molecular basis of disease

09 Jun molecular basis of disease

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300551 Molecular Basis of Disease

School of Science & Health│Learning guide

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Spring 2013

Page 1

Table of Contents

1. Unit details…………………………………………………………………………………………………………………3

Study and attendance expectations……………………………………………………………………………..4

Student workload……………………………………………………………………………………………………………4

Attendance requirements………………………………………………………………………………………………4

Student feedback and improvements to the unit………………………………………………………4

2. Schedule of Learning and Teaching Activities…………………………………………………5

Learning Outcomes…………………………………………………………………………………………………………6

Other Resources………………………………………………………………………………………………………………6

3. Assessment information………………………………………………………………………………………..7

Assessment details………………………………………………………………………………………………………….7

Assessment task 1 : A critical review article (30%)…………………………………………………..8

Assessment task 1 : Standards and Criteria………………………………………………………………..9

Assessment task 2 : Laboratory book (20%)……………………………………………………………10

Assessment task 2 : Standards and Criteria……………………………………………………………..12

Assessment task 3 : Final Examination (50%)…………………………………………………………13

General Submission Requirements……………………………………………………………………………13

Submission…………………………………………………………………………………………………………………….13

Late Submission…………………………………………………………………………………………………………….13

Extension of Due Date for Submission………………………………………………………………………13

Resubmission………………………………………………………………………………………………………………..13

Application for Special Consideration……………………………………………………………………….13

4. Important Information…………………………………………………………………………………………14

Links to Policies…………………………………………………………………………………………………………….14

What is academic misconduct?…………………………………………………………………………………..14

What is non-academic misconduct?………………………………………………………………………….14

Raising concerns…………………………………………………………………………………………………………..15

Assignment Cover Sheet………………………………………………………………………………………………16

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Page 2

1. Unit details

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UNIT DETAILS

Unit Code:

300551

Unit Name:

Molecular Basis of Disease

Level:

3

Contact hours

10

per week:

Assumed

300936 Functional Proteins and Genes

Background:

STAFF

Unit

Dr Mark Temple

Coordinator

Building 21, Room 21.1.09, Campbelltown

and point of

first contact

Phone: 4620 3329

Email: m.[email protected].edu.au

Lecture

Dr Graham Jones

Dr Liza Cubeddu

Staff

Building 21, Room 21.1.36,

Building 21, Room 21.1.02

Campbelltown

Campbelltown

Phone: 4620 3399

Phone: 4620 3343

Email: graham.[email protected].edu.au

Email: l.[email protected].edu.au

CONSULTATION ARRANGEMENTS

Campbelltown

Staff: Dr Mark Temple

Date/Time: Friday 4 pm

Venue: Building 21, Room 21.1.09, Campbelltown

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Text Book

1. Lodish H., Berk, A., Matsudaira, P., Kaiser, C.A., Krieger, M., Scott, M.P., Zipursky, L D., Darnell, J. (2004)“Molecular Cell Biology”, W. H. Freeman and Company.

2. Weinberg R. (2006), The Biology of Cancer, Garland Science.

3. Strachan T. and Read, A.P (2004) Human Molecular Genetics, Garland Science.

Edition: [Session] 2013

© Copyright: University of Western Sydney, 2013. No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or by any information storage and retrieval system, without the prior written permission from the Dean of the School of Science & Health. Copyright for acknowledged materials reproduced herein is retained by the copyright holder. All readings in this publication are copied under licence in accordance with Part VB of the Copyright Act 1968.

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Page 3

Study and attendance expectations

Student workload

For a 10-credit point unit students are expected to work 10 hours per week in total. This means that an average student needs to spend 3-8 hours out of class every week studying this unit. Students are encouraged to read the topic-related material before coming to the lecture in order to follow the presentation.

Attendance requirements

Lectures:

Although lectures are not compulsory, it is highly recommended that students attend lectures and tutorials. During these, all content is discussed and many examples and applications are provided to enhance student learning. The lecture notes available from vUWS are designed to supplement rather than replace live lectures. Material and examples relevant to the assessment tasks are discussed in the lectures.

