Lung function and damage over the life course and the effects of chemical agents

Lead Research Organisation: University of Liverpool
Department Name: Institute of Infection and Global Health

Abstract

Lungs are an essential component of humans and are responsible for the gaseous exchange of oxygen and carbon dioxide. The lung itself is complex and is composed of many different regions, depending on function, and cell types. Over the life course of a person, their lungs are subjected to a range of infections and environmental pollutants, and during conflict the potential use of chemical agents such as ricin and chlorine gas. Special cells in the lung are present that can provide a first defence against infectious and chemical agents. However, such traumas can result in the phenomenon of airway remodelling and result in extreme cases in death or present as lifelong breathing difficulties. Using specialist facilities at the Defence Science Technology Laboratory we have extensive transcriptomic (mRNAs) and proteomic analysis (proteins) of lung tissue subjected to chemical damage. Many thousands of molecules were identified and quantified, as well as detailed clinical information. These datasets were gathered over time and represent an unprecedented window into the effects and consequences of lung damage. The PhD project will use informatics to integrate this data (transcriptomics/proteomics/clinical parameters) to provide an in-silico model of lung damage. This will focus on differential gene expression analysis to identify modified signalling pathways and potential pathways that can be therapeutically targeted. Specific highlighted pathways will be further investigated using ex vivo models of the lung. Thus, the project will involve both computational and wet biology. The project will be based at the University of Liverpool and involve short term research visits to the Defence Science Technology Laboratory located at Porton Down.

Publications

10 25 50
 
Description DiMeN - Flexible funding for skill building
Amount £7,000 (GBP)
Organisation Medical Research Council (MRC) 
Sector Public
Country United Kingdom
Start 09/2018 
End 10/2018
 
Title MinION sequencing 
Description MinION is a handheld sequencing tool developed by the UK company Oxford Nanopore. MinION is portable, real-time, and comes with a relatively low-price-tag (the starter pack costs $1,000). The device contains an array of micro scaffolds that support a polymer membrane containing thousands of embedded nanopores. Once loaded and connected to a power source, an ionic current pass through each nanopore generating a voltage difference across the membrane. During sample preparation "adapter" proteins are ligated to the ends of genomic DNA or cDNA strands. The adaptor proteins direct the strands to the membrane where they pass through the pore in a unidirectional flow. As the nucleic acids are transported through a pore, each base disrupts the current in a unique fashion; allowing the sequence to be obtained. By 2014, the MinION, a hand-held portable sequencing device was introduced to an early access scheme, and in 2015 it became commercially available. During library preparation, genetic material within the sample is not intentionally fragmented, enabling the MinION to generate sequence reads which are substantially longer than other comparative platforms. Traditional sequencing methods rely on the fragmentation and in sillico reassembly of DNA/RNA sequences. This fingerprinting approach can sometimes yield poorly constructed, low quality assemblies, especially when it comes to assembling complex genomic regions and highly identical sequences which can lead to missing information and genomic reduction. Longer read lengths allow for overlapping so that the sequence can be unambiguously reconstructed. Long read lengths also enable the identification of epigenetic modifications and transcript isoforms. Apart from human applications, other organisms such as plants have highly repetitive sequences making it difficult to obtain a complete genome using short read methods. Aside from longer read lengths, MinION also has the advantage of being able to directly sequence native RNA and DNA enabling the detection of individual nucleotide modifications. 
Type Of Material Technology assay or reagent 
Year Produced 2019 
Provided To Others? No  
Impact N/A 
URL https://nanoporetech.com/
 
Description Blue Dot science festival 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact At the start of each day, two people dressed in full hazmat regalia (White paper suit, shoe covers, blue gloves and facemasks) stood at a point on the Bluedot map and infected 250 passers-by. Each infected person received an infected blue sticker, and a sticker pack with instructions to infect 3 people then pass the stickers on. we mapped the spread of the Bluedot fever and identified the source point. This activity sparked questons and discussions about outbreak reponse
Year(s) Of Engagement Activity 2006,2019
URL https://www.discoverthebluedot.com/