Molecular interactions and their impact on life sciences

The behaviour and function of biomolecules represent a fundamental aspect in modulating the activity of micro and macro-scale complexes evolved in cells and tissues. The network of interactions of such biomolecules allow for the formation and regulation of the basic machinery of life, yet is commonly studied under non-physiological conditions. In order to characterise the behaviour and function of such biomolecules, they have to be analysed under relevant conditions, ideally in biofluids, cells or artificial systems which mainly imitate these properties. Recent microfluidic applications present an orthogonal approach for determining the interactions between a wide range of biomolecules, thus allow the study of molecular binding in the condensed phase with no need for extensive dilution, sample immobilisation or changes to the molecular environment from the liquid to the gas phase. As part of my PhD, I capitalised on microfluidic diffusion approaches, developed in the Knowles lab to systematically study the binding and thermodynamics of small heat shock proteins, such as clusterin, αB-crystallin and the Brichos chaperone domain, to aggregated forms of amyloid-beta and α-synuclein, protein aggregates that are associated with a wide range of neurodegenerative diseases. The three chaperones are crucial components of the cellular proteostasis network and characteristically overexpressed during cell stress. Each chaperone type shows distinct binding behaviour to protein aggregates, which can be related to its inhibitory function. While αB-crystallin binding to α-synuclein is entropically driven by conformational rearrangement, the binding of Brichos to amyloid-beta fibrils is shown to be enthalpically driven as it inhibits specifically secondary nucleation processes. In contrast to the specific secondary nucleation inhibition by Brichos, clusterin inhibits specifically fibril elongation of amyloid-beta. I could show that these two specific aggregation processes are affected by the two chaperones, Brichos and clusterin, in a non-cooperative manner. These molecular details are particularly relevant in the context of the rational design of drug molecules that could, potentially in combination, target multiple specific aggregation steps in a selective manner. Therefore, I further screened the binding of a wide range of monoclonal antibodies to either amyloid-beta monomers or fibrils, which are currently at different stages of clinical phase trials for Alzheimer's therapy. I thus show that the obtained stoichiometry and affinity information of the drug correlates with the distinct inhibition mechanisms and consequently provides mechanistic and structural information. In contrast to studying disease related model systems in vitro under homogeneous conditions, measurements in complex body fluids are key in medical applied science, e.g. cancer treatment or immunological characterisation. In my research, I have undertaken the challenge of extending the platform developed above to characterise the binding of a wide range of molecules under complex solution conditions. Preliminary data obtained during my PhD underlines the extraordinary capability of the diffusion-based microfluidics to being applicable for investigating the binding parameters of molecules involved in alloimmunisation in human serum. Along with my main focus on measuring protein interactions with diffusion-based microfluidics, I further developed a technique using selective separation properties, such as particle charge, hydrophobicity, size or immunoaffinity and coupled it with a series of microfluidic devices for an instantaneous and full biophysical characterisation of heterogeneous solutions. This new technique can be used to explore the formation of protein oligomers or protein complexation, characterisation and identification of complex mixtures in the context of amyloid formation and protein homeostasis

Label-Free Protein Analysis Using Liquid Chromatography with Gravimetric Detection.

The detection and analysis of proteins in a label-free manner under native solution conditions is an increasingly important objective in analytical bioscience platform development. Common approaches to detect native proteins in solution often require specific labels to enhance sensitivity. Dry mass sensing approaches, by contrast, using mechanical resonators, can operate in a label-free manner and offer attractive sensitivity. However, such approaches typically suffer from a lack of analyte selectivity as the interface between standard protein separation techniques and micro-resonator platforms is often constrained by qualitative mechanical sensor performance in the liquid phase. Here, we describe a strategy that overcomes this limitation by coupling liquid chromatography with a quartz crystal microbalance (QCM) platform by using a microfluidic spray dryer. We explore a strategy which allows first to separate a protein mixture in a physiological buffer solution using size exclusion chromatography, permitting specific protein fractions to be selected, desalted, and subsequently spray-dried onto the QCM for absolute mass analysis. By establishing a continuous flow interface between the chromatography column and the spray device via a flow splitter, simultaneous protein mass detection and sample fractionation is achieved, with sensitivity down to a 100 μg/mL limit of detection. This approach for quantitative label-free protein mixture analysis offers the potential for detection of protein species under physiological conditions.ERC EPSRC Frances and Augustus Newman Foundation Oppenheimer Early Career Fellowship Nanotechnologies Doctoral Training Centre Fluidic Analytics Lt

Label-Free Protein Analysis Using Liquid Chromatography with Gravimetric Detection.

