Unit convenor and teaching staff |
Unit convenor and teaching staff
Unit convener
Helena Nevalainen
Contact via helena.nevalainen@mq.edu.au
E8C302
Upon appointment
Lecturer, tutor
Anwar Sunna
Contact via anwar.sunna@mq.edu.au
E8C207
Upon appointment
Instructor
Angela Sun
Contact via angela.sun@mq.edu.au
E8A301
Upon appointment
Lecturer, tutor
Morten Andersen
Contact via morten.andersen@mq.edu.au
F7B333
Upon appointment
Unit technician
Elsa Mardones
Contact via elsa.mardones@mq.edu.au
E8A172
Upon appointment
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Credit points |
Credit points
4
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Prerequisites |
Prerequisites
Admission to MRes
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Corequisites |
Corequisites
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Co-badged status |
Co-badged status
CBMS331 and CBMS880
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Unit description |
Unit description
The unit explores particular areas of contemporary molecular and medical biotechnology building on students’ existing knowledge and importantly, showing how science is translated to applications in health, industry and the environment. Lecture topics range from the production of recombinant biomolecules in various cell factories, applications of stem cells to joint repair, and applications of nanoparticles for diagnostics. We will look into recent technical and conceptual developments and how these relate to our personal lives, society and industry. Visiting lecturers from industry and various academic disciplines will lead discussion on their areas of expertise. A special feature for the 700-level students is an exercise on science communication. The unit also has a significant hands-on laboratory component with tutorials and assignment tasks.
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Information about important academic dates including deadlines for withdrawing from units are available at https://www.mq.edu.au/study/calendar-of-dates
On successful completion of this unit, you will be able to:
Practical Reports
These are major reports describing the laboratory experiment in detail with references to literature. The report must be submitted to iLearn by the due date (see below) for checking in turnitin. In addition to the electronic copy, a hard copy is to be submitted to the Science and Engineering Student Centre MUSE, where a submission box will be set up. Campus maps are available at http://www.bgo.mq.edu.au/maps_campus.htm. The Centre is open from 8.30 am to 5.30 pm from Monday to Friday.
Submission
All reports and assignments must be submitted by 5.30 pm on the due date.
Late Submission
Written tasks 10% or less - Students who have not submitted the task by the deadline will be awarded a mark of 0 for the task, except for cases in which an application for Special consideration is made and approved (see below).
Written tasks above 10% -There will be a deduction of 10% of the total available marks made from the total awarded mark for each 24 hour period the submission is late. This penalty does not apply for cases in which an application for Special consideration is made and approved. No submissions will be accepted after marked assignments have been returned to the students.
Non-attendance of assessment
Non-Attendance for Assessable Tasks: If you are unable to attend a practical class, tutorial class or exam due to short-term, serious and unavoidable circumstances, you must submit a Special consideration request at ask.mq.edu.au no later than five (5) working days after the assessment task date or due date. Please also immediately contact the Unit Convenor, Prof Helena Nevalainen (helena.nevalainen@mq.edu.au).
Information on Supplementary Exams: If you receive special consideration for the final exam, a supplementary exam will be scheduled in the interval between the regular exam period and the start of the next session. By making a special consideration application for the final exam you are declaring yourself available for a resit during the supplementary examination period and will not be eligible for a second special consideration approval based on pre-existing commitments. Please ensure you are familiar with the policy prior to submitting an application. You can check the supplementary exam information page on FSE101 in iLearn (bit.ly/FSESupp) for dates, and approved applicants will receive an individual notification one week prior to the exam with the exact date and time of their supplementary examination.
The unit expectation is that you will:
· Attend all lectures or when not possible listen to the recorded lectures
· Attend all practicals and set exercises during the practical hours
· Actively engage in the practical and coursework assessment tasks
· Hand in all practical reports and assessment tasks
· Attend to the Great debate
Name | Weighting | Hurdle | Due |
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Practical reports | 30% | No | Various |
Primer crafting task | 10% | No | 14.9. 2018 |
The Great Debate | 5% | No | Various |
'My Product' Seminar | 10% | No | November 2018 |
Continuing Assessment | 5% | No | Weekly |
Final Examination | 40% | Yes | November 2018 |
Due: Various
Weighting: 30%
Weekly practicals
Report 1
Due: 17-9-2108
Weighting: 12%
Written report on the practical, composed of the results from intensive laboratory work carried out over one week. The report involves substantial writing, thinking and synthesis of the results thus preparing the students for real-life situations and future research projects. There are two additional questions for the students to answer and explore as part of the report.
