Pathology Unit Guide 2022 great and comprehensive PDF

Preview

Summary

hope you enjoyed my notes thanks you and come again next time thanks good bye bye bye bye enjoy the notes again!...

Description

School of Biomedical Sciences

Molecular Medicine PATH2211 6 credit points Semester 1 Crawley Campus

Unit Coordinator: Amber Boyatzis

All material reproduced herein has been copied in accordance with and pursuant to a statutory licence administered by Copyright Agency Limited (CAL), granted to the University of Western Australia pursuant to Part VB of the Copyright Act 1968 (Cth). Copying of this material by students, except for fair dealing purposes under the Copyright Act, is prohibited. For the purposes of this fair dealing exception, students should be aware that the rule allowing copying, for fair dealing purposes, of 10% of the work, or one chapter/article, applies to the original work from which the excerpt in this course material was taken, and not to the course material itself.

© The University of Western Australia 2022

Unit Description Molecular medicine can be defined as the molecular cell biology underlying human disease. Biochemical, biological and bioinformatics techniques are used to describe molecular structures and mechanisms and identify fundamental molecular processes. Knowledge gained from understanding these processes guides us to develop molecular interventions to correct human dysfunction (i.e. pathology). This unit will emphasise basic cellular and molecular phenomena underlying normal human biology rather than the conceptual and observational focus on patients and disease. Content in PATH2211 will reinforce basic concepts in molecular and cellular biology and will provide a framework for the understanding of more complex diagnostic modalities covered in subsequent pathology units. These basic concepts will be contextualised by studying examples of dysfunction at each level (DNA, RNA, protein). The basic precepts will then be expanded to cover in detail the molecular tools that can be used for diagnostic and prognostic assessment. Topics will include: DNA, RNA, protein structure in healthy humans, chromosome structure, function and abnormalities, regulation of gene expression in health and disease and molecular tools in diagnostic and prognostic applications.

Unit rules Prerequisites: SCIE1106, Molecular Biology of the Cell Incompatibility: Nil

Learning outcomes PATH2211 Learning Outcome

(1) Demonstrate an understanding of DNA and chromosome structure and function (2) Demonstrate an understanding of basic gene regulation and structure (3) Describe the implications of altered gene structure (4) Demonstrate an understanding of basic cellular processes and dysfunction (5) Describe examples of metholodologies used in molecular medicine (6) Demonstrate analytical skills in the interpretation of data (7) Demonstrate skills in accessing informatic databases (8) Demonstrate an understanding of genetic and cellular information related to cellular and molecular dysfunction

In-semester tests and final examination

Practical tests, quizzes, worksheets and assignments

Unit Contact Hours Up to 30 hours of lecture content across the semester. All lectures will be provided as recordings. Optional revision sessions may be held synchronously online as needed. 3-hour practical workshops, including self-directed learning activites, throughout semester.

Contact Details Unit Coordinator Amber Boyatzis (she/her) School of Biomedical Sciences Bayliss Building, Rm 3.41 [email protected]

Academic teaching staff Amber Boyatzis ([email protected]) Kathy Fuller ([email protected]) Liz Quail ([email protected]) Mark Cruickshank ([email protected]) Sean Ramsey ([email protected])

Contacting academic and professional staff by email Writing a professional email is a generic skill that you should acquire while at UWA. All email messages should be polite, considerate, and contain correct grammar and spelling. All should begin with an appropriate salutation, e.g. “Dear…”, and end with a suitable closing, e.g., “Regards…”. Please note "madam" or "mdm" is not an acceptable way to address any UWA staff member. Do not expect an answer to an email outside of business hours (Monday – Friday, 09:00 – 17:00). Please check the “Announcements” section in the unit’s LMS page before sending an email as your question may have already been addressed.

Student Feedback In this unit you will be asked to complete Student Experience of Learning and Teaching (SELT) Unit Evaluation questionnaires. Links to these surveys will be sent to your student email later in semester. The feedback you provide in these questionnaires is used by the unit coordinator to modify future delivery and content of the unit, ensuring high quality teaching and learning practices at UWA. Your responses on SELT questionnaires are used by the lecturing and demonstrating staff to develop their individual teaching approaches, unit content and student engagement methods. It may also be used to support excellence in teaching and promotion applications. We really value and do our best to respond to your feedback.

Unit resources Learning Management System (LMS) www.lms.uwa.edu.au For technical assistance with the LMS please do not contact the unit coordinator. If you need help using the LMS visit the Student LMS Help section, contact the University Library for student IT support ,or submit an email enquiry using this form this form.

