Undergraduate final year projects at Huddersfield are 10–12–week long, student–led and research–based. Students spend up to 1.5 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.
Last year (2015–2016) BrykLab offered two types of projects, both very much aligned with our research interests. It is likely that this year’s projects will be very similar; stay tuned for an official announcement in October.
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.
Design, assembly and expression of bacterial plasmids from standardised DNA parts in Escherichia coli
Ability to construct novel genetic circuits from “standardised” DNA–based parts is one of the major themes in synthetic biology. The students in this project will be able to choose a set of DNA parts, assemble them into functional plasmid molecules using Gibson or BioBrick assembly, the two most popular standard methods for joining DNA molecules, and characterise their function depending on the gene assembled. For example, students may assemble and measure the strength of different constitutive promoters that drive expression of a fluorescent protein or assembly a bacterial analogue of an electronic logic gate and measure its performance.
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 1.5 day per week is just over two 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.