Report 2
Due: 15-10-2018
Weighting: 8%
Written report on practical 2. The students have received feedback on their first report and thus should take the advice on board when compiling report 2. This report involves presenting confocal microscopy image material produced in the practical and discussing the observations in detail. Also, the students are requested to answer three additional questions on the topic of fluorescence and produce an executive summary linking together practicals 1 and 2, as part of the report.
Report 3
Due: 05-11-2018
Weighting: 10%
Written report on practical 3. The report concerns detailed analysis using results obtained in the class. There are two additional questions for the students to answer and explore as part of the report.
If not otherwise instructed, the reports should follow the format:
Introduction - stating aims in the last paragraph
Materials and Methods - main points and procedures
Results - with tables and graphs where applicable
Discussion - reflecting on the results and published literature
References - choose one style and stick to it
Answers to questions - separate from other text
Results should consist of tables, diagrams and words in between to tie the story together. Presenting tables, graphs, etc. without any explanation is not acceptable. Every table, graph and diagram should be numbered and have a caption, and you should refer to them in the text by their number. Expected length for an average report is about 5-10 double spaced typewritten pages plus figures and tables. Please answer the questions after the actual report text under a heading ‘Answers to questions’ and number your answers. Marks allocated to each component are given in the class.
Due: 14.9. 2018
Weighting: 10%
Primer crafting task
Due: 14-09-2018
Weighting: 10%
In this exercise, you will look into “turning” peptides to a DNA sequence and design oligonucleotide primers for various purposes in the laboratory such as “catching” a gene and DNA sequencing. This is one of the most essential skills in molecular biology. You will also learn the ropes for peer-assisted marking as you will be marking your classmates work. During the tutorial, you will be given a brief, material to work with and specific questions to answer. Rubric and instructions for peer-assisted marking will also be presented and explained. This assignment will be completed at home and returned before the mid-semester break so that students can mark each others work over the mid-semester break.
Due: Various
Weighting: 5%
The students will be divided into groups of 4-5 people (depending on the total student number) who will be given a topic in the area of biotechnology (drawn out of a hat) which they either have to defend or oppose. The topics will be chosen from those suggested by the students and teaching staff. The groups will know their topic in the previous week so that they can plan ahead their debating strategy. Each debate, chaired by the course convener, will last for 10-20 minutes followed by questions from the audience. The audience will participate in the assessment by voting for the winning team after each debate. This is a good opportunity to practice ethical voting, i.e. voting based on a successful argument and not e.g. because you are good friends with some individuals in one of the debating teams. There will be no individual marks but the collective mark goes to everyone in the group.
Due: November 2018
Weighting: 10%
You will introduce and market an idea for a new biotech product in a seminar presentation. Your task is to convince the audience that the world would be a better place if this product was made available. You will also prepare a snappy A4 Press release describing the product, to be handed to the audience at the seminar.
Due: Weekly
Weighting: 5%
Continuing assessment involves providing a brief answer to a weekly question appearing on iLearn each Wednesday by 5 pm. The question concerns a topic discussed either on the Mon or Tue lecture. You are expected to attend lectures/listen to the lecture recordings and submit a brief answer to the question on iLearn. Your answers must be in by 5 pm on the following Monday. There will be 12 questions overall. The mark will be calculated according to the number of questions answered. Answering all questions will give you the full 5%. This exercise is voluntary; however, it is great practice for the final exam.
Due: November 2018
Weighting: 40%
This is a hurdle assessment task (see assessment policy for more information on hurdle assessment tasks)
This is a hurdle assessment task (see https://staff.mq.edu.au/work/strategy-planning-and-governance/university-policies-and-procedures/policies/assessment for more information on hurdle assessment tasks).
