Chiroptical spectroscopy of biomolecules using chiral plasmonic nanostructures

This thesis explores the potential of chiral plasmonic nanostructures for the ultrasensitive detection of protein structure. These nanostructures support the generation of fields with enhanced chirality relative to circularly polarised light and are an extremely incisive probe of protein structure. In chapter 4 we introduce a nanopatterned Au film (Templated Plasmonic Substrate, TPS) fabricated using a high through-put injection moulding technique which is a viable alternative to expensive lithographically fabricated nanostructures. The optical and chiroptical properties of TPS nanostructures are found to be highly dependent on the coupling between the electric and magnetic modes of the constituent solid and inverse structures. Significantly, refractive index based measurements of strongly coupled TPSs display a similar sensitivity to protein structure as previous lithographic nanostructures. We subsequently endeavour to improve the sensing properties of TPS nanostructures by developing a high through-put nanoscale chemical functionalisation technique. This process involves a chemical protection/deprotection strategy. The protection step generates a self-assembled monolayer (SAM) of a thermally responsive polymer on the TPS surface which inhibits protein binding. The deprotection step exploits the presence of nanolocalised thermal gradients in the water surrounding the TPS upon irradiation with an 8ns pulsed laser to modify the SAM conformation on surfaces with high net chirality. This allows binding of biomaterial in these regions and subsequently enhances the TPS sensitivity levels. In chapter 6 an alternative method for the detection of protein structure using TPS nanostructures is introduced. This technique relies on mediation of the electric/magnetic coupling in the TPS by the adsorbed protein. This phenomenon is probed through both linear reflectance and nonlinear second harmonic generation (SHG) measurements. Detection of protein structure using this method does not require the presence of fields of enhanced chirality whilst it is also sensitive to a larger array of secondary structure motifs than the measurements in chapters 4 and 5. Finally, a preliminary investigation into the detection of mesoscale biological structure is presented. Sensitivity to the mesoscale helical pitch of insulin amyloid fibrils is displayed through the asymmetry in the circular dichroism (CD) of lithographic gammadions of varying thickness upon adsorption of insulin amyloid fibril spherulites and fragmented fibrils. The proposed model for this sensitivity to the helical pitch relies on the vertical height of the nanostructures relative to this structural property as well as the binding orientation of the fibrils

Unraveling metastable Markovian open quantum systems

We analyze the dynamics of metastable Markovian open quantum systems by unraveling their average dynamics into stochastic trajectories. We use quantum reset processes as examples to illustrate metastable phenomenology, including a simple three-state model whose metastability is of classical type, and a two-qubit model that features a metastable decoherence-free subspace. In the three-state model, the trajectories exhibit classical metastable phenomenology: fast relaxation into distinct phases and slow transitions between them. This extends the existing correspondence between classical and quantum metastability. It enables the computation of committors for the quantum phases, and the mechanisms of rare transitions between them. For the two-qubit model, the decoherence-free subspace appears in the unraveled trajectories as a slow manifold on which the quantum state has a continuous slow evolution. This provides a classical (nonmetastable) analog of this quantum effect. We discuss the general implications of these results, and we highlight the useful role of quantum reset processes for analysis of quantum trajectories in metastable systems

Biomacromolecular stereostructure mediates mode hybridization in chiral plasmonic nanostructures

The refractive index sensitivity of plasmonic fields has been exploited for over 20 years in analytical technologies. While this sensitivity can be used to achieve attomole detection levels, they are in essence binary measurements that sense the presence/absence of a predetermined analyte. Using plasmonic fields, not to sense effective refractive indices but to provide more “granular” information about the structural characteristics of a medium, provides a more information rich output, which affords opportunities to create new powerful and flexible sensing technologies not limited by the need to synthesize chemical recognition elements. Here we report a new plasmonic phenomenon that is sensitive to the biomacromolecular structure without relying on measuring effective refractive indices. Chiral biomaterials mediate the hybridization of electric and magnetic modes of a chiral solid-inverse plasmonic structure, resulting in a measurable change in both reflectivity and chiroptical properties. The phenomenon originates from the electric-dipole–magnetic-dipole response of the biomaterial and is hence sensitive to biomacromolecular secondary structure providing unique fingerprints of α-helical, β-sheet, and disordered motifs. The phenomenon can be observed for subchiral plasmonic fields (i.e., fields with a lower chiral asymmetry than circularly polarized light) hence lifting constraints to engineer structures that produce fields with enhanced chirality, thus providing greater flexibility in nanostructure design. To demonstrate the efficacy of the phenomenon, we have detected and characterized picogram quantities of simple model helical biopolymers and more complex real proteins

