Stable isotope probing: Technical considerations when resolving ¹⁵N-labeled RNA in gradients

RNA based stable isotope probing (SIP) facilitates the detection and identification of active members of microbial populations that are involved in the assimilation of an isotopically labeled compound. ¹⁵N-RNA-SIP is a new method that has been discussed in recent literature but has not yet been tested. Herein, we define the limitations to using ¹⁵N-labeled substrates for SIP and propose modifications to compensate for some of these shortcomings. We have used ¹⁵N-RNA-SIP as a tool for analysing mixed bacterial populations that use nitrogen substrates. After incubating mixed microbial communities with ¹⁵N-ammonium chloride or ¹⁵N₂ we assessed the fractionation resolution of ¹⁵N-RNA by isopycnic centrifugation in caesium trifluoroacetate (CsTFA) gradients. We found that the more isotopic label incorporated, the further the buoyant density (BD) separation between ¹⁵N- and ¹⁴N-RNA, however it was not possible to resolve the labeled from unlabeled RNA definitively through gradient fractionation. Terminal-restriction fragment length polymorphism (T-RFLP) analysis of the extracted RNA and fluorescent in situ hybridisation (FISH) analysis of the enrichment cultures provided some insight into the organisms involved in nitrogen fixation. This approach is not without its limitations and will require further developments to assess its applicability to other nitrogen-fixing environments

Towards an Optimal Photonic Network: Optimising Performance, Cost and Flexibility

This thesis investigates optical fibre transmission system technologies, and their impact on network architectures with the objective of lowering unit cost ($/Gb/s/km) of data transmission in long-haul, and ultra long-haul dense wavelength division multiplexing (DWDM) photonic networks. The importance of this work is driven by the exponential growth in Internet traffic of around 40% p.a., and economic pressures constraining network operators’ ability to invest in their networks. Optical transport networks must therefore be designed to meet future bandwidth demands of end users, with optimum performance, cost and flexibility. Dynamic gain equalisers (DGEs) are a key sub-system of ultra long-haul networks, enabling increased un-regenerated transmission reach and elimination of expensive optical-electrical-optical (OEO) regeneration. A theoretical framework was developed integrating models of wideband power variation, together with narrowband nonlinear propagation simulations using the split-step Fourier method. The optimum spacing of the also costly DGEs was determined for a 3,000km network field deployment. Optimum power pre-emphasis profiles were predicted and compared with simple linear calculations, showing <0.7dB performance penalty using the much faster, simplified method. Optical dispersion management schemes were studied, with optical dispersion compensating fibre placed after every other span resulting in 6% cost reduction and little performance degradation compared to compensation after every span. A techno-economic comparison of optical and electronic dispersion compensation (EDC) strategies showed 25% cost reduction using EDC. Tolerance to fibre nonlinearities is reduced compared to optical compensation; splitting the EDC function equally between transmitter and receiver optimises performance. Economic benefits of a single flexible, multi-reach DWDM system were investigated showing almost 20% cost savings compared to separate long-haul and ultra long-haul systems. Finally, the techno-economic benefits of optical bypass in meshed networks were analysed for increasing levels of optical transparency: from OEO regenerated to multi-degree reconfigurable optical add-drop multiplexers (MD-ROADMs), enabling up to 46% cost saving

Facilitating re-use of PhD research data

Paper and presentation given at the Open Repositories 2013 conference, 8-12 July 2013, in Charlottetown, Prince Edward Island, Canada.JIS

User Guide for the Deposit of Data to Open Research Exeter (ORE)

This is a draft guide for the deposit of research data to Open Research Exeter using Globus Online. The guide is subject to change.JIS

E-theses Survival Guide for New PGR Students

A guide to E-theses for new PGR students

Outline of Communications Plan for PGR Open Access Research and Research Data Management Policy

This is a new version of the document. This version was uploaded on 10.05.2013This document outlines the communications plan for the Open Access Research and Research Data Management Policy for PGRs.Jis

Open Exeter: Key Outputs and Sustainability Plans

A poster describing Open Exeter's key outputs and sustainability plans. The poster was shown at the JISC MRD programme workshop in Aston, from 25-26 March 2013.JIS

Checklist for depositing data on Open Research Exeter (ORE)

Before you deposit your digital research data in Open Research Exeter (ORE) you need to select, prepare, organise and document your data, check any legal and ethical issues and decide which level of access you will give to your data. This draft checklist should help you prepare for data deposit.JIS

Open Exeter Advocacy and Communication Strategy

The advocacy and communications plan for the Open Exeter project.JIS

Abstract for IDCC 2013 Poster Sessions

Open Exeter is a JISC-funded project investigating how best to embed good practice in research data management and Open Access in the research lifecycle. This is essential to ensure compliance with funder policies and that the maximum possible benefits of exposing data accrue at an individual and institutional level. So that we can help researchers and postgraduate students to comply with funder and institutional policy, we are developing a range of integrated training courses and resources, using different formats, styles and content tailored for differing audiences.JIS