The final course examination will be 3 hours plus 10 min reading time. The examination will cover all sections of the unit including tutorials and practicals and consists of short answers, problem solving tasks and essay questions. In their answers the students are encouraged to practise critical thinking and expand on ideas rather than just listing facts and figures with no discussion. Dot point-style answering is not allowed. You do not need a calculator in the examination.
The final exam is a hurdle assessment and you will need to get >= 40% of the marks available to meet the hurdle. In the event that you make a serious first attempt at the final exam, you will be provided with an opportunity to sit a new final exam. The Faculty defines a serious attempt as a mark of 10% below the hurdle, which in this instance is a mark between 30-40%. You will NOT be given a second attempt to pass the exam if you get below 30% in your first attempt.
Technology Used
Access to the Internet is necessary for efficient communication and research. General use computers are provided by the University, but it would be advantageous to have your own computer/laptop with internet access.
All calculations during practicals can be carried out using a smart phone. It is also recommended that you will take pictures from the cultivation plates etc to be included in the prac report. Do not use gloves when handling the phone Laboratory reports can be produced using standard Microsoft Office software.
Classes
Timetable: Please check http://www.timetables.mq.edu.au/ for the official timetable of the unit.
Lectures: There are two one-hour lectures per week, Mon 9-10 am and Tue 11 am -12 pm, both in E6A102. The material presented in the lectures is examinable. Please note that there is no text book coverage for a fair amount of the presented material. Therefore, regular attendance to the lectures and careful listening of the recordings is highly recommended. Lecture topics and dates can be found on the unit webpage on iLearn (CBMS880 http://ilearn.mq.edu.au). Lectures will be delivered as scheduled with eCHO recording available through iLearn.
Lecture graphics will be uploaded on CBMS731 iLearn (http://ilearn.mq.edu.au) the day before each lecture. The site also provides you with lecture recordings, videos, images and general data generated in the practicals, and material required for the assignment(s). Announcements facility will be used to communicate information from the unit convener.
Laboratory sessions: Please note that laboratory sessions commence in Week 2. Practical topics and the timetable are available on iLearn. The 4-hour practical sessions will be offered on Tue afternoon from 2-6 pm (Labs 1-2) or Wed morning 9 am-1 pm (Labs 3-4) in E7B349-50. Each student should enrol in one of these sessions and stay within that group throughout the entire semester. Students are required to attend 80% of the laboratory/tutorial sessions although 100% attendance is recommended. It should be noted that missing any practical will make the reporting very difficult since some of the practicals continue over several weeks and plenty of data will be generated every week. Should a student miss a practical for a valid or unavoidable reason, he or she should consult their working pair and other class mates for results and other information generated and shared during the missed session in order to be able to produce a report. The student can also join the other weekly prac class as a temporary guest (in consultation with the convener) and then return to his or her allocated class.
In 2018, a block practical option is offered for up to 30 students over the mid-semester break (Week 39). The labs will be run on 24-28 September from 10 am to 3 pm (Mon-Fri). Some days may go a bit over. Students wishing to attend the block practicals are requested to contact the unit convener in the first week of teaching
In the laboratory: This course will involve laboratory work with microorganisms, DNA samples, proteins and sugars. The experimental techniques feature molecular biology, microbial cultivation, fluorescent microscopy, biochemical analyses and mass spectrometry. Note that there are safety requirements concerning the use of these techniques. All students are required to adhere to the guidelines for safe laboratory conduct provided on iLearn.
You will not be allowed to enter he laboratory unless you are wearing enclosed footwear. When in the lab, wear a laboratory coat and safety glasses - preferably bringing your own. It is recommended that you carry a marking pen (permanent), spatula, scissors and tweezers (and a phone for taking photos).
Instructions for the laboratory experiments and tutorial tasks can be downloaded from iLearn. Instructions for the laboratory experiments can be downloaded from iLearn. It is essential that you bring the notes with you to each class. Additional material may be provided in the class.
You will be required to keep a laboratory book in which the details, results and conclusions of experiments will be recorded. The best format is an A4 ruled notebook that opens flat. This book is to be used in the practicals and the notes taken should be good enough to allow you to repeat the experiment. Tablets and laptops may be used for note-taking but using them may be tricky as you should not wear gloves when typing notes. You are required to write three formal reports on the practical work, a task that will be a lot less painful experience with good notes in hand.
