Biotechnology and Biological Sciences Doctoral Training Programme
   
   
  

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Please note that the list of projects available will be increased over the next few weeks so please check frequently. Project details may also be subject to change before September 2018.

 

 

 

View all our available projects

Molecular genetic studies of spider silk: from natural to synthetic fibres

Description
The rotation will involve both bioinformatic and molecular laboratory elements to provide training in both these areas. Bioinformatic analysis will be made of previously obtained spider silk transcriptome data. Molecular genetic analysis will involve designing and carrying out PCR assays to confirm the location within and amongst silk glands of individual silk transcripts.

Investigation of Metastatic Cancers using a Perfusion Culture Bioreactor

Description
Substrate preference of breast cancer cells. Metastasising cancer cells from specific primary origins tend to recolonise particular secondary sites, for example breast cancer cells most commonly disseminate to the lymph nodes, lungs and bone. Their choice of destination depends largely on the composition of the extracellular matrices present at the secondary location. The aim of this project is to optimise decellularisation protocols for various bovine (or porcine) tissues to enable breast cancer colonisation and harvesting to be achieved with sufficient yield for downstream applications, including clonogenic survival and analysis of genetic stability.

Microbial fuel cells for direct conversion of waste gases into electricity and chemicals

Description
The overall aim of these training projects is to provide proof of concept that a gas fermenting bacterium (Cupriavidus) can be used in a microbial fuel cell to produce electricity and chemicals directly from dirty waste gases.

Regulation of clostridial butanol production by cell-cell communication

Description
This mini project will serve as an introduction to anaerobic microbiology and the biology of the genus Clostridium. Its scientific objective will be the phenotypic characterisation of a C. acetobutylicum quorum sensing mutant.

Biotechnology with a pinch of salt - halophilic enzymes in tandem flow reactions

Description
The goal of this proposal is to assemble a combined enzymatic system that will allow two sequential reactions to take place in flow. This system will generate amines from alcohols via a carbonyl intermediate. Amines are key functional groups of numerous intermediates for pharma and agrochemical applications, and enzymatic synthesis will offer a 'green' alternative to traditional methodologies. To overcome the limitations of mesophilic enzymes such as low stability in organic solvents, a novel system will be based on two halophilic biocatalysts that offer remarkable stability and excellent substrate scope. Both enzymes (HvADH2 and HvAAT1) are from the halophilic archaeon Haloferax volcanii. HvADH2 is exceptionally tolerant to organic solvents, has an unusually broad substrate scope, and shows enhanced stability upon covalent immobilization.

Fungal Sex for Strain Improvement in Biotechnology

Description
Fungi are used in biotechnology for the production of a variety of valuable products including antibiotics, statins, enzymes, and foodstuffs. The overall PhD aims to exploit knowledge of fungal sexual reproduction to allow the development of novel and improved strains of fungi for the food, pharmaceutical, and industrial biotechnology sectors.

Chemicals and fuels from methane gas

Description
During the six weeks rotation, the student will become familiar with the growth and manipulation of methanotrophic organisms and the use of the various gene tools available. Specifically, they will: (i) learn how to cultivate methanotrophic organisms using methane as the sole carbon source; (ii) how to electro-transform and conjugate from E.coli into methanotrophic organisms, how to screen putative mutants by colony PCR and agarose gel electrophoresis; learn how to assemble complex operons via Gibson/USER assembly, and; become familiar with DNA analysis software, CLC Bio WorkBench, DNASTAR and Vector NTI. (iii) undertake CRISPR/Cas9-mediated gene knock-out.

Exploiting cell individuality to improve production by yeast and other fungi

Description
Cell individuality describes the near-universal phenomenon whereby individuals within a population exhibit marked variation in phenotype, despite being genetically uniform. In an industrial production process using microorganisms, this means that only a portion of the population are likely to have optimal production activity and this is likely to be very wasteful. Therefore, harnessing this variation opens great opportunities for marked improvements to production processes.