UWA uses a 24-hour clock Please note that UWA uses a 24-hour clock system for clarity of timings. All teaching and assessment times will be given using this system. Thus, 09:00 equals 9:00 am, 17:00 equals 5:00 pm. All times are given in Australian Western Standard time (+8GMT).

Recommended texts Readings and resources will be placed on the Unit Readings page, available via LMS. The UWA Library holds copies of the following texts. The assigned textbook for this unit is: Strachan T, Read AP. Human molecular genetics. Fifth edition. Boca Raton, Florida: CRC Press; 2019. Copies of this text are available via the UWA Library. Additional textbooks referenced in some lectures are available in the library’s collection. These include, but are not limited to, the following textbooks: Alberts B, Johnson A, Lewis J, Morgan D, Raff M, Roberts K, et al. Molecular biology of the cell. Sixth edition. New York, N.Y: Garland Science, Taylor and Francis Group; 2015.* Griffiths AJF, Doebley J, Peichel C. An Introduction to Genetic Analysis. 12th ed. New York: Macmillan Learning; 2020. * Lewis R. Human genetics: concepts and applications. Twelfth edition. New York, NY: McGraw-Hill Education; 2018. Ch 15.7, Ch13.4 (p.242).* Lodish HF. Molecular cell biology. Eighth edition. New York: W.H. Freeman-Macmillan Learning; 2016. * Pierce BA. Genetics : a conceptual approach. Seventh Edition. New York: Macmillan Learning; 2020. * Strachan T, Goodship J, Chinnery PF. Genetics and genomics in medicine. New York, NY: Garland Science; 2015. * Available online via the UWA library

Unit schedule : Overview Week (starting) 1 (28 Feb)

2 (7 Mar)

3 (14 Mar)

4 (21 Mar)

5 (28 Mar)

6 (4 Apr)

Lectures 1・DNA and chromosome structure 2・DNA and chromosome replication 3・Genes and genome structure 4・Transcription 5・RNA - coding and noncoding 6・Translation 7・Gene mutations 8・Gene Repair 9・Introduction to technologies 10・Mutation detection technologies I 11・Mutation detection technologies II 12・Gene expression technologies 13・Recombinant DNA technologies

7 8 (25 Apr)

9 (2 May)

10 (9 May)

11 (16 May)

12 (23 May)

1・Introduction to workshop sessions

Assessment % unit grade Workshop quizzes and activities ・1%

2・Gene Structure and Bioinformatics Bioinformatics test in your scheduled workshop time

Bioinformatics test ・4%

No session due to PROSH Time to work on SDL 3・LDLR: Bioinformatics

Practical worksheet ・1%

4・LDLR: PCR and Gel Electrophoresis

Practical worksheet ・1% Cytogenetics SDL・2%

Study break

(11 Apr)

(18 Apr)

Practical workshops

14+15・Cell Signalling I + II

5・LDLR: Melt Curve Analysis

Practical worksheet ・1% In-semester Test 1・10%

16・Protein technologies 17・Cytogenetic techniques

6・LDLR: Sequencing

Practical worksheet ・1%

18・Cell cycle, mitosis and meiosis

7・LDLR: Group presentations

Practical presentation ・1%

19+20・Cell Cycle Control I +II

Time to work on LDLR written report

LDLR written report ・13%

21+22・Chromosome abnormalities I + II

8・Flow Cytometry

In-semester Test 2 ・10% Flow cytometry worksheet・5%

23+24・Inheritance I + II

Lecture Schedule Week

Lectures

(Mon)

1 (28 Feb)

2 (7 Mar)

3 (14 Mar)

4 (21 Mar)

5 (28 Mar)

0 ・ DNA chemistry ・Amber Boyatzis* 1 ・DNA & chromosome structure・Amber Boyatzis 2・ ・DNA & chromosome replication・Amber Boyatzis 3・ ・Genes & genome structure・Sean Ramsey 4・ ・Transcription・Sean Ramsey 5・ ・RNA - coding & noncoding・Sean Ramsey 6・ ・Translation・Sean Ramsey 7・ ・Gene mutations・Mark Cruikshank 8・ ・Gene Repair・Mark Cruikshank 9・ ・Introduction to technologies・Amber Boyatzis 10・ ・Mutation detection technologies I・Amber Boyatzis 11・ ・Mutation detection technologies II・Mark Cruikshank

