VIRO3001/3901 Unit of Study Handout!

24th Jan 2012

School of Molecular Bioscience

Virology VIRO3001/ Virology (Advanced) VIRO3901 Semester 1, 2012

Unit of Study Summary This Unit of Study is an introduction to the eld of virology and serves as a basis, and is a strongly recommended prerequisite, Medical and Applied Virology VIRO3002 offered in Semester 2. Virology VIRO3001/VIRO3901 encompasses 4 themes: Virus Classication, Structure and Replication; Animal, Plant and Bacterial Viruses; Concepts of Host/Pathogen Interactions; and Methods and Techniques in Virology. Virus Classication, Structure and Replication: denes what viruses are and how they are classied and introduces common characteristics of various types of viruses, from their taxonomy and structure, to their genome and how their type impacts on replication and viral gene expression. Animal, Plant and Bacterial Viruses: examines viruses from the perspective of host-range, with particular emphasis on how host biology shapes viral replication and poses unique challenges to productive virus infection. Concepts of Host/Pathogen Interactions: this theme illustrates fundamental concepts in viral/host interactions, highlighting viruses associated with human diseases. The immune response to viral infection will be introduced as well as concepts such as viral latency, recombination, cell transformation, methods to control virus infection and the emergence/re-emergence of novel viruses. Prions and unusual infective agents will also be discussed. Methods and Techniques in Virology: this nal theme covers currently used techniques in virology research as well as recent advances in the eld. Lectures in this theme will provide a background and theoretical basis for practical sessions that run concurrently with core lecture delivery.

The hands-on practical component is designed to enhance students practical laboratory skills and to complement the lecture series by giving students practical experience in important laboratory techniques. Tutorials will involve student research presentations on selected topics. Teaching Objectives Teaching in this Unit of Study is aimed at introducing students to the principles of virology including: 1. 2. 3. 4. The structure and replication mechanisms of various viruses Viruses of bacteria, plants and animals Techniques used in virology research Viruses relevant to humans and their control

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VIRO3001/3901 Unit of Study Handout!

24th Jan 2012

Learning Outcomes After completion of this VIRO3001, students should be able to: dene the key characteristics of viruses that distinguish them from other agents of disease such as bacteria, sub-viral particles and prions explain how different classes of viruses replicate, and the impact of genome type on replication and virus structure explain how the immune system is able to combat viral infections and confer immunity, and the various ways viruses have evolved to circumvent this control mechanism perform basic cell culture, uorescence microscopy, diagnostic and molecular techniques used in a modern virology laboratory, and understand the scientic principles behind these techniques explain how anti-viral drugs and vaccination act to limit virus replication explain how viral diseases emerge and the threat posed to public health Students who complete VIRO3901, should additionally be able to: critically evaluate primary scientic literature explain how different scientic approaches are used to support a hypothesis, using illustrative examples Quality of Teaching in this Unit of Study Principles To enhance and facilitate learning in VIRO3001/VIRO3901, students will experience a Unit of Study that: 1. has been designed by experienced educators based on pedagogical principles 2. is enriched with a range of formal and informal learning experiences, face-toface and online 3. provides up-to-date information, strategies and technologies that are relevant to the current scientic community 4. encourages a research-based approach to the study of viruses 5. strives to provide the best possible learning environment Evaluation This Unit of Study will be evaluated annually using either the standard Institute for Teaching and Learning Unit of Study Evaluation Surveys or a discipline-based request for feedback and comment. The outcomes of this Evaluation/feedback will be acted upon and implemented in a timely fashion as appropriate.

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VIRO3001/3901 Unit of Study Handout!