Laboratory:

Laboratory attendance is compulsory A laboratory manual will be made available to you and pre-work is required to be carried out prior to each class.

Student feedback and improvements to the unit

Introduction of clear standards and criteria

Improvements to the Laboratory manual

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Page 4

2. Schedule of Learning and Teaching Activities

Week

Lecture, Fri 2-4 pm, 04.G.14 (LT03)

1

Introduction/ Developmental Biology

(Mark Temple)

2

The role of cancer genetics in disease

(Mark Temple)

3

Functional genomics

Prac 1

(Graham Jones)

4

Inflammatory Bowel Disease

Prac 2

(Graham Jones)

5

Host Genetics and HIV

Prac 3

(Graham Jones)

6

The impact of microarrays on the understanding

Prac 4

of disease

(Graham Jones)

7

DNA repair mechanisms

Prac 5

(Liza Cubeddu)

8

The DNA damage response

Prac 6

(Liza Cubeddu)

Book due at end of

Prac class

9

INTRA-SESSION BREAK

10

Onco-genes and transcription factors in disease

(Mark Temple)

11

Cell cycle regulation and tumour suppressors in

disease

(Mark Temple)

12*

Growth factors and receptors in disease

Assignment due

(Mark Temple)

Monday14/10/13

13

The impact of bioinformatics in understanding

disease

(Mark Temple)

14

Molecular Basis of Disease

(Mark Temple)

.gif”>Learning Outcomes

After satisfactory completion of this unit the student will be able to:

1. Describe the role of genes in the development/differentiation of cells in multicellular organisms.

2. Describe DNA replication and the molecular mechanisms involved in the repair process of mutagenesis and the effects of gene dosage, genomic imprinting and teratogenesis.

3. Explain the basic principles involved in the mutagenic processes behind radiation, diet and oxidative stress.

4. Explain the basis of cancer genetics and the role of growth factors and receptors, oncogenes and transcription factors, the cell cycle and suppressor proteins on the cancer state.

5. Understand the principles of functional genomics.

6. Explain the principles of metabolomics and its relevance for disease diagnosis and prognosis.

7. Appreciate the importance of model organisms for the understanding of human cell biology.

8. Access and interpret information from the scientific literature in the areas of study.

9. Development and extension of laboratory skills for basic molecular biology.

Other Resources

University

Find out about life outside the lecture theatre – news and events, services and facilities,

life

career information and more!

http://www.uws.edu.au/currentstudents/current_students/services_and_facilities

E-Learning

Check your vUWS sites regularly for unit announcements and to keep up with online

discussions. If you do not have access to vUWS please contact e-learning on

https://vuws.uws.edu.au/

Disability

Students with a disability should visit:

Service

http://www.uws.edu.au/currentstudents/current_students/getting_help/disability_servic

es

Course and

This site provides information on pre-requisites, co-requisites and other matters

unit rules

concerning how your course is structured.

http://www.uws.edu.au/currentstudents/current_students/managing_your_study/enrolm

ent/course_and_unit_rules

Student

The Student Learning Unit (SLU) can offer you assistance in writing good exam

Learning

essays. Visit: http://www.uws.edu.au/campuses_structure/cas/services_facilities/slu

Unit

Policies

This site includes the full details of policies that apply to you as a UWS student.

http://www.uws.edu.au/policies/a-z

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Page 6

.gif”>3. Assessment information

Assessment details

There are three assessments in this unit designed to enable students to demonstrate that they have achieved the learning outcomes outlined above. Completion of all assessment items is necessary to receive a final mark in the unit. Achievement of at least 50% overall is required to pass the unit. There is no requirement that each individual assessment must be passed in order to pass the unit.

Assessment task

Learning

Due

Weight

outcomes

Assignment task 1 : A critical review

1.

