Course Title: Apply electrophoretic techniques

Part B: Course Detail

Teaching Period: Term1 2011

Course Code: ONPS5210C

Course Title: Apply electrophoretic techniques

School: 155T Vocational Health and Sciences

Campus: City Campus

Program: C5183 - Diploma of Laboratory Technology (Biotechnology)

Course Contact: Kirsten Balding

Course Contact Phone: +61 3 9925 4283

Course Contact Email: Kirsten.balding@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

PMLTEST303B - Prepare working solutions OR PMLTEST402A - Prepare, standardise and use solutions
PMLTEST404A - 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:

PMLTEST512A Apply electrophoretic techniques

Element:

Establish client needs and schedule analysis

Performance Criteria:

1           Liaise with client or sample provider to determine client needs and sample history

2           Record sample description, compare with specification and record and report discrepancies

3           Identify non-routine samples and the possible need to vary enterprise procedures

4           Seek advice from supervisor about any proposed variations and document all approved changes

5           Schedule analysis using enterprise procedures

Element:

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:

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.

Element:

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:

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

                  Prepare validation checks for analytical portion(s)

Element:

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

                Troubleshoot analytical procedure or equipment problems which have led to atypical data or results

Element:

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

                Check calibration status of instrument and perform calibration using specified standards and procedures, if applicable


Learning Outcomes



Details of Learning Activities

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


Teaching Schedule


Semester 1, 2011

 

 

FOR LONG EXPERIMENTS THEORY & PRAC CLASSES ARE MERGED TOGETHER

Part 1 - DNA

Date (week of)

week


 

THEORY 1 Hour



PRAC 4 Hours

Assessment



7/2

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


14/2

2

Visualising 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)

Weekly quiz 1

21/2

3

Quantifying DNA using agarose electrophoresis and fluorimeter methods.



1. Pipetting Workshop (Eppendorf*)

*Refresher - using pipettes

*How to calibrate pipettes

 

 

2. Agarose Gels II How much & how pure is my DNA?
(fluorimetry versus agarose gel determination)

Weekly quiz 2

 

 

 

 

Experiment for Prac Report1
agarose gels II only

28/2

4

Which allele(s) of Alu
is in your DNA? How can you tell from the electrophoresis results?

 

Electrophorese Mol Gen
Alu PCR products gel electrophoresis

 

*Emerging technology: agarose gels e-Gels (Invitrogen)
 


Weekly quiz 3

 

 

7/3

5


Electrophoresis of RNA (Northern Blotting); Electrophoresis of Genomic DNAs (Pulsed field gel electrophoresis, Southern Blotting)

 

 

Prac report 1 do activity in class
– annotating gel photos

Weekly quiz 4

Prac report 1 due – do and submit in class

14/3

6

Intro to DNA sequencing & Capillary Electrophoresis

DNA Sequencing
(AGRF Sequencing facility visit)

Weekly quiz 5


21/3

7

Update logbooks

(no theory topic this week)

 

Update logbooks at home/ last date to sign off any term 1 entries

Logbooks due by 5pm Thursday

28/3  8  Revision (at home)  

4/4

9

Exam week - Test 1

 

Test 1



 

Program is subject to change

*To be confirmed


 

Electrophoresis Lab
Course Outline cont’d…






Part 2: Protein

Date

Week


 

THEORY (1 Hour)



PRAC (4 Hours)


Assessment



 

 

 

 

 

11/4

10

1. Protein 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*)

Weekly quiz 6

18/4 &25/4 (split week)

11

Intro to SDS-PAGE,

2. Calc size of proteins using SDS-PAGE

 

 

Lab class held on 21st April
(so 28th is vacation)

1. Preparing solutions
– protein agarose electrophoresis.

 

2. Protein agarose Electrophoresis of Serum Haemoglobins


(Helena Labs*) 


 

3. Preparing solutions
 - Western Blotting
 

 

Weekly quiz 7

21 Apr – 27th Apr     Student vacation

2/5

12



SDS-PAGE of Albumin. *Prac Report 2




Weekly quiz 8

 

Prac Report 2

SDS-PAGE of Albumin

 

9/5

13

Dotblot Immunoassay, Western transfer & Westernblot Immunoassay

1. Record & analyse
    SDS- PAGE result. 

 

2. Calculate size of albumin.

3. Dotblot - a simple
    immunoassay.

Weekly quiz 9

16/5

14

SDS - PAGE of a mixture of proteins &
Western Transfer of an SDS-PAGE gel.

Weekly quiz 10

(prac report due)

 

23/5

15

1. Western blot immunoassay

 

 

2. Emerging technology – western blotting

    iBlot demonstration (Invitrogen*)


Logbooks due

30/5

16

REVISION

 

 



Week of 6/6

17

Exam Week   Test 2


Test 2



Week of 13/6

18

Alternative assessments if required

 

 

 

      

 

Program is subject to change

* To be confirmed


Learning Resources

Prescribed Texts

Boyer R (2006) Biochemistry Laboratory Modern Theory and Techniques, Benjamin Cummings
Carlton Library Call No. 572.078 B791

The text has nice information about both Electrophoresis and Chromatography Techniques. There should be a number of copies on the library that you can borrow.


References

Electrophoresis Lab Manual. The Lab manual will be provided online via blackboard in the first week of semester (you will be notified by email when it is available). Students are required to print the ENTIRE lab manual at the START of semester and bring it to ALL lab classes.