(4 Apr)

12・ ・Gene expression technologies・Mark Cruikshank 13・ ・Recombinant DNA technologies・Mark Cruikshank

(11 Apr)

Study break

6

7 (18 Apr)

8 (25 Apr)

9 (2 May)

10 (9 May)

11 (16 May)

12 (23 May)

14+15・ ・Cell Signalling I and II・Sean Ramsey 16・ ・Protein technologies ・ Amber Boyatzis 17・ ・Cytogenetic techniques・ ・ Amber Boyatzis 18・ ・Cell cycle, mitosis & meiosis・Liz Quail 19+20・ ・Cell Cycle Control I and II・Liz Quail 21+22・ ・Chromosome abnormalities I + II・Liz Quail 23+24・ ・Inheritance I + II・Liz Quail

*The content of this lecture is essential background for this unit, but is not directly assessed.

Practical Workshop Sessions Assessments relating to the practical workshop sessions total 30% of the overall unit marks.

Practical Workshop Schedule Week (Mon)

1 (28 Feb)

2 (7 Mar)

3 (14 Mar)

4 (21 Mar)

5 (28 Mar)

6 (4 Apr) (11 Apr)

7 (18 Apr)

8 (25 Apr)

9 (2 May)

10 (9 May)

11 (16 May)

Practical workshops 1・ ・Introduction to workshop sessions・Amber Boyatzis 2・ ・Gene Structure and Bioinformatics・Mark Cruickshank Bioinformatics test in your scheduled workshop time No session due to PROSH ・Opportunity to complete SDL 3・ ・LDLR: Bioinformatics・Amber Boyatzis / Sean Ramsey 4・ ・LDLR: PCR and Gel Electrophoresis・Amber Boyatzis / Sean Ramsey Study Break 5・ ・LDLR: Melt Curve Analysis・Amber Boyatzis / Sean Ramsey 6・ ・LDLR: Sequencing・Amber Boyatzis / Sean Ramsey 7・ ・LDLR: Presentations of findings・Amber Boyatzis / Sean Ramsey No formal session・ Time to work on LDLR write-up 8・ ・Flow Cytometry・Kathy Fuller

12 (23 May)

Attendance You must attend practical sessions online on Tuesdays OR Wednesdays from 09:00 -11:45. The E-learning Suite in the J Robin Warren Library at QE2 is also resesrved for this unit during the workshop session times. Please check CAS and attend your allocated sessions only. During each practical session your interaction and performance will be assessed. You will be required to submit work in-class during most practical sessions. To this end, you must attend each practical session. If you do not attend your designated practical session, you will receive a mark of zero for that part of the practical assessment.

You are required to keep accurate practical notes during all practical sessions and may be required to submit these for assessment at any time during the semester. You do not need to purchase a notebook for your practical notes, but are asked to use the practical work sheets for your note taking.

Microsoft Teams (teams.microsoft.com) Three workshops in this unit will be delivered via Microsoft Teams. Microsoft Teams is a program which will allow us to conduct interactive workshops easily throughout the semester. You will need to navigate to the MS Teams site, and then log in using your UWA credentials. You should attend your workshop session on MS Teams at the time allocated on CAS. Before the first scheduled online workshop please make yourself familiar with the code of conduct, which will be posted both on the LMS site, and within MS Teams. We expect you to “arrive” 5-10 minutes prior to each session, as you would for an in-person class. During the workshops, each group will be using MS Teams to complete your worksheets together. At the end of each of the LDLR workshops, each group’s shared word document will be considered to be your completed and submitted worksheet. Lecturers and workshop facilitators will NOT reply to private messages (chats) sent via MS Teams. Please direct queries to academic staff via email only. You may use MS Teams to engage in peer-assisted learning through posting in the “general” channel. Whilst teaching staff may contribute in this channel from time to time, please do NOT expect them to be checking, moderating or otherwise contributing to these discussions.