24th Jan 2012

Reaction to student feedback VIRO3001/VIRO3901 strives to become a dynamic unit of study and continual feedback will be sought and suggestions to improve effectiveness of teaching and learning will be implemented. Suggestions obtained from previous student feedback from other units of study in the Discipline of Microbiology that have been adopted for VIRO3001/VIRO3901 include: the unit is web-based for greater exibility and accessibility of unit support material, and recordings of lectures and lecture summaries the lecture and practical content has been designed into theme areas and includes scientically up-to-date and interesting material relevant to the elds of general and some medical virology, delivered by active researchers tutorials have been designed to encourage active student involvement emphasis of assessment will be on understanding the presented material rather than on regurgitation of the information implementation of online formative self-assessment constructive feedback on progress will be provided to all students in a timely fashion Statement by Unit of Study Coordinator I am committed to effective University teaching of the highest standard and have an open-door policy for student consultation. I am striving to improve the quality of teaching and learning in this Unit of Study in order to encourage students to learn effectively. All staff teaching in this Unit supports this process. I trust that students will be challenged in VIRO3001/VIRO3901 to reach their full potential and enjoy themselves in the process. Dr Tim Newsome, Unit of Study Co-ordinator. Contact Web Pages: eLearning Unit of Study Co-Ordinator: Dr Tim Newsome Rm 562, Biochemistry/Microbiology Building G08 Email: tim.newsome@sydney.edu.au, phone: 9351-2907 Teaching Assistant: Dr Deborah Blanckenberg Room 535, Biochemistry/Microbiology Building G08 Email: deborah.blanckenberg@sydney.edu.au, phone: 9351-2540 Administrative Assistant (Student Service): Room 435, Biochemistry/Microbiology Building G08 Phone: 9036-5417; FAX: 9351-4726 Additional lecturers: A/Prof Allison Abendroth Dr Russell Diefenbach Dr Jacquelyn Horsington Dr Gary Muscatello A/Prof Barry Slobedman Prof Peter Waterhouse A/Prof Kevin Downard Prof Peter Reeves

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VIRO3001/3901 Unit of Study Handout!

24th Jan 2012

Lectures VIRO3001/3901: Lectures will be held at 10AM on Thursdays and Fridays at 10AM in Carslaw Lecture Theatre 373. VIRO3901 only: Lectures in the advanced lecture series will be held on Monday at 10:00am in New Law School Annexe SR 340 in teaching weeks 3 and 913 only. See the schedule at the end of this document for exact dates of lectures. Attendance is strongly recommended for a full understanding and engagement of the material delivered. Practical Classes and Tutorials Students are required to bring their own lab coat to the practical classes and tutorials. Failure to do so will result in exclusion from the session in compliance with the Australian Standards for Safety in Microbiological Laboratories AS/NZS 2243.3: 2003. Practical Classes start in Week 2 and will be held on Thursday OR Friday from 1:00 5:00 pm in Lab 542 (level 5) or 300 (level 3) in the Biochemistry and Microbiology Building GO8. Students will be centrally allocated to one of these sessions. The practical classes are designed to complement and enhance the theoretical background provided in the lectures and give the opportunity of hands-on experience in some of the current and cutting-edge virology techniques. The six practical classes will cover: sterile techniques of eukaryotic cell culture including passaging adherent cell lines, counting cells using a haemocytometer with phase contrast microscopy and assessing cell viability using Trypan Blue exclusion observing various cytopathic effects on host cells caused by viruses and determining PFU using a plaque assay understanding and performing of serological techniques such as the haemagglutinin assay and ELISA test to determine the presence of viral agents enhanced knowledge of currently used molecular biology techniques in virology including PCR, uorescence microscopy and immunoblotting with one detailed hands-on example for each application. Attendance at practical classes will require electronic submission of a small number of pre-class questions addressing safety and the background to the practical class. These also form part of the assessment for this unit of study. Practical classes 13 will include a short piece of continuous assessment based on the practical class to be handed in by the end of the class. Assessment for practical classes 46 will comprise a written project report covering material from these classes. Tutorials form part of the practical course and will be held on 3 specied days (see practical schedule at the end of this hand-out). These will be held from 1:003:00pm (in your usual practical allocated time) on Thursdays OR Fridays in weeks 1012. Students will be assigned into small groups of 3-4. Each group will select from a list of supplied topics, that will be available during the rst practical class, an area on which they will research and then present a short (15 minute) Powerpoint presentation to the rest of the demonstrator group. Presenting research results orally is an important way of communicating data and ideas, and students in this Unit will have the opportunity to
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VIRO3001/3901 Unit of Study Handout!

