Course Title: Apply electrophoretic techniques

Part B: Course Detail

Teaching Period: Term1 2012

Course Code: ONPS5662C

Course Title: Apply electrophoretic techniques

School: 155T Vocational Health and Sciences

Campus: City Campus

Program: C5282 - Diploma of Laboratory Technology (Biotechnology)

Course Contact: Amberlee Mitton

Course Contact Phone: +61 3 9925 8053

Course Contact Email: amber.mitton@rmit.edu.au


Name and Contact Details of All Other Relevant Staff

Nominal Hours: 100

Regardless of the mode of delivery, represent a guide to the relative teaching time and student effort required to successfully achieve a particular competency/module. This may include not only scheduled classes or workplace visits but also the amount of effort required to undertake, evaluate and complete all assessment requirements, including any non-classroom activities.

Pre-requisites and Co-requisites

MSL973002A  - Prepare working solutions OR MSL974001A - Prepare, standardise and use solutions
MSL974003A   - Perform chemical tests and procedures.

Course Description

This unit of competency covers the ability to analyse samples using electrophoretic techniques. The unit also includes establishing client needs for routine and non-routine samples, optimising enterprise procedures and instruments for specific samples, obtaining valid and reliable data and reporting test results. Personnel are required to recognise atypical test data/results and troubleshoot common analytical procedure and equipment problems.


National Codes, Titles, Elements and Performance Criteria

National Element Code & Title:

MSL975008A Apply electrophoretic techniques

Element:

1. Establish client needs and schedule analysis

Performance Criteria:

1.1.    Liaise with client or sample provider to determine client needs and sample history
1.2.    Record sample description, compare with specification and record and report discrepancies
1.3.    Identify non-routine samples and the possible need to vary enterprise procedures
1.4.    Seek advice from supervisor about any proposed variations and document all approved changes
1.5.    Schedule analysis using enterprise procedures

Element:

2.    Prepare samples and standards

Performance Criteria:

2.1.    Obtain a representative analytical portion of the laboratory sample
2.2.    Prepare sample in accordance with testing requirements
2.3.    Prepare validation checks for analytical portion

Element:

3.    Set up and optimise instrument

Performance Criteria:

3.1.    Perform pre-use and safety checks in accordance with enterprise procedures
3.2.    Start up and condition the instrument using enterprise procedures
3.3.    Optimise instrumental parameters to suit sample and test requirements
3.4.    Check calibration status of instrument and perform calibration using specified standards and procedures, if applicable

Element:

4.    Perform analysis

Performance Criteria:

4.1.    Measure analyte response for standards, validation checks and samples
4.2.    Conduct sufficient measurements to obtain reliable data
4.3.    Return instruments to standby or shutdown condition as required

Element:

5.    Process and analyse data

Performance Criteria:

5.1.    Confirm data is the result of valid measurements
5.2.    Perform required calculations and ensure results are consistent with standards or estimations and expectations
5.3.    Record results with the appropriate accuracy, precision and units
5.4.    Analyse trends in data and/or results and report out of specification or atypical results promptly to appropriate personnel
5.5.    Troubleshoot analytical procedure or equipment problems which have led to atypical data or results

Element:

6.    Maintain a safe work environment

Performance Criteria:

6.1.    Identify risks, hazards, safety equipment and control measures associated with sample handling, preparation and analytical method
6.2.    Use personal protective equipment and safety procedures specified for test method and materials to be tested
6.3.    Minimise the generation of wastes and environmental impacts
6.4.    Ensure the safe disposal of laboratory wastes
6.5.    Clean, care for and store equipment and consumables in accordance with enterprise procedures

Element:

7.    Maintain laboratory records

Performance Criteria:

7.1.    Enter approved data and results into laboratory information management system
7.2.    Maintain equipment logs in accordance with enterprise procedures
7.3.    Maintain security, integrity and traceability of samples and documentation
7.4.    Communicate results to appropriate personnel


Learning Outcomes



Details of Learning Activities

Lab classes and Record keeping
Lectures/Workshops
Team meetings
Presentations
Exams
Reports and Assignments
Online theory and quizzes
Research
Fieldtrips


Teaching Schedule


Program is subject to change
FOR LONG EXPERIMENTS THEORY & PRAC CLASSES ARE MERGED TOGETHER


Part 1 - DNA

Date
(week
of)   
 week THEORY
(at home)
 PRAC 4 Hours Assessment
6/2
1
 Intro to Electrophoresis
**On campus class** 
   No lab class this week
, but print lab manual and do calculations at home for week 2 solution making
Week 1 quiz
(in class)
13/2
2Visualising DNA:
 3 useful stains, Molecular weight markers,
Gel concentrations 
 Agarose Gels I: Frankenstein Gels - Separating DNA with different % gels.

