Biotechnology Exemplar Projects

 
Exemplar projects led by UoN
   
Studies of spider silk for biotechnology: From natural to synthetic fibres  Spider silks display a remarkable array of properties that make them an area of great interest in biotechnological research. Individual silks demonstrate many of the desired properties needed for a biomaterial; they can be tough, biocompatible and have remarkable tensile strength. Some silks are as strong and tough as Kevlar and steel, while others retain their strength and structure in extreme environments. This makes spider silk an especially interesting candidate for both bioengineering and medical applications. However, it is relatively difficult to farm spiders due to their cannibalistic nature. Recent technological advancements have enabled the recombinant production of artificial miniaturised spider silk proteins (spidroins) in bacterial and eukaryotic hosts. Optimisation of the design of recombinant silk proteins relies on our understanding not only of what is transcribed, but of the translation and assembly of native silk proteins. The structure of silk genes and their protein products can vary between both silk type and spider species. Understanding the importance of each of these processes will allow a rational design approach to recombinant silks. This project aims to shed light on the complex genetic regulation of spider silk genes, especially those used by spiders that live in extreme environments, and use this information to create synthetic silk proteins. 2017-2021
Understanding the role of DNA repair proteins in CRISPR-mediated gene editing Over the last decade, the number of technologies available for genome editing has exploded, providing researchers with new approaches for the manipulation of DNA and RNA in prokaryotes and eukaryotes. Much of this development has been built around the CRISPR-Cas systems of adaptive immunity. The front-runners of this new platform which target DNA, the Class II Cas-enzymes Cas9 and Cas12a, rely on the repair of DNA double-strand breaks (DDSBs) by host DNA-repair enzymes for successful editing. This has highlighted crucial supporting roles for DNA repair systems in the success of genome manipulation. Data are beginning to emerge regarding the identities of DNA repair enzymes associated with successful genome editing in human cells, including enzymes such as the PolQ-like Helicase HelQ, ssDNA bind protein RPA and CtIP, a promoter of end resection at DDSBs. This project aims to explore interactions of HelQ and RPA with Cas9 and Cas12a at the site of R-loops using synthetic DNA substrates. This will be further supported by measuring the efficiency of editing through the use of cell-free systems derived from knockout cell-lines of DNA-repair proteins such as HelQ and CtIP, building towards the hypothesis that the role of such proteins is to remove the roadblock that Cas-enzymes present to DNA-repair systems such as the HR, SDSA and FA pathways. 2016-2020 
Structural characterisation of the β-barrel assembly machinery (BAM) complex in Campylobacter jejuni Biotech 2016-2020 The cell envelope of Gram negative bacteria has an inner membrane (IM) and an outer membrane (OM) separated by periplasm. Folding of proteins into the IM is well understood and involves post-ribosomal transport by SecA/B and folding/assembly into the IM by the SecYEG complex using a lateral release mechanism. However, understanding how OM proteins reach their final folded state in the outer membrane remains incomplete. Recent evidence indicates the majority of folding and assembly at the OM is facilitated by the β-barrel assembly machinery (BAM) complex. The BAM complex is conserved and essential in Gram negative bacteria with orthologues existing in mitochondria and chloroplasts, which highlights its essential role and potential as an “Achilles heel” in Gram-negative organisms. This project is focused on the BAM complex from an important pathogen, Campylobacter jejuni, a major cause of food spoilage, food poisoning and the more severe (or lethal) Guillain-Barré syndrome. We aim to clone and recombinantly express the components of the BAM complex alongside periplasmic chaperones and laterally involved partner proteins from LPS biosynthesis to determine structure and study interactions of the OM transport pathway. We will utilise circular dichroism, X-ray scattering, electron microscopy, and advanced computing to obtain a structural and biophysical characterisation of the complex in an effort to understand the unique OM protein folding mechanism and to generate a template for pharmacological control of this pathogen.  2016-2020

 

Exemplar projects led by NTU
  
Development of a Defined and Reproducible 3 Dimensional Matrix in Vitro model to Evaluate Angiogenesis and Vascular Condition; A Novel System Entirely Devoid of Animal Components or  Cells 

One of the most elementary pieces of data sought for many medical treatments, including  medicines and interventional therapies like biomedical device implantation, is the treatment’s angiogenic potential; the capacity of the material, agent or medicine to drive neo-vascularisation towards itself. Angiogenesis is a double edged sword. Whilst blood vessels bring nutrient rich tissue fluid to a tissue compromised by damage or disease allowing integration of the treatment with host tissues and avoiding tissue breakdown and necrosis, with the new vessels comes the host defence immune cells, that includes macrophages with the capacity to degrade the treatment and inhibit the function and proliferation of the cells required to provide for a successful clinical outcome. It is therefore of paramount importance during the development of any biomedical device or pharmaceutical agent that the angiogenic potential is characterised and ideally defined by design. This research investigates the provision of a 3D gel with and without cells for use in vitro using tissue engineering systems to produce a 3D cell culture tissue model to replace animal models for the evaluation of the angiogenic potential of material and soluble substances.  The approach offers the potential to provide a highly reproducible and well defined model to replace current animal models (subcutaneous implantation, CAM assay, corneal implantation, skin flap models) for the study of the angiogenic potential of exogenous factors including medicines be they biomaterials and/or agents of pharmaceutical interest. 

 
Deep Learning for Improved Rational Protein Engineering Informatics  Protein engineering has the potential to transform synthetic biology. Deep learning is a versatile and powerful paradigm of machine learning that can learn rich representations from raw data. This project is applying deep learning Long-Short-Term-Memory (LSTM) models to abundant (publicly available) unlabelled protein sequence data towards learning unique statistical vector representations that are semantically rich, and structurally and biophysically grounded. The results will be tested on challenging stability and function tasks and will be compared against the state-of-the-art. The improved representations will be used to evoke deep protein design, and facilitate protein comparisons at any evolutionary depth.

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