Making a new DNA cut and paste gene editing tool using CRISPR protein fusions

Description
Modelling and analysis of atomic resolution structures fo Cas9, Cpf1, Casposon-Cas1 and Cas8/CasA. To test for protein production of novel fusions of these CRISPR gene editing enzymes as a pilot for testing DNA cut and paste activities. Simple genetic analysis to assess gene-fusion function.

Discovery and characterisation of copy number variation in the chicken genome

Description
This mini-project will begin by applying bioinformatic analysis of chicken (or cattle) genome sequences to develop a pipeline for defining and genotype-calling CNVs. This will use a collection of genome sequences available in Nottingham (Prof. Olivier Hanotte) augmented by genome sequences from collaborators elsewhere.

Decoding the molecular basis of antigenic variation in animal African trypanosomes

Description
Tagging and localisation of potential antigenic surface proteins of Trypanosoma congolense. During the rotation, students will investigate the surface composition of the major causative species of Animal African Trypanosomiasis (AAT) by endogenous locus tagging and subcellular localization of putative variable surface proteins.

Unravelling Animal African Trypanosomiasis: Starve the Parasite, Feed the World

Description
In this rotation, students will carry out the first steps towards the definition of molecules that are critical to animal African trypanosomes. In the main project, identified molecules will be tested for biological functions and parasite viability, potential as drug targets and in vaccine development.

Fungal sex hormones as novel agents for disease control

Description
Fungi are responsible for a number of devastating plant diseases. However, fungi are also used for the beneficial production of various foodstuffs and valuable pharmaceuticals and other metabolites. This project aims to identify whether fungal sexual reproduction can be exploited to produce hormonal factors that might be used as novel growth regulators.

From pests to paradise: control and conservation of molluscan biodiversity

Description
During the lab rotation the student will receive training in several of the techniques that are a necessary component of the larger PhD project. Depending upon the existing skills of the student, these are likely to include a range of molecular biology techniques (e.g. DNA extraction, PCR, RNA methods), analysis (e.g. mapping genes to chromosomes), simple (e.g BLAST searching) and more advanced bioinformatics (e.g. phylogenetics, introduction to biolinux).

Understanding and harnessing endosymbiont infections to boost the benefits of invertebrate biocontrol

Description
Use of next-generation sequencing techniques and bioinformatic analysis to identify and characterise bacterial endosymbionts in invertebrate hosts.

Assessing the potential of ladybird alkaloids as pesticides

Description
The mini project will be closely related to the main project but will focus more on the electrophysiological techniques that will be employed. The student will patch clamp the TE671 human muscle cell line and obtain nicotinic acetylcholine receptor (nAChR) currents in response to ACh. They will also express mammalian nAChR subunits that are known to function in Xenopus oocytes and measure some of their basic electrophysiological properties using two-electrode voltage-clamp. On successful completion of this part of the project they will investigate the actions of a novel alkaloid alongside an antagonist known to inhibit nAChRs.

The effect of diet on oxidative stress, immune gene expression and parasite resistance in fish

Description
Students will carry out a short-term dietary manipulation on lab-raised stickleback, culture immune (head-kidney) cells from different treatment groups and conduct fluorescence-based cellular assays of oxidative stress on these cell populations.

Determining the Incidence of the Sheep Liver Fluke (Fasciola hepatica) in Snail Intermediate Hosts.

Description
Freshwater snail intermediate hosts of the Family Lymnaeidae will be collected from local populations and parasites isolated, with emphasis on the sheep liver fluke Fasciola hepatica.

Developing a bovine monoclonal antibody platform

Description
The project will characterise bovine monoclonal antibodies for their ability to neutralise important livestock virus infections. Techniques will include antibody cloning, expression and analysis using live virus culture.

Assessing the risk of bornavirus infection in UK livestock and interrogating wildlife reservoirs

Description
Bornaviruses are a cause of serious neurological disease in a variety of humans, animals and birds. In livestock, especially sheep, infection invariably leads to death in cases where overt symptoms are evident. The cost to the farming industry, especially in parts of the world where the virus is thought to be endemic, is considerable.
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Biotechnology and Biological Sciences Doctoral Training Programme

The University of Nottingham
University Park
Nottingham, NG7 2RD

Tel: +44 (0) 115 8466946
Email: bbdtp@nottingham.ac.uk