Preparing solutions -  Agarose gel electrophoresis (calculations)
Week 2 quiz
20/2
3 Quantifying DNA using agarose electrophoresis and fluorimeter methods. Agarose Gels II How much & how pure is my DNA?
(fluorimetry versus agarose gel determination)   
Week 3 quiz
27/2     
4Which allele(s) of Alu
is in your DNA? How can you tell from the electrophoresis results?
 Electrophorese Mol Gen
Alu PCR products gel electrophoresis
Week 4 quiz
5/35 Electrophoresis of RNA (Northern Blotting); Electrophoresis of Genomic DNAs (Pulsed field gel electrophoresis, Southern Blotting)   1. Pipetting Workshop (Eppendorf*)
*Refresher - using pipettes
*How to calibrate pipettes 

2. Prac report 1 do activity in class – annotating gel photos
Week 5 quiz
Prac report 1 due – do and submit in class
   
12/3   
6Intro to DNA sequencing & Capillary Electrophoresis      
 DNA Sequencing*
(AGRF Sequencing facility visit)
Week 6 quiz
19/3              
7Update logbooks
(no theory topic this week)
 Update logbooks at home/ last date to sign off any term 1 entriesLogbooks due by 5pm Thursday
26/3   
8Revision (at home)
  
2/4        
9 Exam week    
 6/4 = Good Fri
Test 1
 
  Part 2: Protein   
Date
(week
of)
Week
THEORY (1 Hour) PRAC (4 Hours)     Assessment
6th
Apr –
12th
Apr    
 Student vacation
  
16/4  
10Protein Electrophoresis Types of gels: agarose, cellulose acetate,
SDS-PAGE & MW calculations. 
1. Prepare solutions for protein agarose gel & SDS- PAGE.

2. Agarose Gel Electrophoresis of Serum Proteins

(Helena Labs*) 
Week 10 quiz
23/4
11Intro to SDS-PAGE,
Calc size of proteins using SDS-PAGE
1. Preparing solutions
– protein agarose electrophoresis.
2. Protein agarose Electrophoresis of Serum Haemoglobins (Helena Labs*) 
3. Preparing solutions
 - Western Blotting 
Week 11 quiz
30/4
12 Quiz
 SDS-PAGE of Albumin. Prac Report 2Week 12 quiz
Prac Report 2
SDS-PAGE of Albumin
7/5   
13Dotblot Immunoassay, Western transfer & Westernblot Immunoassay   
    1. Record & analyse SDS- PAGE result.  
    2. Calculate size of albumin.
    3. Dotblot - a simple immunoassay.
  
Week 13 quiz
14/5   
14 Quiz SDS-PAGE of a mixture of proteins & Western Transfer of an SDS-PAGE gel.    Week 14 quiz (prac report due)
21/5
15 Quiz1. Western blot immunoassay
2. Emerging technology – western blotting:     iBlot demonstration (Invitrogen/LifeTechnologies*)
Week 15 quiz
Logbooks due
 28/5
16 REVISION   
Week
of 4/6
17 Exam Week
   Test 2 Test 2
Week
of
11/6
18Alternative assessments if required  Alt Exam if required
   Program is subject to change
* To be confirmed
  


Learning Resources

Prescribed Texts

Lab Manual - Term 1 (DNA)
Lab Manual - Term 2 (Protein)
Both Lab manuals are available from the course Blackboard. Please print the manual in time for the week 1 class. Print the whole manual at the start of the semester - bring it to class each week so you have the instructions for each experiment. The Term 2 Manual will be available towards the beginning of term 2.

Resources available on Blackboard for this course


References


Other Resources

Lab coat, Gloves, Safety goggles (some are available in the lab), Appropriate shoes.
Logbook (a bound book, NOT spiral) - it needs only to be short - 30 pages or so is sufficient.