The Economic Contribution of the Pharmaceuticals Sector in Scotland

The pharmaceuticals sector is a significant contributor to the Scottish economy and a key player in Scotland's life sciences sector. In this report, we use our detailed model of the Scottish economy to quantify the economic impact and wider spill-over effects of Scotland's Manufacturing of Pharmaceuticals sector. This report also includes analysis that considers a broader group of pharmaceutical contributors, which is most representative of ABPI members, that we call the 'Wider Pharmaceuticals sector'. Additionally, this report models the impact of the Life Sciences sector – a Scottish Government 'Growth Sector'. This report goes beyond economic impact assessment, highlighting these sectors' wider impact on the Scottish economy

Scotland's Budget Report 2023

When Deputy First Minister (DFM) and Finance Secretary Shona Robison rises next week to present her first Scottish Budget, she will do so against one of the most challenging fiscal backdrops in the history of Scottish devolution. The Scottish economy has not performed as badly as many had anticipated, with no recession this year, but growth has been essentially non-existent for the past two years. And with the Bank of England set to keep interest rates higher for longer than previously anticipated, the Scottish Fiscal Commission’s (SFC) forecasts are likely to follow the pattern presented by the Office for Budget Responsibility for the whole of the UK – slower growth and higher inflation than at their previous update. Between the Medium-Term Financial Strategy (MTFS) in May and the Autumn Budget Revision, spending pressures – mostly on pay – had increased by £930m. Since then, there have been £520m-worth of spending cuts announced; there is £380m in additional Barnett funding; and £260m in additional borrowing and use of the Scotland Reserve. This leaves the prospective position of the Scottish Government in 2023-24 at £232m, which might mean not all of the cuts announced by the DFM on the eve of the Autumn Statement are necessary. But the situation for 2024-25 is much more difficult. Part of it was already in the MTFS, with resource spending plans already outstripping funding by £1bn and capital plans £450m larger than projected funding. As the Scottish Government must balance funding sources with expenditures, this was clearly always unsustainable. More positive Income Tax net revenues in outturn and forecast are likely to add around £970m to funding available next year, and there are £310m of Barnett consequentials to add – plus an additional £180m additional funding to compensate for the devolution of winter fuel payments. In total, funding is £1,455m higher than expected in May. But spending pressures are also higher, with higher-than-budgeted-for pay awards creating ongoing difficulties. Assuming the higher scenario for pay this year and next from the MTFS – themselves probably too low for what actually happened – would add about £500m to spending. Adding in winter fuel payments expenditure brings spending plans to £646m above the MTFS – meaning a £780m improvement to the net funding position. This is before any of the additional spending commitments made by the Scottish Government, which have been numerous in recent months. First Minister Humza Yousaf said in October it would be ‘fully funded’ – which of course depends on what councils would have done in the absence of the freeze. If we assume they would have mirrored last year’s increases, we estimate compensation would run to £330m. The First Minister (FM) also announced so an additional £100m for NHS waiting list reduction. And at least £325m of the DFM’s ‘savings’ announced in Parliament on 21 November were actually reprofiling of spending into future years, when plans already exceeded projected funds using May’s forecasts. On the basis of announced policy and commitments, we estimate that the net funding gap is £1,465m for 2024-25: £799m on resource and £665m on capital. In the report, we also look at the outlook for spending and tax. We analyse how public sector employment has been evolving in Scotland relative to other areas of the UK; what capital borrowing plans using Scottish Government bonds might mean for capital spending; and how social security spending has been evolving. On the tax side, we have updated our analysis of how much proposed Income Tax policies would raise under our understanding of the SFC’s methodology; what reforms to smooth out marginal tax rates might look like; what the consequences of the council tax freeze are for the revenues and for households; the cost of matching reliefs on non-domestic rates; and the practical difficulties in introducing new taxes to combat short-term funding gaps

Single-nanowire spectrometers.

Spectrometers with ever-smaller footprints are sought after for a wide range of applications in which minimized size and weight are paramount, including emerging in situ characterization techniques. We report on an ultracompact microspectrometer design based on a single compositionally engineered nanowire. This platform is independent of the complex optical components or cavities that tend to constrain further miniaturization of current systems. We show that incident spectra can be computationally reconstructed from the different spectral response functions and measured photocurrents along the length of the nanowire. Our devices are capable of accurate, visible-range monochromatic and broadband light reconstruction, as well as spectral imaging from centimeter-scale focal planes down to lensless, single-cell-scale in situ mapping.EPSRC (EP/M013812/1, EP/L016087/1), the Royal Commission for the Exhibition of 1851, CRUK Pioneer Award (C55962/A24669), , Business Finland (A-Photonics), Academy of Finland, ERC (834742), EU Horizon 2020 (820423), the Cambridge Trust, the Royal Society