You are to write a review article describing

8

Week 12

30%

key factors associated with the molecular

basis of disease in the style of a scientific

review publication

Assessment task 2 : Laboratory book

2.

You are expected to keep compliant

9

Week 8

20%

laboratory notebook

Assessment task 3 : Final examination

3.

Consist of a combination multiple choice

1, 2, 3, 4, 5,

Exam period

50%

and/or short answer and/or essay questions.

6, 7

Duration is 3 hours

TOTAL

100%

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.gif”>Assessment task 1 : A critical review article (30%).

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One of the most widely read story in “Technology Review” was “Do You Want to Live Forever?”’ a profile of Dr. Aubrey de Grey. De Grey believes that disease and aging can be treated and defeated. In this article he proposes approaching aging as a problem in engineering through “Strategies for Engineered Negligible Senescence (SENS).” Through SENS he claims to identify the 7 causes of human aging and proposes how each cause might be circumvented.

This assignment is to be carried out in pairs. Together you are to critique SENS from two different view points. Firstly that SENS is so wrong that they are unworthy of learned debate and secondly that SENS is worthy of serious consideration. You are expected to question the information and opinions from general literature and media sources and from relevant peer reviewed articles. Explain the background science and discuss whether the proposals are feasible. Together you are to present a final evaluation of SENS in relation to the molecular basics of disease and discuss whether circumvention by SENS is either highly speculative or grounded in fact.

As background material listen to Aubrey de Grey at TED:

http://www.ted.com/speakers/aubrey_de_grey.html

A PDF copy of the “Do You Want to Live Forever?” article is available on the vUWS website (note, this is NOT a peer reviewed article). As you critique the proposals it is important that you reference science material primarily from peer reviewed sources rather than popular web sites, text books or other commentary.

Use the Author Date format for in-text citations and referencing based on Harvard style: http://library.uws.edu.au/FILES/cite_Harvard.pdf

The maximum length is to be 2000 words (excluding, figure legends and references).

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A signed hard copy of the assignment cover sheet is to be given to Dr Mark Temple (Office 21.1.09) and an electronic copy of the assignment is to be submitted via the turnitin link (in the assignment folder on the units vUWS site) before 5 pm Monday of Week 12 (14th Oct 2013).

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Page 8

.gif”>Assessment task 1 : Standards and Criteria

Research

Standards

report

Criteria

High

Distinction

Credit

Pass

Fail

Distinction

Quality of

Is a balanced

Is a balanced

Shows

Shows

Poor summary

Critique

discussion and

discussion of

understanding

awareness

and evaluation of

10%

evaluation of

the strengths,

of the topic

of the

the articles.

the strengths,

weakness of

from different

proposal

weakness and

the articles.

perspectives

from

notable features

different

of the articles.

perspectives

Quality of

Scientific

Scientific

Scientific

Scientific

Scientific

written

content is fully

content is

content is

Content is

Content is poorly

scientific

stated,

mostly well

stated, and

stated, and

stated, and

content

comprehended

stated,

discussed

poorly

poorly discussed

10%

and discussed.

comprehended

discussed

and discussed

Research

Information is

Information is

Information is

Information

Information is

ability and

primarily from

mostly from

sometimes

is gathered

gathered from a

quality of

many peer

few peer

from few peer

from text

unreliable or

sources

reviewed

reviewed

reviewed

books and

unacknowledged

5%

sources.

sources.

sources, text

internet sites

sources.

books and

quality

internet sites

Format and

Format, layout,

Format,

Format,

Format,

Poorly structure

organisation

Reference list,

layout,

layout,

layout,

with missing

5%

Author-Date

Reference list,

Reference list,

Reference

sections and

citations,

Author-Date

Author-Date

list, Author-

major errors or

Tables and

citations,

citations,

Date

no Author-Date

Figures are

Tables and

Tables and

citations,

citations.