Overview of Assessment

Assessments for this course typically consist of:
 

  • Class activities
  • Reports
  • Presentations
  • Exams
  • Online Quizzes
  • Logbook records of experiments


Assessment Tasks


#1    
Assessment Task:   Prac Report 1, Agarose Electrophoresis of DNA    
Done (wk):    3    
Due (wk): 5    
% : 15%    
Maps to NTIS Performance Criteria*:    1.1-5, 2.1-3, 3.1-4, 4.1-3, 5.1-5
Maps to NTIS Skills & Knowledge*: RS:1, 4-14, RK:8, 9 10, 12, 13

#2    
Assessment Task:   Test 1
Done (wk):  9    
Due (wk): on day   
% : 25%    
Maps to NTIS Performance Criteria*:    n/a    
Maps to NTIS Skills & Knowledge*: RS:1-12, RK:1-10

#3
Assessment Task:   Prac Report 2, SDS PAGE of Albumin    
Done (wk): 12    
Due (wk): 14    
% :  15%    
Maps to NTIS Performance Criteria*:    1.1-5, 2.1-3, 3.1-4, 4.1-3, 5.1-5
Maps to NTIS Skills & Knowledge*: RS:1, 4-14, RK:8, 9 10, 12, 13

#4    
Assessment Task:   Test 2
Done (wk): 17    
Due (wk): on day   
% :  25%    
Maps to NTIS Performance Criteria*:     n/a    
Maps to NTIS Skills & Knowledge*:RS:1-12, RK:1-10

#5    
Assessment Task:   Logbook
Done (wk): all    
Due (wk):each week/ submit in week 15    
% : Satisfactory
Maps to NTIS Performance Criteria*:    7.1-4    
Maps to NTIS Skills & Knowledge*: RS:1-12, RK:3,12

#6    
Assessment Task:   Weekly Quizzes    
Done (wk): A quiz most weeks    
Due (wk): Thursday of most weeks*    
% :  20% AND must have an average pass for all quizzes.     
Maps to NTIS Performance Criteria*:    5.1-5, 6.1-5   
Maps to NTIS Skills & Knowledge*: RS:1-10, RK:1-13

#7    
Assessment Task:   Attendance/ In class observations    
Meet 80% attendance requirement AND have satisfactory (competent) performance     
Done (wk): all    
Due (wk): all   
% : Satisfactory    
Maps to NTIS Performance Criteria*:    All i.e 1.1-5, 2.1-3, 3.1-4, 4.1-3, 5.1-5, 6.1-5, 7.1-4    
Maps to NTIS Skills & Knowledge*: RS:1-14, RK:1-13

Total     100%        
Important information about assessment

 

To pass the course you need to pass, on average, each type of assessment (tests, reports, assignments, quizzes, logbooks). For example, if there are two tests you need to have an average of 50% to pass. But you also need to have passed the other assessments as well. You can’t make up marks from one type of assessment to another (eg pass the tests but fail the prac reports).

 

This means:

    You need an average pass grade from all the quizzes to pass the course
    You need an average pass grade from both theory exams to pass the course
    You need to pass the logbook component of the course to pass the course.
     If you miss a prac class you should provide a copy of your medical certificate or other evidence (court appearance, funeral notice, statutory declaration) to the teacher.
    You need to pass the prac reports to pass the course.
    You need to pass the prac exam to pass the course.

 

Additional assessment may be provided at the discretion of the Program Coordinator if your average test mark is above 45% and you have passed all other assessments.

 

Students must attend at least 80% of practical classes. If you miss a prac class you should provide a copy of your medical certificate or other evidence (court appearance, funeral notice, statutory declaration) to the teacher.

 

Extension of time for submission of assessable work:

A student may apply for an extension of up to 7 days from the original due date

They must lodge the application form (available on the web) at least the day before the due date

The application is lodged with the School Admin Office on Level 6, Bdg 51

Late work that is submitted without an application for an extension will not be corrected, and therefore will receive a zero grade.

 

Students requiring longer extensions must apply for Special Consideration  (form available on the Web)

For missed assessments such as exams- you (& your doctor if you are sick) must fill out a special consideration form. This form must be lodged at the HUB or online with supporting evidence (eg medical certificate), prior to, or within, 48 hours of the scheduled time of examination.


Assessment Matrix

Other Information

Do each week’s Quiz before the Lab class to help you prepare.
The quizzes are designed to help you prepare for each lab class. Each week you should read through the notes available from Blackboard as well as the lab manual and then do the quiz. The more preparation you do before class, the easier (and faster!) will be your lab experience, and you’ll learn a lot more too!
Each quiz is available from when it is released until the start of prac class time.  Network or technical difficulties will not be accepted as a valid excuse for not having done the quiz, so…

…give yourself the best chance of getting the quiz done successfully:

•    Use  a computer with a reliable network connection
•    Don’t leave the quiz till the last moment  
•    Make sure you know how to submit the quiz properly
•    Ask the teacher if you are not sure if your quiz has been submitted

Remember that you need to pass the quizzes on average to be able to pass the course.
See the assessment section for full details.

