Metagenomic analysis of the gut microbiome of the common black slug Arion ater in search of novel lignocellulose degrading enzymes

Some eukaryotes are able to gain access to well-protected carbon sources in plant biomass by exploiting microorganisms in the environment or harbored in their digestive system. One is the land pulmonate Arion ater, which takes advantage of a gut microbial consortium that can break down the widely available, but difficult to digest, carbohydrate polymers in lignocellulose, enabling them to digest a broad range of fresh and partially degraded plant material efficiently. This ability is considered one of the major factors that have enabled A. ater to become one of the most widespread plant pest species in Western Europe and North America. Using metagenomic techniques we have characterized the bacterial diversity and functional capability of the gut microbiome of this notorious agricultural pest. Analysis of gut metagenomic community sequences identified abundant populations of known lignocellulose-degrading bacteria, along with well-characterized bacterial plant pathogens. This also revealed a repertoire of more than 3,383 carbohydrate active enzymes (CAZymes) including multiple enzymes associated with lignin degradation, demonstrating a microbial consortium capable of degradation of all components of lignocellulose. This would allow A. ater to make extensive use of plant biomass as a source of nutrients through exploitation of the enzymatic capabilities of the gut microbial consortia. From this metagenome assembly we also demonstrate the successful amplification of multiple predicted gene sequences from metagenomic DNA subjected to whole genome amplification and expression of functional proteins, facilitating the low cost acquisition and biochemical testing of the many thousands of novel genes identified in metagenomics studies. These findings demonstrate the importance of studying Gastropod microbial communities. Firstly, with respect to understanding links between feeding and evolutionary success and, secondly, as sources of novel enzymes with biotechnological potential, such as, CAZYmes that could be used in the production of biofuel

The culture of scientific research.

In 2014, the UK-based Nuffield Council on Bioethics carried out a series of engagement activities, including an online survey to which 970 people responded, and 15 discussion events at universities around the UK to explore the culture of research in the UK and its effect on ethical conduct in science and the quality of research. The findings of the project were published in December 2014 and the main points are summarised here. We found that scientists are motivated in their work to find out more about the world and to benefit society, and that they believe collaboration, multidisciplinarity, openness and creativity are important for the production of high quality science. However, in some cases, our findings suggest, the culture of research in higher education institutions does not support or encourage these goals or activities. For example, high levels of competition and perceptions about how scientists are assessed for jobs and funding are reportedly contributing to a loss of creativity in science, less collaboration and poor research practices. The project led to suggestions for action for funding bodies, research institutions, publishers and editors, professional bodies and individual researchers

New limits on "odderon" amplitudes from analyticity constraints

In studies of high energy $pp$ and $\bar pp$ scattering, the odd (under crossing) forward scattering amplitude accounts for the difference between the $pp$ and $\bar pp$ cross sections. Typically, it is taken as $f_-=-\frac{p}{4\pi}Ds^{\alpha-1}e^{i\pi(1-\alpha)/2}$ ($\alpha\sim 0.5$), which has $\Delta\sigma, \Delta\rho\to0$ as $s\to\infty$, where $\rho$ is the ratio of the real to the imaginary portion of the forward scattering amplitude. However, the odd-signatured amplitude can have in principle a strikingly different behavior, ranging from having $\Delta\sigma\to$non-zero constant to having $\Delta\sigma \to \ln s/s_0$ as $s\to\infty$, the maximal behavior allowed by analyticity and the Froissart bound. We reanalyze high energy $pp$ and $\bar pp$ scattering data, using new analyticity constraints, in order to put new and precise limits on the magnitude of ``odderon'' amplitudes.Comment: 13 pages LaTex, 6 figure

Single-Carbon Atom Insertion into Aromatic Heterocycles

The desire for highly selective and general methods for the functionalisation of complex molecules is particularly prevalent in the field of drug discovery, as the facile modification of pre-existing entities can lead to the rapid diversification of existing drug libraries. In turn, this could lead to the more efficient identification of potential drug candidates. Building upon the general theme of skeletal editing, this thesis details the development of methodologies to transform heteroaromatic scaffolds – namely indoles and pyrroles - by the insertion of a single carbon atom. The work described in Chapter 2 outlines the development of a methodology to achieve the ring expansion of indoles via a cyclopropanation/fragmentation strategy to the corresponding quinoline with the use of zinc carbenoids. While the desired transformation was achieved in modest yields, the highly reactive nature of the carbenoid intermediate led to poor compatibility with unprotected indoles, while protected indoles proved inert in most cases. Chapter 3 details the development and application of a robust protocol to achieve carbon atom insertion by a similar strategy, employing arylchlorodiazirines as photo-activated carbene precursors. Protection of the indole nitrogen proved key to high conversion and – along with the tuning of the reaction solvent – allowed for precipitation of the azinium salt product and facile isolation by filtration. An extensive substrate scope revealed tolerance of a range of functional groups, both on the azole and diazirinyl partners. The exploration of substrate scope was assisted by a robustness screen of a number of medicinally-relevant functional groups, revealing the potential application to complex molecules. Consequently, the methodology was applied to the modification of tryptophan and tryptophan-containing peptides. Functionalisation of the azinium salt products was also explored, focusing in particular on reduction chemistry to give access to a range of three-dimensional architectures. A hazard assessment of arylchlorodiazirines was also carried out as literature reports have often noted their thermal instability though extensive analysis has not yet been undertaken. The explosive nature of arylchlorodiazirines was analysed by the use of differential scanning calorimetry (DSC). From this data, along with predictors derived from it, the thermal stability of these diazirines was assessed and measures to avoid potential hazards were proposed and discussed