24th Jan 2012

learn how to effectively communicate these. The presentation will be assessed and will contribute to the practical component. Attendance by all students at the tutorials is expected and forms part of the continuous assessment. Practical Manual A printed practical manual will be provided free-of-charge in the rst practical session. An online version of the practical manual will also be available via the online PebblePad portal (a link will be provided on the VIRO3X01 eLearning site). Textbooks Recommended Textbook: Introduction to MODERN VIROLOGY by N.J. Dimmock, A.J. Eaton & K.N. Leppard; 6th ed 2007, Blackwell publishing. Approximately $65 from Co-op Bookshop. We have recently integrated this textbook due to a signicant escalation in price of the new edition of the previous textbook, nonetheless Flint (see below) is an excellent textbook and students planning on taking VIRO3001 and 3002 might nd the purchase of a new or second-had copy worthwhile as Flint is an extremely comprehensive text that deals with many topics more thoroughly than Dimmock. Copies of Dimmock and both editions of Flint are available in the Medical and SciTech libraries. Reference Books: Principles of Virology - Molecular Biology, Pathogenesis, and Control of Animal Viruses by Flint, S. J.; Enquist, L.W.; Racaniello, V. R., and Skalka, A. M.; 2nd ed., 2004, ASM Press. 3rd edition available 2009. Basic Virology by Wagner, E.K. et al; 3rd ed., 2008, Blackwell. Virus Taxonomy by Fauquet C. et al; 2005, Elsevier. Several copies of all the above books are available in Medical and SciTech libraries. Deadlines Assignments and Reports must be handed in by certain deadlines. Failing to meet these deadlines will incur mark deductions of 10% of the total mark available for every day past the due date. Deadlines are the absolute latest time points by which such assignments need to be submitted without being penalised, but early submissions will be gladly accepted. Refer to policies on the VIRO3001 eLearning website. Pre-class assessments for practical classes 1-5 must be completed and submitted electronically at 5pm the day before the relevant class. Special Consideration Any student who believes that their performance has been or may be adversely affected by illness or other misadventure may request special consideration to the circumstances from the Faculty. Such a request must be made following the guidelines below within seven (7) days of the assessment task for which you are seeking consideration (ie 7 days from the assignment due date or date of examination) and must be accompanied by appropriate documentary evidence (eg medical certicate, police report, or other) For detailed guideline refer to: University of Sydney guidelines for Special Consideration
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VIRO3001/3901 Unit of Study Handout!

24th Jan 2012

School of Molecular Bioscience guidelines for Special Consideration Attendance Requirements All students are expected to attend all lectures, practical classes, tutorials, and case studies. A variety of notes, handouts, data sheets, and information provided throughout the Unit of Study are intended to supplement the lectures not to substitute for them. Absences from all scheduled practical sessions, tutorials and case studies must be explained and supported by appropriate documentation. Even if special consideration has been granted, it is the students responsibility to know and understand the material covered in the missed session. Please note that the Faculty of Science has a minimum 80% attendance requirement for a student to pass any unit of study (Faculty of Science Handbook 2012). Unit of Study Standards The grade descriptors for this unit are in line with the University of Sydney Academic Board Resolutions for Assessment. The following Grade Descriptors are to be read in conjunction with the specic criteria and learning outcomes being assessed for each assessment task. Taken together, these will indicate to you how we have gone about assessing your work in this unit.
Grade High distinction (85-100) Descriptors Work of exceptional standard Explanation / Interpretation Complete mastery of topics showing extensive assimilation; treatment of tasks show an advanced synthesis of ideas; demonstration of initiative, complex understanding and analysis; work is well presented; all criteria addressed and learning outcomes achieved to a high level Work of superior standard Excellent achievement, consistent evidence of deep understanding and application of knowledge; treatment of tasks show advanced understanding of topics; demonstration of initiative, complex understanding and analysis; work is well-presented; all criteria addressed and learning outcomes achieved strongly Highly competent work Condent in explaining microbial processes, with evidence of solid demonstrating potential for higher understanding and achievement; occasional lapses indicative of unresolved study issues; treatment of tasks show a good understanding of topic; work is wellpresented with a minimum of errors; all criteria addressed and learning outcomes achieved clearly Work of acceptable standard Satisfactory level of engagement with and understanding of topic; some inconsistencies in understanding and knowledge of microbes in infection; work is adequately presented, with some errors or omissions, most criteria addressed and learning outcomes achieved adequately Work not of acceptable standard Unsatisfactory achievement and engagement with the discipline; inadequate or fundamental misunderstanding of topics; most criteria and learning outcomes not clearly or adequately addressed or achieved; lack of effort/ involvement in the unit

