Solved by a verified expert:300551 Molecular Basis of Disease
School of Science & Health│Learning guide
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
Page 2
1. Unit
details
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: [email protected]
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: [email protected]
Email: [email protected]
CONSULTATION ARRANGEMENTS
Campbelltown
Staff: Dr Mark Temple
Date/Time: Friday 4 pm
Venue: Building 21, Room 21.1.09,
Campbelltown
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.
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
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)
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
Page 6
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%
Page 7
Assessment
task 1 : A critical review article (30%).
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).
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).
Page 8
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%
Page 9
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.
Page 10
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.
Page 11
Assessment
task 2 : Standards and Criteria
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 Page 12 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 Page 13 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. Page 14 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 [email protected]. 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
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