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Module Specifications

Current Academic Year 2012 - 2013
Please note that this information is subject to change.

Module Title Adv Lab Techniques in Molecular Biology
Module Code BE480
School School of Biotechnology
Online Module Resources

Module Co-ordinatorSemester 1: Dermot Walls
Semester 2: Dermot Walls
Autumn: Dermot Walls
NFQ level 8 Credit Rating 5
Pre-requisite None
Co-requisite None
Compatibles None
Incompatibles None
Description
This module aims to familiarise students with commonly used in vitro and in silico techniques in molecular evolution and human molecular genetics.

Learning Outcomes
1. Prepare and assess biological sequence data sets and estimate phylogeny using a variety of methods.
2. Operate the computer based maximum parsimony method using real biologial data.
3. Apply statistical and mathematical apporaches to determine protein selective pressures/protein evolution.
4. Use polymorphism databases to identify SNPs and their linkage disequilibrium patterns.
5. Design and apply a SNP genotyping assay and discover the frequency in a population.
6. Design and execute a relative Q-PCR assay to measure the mRNA levels of a specific gene and interpret results.



Workload Full-time hours per semester
Type Hours Description
Lab18In silico tools for genetics and comparative genomics
Independent learning time44.5full access to server all week for practicing manipulations using UNIX scripting and UNIX language, high throughput bioinformatics basic skills
Lab18Molecular genetic techniques (wet bench)
Independent learning time44.5report writing, reading of specified materials and independent learning time
Total Workload: 125

All module information is indicative and subject to change. For further information,students are advised to refer to the University's Marks and Standards and Programme Specific Regulations at: http://www.dcu.ie/registry/examinations/index.shtml

Indicative Content and Learning Activities
Commonly used in silico techniques to assess molecular evolution and patterns in sequence data.
Phylogenetic/genomics: Basic methods in identifying relationships amongst expressed proteins. Practical experience in phylogeny reconstruction, Long Branch Attraction(LBA) and evolutionary rate variation. Case Study for pjhylogenetics: The Florida dentist case will be used to determine whether the accused was guilty or infecting individuals in a population with HIV using phylogenetic methods.Selection analysis: Practical experience in statistical approaches and methods in comparative genomic analyses and producing statistically robust results..

Commonly used in vitro techniques in human molecular genetics to assess gene expression..
SNP genotyping forms the basis of porjects such as the HapMap that will facilitate efforts to dientify the genetic risk factors associated with common disease. The module aims to teach students how to access nucleotide-based databases such as dbSNP and HapMap in order to design and interpret a SNP genotyping assay for a gene of interest.Relative Q-PCR. Microarrays are now widely used technique for analysiing global gene expression patterns. However, specific gene expression differences require validation by an independent method such as Relative Q-PCR (or Real time PCR). The module aims to teach students how to design and interpret a gene-specific Q-PCR assay, including how to identify the most appropriate endogenous control under particular experimental coniditions..

Assessment Breakdown
Continuous Assessment100% Examination Weight0%
Course Work Breakdown
TypeDescription% of totalAssessment Date
Computerised test/examReports from in vitro and in silico work100%Other
Reassessment Requirement
Resit arrangements are explained by the following categories;
1 = A resit is available for all components of the module
2 = No resit is available for 100% continuous assessment module
3 = No resit is available for the continuous assessment component
This module is category 2
Indicative Reading List
  • Campbell and Heyer: 0, Genomics, Proteomics and bioinformatics, 2,
  • Higgs and Attwood: 0, Bioinformatics and Molecular evolution,
  • Edwards: 2004, Real-Time PCR: An essential guide, Horizon Bioscience (Thompson Scientific),
  • HapMap User Guide online: 0, user guide,
  • dbSNP user guide online: 0, user guide,
  • LightCycler 480 user guide: 0, user guide,
  • Page and Holmes: 0, Molecular Evolution: a phylogenetic approach,
Other Resources
None
Array
Programme or List of Programmes
GCBBSc in Genetics & Cell Biology
Timetable this semester: Timetable for BE480
Date of Last Revision26-MAY-08
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