Single-Carbon Atom Insertion into Aromatic Heterocycles

The desire for highly selective and general methods for the functionalisation of complex molecules is particularly prevalent in the field of drug discovery, as the facile modification of pre-existing entities can lead to the rapid diversification of existing drug libraries. In turn, this could lead to the more efficient identification of potential drug candidates. Building upon the general theme of skeletal editing, this thesis details the development of methodologies to transform heteroaromatic scaffolds – namely indoles and pyrroles - by the insertion of a single carbon atom. The work described in Chapter 2 outlines the development of a methodology to achieve the ring expansion of indoles via a cyclopropanation/fragmentation strategy to the corresponding quinoline with the use of zinc carbenoids. While the desired transformation was achieved in modest yields, the highly reactive nature of the carbenoid intermediate led to poor compatibility with unprotected indoles, while protected indoles proved inert in most cases. Chapter 3 details the development and application of a robust protocol to achieve carbon atom insertion by a similar strategy, employing arylchlorodiazirines as photo-activated carbene precursors. Protection of the indole nitrogen proved key to high conversion and – along with the tuning of the reaction solvent – allowed for precipitation of the azinium salt product and facile isolation by filtration. An extensive substrate scope revealed tolerance of a range of functional groups, both on the azole and diazirinyl partners. The exploration of substrate scope was assisted by a robustness screen of a number of medicinally-relevant functional groups, revealing the potential application to complex molecules. Consequently, the methodology was applied to the modification of tryptophan and tryptophan-containing peptides. Functionalisation of the azinium salt products was also explored, focusing in particular on reduction chemistry to give access to a range of three-dimensional architectures. A hazard assessment of arylchlorodiazirines was also carried out as literature reports have often noted their thermal instability though extensive analysis has not yet been undertaken. The explosive nature of arylchlorodiazirines was analysed by the use of differential scanning calorimetry (DSC). From this data, along with predictors derived from it, the thermal stability of these diazirines was assessed and measures to avoid potential hazards were proposed and discussed

The construction of an electron diffraction unit

Call number: LD2668 .T4 1950 J69Master of Scienc

Analysis of the gut microbiome of the common black slug Arion ater : in search of novel lignocellulose degrading enzymes

Some eukaryotes are able to gain access to otherwise well-protected carbon sources in plant biomass by exploiting microorganisms in the environment, or harboured in their digestive system. One such organism is the European black slug, Arion ater, which takes advantage of a gut microbial consortium that can break down plant tissues, including the widely available, but difficult to digest, carbohydrate polymers in lignocellulose. This ability is considered to be one of the major factors that have enabled A. ater to become one of the most widespread plant pest species in Western Europe and North America. Here we have identified the A. ater gut environment as a target for metagenomic study through identification of cellulolytic activity of bacterial origin. Next generation sequencing technology was used to characterize the bacterial diversity and functional capability of the gut microbiome of this notorious agricultural pest. Over 6 Gbp of gut metagenomic community sequences were analysed to reveal populations of known lignocellulose-degrading bacteria, along with abundant well-characterized bacterial plant pathogens. This study also revealed a repertoire of more than 3,000 carbohydrate active enzymes (CAZymes), indicating a microbial consortium capable of degradation of all components of lignocellulose, including cellulose, hemicellulose, pectin and lignin. Together, these functions would allow A. ater to make extensive use of plant biomass as a source of nutrients. This thesis demonstrates the importance of studying microbial communities in understudied groups such as the gastropods, firstly with respect to understanding links between feeding and evolutionary success and, secondly, as sources of novel enzymes with biotechnological potential, such as CAZYmes that could be used in the production of biofuel

Good governance and the development of an ethical framework for the UK National Screening Committee

Following COVID-19, good governance of public health is self-evidently a priority. Those who have governance responsibilities should act with integrity, and public health interventions should be both effective and ethically sound. In this context, this article focuses on the work recently undertaken by the UK National Screening Committee (NSC) in reviewing how it engages with and resolves the ethical questions raised by health screening. The article sketches the context for this review and the challenges faced; it describes the review process and the principal review outputs (including the ethical framework); and it reflects on a number of issues that are provoked by the ethical framework. Given the post-pandemic re-organisation of public health, the importance of embedding ethics in screening practice is underlined. If the United Kingdom is to be a standard-bearer for world-leading screening, it is essential that the NSC sustains its commitment to the ideals of good governance

Probe Footprint Estimation in Eddy-Current Imaging

Eddy-current imaging has been described in detail in previous publications [1,2,3]. As with other imaging systems, the image of an object represents blurring of the structures of the object by the system point spread function (PSF). Differing from other imaging systems, the PSF is very large and causes great spatial blurring of the object. This is because the eddy-current probe is a coil; its active area is much greater than the size of a beam of light, sound, or x-ray