The detection and analysis of proteins in a label-free manner under native solution conditions is an increasingly important objective in analytical bioscience platform development. Common approaches to detect native proteins in solution often require specific labels to enhance sensitivity. Dry mass sensing approaches, by contrast, using mechanical resonators, can operate in a label-free manner and offer attractive sensitivity. However, such approaches typically suffer from a lack of analyte selectivity as the interface between standard protein separation techniques and micro-resonator platforms is often constrained by qualitative mechanical sensor performance in the liquid phase. Here, we describe a strategy that overcomes this limitation by coupling liquid chromatography with a quartz crystal microbalance (QCM) platform by using a microfluidic spray dryer. We explore a strategy which allows first to separate a protein mixture in a physiological buffer solution using size exclusion chromatography, permitting specific protein fractions to be selected, desalted, and subsequently spray-dried onto the QCM for absolute mass analysis. By establishing a continuous flow interface between the chromatography column and the spray device via a flow splitter, simultaneous protein mass detection and sample fractionation is achieved, with sensitivity down to a 100 μg/mL limit of detection. This approach for quantitative label-free protein mixture analysis offers the potential for detection of protein species under physiological conditions.ERC EPSRC Frances and Augustus Newman Foundation Oppenheimer Early Career Fellowship Nanotechnologies Doctoral Training Centre Fluidic Analytics Lt

Project HyBuJET

A conceptual Hypersonic Business Jet (HyBuJet) was examined. The main areas of concentration include: aerodynamics, propulsion, stability and control, mission profile, and atmospheric heating. In order to optimize for cruise conditions, a waverider configuration was chosen for the high lift drag ratio and low wave drag. The leading edge and lower surface of a waverider was mapped out from a known flow field and optimized for cruising at Mach 6 and at high altitudes. The shockwave generated by a waverider remains attached along the entire leading edge, allowing for a larger compression along the lower surface. Three turbofan ramjets were chosen as the propulsion of the aircraft due to the combination of good subsonic performance along with high speed propulsive capabilities. A combination of liquid silicon convective cooling for the leading edges with a highly radiative outer skin material was chosen to reduce the atmospheric heating to acceptable level

Rational design of a conformation-specific antibody for the quantification of Aβ oligomers.

Protein misfolding and aggregation is the hallmark of numerous human disorders, including Alzheimer's disease. This process involves the formation of transient and heterogeneous soluble oligomers, some of which are highly cytotoxic. A major challenge for the development of effective diagnostic and therapeutic tools is thus the detection and quantification of these elusive oligomers. Here, to address this problem, we develop a two-step rational design method for the discovery of oligomer-specific antibodies. The first step consists of an "antigen scanning" phase in which an initial panel of antibodies is designed to bind different epitopes covering the entire sequence of a target protein. This procedure enables the determination through in vitro assays of the regions exposed in the oligomers but not in the fibrillar deposits. The second step involves an "epitope mining" phase, in which a second panel of antibodies is designed to specifically target the regions identified during the scanning step. We illustrate this method in the case of the amyloid β (Aβ) peptide, whose oligomers are associated with Alzheimer's disease. Our results show that this approach enables the accurate detection and quantification of Aβ oligomers in vitro, and in Caenorhabditis elegans and mouse hippocampal tissues

Three-dimensional cometary dust coma modelling in the collisionless regime: strengths and weaknesses

Inverse coma and tail modelling of comets based on the method developed by Finson & Probstein is commonly used to analyse cometary coma images. Models of this type often contain a large number of assumptions that may not be constrained unless wide temporal or spectral coverage is available and the comets are bright and at relatively small geocentric distance. They are used to predict physical parameters, such as the mass distribution of the dust, but rarely give assessments of the accuracy of the estimate. A three-dimensional cometary dust coma model in the collisionless regime has been developed to allow the effectiveness of such models to constrain dust coma properties to be tested. The model is capable of simulating the coma morphology for the following input parameters: the comet nucleus shape, size, rotation, emission function (including active fraction and jets), grain velocity distribution (and dispersion), size distribution, dust production rate, grain material and light scattering from the cometary dust. Characterization of the model demonstrates that the mass distribution cannot be well constrained as is often assumed; the cumulative mass distribution index ? can only be constrained to within ±0.15. The model is highly sensitive to the input grain terminal velocity distribution so model input can be tested with a large degree of confidence. Complex secondary parameters such as jets, rotation and grain composition all have an effect on the structure of the coma in similar ways, so unique solutions for these parameters cannot be derived from a single optical image alone. Multiple images at a variety of geometries close in time can help constrain these effects. The model has been applied to photometric observations of comets 126P/IRAS and 46P/Wirtanen to constrain a number of physical properties including the dust production rate and mass distribution index. The derived dust production rate (Qdust) for 46P/Wirtanen was 3+7/1.5 kg s1 at a pre-perihelion heliocentric distance of 1.8 au, and for P/IRAS was 50+100/20 kg s1 at a pre-perihelion heliocentric distance of 1.7 au; both comets exhibited a mass distribution index ? = 0.8 ± 0.15

Secondary nucleation and elongation occur at different sites on Alzheimer's amyloid-β aggregates.

