PROTEOMICS AND GENOMICS

BIO5PAG

2018

Credit points: 15

Subject outline

In this subject, students will gain theoretical experience with molecular biology, protein expression (in prokaryotes and eukaryotic systems) and protein chemistry techniques most commonly used in the early stages of proteomics and genomics research. The students will also learn the next generation cloning techniques such as 'Gibson Assembly', 'In-­Fusion', 'SLICE', 'LIC' and 'TA' cloning etc. Along with molecular biology and protein chemistry fundamentals, students will also learn more advanced technologies such as Isothermal Loop Amplification PCR, Strand displacement PCR, CRISPR-­mediated gene editing, Next Gen Sequencing and mass spectrometry. In workshops, which are an integral part of this subject, students will learn about practical problem solving related to various subjects taught in this course. Students will also use online data analysis software to identify DNA and protein molecules and algorithms to identify CRISPR gene targets. In completing tasks for this subject, students are expected to gain confidence in applying their knowledge to future research problems.

 




SchoolSchool of Molecular Sciences/LIMS

Credit points15

Subject Co-ordinatorHamsa Puthalakath

Available to Study Abroad StudentsYes

Subject year levelYear Level 5 - Masters

Exchange StudentsYes

Subject particulars

Subject rules

Prerequisites Must be enrolled in one of the following courses: SGBB, SMBB, SMBM, SMBT, SMNT, SZHSMN, SZHSN or SZHSNT. All other students require coordinator approval.

Co-requisitesN/A

Incompatible subjectsN/A

Equivalent subjectsN/A

Special conditionsN/A

Graduate capabilities & intended learning outcomes

01. Use bioinformatic software to analyse and critically interpret genetic or proteomic data

Activities:
During the workshops, students will be provided with an experimental outline and a theoretical set of data. Students will need to analyse the data using standard bioinformatic software. Upon completing these exercises, students will be asked to make a recommendation about what type of experiment they would perform next. These activities will form the basis of a number of worksheets that must be submitted for assessment.

02. Solve mathematical problems and perform calculations commonly used in a laboratory setting and critically analyze the results

Activities:
Throughout the lecture series, students will be provided with opportunities to improve their quantitative literacy skills through completing a number of exercises that examine experimental design and setup. Students will be expected to apply these skills to equivalent problems that are embedded in the worksheets that are delivered in the weekly workshops.

03. Compile, report, interpret and transmit scientific information in a meaningful and clear context

Activities:
At the beginning of the semester, students will be allocated a cDNA accession number from the database. They will need to design an experimental strategy that will allow them to clone the cDNA, express and purify the protein, and finally confirm that it is the correct protein sequence. Students wil also design using an online algorithm guide sequences gene via CRISPR technology. Workshop activities will support students in developing the skills to complete this assignment.

04. Demonstrate an understanding of advanced theoretical concepts in molecular biology and protein chemistry

Activities:
By completing the exercises presented in the lectures and workshops, students should develop a high level of the theoretical knowledge in the areas of molecular biology and protein chemistry. This knowledge will be assessed through the final subject exam and the written quiz.

05. Interpret and critically evaluate experimental data

Activities:
As a part of the worksheet exercises, students will be required to evaluate and interpret experimental data related to the outcomes of mass spectrometry and other experiments.

Subject options

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Start date between: and    Key dates

Melbourne, 2018, Semester 2, Day

Overview

Online enrolmentYes

Maximum enrolment sizeN/A

Enrolment information

Subject Instance Co-ordinatorHamsa Puthalakath

Class requirements

Lecture Week: 32 - 43
One 2.0 hours lecture per week on weekdays during the day from week 32 to week 43 and delivered via face-to-face.

WorkShop Week: 32 - 43
One 2.0 hours workshop per week on weekdays during the day from week 32 to week 43 and delivered via face-to-face.

Assessments

Assessment elementComments% ILO*
1 x 1,000-word assignmentEach student will be allocated a cDNA from the NCBI database. They will need to design a strategy to clone the cDNA, express and purify the protein, analyse by tryptic digest and mass spectrometry and finally design a CRISPR guide for genome editing. The integrated assignment will run from week 2 -10. Students should apply the knowledge they are developing throughout the classes to progressively complete th20 01, 03, 04
1 x 2-hour written examinationStudents will have a set time frame (120 min) to complete a series of questions covering all aspects of the subject curriculum. Questions may be theoretical, technical or analytical in nature.30 02, 04, 05
7 x problem based workshop scenario reports (5% each) (2,000-words equivalent total)Each workshop is based on the theme/subject that was taught in the previous lecture. The students may be asked to critically assess and write a report on a technical video or may be given a proteomics/molecular genetics-­based problem to be solved. Students are expected to use online, web-­based tools to solve these problems including BLAST, BLAT (UCSC genome browser) and ExPASy (SIB Bioinformatics Resource35 01, 02, 04, 05
1 x 1-hour multiple choice quizStudents will be asked to complete a series of questions covering key concepts outlined in the lecture material or provide answers to a problem-­#solving activity.15 02, 04, 05