Next Generation Science at the University of Dundee

Studying abroad the University of Dundee — one of GEO’s newest programs in the sciences — is not your typical overseas experience. You’ll swap lecture halls and classrooms for practical work as a research scientist. Join labs such as the Hunter Group, who are searching for novel anti-microbial drugs using next generation genome sequencing. Students who study abroad in the spring semester can join the following practical projects (or similar ones like them):

Bioinformatics Project – Next Generation Genome Sequencing

Faculty Lead: Prof. David Martin
Modern DNA sequencing techniques, so called ‘next generation sequencing’, allow us to rapidly determine the sequence of a genome of interest. In particular it is relatively straightforward to determine the genome sequence for prokaryotes. In this practical we will start with a set of simulated next generation sequencing data for a prokaryote. You will then assemble that genome using exactly the same tools and techniques that a research scientist would. This will give a set of genomic fragments which should contain the genes in which we are interested.

Microbial Cell Biology Project

Faculty Lead: Prof. Nicola Stanley-Wall
Genetics deals with the molecular structure and function of genes in a cell or organism. Experimental techniques that manipulate the genetics of an organism have provided a wealth of knowledge regarding gene function. Indeed non-biased genetic screen (such as random mutagenesis) allow researchers to gain insight at the molecular level to processes that otherwise would remain a mystery. In this practical, you will develop the knowledge and technical skills to apply molecular genetics to the analysis of bacterial physiology.

Molecular Biochemistry Project – Purified Proteins

Faculty Lead: Prof. Joost Zomerdijk
The overall goal of this practical is to allow you to gain experience of protein expression and purification, SDS-polyacrylamide gel electrophoresis (SDS-PAGE), Western blot analysis, enzyme assays and potentially protein crystallization.

Plant Sciences Project – Agrobacterium

Faculty Lead: Prof. Edgar Huitema
Crop plants and their diseases have played a major part in the rise and demise of civilizations, mass emigration and population growth. The study of plants and the causal agents of disease have always featured prominently in the biological sciences and consequently, helped revolutionise our understanding of cellular processes. Ironically, the identification and subsequent adaptation of one plant pathogen, Agrobacterium tumefaciens, has helped revolutionise Molecular Plant biology, Biotechnology and now synthetic biology. In this practical course, you will use Agrobacterium as a tool to study the interaction between the devastating oomycete pathogen Phytophthora infestans (late blight of potato, cause of the Irish Potato Famine) and its host(s) Nicotiana benthamiana and potato (Solanum tuberosum).

Synthetic Biology Project – Biobricks

Faculty Lead: Prof. David Booth
Synthetic Biology is a modern, forward-looking field with its roots in molecular genetics that aims to allow the design of new biological systems. It is a multidisciplinary field that involves fundamental science such as chemistry, biology, physics and mathematics, coupled with the principles of engineering, electrical and electronic engineering, and computer science. Whole systems biology and modelling approaches are also intimately linked with Synthetic Biology. In 2003 the REGISTRY OF STANDARD BIOLOGICAL PARTS (http://partsregistry.org/Main_Page) was founded by Tom Knight at Massachusetts Institute of Technology, Cambridge, USA. This was an ambitious initiative in the early days of Synthetic Biology with the aim of setting up a free and open collection of DNA fragments that could be used to build the device or organism of your dreams. With it came the concept of standardised “BIOBRICKS”, which are thousands of different pieces of DNA, all cloned the same way and following the same design principles, that could be snapped together to build a biological device. The overall aim of this practical is to design, build and characterise a biobrick with a temperature sensitive RNA. You will be fully briefed on the specifics of the biobricks that can be produced during the introductory session/workshop. You will be able to choose from a broad selection of biobricks already available at the University of Dundee in order to help express and characterise your new biobrick.

Drug Design Projects

Working under the leadership of a Dundee faculty member, you’ll work in the areas of new drug discovery and design, investigating topics such as:

• Synthesis of sulfonamides and hydroxamates from benzoic acid derivatives
• A comparison of coupling agents in the synthesis of 2-fluoro benzohydroxamic acid and 2-(trifluoromethyl) benzohydroxamic acid

Molecular Ecology Project

Faculty Lead: Prof. David Martin 
Observation of large mammals in Scotland is difficult. It requires considerable field craft and is timeconsuming and expensive. A more convenient approach is to use surrogate measures such as scat, or droppings. Identification of species from fresh scat in the field is usually straightforward but often scat samples are older and reliable identification between two species of similar size and of similar habitat is not possible. Animals shed epithelial cells in their scat, and the DNA from these can be recovered and amplified via PCR. The aim of this project is to design a suitable set of PCR primers that will allow the amplification of a region of the mitochondrial genome that contains a restriction enzyme site specific for one of a species pair but not the other.