Logbook Assessment
Your logbook must be signed off after completion each week by both the student AND the teacher.
The teacher will also signoff your logbook on the class sheet as a central record.

The central record is the evidence record that is required to show that your logbook has been signed off by you, the student, and the teacher.

IT IS THE STUDENT’S RESPONSIBILITY TO GET THEIR WORK SIGNED OFF EVERY WEEK.
(If you miss the class you do not need to get the sheet signed off – the teacher will record this as an absence). If a logbook is not signed off, that week’s grade will be NYC* unless you were absent.

*NYC = not yet competent

When is a lab performance considered “competent’ (ie when can a logbook be signed off)?
Logbooks will only be signed off when the student has followed and completed a method adequately, and is therefore considered competent for that experiment.

This is evidenced by:

THE LOGBOOK WILL ONLY BE SIGNED OFF BY THE TEACHER AFTER THE FOLLOWING:

1.    Your performance during the lab class is satisfactory
2.    Show date of analysis/results at top of page at start of experimental record in logbook,
3.    Attach loose pages to logbook securely (use tape or staples),
4.    Include raw and analysed results in logbook as appropriate to particular method (see lab manual)
5.    You have cleaned up lab work area and equipment adequately
6.    You have signed off logbook entry once record of results and the clean up are completed

IDEALLY THE LOGBOOK IS SIGNED OFF ON THE DAY OF THE EXPERIMENT.
If this is not possible due to time constraints (the teacher will let you know when this is the case), you can get the logbook signed off WITHIN 2 WEEKS of doing the experiment.

Attendance/Class observations
Students need to attend at least 80% of classes so that skills can be learned and practices, and so that sufficient observations to determine satisfactory (competent) lab work.

When is a prac performance considered “not yet competent’?
(ie when will a logbook not be signed off?)

Performance will be considered to be ‘not yet competent’ for an experiment if:

•    The Student doesn’t attend class long enough to complete the experiment
•    The Student doesn’t finish the procedure in a reasonable time
(nominally by the time class finishes – excluding when there are logistic issues that mean few/no one in the class finishes).
•    The student doesn’t contribute to the group effort adequately
•    Results are a debacle – several errors/extensive lack of following SOP (method).
•    The experiment is not conducted in a safe manner
•    The lab area and equipment are not adequately cleaned up

In the case of a not yet competent result, it is noted that there is no opportunity to repeat that particular experiment due to scheduling of classes. In this case, to achieve competency other experiments during the course should be done to a ‘competent’ level and the student should show a good amount of improvement as semester goes along as evidenced by observations in class by the teacher.
 

Booklist

1.    A logbook is required for this course to record all experimental details. The logbook must be brought to class each week and signed off by the teacher.
The book needs to be a bound NON-SPIRAL exercise book.

Completion of experimental records in the logbook trains students how to keep good records that can be used as “proof of discovery”. These logbooks form legal documents that can be used to prove discovery for Intellectual Property & patenting purposes & thus form an important part of the electrophoresis course. Because pages can easily be ripped out of SPIRAL bound books,
SPIRAL bound books ARE NOT ACCEPTABLE.

All loose pages should be attached to the logbook as soon as possible. This is so that important experimental records do not get lost.

The logbook is to be submitted at the end of the semester – see the assessment guide.


2.    Resources available from Blackboard including:
•    Theory notes and worksheets
•    Videos and diagrams that show each electrophoretic technique used in class
•    Links to internet resources
•    Online quizzes

Time Allowance for this course
The 100 nominal hours for this unit are allocated as follows:

Aspect                         Breakdown (hours)                                       Total (hours)
theory at home             (1hr*7)+(1hr*5)+5  + 4                                       17
online weekly quiz        10 quizzes * 1.5hr                                              15
revision at home           2 * 5hrs                                                              10
exams 1&2                   2 * 1.5hr                                                               4
alt asst (if required)      1 hr                                                                      1
prac                              (7*4hr) +(3*5hr)                                                  43
fieldtrip                         4hr                                                                       4
report write ups            2 * 3hr                                                                 6
         
                                                                                         Total Hours  100

 

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