The lectures and practicals link together to support the overall learning. Questions related to the practicals are formulated so that you will have the opportunity to use the information acquired in the class and provided in the lectures. You are expected to consult scientific literature for additional information and inspiration. The students will have plenty of time for hands-on laboratory work and opportunities to discuss their findings and potential problems with the demonstrator and class mates. It is important to keep in mind that experiments with living organisms can produce surprising results or sometimes no results at all! If that should happen, your task would be to find reasons for the unexpected outcome(s). There are no pre-set ‘correct’ results to the laboratory work and it is important to learn how to continue with the experiment in the face of the unexpected. Similarly, there may be modifications or additions to the instructions printed in the practical notes provided, depending on the course the experiments may take.
The Great Debate: The debates will be carried out at the time slot allocated for the laboratory class (i.e. 2-6 pm on Tue or 9 am-1 pm on Wed). The venue will be announced later.
Tutorials: Tutorials (codon optimisation and namesake peptide) are run as part of the practical sessions. Previously announced locations for these activities may change so stay tuned (please consult iLearn). Tutorial material, which forms part of the material submitted for assessment and/or examination, will be made available on iLearn.
Required Materials and/or Recommended Readings
Biotechnology draws from different disciplines and technologies. The recommended textbooks will give you a good general introduction to (Thieman and Palladino) or deeper knowledge on (Clark and Pazdernik) these areas and provide further reading as well as useful websites for more in depth studies. The books also provide good questions at the end of each chapter to test your learning.
Textbooks:
William J. Thieman and Michael A. Palladino (2012): Introduction to Biotechnology, 3rd edition. Pearson Benjamin-Cummings Publishing Company, San Francisco CA.
David P. Clark and Nanette J. Pazdernik (2016): Biotechnology, 2nd edition. Elsevier, China. This book also provides an online study guide available with the textbook.
The books is available at the University Bookshop. Please note that while the books provide an anchor for the studies, plenty of additional and examinable information will be provided in the lectures.
Almost every issue of the mainstream biotechnology journals will contain scientific papers related to the lecture material. Journals such as ‘Biotechnology’ and ‘Trends in Biotechnology’ are subscribed by the MQ Library and a good amount of the relevant journals are accessible through electronic databases such as PubMed (http://www.ncbi.nlm.nih.gov/pubmed/). Please take some time to browse through the journals for papers that you find interesting. Getting familiar with the format in which scientific papers are presented will be of great help in your own report writing.
Unit Website
The official CBMS731 website is: ilearn.mq.edu.au
You will be asked for a username and password. Your username is your student number. If you have trouble logging in, please follow the help instructions given on the web page before contacting your lecturer academic staff. You may also contact the
Help Desk:
Phone: 9850-HELP (4357)
Freecall: 1800 063 191
Email: http://help.mq.edu.au/
CBMS331/731/880 Molecular and Medical Biotechnology, lecture topics 2018 Two one-hour lectures per week, on Mon in E6A102 at 9-10 am and on Tue from 11 am -12 pm.
The many faces of biotechnology- the big picture |
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1. Course introduction - contribution of biotechnology to modern life (HN) |
Mon 30.7 |
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Molecular biotechnology |
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Molecular aspects of biotechnology revisited |
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2. The toolbox for genetic engineering- making a recombinant protein (HN) |
Tue 31.7 |
3. Genetic engineering- power tools and considerations (HN) |
Mon 6.8 |
4. Biotechnology pipeline- linking the ‘omics’ (HN) |
Tue 7.8 |
5. Protein secretion and quality control (HN) |
Mon 13.8 |
6. Protein secretion, the way out (HN) |
Tue 14.8 |
7. Modern approaches into protein engineering (AS) |
Mon 20.8 |
8. Basic concepts in synthetic biology (LB) |
Tue 21.8 |
9. Making a synthetic yeast chromosome (HG) |
Mon 27.8 |
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Making recombinant products |
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10. Microbes as cell factories (HN) |
Tue 28.8 |
11. Cell cultures and transgenic animals (HN) |
Mon 3.9 |
12. What about transgenic plants? (HN) |
Tue 4.9 |
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Fluorescence in biotechnology |
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13. Fluorescence instrumentation and applications in biotechnology (LP) |
Mon 10.9 |
14. Flow cytometry as a tool in biotechnology (MO) |
Tue 11.9 |
BREAK 15.9. – 1.10.