Other Resources

Students require labcoat, gloves and other standard PPE for working in a laboratory.
Students need to bring a NON-SPIRAL logbook to ALL lab classes. (more information below).


Overview of Assessment

Assessments for this course typically consist of:
• Class activities
• Assignments
• Presentations
• Exam


Assessment Tasks

Assessment Guide 2011 - Apply electrophoretic techniques (ONPS5210C/PMLTEST512A)



#

Title

Assessment Task

Done (wk)

Due
(wk)

%

Maps to NTIS Performance Criteria*

Maps to NTIS
Skills & Knowledge*

1

Prac Report 1

Agarose Electrophoresis
of DNA

3

5

15%

1.1-5
2.1-3
3.1-4
4.1-3
5.1-5

 RS:
1, 4-11

RK:
8, 9 10, 12, 13

2

Test 1

 

Test 1

9

 

20%

 n/a

RS:
1-10

RK:
1-10

3

Prac Report 2

 

SDS PAGE of Albumin

12

14

15%

1.1-5
2.1-3
3.1-4
4.1-3
5.1-5

 

 RS:
1, 4-11

RK:
8, 9 10, 12, 13

4

Test 2

 

Test 2

17

 

20%

n/a

 RS:
1-10

RK:
1-10

5

Logbook

 

Logbook

all

15

15%

 7.1-4

 RS:
1-10
 
RK:
3,12

6

Weekly Quizzes

A quiz each week

all

By start of prac – no quiz, no entry to prac

Best 5 each worth 3%
(ie 15% total) AND must have an average pass for all quizzes. Quiz must be done before entry to that week’s prac class

 5.1-5
6.1-5

 RS:
1-10

RK:
1-13

7

Attendance

Meet 80% attendance requirement

all

 

satisfactory

All i.e
1.1-5
2.1-3
3.1-4
4.1-3
5.1-5
6.1-5
7.1-4

 RS:
1-12

RK:
1-13

 

 

 

 

 

Total

100%

 

 

 

·       NOTE: The weekly quiz must be done before start of prac session.
No quiz = No entry to prac. NO EXCEPTIONS.

·       Students must attend at least 80 % of practical classes to pass the course.

·       Students must pass all of the assessment tasks to pass the Learning Unit.

·       All prac reports must be satisfactory to pass the subject. If they are not satisfactory, you will be given an opportunity to resubmit. If you are absent from a session nominated for a formal report it is your responsibility to negotiate a replacement report with the teacher. You MUST submit the number of required reports in order to pass the course.

·       *** You agree to & abide by the anti-plagiarism statement when submitting your report ***



Assessment Matrix

Other Information



 

To gain entry to each week’s prac class, you need to have done the weekly quiz for that week. The teacher will check at the start of class who has done the quiz, and therefore who is eligible to do the prac. By doing the quiz you show that you have prepared for the class, which increases your and everyone else in the lab’s safety.

 

The quiz is available from when it is released (earlier in the week) 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 the quizzes impact your practical attendance.
You must attend at least 80% of classes to be able to pass the course.

 

 

 


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). YOU WILL BE CONSIDERED NYC* FOR THAT WEEK UNTIL THE CENTRAL RECORD IS SIGNED OFF or YOU ARE MARKED ABSENT.

 

*NYC = not yet competent

 

When is a prac 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 IS DONE:

 

  1. Show date of analysis/results at top of page at start of experimental record in logbook,
  2. Attach loose pages to logbook securely (use tape or staples),
  3. Include raw and analysed results in logbook as appropriate to particular method (see lab manual)
  4. You have cleaned up lab work area and equipment adequately
  5. 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.

 

See the next page for how you can also get a grade of NYC for a practical session.


 

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

 

A student is 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 (record reason for NYC grade)
  • The attitude and work ethic of the student while doing experiments is considered appropriate by the teacher

 

 
 

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.     R. Boyer (2006) Biochemistry Laboratory. Pearson Benjamin Cummings USA

This is the text for this course.

 

 

3.     J Crowe, T. Bradshaw, P. Monk (2006)
Chemistry for the Biosciences. The essential concepts. pp 274-277 
Oxford University Press, Oxford.

This is available from the RMIT Library’s eReserve collection & is available after login from the following link:

http://digital.lib.rmit.edu.au/ereserve/notes07/onps5201c/31259007839827.pdf


The link can also be accessed from the Electrophoresis Learning Hub site in the External Links section:

 COURSES > APPLY ELECTROPHORETIC TECHNIQUES > EXTERNAL LINKS
and also in the week 1 folder

 

 

4.     Kaplan, Lawrence A., Pesce, Amadeo J. & Kazmierczak, Steven C. (2003)
Clinical chemistry: theory, analysis, correlation, 4th ed. St. Louis, Mo, Mosby
Chapters 5,6,7 & 10.
This is available from the RMIT Library’s eReserve collection & is available after login from the following link:

http://digital.lib.rmit.edu.au/ereserve/notes06/onps5179l-5131/31259007735140.pdf

The link can also be accessed from the Electrophoresis Learning Hub site in the External Links section:

 COURSES > APPLY ELECTROPHORETIC TECHNIQUES > EXTERNAL LINKS

 

 

 

 

Course Overview: Access Course Overview