Distinction (75-84)

Credit (65-74)

Pass (50-64)

Fail (<50)

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VIRO3001/3901 Unit of Study Handout!

24th Jan 2012

Assessment
Task Practical: Pre-class assessment Purpose Due Date Weight 40% total

Preceding Practical classes 1-5 students are required to 5pm the day 5 x 1% complete a brief very short answer/MCQ assessment covering before Prac safety aspects of the upcoming class and familiarity with the procedural and theoretical aspects experiments to be undertaken. Completion of the pre-class assessment is a requirement for attendance and students will receive feedback based upon their performance. Continuous This assessment tests the students comprehension of the End of Pracs 3 x 2% assessment background material, the results obtained and their interpretation 1-3 and assimilation of the results. There is a continuous assessment for Practical classes 1-3 and they must be handed in by the end of class and students will receive feedback on their performance. Project This assessment replaces the continuous assessment for 5pm, 21st May 7% Practical classes 4-6, which are thematically linked and involves the characterisation of a recombinant virus through classical and modern virological techniques. Presentations This is a group activity (3-4 students) and concerns the Submitted 5pm, 7% presentation of a primary piece of literature including the 14th May. analysis experimental techniques used in current virological Delivered research, linking the theory covered in the core lecture stream Weeks 10-12 with the techniques studied in the Practical classes. Theory of Qualitatively assess achievement of unit learning outcomes of Formal exam 15% Prac exam your: period Understand and apply the scientic principles behind basic cell culture, uorescence microscopy, diagnostic and molecular techniques used in a modern virology laboratory. Identify and apply the concepts of positive and negative controls to experiments conducted in virological research This assessment comprises 20 multiple choice questions (no negative marking). A more detailed description of learning outcomes is found in summaries in the Practical class manual. eLearning This assessment will provide formative assessment in the style Available Week Formative quiz of the Theory of Prac exam and cover the learning outcomes 10 (see above) of this part of the course. The quiz is optional and can be attempted an unlimited number of times and online feedback is provided.

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VIRO3001/3901 Unit of Study Handout! Theory: Theory examination

24th Jan 2012 60% total 60% total

eLearning quiz

Qualitatively assess achievement of unit learning outcomes of Formal exam your: period dene the key characteristics of viruses that distinguish them from other agents of disease such as bacteria, subviral particles and prions explain how different classes of viruses replicate, and the impact of genome type on replication and virus structure explain how the immune system is able to combat viral infections and confer immunity, and the various ways viruses have evolved to circumvent this control mechanism explain how anti-viral drugs and vaccination act to limit virus replication explain how viral diseases emerge and the threat posed to public health This assessment comprises 40 multiple choice questions (no negative marking) and 8 short answer questions. A more detailed description of learning outcomes is found in lecture summaries. These assessments will provide formative assessment in the Available style of the Theory examination and cover the learning outcomes Weeks 5, 10 (see above) of this part of the course. The quizzes is optional and 13 and can be attempted an unlimited number of times and online feedback is provided.Three quizzes are provided that each cover approximately a third of the core lecture series.