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15. Making products on a large scale (HN) |
Tue 2.10 |
Medical biotechnology |
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Sweet biotechnology |
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16. Selected aspects of protein glycosylation (MA) |
Mon 8.10 |
17. Biological functions of protein glycosylation (MA) |
Tue 9.10 |
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Nanobiotechnology applications in biomedicine |
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18. Microfluidics in cell separation (ML) |
Mon 15.10 |
19. Leading concepts and applications of nanotechnology (AC) |
Tue 16.10 |
20. Nanobiotechnology in cancer diagnostics (AC) |
Mon 22.10 |
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Biomolecules and their applications |
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21. Bioinformatics and combinatorial chemistry in drug design (SR) |
Tue 23.10 |
22. DNA as evidence in forensic science (HN) |
Mon 29.10 |
23. The promise of biopharmaceuticals (HN) |
Tue 30.10 |
24. Quick guide to stem cells and their applications (HN) |
Mon 5.11 |
25. Course summary | Tue 6.11 |
Please note that there may be changes to the visiting lecturers; these changes will be announced on iLearn Announcements. Attendance to the lectures is not compulsory but is strongly encouraged. Some lectures will be supported by video material also made available on iLearn. Lecturers: HN- Prof Helena Nevalainen, MQ CBMS (helena.nevalainen@mq.edu.au) LB- Dr Louise Brown, MQ CBMS (louise.brown@mq.edu.au) AS- Dr Anwar Sunna, MQ CBMS (anwar.sunna@mq.edu.au) LP- Dr Lindsay Parker, MQ, Biological Sciences (lindsay.parker@mq.edu.au) ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP) MO- Dr Martin Ostrowski, MQ, CBMS (martin.ostrowski@mq.edu.au) SR- Prof Shoba Ranganathan, MQ CBMS (shoba.ranganathan@els.mq.edu.au) MA- Dr Morten Thaysen-Andersen, MQ CBMS (morten.andersen@mq.edu.au) ML- Dr Ming Li, MQ, School of Engineering (ming.li@mq.edu.au) AC- Dr Andrew Care, MQ CBMS (andrew.care@mq.edu.au) ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP)
Practical sessions The 4 hour practical sessions will be offered on Tue afternoon from 2-6 pm in E7B349-50 (Groups 1, 2) or Wed morning 9 am-1 pm (Groups 3,4). Each student should enrol in one of these sessions and stay within that group throughout the entire semester. Attendance to all sessions allocated to your group is recommended.
Practicals:
Practical 1 Genetic transformation of the filamentous fungus Trichoderma reesei Tue 7.8. Plate conidia for bombardment Wed 8.8. Coat microparticles with DNA and shoot
Tue 14.8. Count transformants and restreak on PDA-HygB plates Wed 15.8. Streak transformant conidia for DNA isolation
Codon optimisation tutorial TBA
Tue 21.8. Isolate chromosomal DNA from transformants for PCR Wed 22.8. Design primers for PCR to check the transformants
Tue 28.8. Check the quality of chromosomal DNA Wed 29.8. Run PCR on transformants
Primer crafting task handed out and discussed in the class
Tue 4.9. Check PCR products by agarose gel electrophoresis and take Wed 5.9. photographs
Wrapping up Practical 1
Practical 2 Fluorescent labelling of fungal cell membranes and cellular localisation of the DsRed1 protein
Tue 11.9. Staining of the DsRed-expressing transformants and the Wed 12.9. non-transformant with an ER specific dye Inspection of specimens using confocal microscopy
Executive summary, peptide clinic and refreshments Writing room and APAF Conference room
No prac on 2 or 3 Oct
Practical 3. Analysis of N-linked glycans on the native lactoferrin glycoprotein isolated from human and bovine milk
Tue 9.10. Sample preparation of native and recombinant lactoferrin Wed 10.10. Release of oligosaccharides by enzyme treatment
Wrapping up Practical 2
Tue 16.10. Purification and analysis of oligosaccharides by liquid Wed 17.10. chromatography-mass spectrometry and interpretation of data
Wrapping up Practical 3
Tue 23.10. The Great Debate I TBA Wed 24.10.