The aggregates of the Aβ peptide associated with Alzheimer's disease are able to both grow in size as well as generate, through secondary nucleation, new small oligomeric species, that are major cytotoxins associated with neuronal death. Despite the importance of these amyloid fibril-dependent processes, their structural and molecular underpinnings have remained challenging to elucidate. Here, we consider two molecular chaperones: the Brichos domain, which suppresses specifically secondary nucleation processes, and clusterin which our results show is capable of inhibiting, specifically, the elongation of Aβ fibrils at remarkably low substoichiometric ratios. Microfluidic diffusional sizing measurements demonstrate that this inhibition originates from interactions of clusterin with fibril ends with high affinity. Kinetic experiments in the presence of both molecular chaperones reveal that their inhibitory effects are additive and noncooperative, thereby indicating that the reactive sites associated with the formation of new aggregates and the growth of existing aggregates are distinct

Vitamin D and mortality: Individual participant data meta-analysis of standardized 25-hydroxyvitamin D in 26916 individuals from a European consortium

Source at http://doi.org/10.1371/journal.pone.0170791Background:Vitamin D deficiency may be a risk factor for mortality but previous meta-analyses lacked standardization of laboratory methods for 25-hydroxyvitamin D (25[OH]D) concentrations and used aggregate data instead of individual participant data (IPD). We therefore performed an IPD meta-analysis on the association between standardized serum 25(OH)D and mortality.Methods:In a European consortium of eight prospective studies, including seven general population cohorts, we used the Vitamin D Standardization Program (VDSP) protocols to standardize 25(OH)D data. Meta-analyses using a one step procedure on IPD were performed to study associations of 25(OH)D with all-cause mortality as the primary outcome, and with cardiovascular and cancer mortality as secondary outcomes. This meta-analysis is registered at ClinicalTrials.gov, number NCT02438488.Findings:We analysed 26916 study participants (median age 61.6 years, 58% females) with a median 25(OH)D concentration of 53.8 nmol/L. During a median follow-up time of 10.5 years, 6802 persons died. Compared to participants with 25(OH)D concentrations of 75 to 99.99 nmol/L, the adjusted hazard ratios (with 95% confidence interval) for mortality in the 25(OH)D groups with 40 to 49.99, 30 to 39.99, and Interpretation:In the first IPD meta-analysis using standardized measurements of 25(OH)D we observed an association between low 25(OH)D and increased risk of all-cause mortality. It is of public health interest to evaluate whether treatment of vitamin D deficiency prevents premature deaths

National trends in total cholesterol obscure heterogeneous changes in HDL and non-HDL cholesterol and total-to-HDL cholesterol ratio : a pooled analysis of 458 population-based studies in Asian and Western countries

Background: Although high-density lipoprotein (HDL) and non-HDL cholesterol have opposite associations with coronary heart disease, multi-country reports of lipid trends only use total cholesterol (TC). Our aim was to compare trends in total, HDL and nonHDL cholesterol and the total-to-HDL cholesterol ratio in Asian and Western countries. Methods: We pooled 458 population-based studies with 82.1 million participants in 23 Asian and Western countries. We estimated changes in mean total, HDL and non-HDL cholesterol and mean total-to-HDL cholesterol ratio by country, sex and age group. Results: Since similar to 1980, mean TC increased in Asian countries. In Japan and South Korea, the TC rise was due to rising HDL cholesterol, which increased by up to 0.17 mmol/L per decade in Japanese women; in China, it was due to rising non-HDL cholesterol. TC declined in Western countries, except in Polish men. The decline was largest in Finland and Norway, at similar to 0.4 mmol/L per decade. The decline in TC in most Western countries was the net effect of an increase in HDL cholesterol and a decline in non-HDL cholesterol, with the HDL cholesterol increase largest in New Zealand and Switzerland. Mean total-to-HDL cholesterol ratio declined in Japan, South Korea and most Western countries, by as much as similar to 0.7 per decade in Swiss men (equivalent to similar to 26% decline in coronary heart disease risk per decade). The ratio increased in China. Conclusions: HDL cholesterol has risen and the total-to-HDL cholesterol ratio has declined in many Western countries, Japan and South Korea, with only a weak correlation with changes in TC or non-HDL cholesterol.Peer reviewe