Formative

The Theory of Prac exam (30 minutes) and the Theory exam (120 minutes) will be held as a single exam paper during the formal examination period. To pass VIRO3001 students must pass the Practical assessment AND pass the Theory assessment. Additional Assessment task for VIRO3901students only: In Week 13, VIRO3901 students will sit a short theory exam and be required to: Answer 1 from 2 essay questions based on VIRO3901 advanced lecture series, a A mark in excess of 65% achieved in the essay will achieve a bonus of up 7 marks to be added to the total mark for the theory component of the assessment. To pass VIRO3901 students must pass the essay question based on the advanced lecture series, fail to do so will result in the student being assessed as VIRO3001 students. For all students: At the end of semester all marks may be scaled in accordance with Faculty of Science guidelines. In the case of further assessment required due to illness or misadventure, these may take the form of written and/or oral examinations and will be held in the week commencing 2nd July,012. Plagiarism Policy A summary of examples of plagiarism and means to avoid them that are appropriate for students enrolled in the Faculty of Science Handbook 2012. With each item of assessment that you submit, you will be required to attach a signed compliance statement agreeing that you have read, understood and have complied with this plagiarism policy.
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VIRO3001/3901 Unit of Study Handout!

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Language Students from non-English speaking backgrounds who experience difculties with writing skills, comprehension, communications or examinations are encouraged to seek help from the Learning Centre. Students born outside Australia, even if they do not experience difculties in understanding, writing or expressing themselves, may be particularly vulnerable in an examination where the emphasis is on rapid and succinct expression. 4th Year Honours Students interested in the Microbiology Honours Program should contact Dr Tim Newsome or Dr Hannah Nicholas.

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Week

Date

Lectures
10AM Thursday Carslaw LT 373 10AM Friday Carslaw LT 373 2 Intro to Viruses
Tim Newsome

Practicals
1-5PM Thursday/Friday Lab 300/542 G08

Tutorials
1-3PM Thursday/Friday T.B.C.

3901 Lectures
10AM Monday New Law School SR 340

Week 1 Week 2 Week 3 Week 4 Week 5

5-Mar 12-Mar 19-Mar 26-Mar 2-Apr

1 Course Intro
Tim Newsome

3 Classication
Tim Newsome

4 Virus Structures
Tim Newsome

Practical Intro Practical 1: Cell Culture Practical 2: Cytopathic Effect Intro to 3901

5 Cell Culture
Tim Newsome

6 DNA Viruses
Tim Newsome

7 RNA viruses
Tim Newsome

8 Bacteriophage I
Peter Reeves

9 Bacteriophage II
Peter Reeves

Good Friday Easter

Week 6 Week 7 Week 8 Week 9 Week 10 Week 11 Week 12 Week 13

16-Apr 23-Apr 30-Apr 7-May 14-May 21-May 28-May 4-Jun

10 Molecular Tech
Tim Newsome

11 Plant Viruses I
Peter Waterhouse

Practical 3: Serology Practical 4: PCR Practical 5: Immunoblot Practical 6: Immunouorescence Student Presentations I Student Presentations II Student Presentations III AL1 Hendra virus outbreak
Gary Muscatello

12 Plant Viruses II
Peter Waterhouse

13 Viruses in Livestck
Jacq Horsington

14 Animal Viruses
Tim Newsome

15 Immune Resp I
Allison Abendroth

16 Immune Resp II
Allison Abendroth

17 Herpesviruses
Russell Diefenbach

18 Retroviruses
Barry Slobedman

19 Latency
Barry Slobedman

AL2 Hendra virus outbreak

Gary Muscatello

20 Inuenza
Kevin Downard

21 Cell transformation
Tim Newsome

AL3 Virus Transport

Tim Newsome

22 Prions
Jacq Horsington

23 Control of Viruses
Jacq Horsington

AL4 Virus Transport

Tim Newsome

24 Emerging Viruses
Tim Newsome

25 Course Summary
Tim Newsome

Exam