highly

Figures are

Figures are

Tables and

organized,

organized,

organized,

Figures are

demonstrates

demonstrates

with minor

highly

logical

logical

errors

organized,

sequencing and

sequencing

with major

structure.

and structure.

errors

TOTAL 30%

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Page 9

.gif”>Assessment task 2 : Laboratory book (20%)

Guide to keeping a laboratory notebook

A notebook should be kept for laboratory experiments only using a Scientific Notebook or other bound book. The notebook should be written in ink, and each page signed and dated. Mistakes are not to be erased but should be marked out with a single line. Try to keep your notebook with the idea that someone else must be able to read and understand what you have done. The notebook should always be up-to-date and can be collected at any time.

Index: An index containing the titleof each experiment and the page number should be included atthe beginning of the notebook.

Essentially everything you do in the laboratory should be in your notebook. The notebook should be organized by experiment. Start each new experiment on a new page. The top of the page should contain the title of the experiment, the date, and the page number. The page number is important for indexing, referring to previous experiments, and for labelling materials used in a given experiment. If an experiment spans more than one page, note the page on which the experiment continues if it’s not on the next page.

No data is to be recorded on loose sheets of paper or on the protocol sheets.

Title/Purpose: Every experiment should have a title and it should be descriptive. An examplewould be “Small-scale preparation of plasmid pUC19 for ……”.

When starting a new weeks entry, it is a good idea to introduce and write up the overall strategy prior to beginning, this may take the form of a flow diagram or a written section. This serves two purposes.

• First, it forces you to think about what you are doing and why,…. and sometimes things look differently when written down than they do in your head.

• Second, ideas can be patented, and a thorough description of your hypothesis and experimental strategy with appropriate documentation can be helpful for any future intellectual property issues.

Background information:This section should include any information that is pertinent to theexecution of the experiment or to the interpretation of the results. For example, if it is a repeat experiment, state what will be done differently to get the experiment to work. A simple drawing of the plasmid, PCR product expected or chemical to be used can be helpful. This is not like an introduction to a paper. Include anything that will be helpful in carrying out the experiment and deciphering the experiment at a later date. For the most part, notebooks are not written just for today but for you or somebody else to read in the future.

Materials:This section should include the key materials, i.e., solutions or equipment, that will beneeded. It is not necessary to include every piece of lab equipment required, i.e. vortexer, pipetman, etc, but you should include any specialized equipment and the manufacturer, i.e., a image documentation equipment or PCR instrument. Composition of all buffers should be included unless they are standard or are referenced. Pre-packaged kits should be identified as to the name of the kit, the vendor, and the catalogue number. Biological samples should be identified by genus and species, strain number, tissue type, and/or genotype with the source of the material identified.

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.gif”>Enzymes should be identified by name, vendor, and concentration. DNA samples should be identified as to

• type of DNA, i.e., chromosomal, plasmid, etc,

• purity (miniprep, gel purified, PCR product)

• concentration, if known

• source, (include prior experiment number if the DNA was isolated in a previous experiment).

Include all calculations made in preparing solutions. The sequence of all oligonucleotides must be included or referenced. Agarose gels should be identified by percentage and buffer used. If any of these materials were used in previous experiments, include only the reference to that earlier experiment, do not repeat the information again.

Procedure: Write down exactly what you are going to do before you do it and make sure youunderstand each step before you do it.

• You should include everything you do including all volumes and amounts; many protocols are written for general use and must be adapted for a specific application.

• Writing a procedure out helps you to remember and to understand what it is about. It will also help you to identify steps that may be unclear or that need special attention.

• Some procedures can be several pages long and include more information than is necessary in a notebook.

Flow charts are sometimes helpful for experiments that have many parts. Tables are also useful if an experiment includes a set of reactions with multiple variables. It is good practice to check off steps as they are completed or reagents as they are added to prevent you from losing you place or for forgetting to add something.

