Undergraduate final year projects at Huddersfield are 10–12–week long, student–led and research–based. Students spend up to 2 days per week doing lab– or computer–based research and, based on their results, prepare their dissertations and presentations. They choose and rank five of the projects proposed each year by members of staff and are assigned a project based on their second year grades, in order of preference.
Like last year, we offer projects very much aligned with our research interests, although this year we place more emphasis on the weasel project.
How do weasels change colour?
Weasels from the genus Mustela are small and widespread carnivorous mammals. Two subspecies of least weasels living in sympatry in northeastern Poland exhibit marked differences in coat coloration in winter: M. n. nivalis rapidly turns white when days shorten, while M. n. vulgaris, recently invading north, remains of brownish colour throughout the winter. The change provides camouflage and increases survival on snow for M. n. nivalis, however the mechanism of coat colour change is unknown. This project will select genes and/or promoter sequences of the melatonin–receptor genes and others, likely involved in coat colouration, based on literature and database searches and then proceed to design and test primers to amplify the transcripts or genomic regions of interest. Finally, the amplified regions will be sequenced and analysed in relation to known polymorphisms involved in coat colour changes in other animals.
Literature mining, database mining, multiple sequence alignment, DNA/RNA isolation from tissue, primer design, polymerase chain reaction (PCR), agarose gel electrophoresis, DNA sequencing.
Hubbard, J. K., Uy, J. A. C., Hauber, M. E., Hoekstra, H. E. & Safran, R. J. Vertebrate pigmentation: from underlying genes to adaptive function. Trends Genet 26, 231–239 (2010).
Lebarbenchon, C., Poitevin, F., Arnal, V. & Montgelard, C. Phylogeography of the weasel (Mustela nivalis) in the western-Palaearctic region: combined effects of glacial events and human movements. Heredity 105, 449–462 (2010).
This is a project for students who are expected to work on different pathways or elements of pathways involved in coat colour development. Each student is expected to test and validate at least three candidate sequences. A PhD student may supervise students during their work.
Electronic logic gates in Escherichia coli
Ability to construct novel genetic circuits from “standardised” DNA–based parts is one of the major themes in synthetic biology. The student in this project will be tasked with assembly and characterisation of at least two different genetic circuits in E. coli that will emulate behaviour of electronic logic gates. Up to three constructs will be assembled using PCR and BioBrick assembly, one of the most popular standard methods for joining DNA molecules, and their behaviour characterised via flow cytometry.
Literature mining, DNA manipulation in silico (Gibson Assembly, BioBrick Assembly, restriction digestion and ligation, cloning), plasmid DNA isolation from bacteria, Gibson Assembly, BioBrick Assembly, cloning, bacterial transformation, bacterial culture, agarose gel electrophoresis, PCR, sequencing, gene expression measurement (enzymatic and/or fluorescent).
This is a project for students who are expected to work on assembly or measurements of different sets of parts. Each student is expected to assemble and validate at least three constructs of their own choosing. A PhD student may supervise students during their work.
Cameron, D. E., Bashor, C. J. & Collins, J. J. A brief history of synthetic biology. Nat Rev Microbiol (2014). doi:10.1038/nrmicro3239
Kelwick, R., MacDonald, J. T., Webb, A. J. & Freemont, P. Developments in the tools and methodologies of synthetic biology. Frontiers in Bioengineering and Biotechnology 2, 60 (2014).
- SnapGene (Mac + Windows) – in my opinion the best software for manipulating and visualising DNA sequences, by a long shot. Paid, but worth it, and there is a free trial available for a month. A very nice and free (donationware) alternative: ApE (Mac + Windows).
Word of wisdom
Last but not least, ten weeks at up to two days per week is less then three weeks of hands–on lab– or computer–based work in total. It is hard to overstate the fact that this is a very short amount of time for any project in biology and it is especially unforgiving if the project is wet lab–based. Preparation, regular participation in lab meetings and good work ethics are crucial to the success of the project.