined by scholarly activity, as well as familiarity with evolving practice of the discipline.
GQ2	Critical thinking and problem solving Critical thinking and problem solving are the questioning of ideas, evidence and assumptions in order to propose and evaluate hypotheses or alternative arguments before formulating a conclusion or a solution to an identified problem.
GQ3	Oral and written communication Effective communication, in both oral and written form, is the clear exchange of meaning in a manner that is appropriate to audience and context.
GQ4	Information and digital literacy Information and digital literacy is the ability to locate, interpret, evaluate, manage, adapt, integrate, create and convey information using appropriate resources, tools and strategies.
GQ5	Inventiveness Generating novel ideas and solutions.
GQ6	Cultural competence Cultural Competence is the ability to actively, ethically, respectfully, and successfully engage across and between cultures. In the Australian context, this includes and celebrates Aboriginal and Torres Strait Islander cultures, knowledge systems, and a mature understanding of contemporary issues.
GQ7	Interdisciplinary effectiveness Interdisciplinary effectiveness is the integration and synthesis of multiple viewpoints and practices, working effectively across disciplinary boundaries.
GQ8	Integrated professional, ethical, and personal identity An integrated professional, ethical and personal identity is understanding the interaction between one’s personal and professional selves in an ethical context.
GQ9	Influence Engaging others in a process, idea or vision.

Outcome map

Learning outcomes	Graduate qualities
Learning outcomes

Responding to student feedback

This section outlines changes made to this unit following staff and student reviews.

This is the first time this unit has been offered.

Additional information

Work, health and safety

This WHS information is for information only as it applies to standard practical delivery.

We are governed by the Work Health and Safety Act 2011, Work Health and Safety Regulation 2011 and Codes of Practice. Penalties for non-compliance have increased. Everyone has a responsibility for health and safety at work. The University’s Work Health and Safety policy explains the responsibilities and expectations of workers and others, and the procedures for managing WHS risks associated with University activities.

General laboratory safety rules

No eating or drinking is allowed in any laboratory under any circumstances
A laboratory coat and closed-toe shoes are mandatory
Follow safety instructions in your manual and posted in laboratories
In case of fire, follow instructions posted outside the laboratory door
First aid kits, eye wash and fire extinguishers are located in or immediately outside each laboratory
As a precautionary measure, it is recommended that you have a current tetanus immunisation. This can be obtained from University Health Service: unihealth.usyd.edu.au/

Many of the microorganisms that will be studied in class may cause disease if mishandled. Therefore, great care to maintain good microbiological techniques must be taken when handling cultures, slides and other materials that contain or have been in contact with living microorganisms.

Behaviour and activities in the laboratory must comply with Australian Standard AS/NZS 2243.3:2010: Safety in laboratories Part 3: Microbiological aspects and containment facilities. The Standard is available via the link under Prac Resources in the Canvas MIMI2x02 Microbes, Infection & Immunity site. As you will gain experience handling potentially pathogenic microbes in this unit of study, your immune status is important. You are strongly advised to contact the unit coordinator if you have any predisposing condition or issue that might be relevant to your participation in these practical sessions.

Disclaimer

The University reserves the right to amend units of study or no longer offer certain units, including where there are low enrolment numbers.

To help you understand common terms that we use at the University, we offer an online glossary.

Current students

Overview

Overview

Unit details and rules

Teaching staff

Assessment

Assessment

Assessment summary

Assessment criteria

Late submission

Academic integrity

Learning support

Learning support

Simple extensions

Special consideration

Using AI responsibly

Weekly schedule

Weekly schedule

Study commitment

Learning outcomes

Learning outcomes

Graduate qualities

Outcome map

Responding to student feedback

Responding to student feedback

Additional information

Additional information

Work, health and safety

Disclaimer

On this page

Useful links

Media

Student links

About us

Connect

Current students

MICR3921: Microbes in Health and Disease (Advanced)

Semester 1, 2022 [Normal day] - Camperdown/Darlington, Sydney

Overview

Overview

Unit details and rules

Teaching staff

Assessment

Assessment

Assessment summary

Assessment criteria

Late submission

Academic integrity

Learning support

Learning support

Simple extensions

Special consideration

Using AI responsibly

Weekly schedule

Weekly schedule

Study commitment

Learning outcomes

Learning outcomes

Graduate qualities

Outcome map

Responding to student feedback

Responding to student feedback

Additional information

Additional information

Work, health and safety

Disclaimer

On this page

Useful links

Media

Student links

About us

Connect