Results: This section should include allraw data, including gel photographs, printouts, gel images,etc. All lanes on gel photographs must be labelled and always identify the source and the amount of any standards. This section should also include your analyzed data, for example, identification of products, calculations etc. All images should be labelled eg Fig. 1. Also give the Figure a meaningful title and a short description (legend). Be sure to refer to the Figure in your text (narrative/ description etc).

Conclusions/Summary: This is one of the most important sections. You should summarize all ofyour results, even if they were stated elsewhere and state any conclusions you can make. If the experiment didn’t work, what went wrong and what will you do the next time to try to trouble shoot?

Questions: There are questions to be written up as part of your preparation for each weeks class.These are intended to supplement your background knowledge so that you have a better appreciation of what you are doing and why you are doing it.

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.gif”>Assessment task 2 : Standards and Criteria

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High

Distinction

>=17%

Distinction

15 < 17% Credit 13 < 17% Pass 10 < 13% Fail < 10% Standards and Criteria All required sections are present and are formatted correctly (including name of lab partner, title of the exercise, date work was done) Notebook is neat, orderly and legible Tables, graphs and data are used appropriately and are of proper size and format Pages are dated and signed Proper protocols are followed in regard to errors, empty space, etc. Procedural Outline concisely written in student’s own words Changes to procedure are noted Results section is written in complete sentences and is a complete recounting of what was done and what was observed All required sections are present and are formatted correctly Notebook is by and large neat, orderly and legible Tables, graphs and data are used appropriately and are of proper size and format Most pages are dated and signed Proper protocols are followed in regard to errors, empty space, etc. Procedural Outline written in student’s own words Changes to procedure are noted Results section is generally written in complete sentences and is a complete recounting of what was done and what was observed, although there may be occasional lapses Most required sections are present, although some may be formatted incorrectly Notebook has significant lapses of neatness, orderliness and legibility Necessary tables, graphs and data are present, but are lacking in some way (e. g., table headings, graph axis labels, etc.) Only a few pages are dated or signed Haphazard application of proper protocols regarding errors, empty space, etc. Procedural Outline largely a repetition of given material Changes to procedure may be noted Results section consists mainly of random observations and jotted down numbers One or more required sections are missing or formatted incorrectly Necessary tables, graphs and data are present, but are lacking in several important features Pages are not dated or signed Haphazard application of proper protocols regarding errors, empty space, etc. Procedural Outline essentially a copy of the given procedure with minor changes Changes to procedure are not noted Results section consists mainly of random observations and jotted down numbers or results are recorded in the Procedural Outline May have only one or two sections present or labelled properly Illegible writing, haphazard placement of records within the notebook Missing tables, graphs and data, what is present is not formatted properly Pages are not dated or signed No apparent set of rules used to prepare the notebook Procedural Outline is a simple recopying of the laboratory exercise with minor changes Changes to procedure are not noted Results are missing or consist only of numbers presented without context .jpg">

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.gif”>Assessment task 3 : Final Examination (50%)

The exam is to be held in the Examimations period following Stuvac.

Criterion

Standards

Fail: achieve less than 50% of marks

Pass: achieve 50-64% marks

Produce the correct answer

Credit: achieve 65-74% marks

Distinction: achieve 75-84% marks

High Distinction: achieve 85% or greater marks

General Submission Requirements

Submission

All assignments must be submitted by the specified due date and time, using a completed and signed Assignment Cover Sheet provided in the last page of this document.

Complete your assignment, attach a completed and signed Assignment Cover Sheet, and follow the individual assessment items instructions on how to submit.

Late Submission

If you submit a late assessment, without receiving approval for an extension of time, (see next item), you will be penalised by 10% per day for up to 10 days. In other words, marks equal to 10% of the assignment’s weight will be deducted from the mark awarded.

For example, if the highest mark possible is 50, 5 marks will be deducted from your awarded mark for each late day

Saturday and Sunday each count as one calendar day

Assessments will not be accepted after the marked assessment task has been returned to students This is consistent with Clause 50 of the University of Western Sydney’s Assessment Policy – Criteria and Standards-Based Assessment.