Tue 30.10. The Great Debate II TBA Wed 31.10.
For CBMS731 only: Seminar presentations
Tue 6.11. or TBA Wed 7.11.
Note that a block practical is organised during the mid-semester break (week 39). We are looking for 32 volunteers to attend this mode of practicals. Please list your name on iLearn for expression of interest. |
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Macquarie University policies and procedures are accessible from Policy Central (https://staff.mq.edu.au/work/strategy-planning-and-governance/university-policies-and-procedures/policy-central). Students should be aware of the following policies in particular with regard to Learning and Teaching:
Undergraduate students seeking more policy resources can visit the Student Policy Gateway (https://students.mq.edu.au/support/study/student-policy-gateway). It is your one-stop-shop for the key policies you need to know about throughout your undergraduate student journey.
If you would like to see all the policies relevant to Learning and Teaching visit Policy Central (https://staff.mq.edu.au/work/strategy-planning-and-governance/university-policies-and-procedures/policy-central).
Macquarie University students have a responsibility to be familiar with the Student Code of Conduct: https://students.mq.edu.au/study/getting-started/student-conduct
Results shown in iLearn, or released directly by your Unit Convenor, are not confirmed as they are subject to final approval by the University. Once approved, final results will be sent to your student email address and will be made available in eStudent. For more information visit ask.mq.edu.au.
Macquarie University provides a range of support services for students. For details, visit http://students.mq.edu.au/support/
Learning Skills (mq.edu.au/learningskills) provides academic writing resources and study strategies to improve your marks and take control of your study.
Students with a disability are encouraged to contact the Disability Service who can provide appropriate help with any issues that arise during their studies.
For all student enquiries, visit Student Connect at ask.mq.edu.au
For help with University computer systems and technology, visit http://www.mq.edu.au/about_us/offices_and_units/information_technology/help/.
When using the University's IT, you must adhere to the Acceptable Use of IT Resources Policy. The policy applies to all who connect to the MQ network including students.
Our postgraduates will demonstrate a high standard of discernment and common sense in their professional and personal judgment. They will have the ability to make informed choices and decisions that reflect both the nature of their professional work and their personal perspectives.
This graduate capability is supported by:
Our postgraduates will be able to demonstrate a significantly enhanced depth and breadth of knowledge, scholarly understanding, and specific subject content knowledge in their chosen fields.
This graduate capability is supported by:
Our postgraduates will be capable of utilising and reflecting on prior knowledge and experience, of applying higher level critical thinking skills, and of integrating and synthesising learning and knowledge from a range of sources and environments. A characteristic of this form of thinking is the generation of new, professionally oriented knowledge through personal or group-based critique of practice and theory.
This graduate capability is supported by:
Our postgraduates will be capable of systematic enquiry; able to use research skills to create new knowledge that can be applied to real world issues, or contribute to a field of study or practice to enhance society. They will be capable of creative questioning, problem finding and problem solving.
This graduate capability is supported by:
Our postgraduates will be able to communicate effectively and convey their views to different social, cultural, and professional audiences. They will be able to use a variety of technologically supported media to communicate with empathy using a range of written, spoken or visual formats.
This graduate capability is supported by:
Our postgraduates will be ethically aware and capable of confident transformative action in relation to their professional responsibilities and the wider community. They will have a sense of connectedness with others and country and have a sense of mutual obligation. They will be able to appreciate the impact of their professional roles for social justice and inclusion related to national and global issues
This graduate capability is supported by:
The Namesake peptide task has been changed to Primer crafting task and peer-assessment.
In 2018, a block practical option is offered for up to 30 students over the mid-semester break (Week 39). The labs will be run on 24-28 September from 10 am to 3 pm (Mon-Fri). Some days may go a bit over. Students wishing to attend the block practicals are requested to contact the unit convener in the first week of teaching.