Assessment Mechanism Assessment % unit grade

Practical sessions 30%

In-semester tests 20% Final Examination 50%

Weighting

Date

Workshop quizzes, activities and worksheets

6 x 1% ea

During relevant workshop sessions

Bioinformatics test

4%

15 / 16 of March

Cytogenetics SDL

2%

Fri 8 April 23:30

LDLR written report

13%

Fri 13 May 23:30

Flow cytometry worksheet

5%

Fri 20 May 23:30

In-semester Test 1 Lecture content, weeks 1-5

10%

Tue 12 April 18:00

In-semester Test 2 Lecture content, weeks 6-10

10%

Tue 17 May 18:00

Final Examination

50%

TBA

Ethical Scholarship, Academic Literacy and Academic Misconduct Ethical scholarship is the pursuit of scholarly enquiry marked by honesty and integrity. Academic Literacy is the capacity to undertake study and research, and to communicate findings and knowledge, in a manner appropriate to the particular disciplinary conventions and scholarly standards expected at university level. Academic misconduct is any activity or practice engaged in by a student that breaches explicit guidelines relating to the production of work for assessment, in a manner that compromises or defeats the purpose of that assessment. Students must not engage in academic misconduct. Any such activity undermines an ethos of ethical scholarship. Academic misconduct includes, but is not limited to cheating, or attempting to cheat, through: • Collusion • Inappropriate collaboration • Plagiarism • Misrepresenting or fabricating data or results or other assessable work • Inappropriate electronic data sourcing/collection • Breaching rules specified for the conduct of examinations in a way that may compromise or defeat the purposes of assessment. Penalties for academic misconduct vary according to seriousness of the case and may include the requirement to do further work or repeat work; deduction of marks; the award of zero marks for the assessment; failure of one or more units; suspension from a course of study; exclusion from the University, non-conferral of a degree, diploma or other award to which the student would otherwise have been entitled.

Refer to the Academic Integrity policy

Final Examination – 50% of your overall unit grade The final examination will assess all unit-level learning outcomes (all unit content). It will be delivered online, be of approximately 2 hours duration, and will be open-book. Further information on the exam format will be available closer to the time. DATE: TBA

In-Semester Tests There are TWO in-semester tests contributing 20% of your overall unit grade (10% each). You will be assessed on lecture content only. These tests will be delivered online and will be open-book. Test 1: Tuesday, April 12 at 18:00 Online. Test 1 will cover lecture content from Weeks 1 to 5, inclusive. Test 2: Tuesday, May 17 at 18:00 Online. Test 2 will cover lecture content from Weeks 6 to 10, inclusive. Please note these tests may appear as a face-to-face class on your CAS. These assessments have since been modified for online delivery.

Practical Workshop Assessments The assessments relataing to the practical workshops contribute 30% of your overall unit grade. Practical workshop

Assessment

Weighting

1・Introduction to workshop sessions

In- workshop quizzes and activities

1%

2・Gene Structure and Bioinformatics

Bioinformatics test

4%

Cytogenetics Self-Directed Learning Activity (SDL)

Cytogenetics SDL worksheet

2%

3・LDLR: Bioinformatics

Practical worksheet (group submission)

1%

4・LDLR: PCR and Gel Electrophoresis

Practical worksheet (group submission)

1%

5・LDLR: Melt Curve Analysis

Practical worksheet (group submission)

1%

6・LDLR: Sequencing

Practical worksheet (group submission)

1%

7・LDLR: Group presentations

Practical presentation (group submission)

1%

LDLR Practical series Workshops 3-7

LDLR written report

13%

8・Flow Cytometry

Flow cytometry worksheet

5%

Accessing LMS tests and assessments You may be required to use multi-factor authentication to access the LMS and other UWA services. This involves receiving a code or SMS to your phone in order to log in to the system. If you have a scheduled assessment administered via the LMS you will need to ensure ahead of time that your phone is available to you and working properly. In the event that your phone is not functioning or available to you, you will need to contact the UWA Library to reset the multi-factor authentication for your account. You can email them ([email protected]) contact by phone (+61 8) 6488 2342, or use the chat function on the library website (library.uwa.edu.au). It is your responsibility to make arrangements so that you can access the LMS in order to complete your assessments. Please note that you can set alternate phone numbers and email addresses as a backup for receiving the multi-factor authentication code. We STRONGLY suggest that you do this as soon as possible as, in the event of a mishap with your phone, doing so will allow you to log in and complete the assessment without having to receive immediate IT support.

Assessment Word Limits Where a submitted assignment exceeds the word limit, a penalty of 1 per cent of the total mark allocated for the assessment task applies for each 1 per cent in excess of the word limit, or the marking ceases once the word limit is reached. For details, please see section 5.3.3 of the University’s assessment policy document.

Policy on Referencing Written Work All written work must be correctly referenced using the Vancouver referencing system. Health and Medical Sciences primarily use this referencing system; therefore students must learn and use this system. Further guidelines on referenc...