Unbiased metabolome screen leads to personalized medicine strategy for amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis is a rapidly progressive neurodegenerative disease that affects 1/350 individuals in the United Kingdom. The cause of amyotrophic lateral sclerosis is unknown in the majority of cases. Two-sample Mendelian randomization enables causal inference between an exposure, such as the serum concentration of a specific metabolite, and disease risk. We obtained genome-wide association study summary statistics for serum concentrations of 566 metabolites which were population matched with a genome-wide association study of amyotrophic lateral sclerosis. For each metabolite, we performed Mendelian randomization using an inverse variance weighted estimate for significance testing. After stringent Bonferroni multiple testing correction, our unbiased screen revealed three metabolites that were significantly linked to the risk of amyotrophic lateral sclerosis: Estrone-3-sulphate and bradykinin were protective, which is consistent with literature describing a male preponderance of amyotrophic lateral sclerosis and a preventive effect of angiotensin-converting enzyme inhibitors which inhibit the breakdown of bradykinin. Serum isoleucine was positively associated with amyotrophic lateral sclerosis risk. All three metabolites were supported by robust Mendelian randomization measures and sensitivity analyses; estrone-3-sulphate and isoleucine were confirmed in a validation amyotrophic lateral sclerosis genome-wide association study. Estrone-3-sulphate is metabolized to the more active estradiol by the enzyme 17β-hydroxysteroid dehydrogenase 1; further, Mendelian randomization demonstrated a protective effect of estradiol and rare variant analysis showed that missense variants within HSD17B1, the gene encoding 17β-hydroxysteroid dehydrogenase 1, modify risk for amyotrophic lateral sclerosis. Finally, in a zebrafish model of C9ORF72-amyotrophic lateral sclerosis, we present evidence that estradiol is neuroprotective. Isoleucine is metabolized via methylmalonyl-CoA mutase encoded by the gene MMUT in a reaction that consumes vitamin B12. Multivariable Mendelian randomization revealed that the toxic effect of isoleucine is dependent on the depletion of vitamin B12; consistent with this, rare variants which reduce the function of MMUT are protective against amyotrophic lateral sclerosis. We propose that amyotrophic lateral sclerosis patients and family members with high serum isoleucine levels should be offered supplementation with vitamin B12

Low expression of EXOSC2 protects against clinical COVID-19 and impedes SARS-CoV-2 replication

New therapeutic targets are a valuable resource for treatment of SARS-CoV-2 viral infection. Genome-wide association studies have identified risk loci associated with COVID-19, but many loci are associated with comorbidities and are not specifictohost–virus interactions. Here, we identify and experimentally validate a link between reduced expression of EXOSC2 and reduced SARS-CoV-2 replication. EXOSC2 was one of the 332 host proteins examined, all of which interact directly with SARS-CoV-2 proteins. Aggregating COVID-19 genome-wide association studies statistics for genespecific eQTLs revealed an association between increased expression of EXOSC2 and higher risk of clinical COVID-19. EXOSC2 interacts with Nsp8 which forms part of the viral RNA polymerase. EXOSC2 is a component of the RNA exosome, and here, LC-MS/MS analysis of protein pulldowns demonstrated interaction between the SARS-CoV-2 RNA polymerase and most of the human RNA exosome components. CRISPR/Cas9 introduction of nonsense mutations within EXOSC2 in Calu-3 cells reduced EXOSC2 protein expressionandimpededSARS-CoV-2replicationwithoutimpacting cellular viability. Targeted depletion of EXOSC2 may be a safe and effective strategy to protect against clinical COVID-19

Bedrock geology of DFDP-2B, central Alpine Fault, New Zealand

<p>During the second phase of the Alpine Fault, Deep Fault Drilling Project (DFDP) in the Whataroa River, South Westland, New Zealand, bedrock was encountered in the DFDP-2B borehole from 238.5–893.2 m Measured Depth (MD). Continuous sampling and meso- to microscale characterisation of whole rock cuttings established that, in sequence, the borehole sampled amphibolite facies, Torlesse Composite Terrane-derived schists, protomylonites and mylonites, terminating 200–400 m above an Alpine Fault Principal Slip Zone (PSZ) with a maximum dip of 62°. The most diagnostic structural features of increasing PSZ proximity were the occurrence of shear bands and reduction in mean quartz grain sizes. A change in composition to greater mica:quartz + feldspar, most markedly below c. 700 m MD, is inferred to result from either heterogeneous sampling or a change in lithology related to alteration. Major oxide variations suggest the fault-proximal Alpine Fault alteration zone, as previously defined in DFDP-1 core, was not sampled.</p