Welcome to BrykLab.

Undergraduate projects

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, however this year we (finally!) place more emphasis on the computational aspects of our research.

Divergence times between Apodemus and its close relatives based on whole-genome, high-density genotyping data

A student in this project will be tasked with calculating the sequence divergence and divergence time between Apodemus flavicollis and A. sylvaticus and their close relatives such as other species of Apodemus, Mus musculus, Peromyscus, Rattus norvegicus and others, for which it will be possible to recover homologous sequences.

We have previously obtained high-density, whole-genome genotyping data for 80+ wood and yellow-necked mice (Apodemus flavicollis and sylvaticus) from several populations in North-Eastern Poland. From each individual we have 20000+ SNP markers selected from over 10000 genetic loci. There is no well-established way of calculating of sequence divergence from thousands of loci and SNP markers and therefore several different approaches and checks to identify the accurate and reliable way of completing the project need to be undertaken.

Techniques Involved

RAD-seq, Stacks pipeline, R programming, shell programming, high-performance computing, database mining, literature mining.

Introductory papers

Construction of SNP-based pedigrees from the whole-genome genotyping data in the wild wood and yellow-necked mice Apodemus flavicollis and sylvaticus

A student in this project will be tasked with investigating how the individuals from the same population of Apodemus are related, based solely on 20000+ SNP markers from each individual. This is a non-trivial task as, counterintuitively, the more markers one has, the less accurate traditional pedigree construction approaches become. The student’s goal would be to analyse the data: select the right packages and programming tools, select the most informative SNPs (or use all of them), identify and test an appropriate positive control for your method and produce a reliable way of constructing pedigrees from high-density, whole-genome markers.

Techniques Involved

RAD-seq, Stacks pipeline, R programming, shell programming, high-performance computing, database mining, literature mining.

Introductory papers

Construction of genetic circuits 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 one or more of genetic circuits in E. coli. They will be: α-subunit of β-galacosidase gene under control of constitutive or inducible promoter, quorum sensing system based on Vibrio fischeri AHL and a NOT logic gate based on phage λ cI protein.

The constructs will be assembled using PCR and Gibson Assembly and their behaviour characterised via an appropriate techniques such as Müller assay or flow cytometry. The successful constructs will become a part of our collection at practicalsyntheticbiology.net and Addgene.

Techniques Involved

Literature mining, DNA manipulation in silico (Gibson Assembly, cloning), plasmid DNA isolation from bacteria, Gibson 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 constructs of their own choosing. A PhD student may supervise students during their work.

Introductory papers

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.