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BIO8044 : Biotechnology: Advanced Topics

  • Offered for Year: 2019/20
  • Module Leader(s): Dr Jon Marles-Wright
  • Lecturer: Dr Thomas Howard, Professor William Willats, Professor Angharad MR Gatehouse, Professor Chris Tapsell, Dr James Stach, Dr Timothy Boswell, Dr Maxim Kapralov
  • Owning School: Natural and Environmental Sciences
  • Teaching Location: Newcastle City Campus
Semester 1 Credit Value: 20
ECTS Credits: 10.0


1.       To elaborate the methods for and uses of genes and genome sequencing.

2.       To elaborate methods for the design of experiments.

3.       To elaborate the use of cell-free systems for biotechnology applications.

4.       To elaborate different microbial systems used to express recombinant proteins.

5.       To elaborate the methodologies underlying genetic engineering of plants and animals (both vertebrates and invertebrates) from first principles including construction of transgenes and techniques for introducing them into plant/animal cells.

6.       To elaborate the use of RNA interference as a means of gene silencing to understand gene function.

7.       To elaborate the use of different omics technologies to understand cellular systems and to inform metabolic engineering applications.

8.       To elaborate genome mapping strategies through different molecular markers.

9.       To elaborate methods for protein design.

10.       To elaborate the design and construction of synthetic genomes.

11.       To promote detailed critical analysis of, and engagement with, the latest developments in the field.

Outline Of Syllabus

An introduction to the applications of basic understanding of cell & molecular biology will be provided to appreciate the principles, methods & systems used as foundations for various agricultural, pharmaceutical, medical & biotechnology industries. Areas range from applications in fundamental tools like DNA sequencing to expressing recombinant proteins for research or commercial applications, to generating improved varieties of crop plants & livestock through genetic engineering, & the directed engineering of proteins for increased activity & novel functions. The use of omics methods for studying cellular systems & functional molecular markers as well as marker-assisted breeding will be covered. Technologies for gene silencing such as RNAi will be addressed. Synthetic biology methods such as the implementation of measurement standards & statistical design of experiments approaches will be covered. DNA technologies including genome editing & the construction of synthetic genomes will be explored.

Fundamentals of Gene Transfer to Plant & Animal Cells
•       Design of transgene constructs for use in plants and animals • Genetic modification of plant & animal cells
Methods & Applications of Transgenesis in Crops
•       Plant Transformation using Agrobacterium-mediated transformation and biolistic transformation • Other techniques for developing novel crops/traits
•       Unintended effects of transformation
Methods & Applications of Transgenesis in Invertebrate Model Organisms
•       Nematode worm (C. elegans) transgenesis
• Insect transgenesis
The Mouse as a Platform for development of Animal Transgenic Technology
•       Methods & applications of mouse transgenesis
Animal Cloning
•       Introduction to animal cloning methods and applications for animal transgenesis
Microorganisms as Expression Systems
•       Expression vectors (Components of an expression vector; Constitutive and inducible promoters; Assembly of expression constructs; Targeting and tagging of protein products)
•       Bacterial expression systems
•       Yeast expression systems
•       Comparison of expression systems
•       Methodologies for protein design and engineering
Bioinformatics & Genome Analysis
•       Next generation sequencing
•       Gene & Sequencing
•       From Gene to Function, Gene Expression & Silencing
•       ESTs, and expression databases
RNA Interference (RNAi)
•       Understanding gene function through RNAi
•       Use of RNAi to control insect pests
Omics technologies to study & engineer cellular systems
•       Methodologies for studying the proteome of an organism
•       What are molecular markers? (Isoenzymes and protein isoforms; RFLPs; RAPDs; AFLPs & other PCR-based markers)
•       Relationships between “classical” and molecular markers and maps (Construction of gene maps)
•       Molecular markers in plant breeding (Map based cloning and QTLs)
•       Metabolic engineering
Synthetic biology technologies
•       The implementation of standards for measuring the activity of genetic constructs in different biological contexts
•       Use of Statistical Design of Experiments approaches
•       Design and construction of synthetic genomes
•       Genome editing technologies
Antibody technology
•       Phage display
•       ELISA
•       Production of monoclonal antibodies
On completion of the module students should have:
•       a detailed knowledge of the methods by which transgenes are constructed and introduced into plant or animal cells.
•       an awareness of historical context and development of plant transformation and expression of valuable traits.
•       an awareness of historical context and development of animal transgenesis and cloning.
•       Appreciate the limitations imposed by species differences in the use of specific transgenic methodologies.
•       a detailed knowledge of the construction and use of microbial expression systems for production of recombinant proteins.
•       an understanding of proteomics for the identification and development of functional molecular markers.
•       an understanding of the main molecular tools for synthetic bio

Teaching Methods

Teaching Activities
Category Activity Number Length Student Hours Comment
Guided Independent StudyAssessment preparation and completion12:002:00Mid-semester Test
Guided Independent StudyAssessment preparation and completion12:002:00Final Exam
Guided Independent StudyAssessment preparation and completion240:3012:00Revision for final exam
Guided Independent StudyAssessment preparation and completion55:3027:30Practical reports
Scheduled Learning And Teaching ActivitiesLecture241:0024:00N/A
Guided Independent StudyAssessment preparation and completion160:154:00Revision for mid-semester test
Scheduled Learning And Teaching ActivitiesPractical53:0015:00N/A
Guided Independent StudyDirected research and reading241:0024:00N/A
Scheduled Learning And Teaching ActivitiesFieldwork26:0012:00N/A
Guided Independent StudyIndependent study153:3053:30Study of lectures, ReCap, Blackboard etc.
Guided Independent StudyIndependent study241:0024:00Consolidation of lectures
Teaching Rationale And Relationship

The lectures will provide students with the background information on DNA techniques and the labs will allow them to think in more practical terms how to get information from experiments and computer based data analysis. The labs give them the opportunity to practise the techniques discussed in the lectures and to learn how to interpret the data and report the experiments in an appropriate format, preparing them for their future project. The field trips will allow students to see some of the techniques they are studying in use in an industrial setting.

Assessment Methods

The format of resits will be determined by the Board of Examiners

Description Length Semester When Set Percentage Comment
Written Examination1201A50N/A
Other Assessment
Description Semester When Set Percentage Comment
Case study1M30Based on 5 practicals
Prob solv exercises1M20Online MCQ test
Assessment Rationale And Relationship

The written exam, practical report and mid-semester test will assess the students’ understanding of the subject. The mid-semester test will also act to check students' progress with, and understanding of, the module content.

Study Abroad students may request to take their exam before the semester 1 exam period, in which case the format of the paper may differ from that shown in the MOF. Study Abroad students should contact the school to discuss this.

Reading Lists