Extension of Due Date for Submission

Extensions are only granted in exceptional circumstances. To apply for an extension of time:

Locate an application form via the UWS homepage or copy the following link: http://www.uws.edu.au/__data/assets/pdf_file/0004/118273/Request_for_Extension_RO_00205_01 12.pdf

Application forms must be submitted to the Campus Co-ordinator

Requests for extension should be made no later than 3 working days before the due date of an assignment or other assessment item including web-based quizzes

Appropriate, supporting documentation must be submitted with the application

An application for an extension does not automatically mean that an extension will be approved Assessments will not be accepted after the marked assessment task has been returned to students

Resubmission

Resubmission of assessment items will not normally be granted if requested

Application for Special Consideration

It is strongly recommended that you attend all scheduled learning activities to support your learning. If you have suffered misadventure, illness, or you have experienced exceptional circumstances that have prevented your attendance at class or your completion and submission of assessment tasks you

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Page 13

.gif”>may need to apply for Special Consideration via the UWS website http://www.uws.edu.au/currentstudents/current_students/services_and_facilities/special_considerati on2or the Student Centre. Special Consideration is not automatically granted. It is your responsibility to ensure that any missed content has been covered. Your lecturer will give you more information on how this must be done.

4. Important Information

Links to Policies

The University has a number of policies that relate to teaching and learning. Important policies affecting students include:

§ Assessment Policy

§ Bullying Prevention Policyand Guidelines

§ Enrolment Policy(includes a section on the UWS Student Email Account)

§ Examinations Policy

§ Misconduct – Student Academic Misconduct Policy(see extract below)

§ Misconduct – Student Non-academic Misconduct Policy(see extract below)

§ Review of Grade Policy

§ Sexual Harassment Prevention Policy

§ Special Consideration Policy

§ Teaching and Learning – Fundamental Code

There are two policies that relate to misconduct – academic and non-academic misconduct. Breaches of these policies can have very serious consequences. It is essential that you are familiar with these policies and how to avoid misconduct of any type.

What is academic misconduct?

Academic misconduct may involve plagiarism, collusion or cheating. Plagiarism involves submitting or presenting work in a unit as if it were the student’s own work when, in fact, it was not. Collusion includes inciting, assisting, facilitating, concealing or being involved in plagiarism, cheating or other academic misconduct with others. Cheating includes dishonest conduct (or attempted dishonest conduct) in exams.

For the full definition of academic misconduct and the consequences of such behaviour, you are advised to read the Misconduct – Student Academic Misconduct Policy in its entirety (refer to http://policies.uws.edu.au/view.current.php?id=00051).

There are many resources to help you avoid academic misconduct. Library staff can help you with referencing and the Student Learning Unit can assist with academic writing and plagiarism. If you are unsure about any of your work you should also ask your tutor or lecturer for advice and feedback. The University also has text matching software (called Turnitin) which can help you check to see if your work might have problems. You can access Turnitin on the vUWS site for this unit.

What is non-academic misconduct?

Non-academic misconduct includes unlawful activities and crimes, falsifying documents (like a medical certificate or academic records), harassing other students (or staff), stealing or damaging university property (like library books or computers) and disrupting other students or staff. These are just some of the types of non -academic misconduct and while these things are rare they do happen. If you believe you have been the victim of non-academic misconduct or you are aware of any academic misconduct it is very important that you report it.

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.gif”>You should report all matters of non-academic misconduct directly to the Dean or the head of the relevant section of the University. For example, you can report matters to the Manager of Security on your campus or to the Campus Provost or the Dean of your school. You must do this in writing. You may write to the Dean on g.[email protected].edu.au.

Raising concerns

If you have a concern about this unit please contact your lecturer or tutor in the first instance. If the matter is not resolved, then you may contact the unit coordinator (see inside front cover). If you would prefer to speak to someone else, you are advised to contact the Director of Academic Program responsible for th