Search

Plasmonic devices offer the possibility of passively detecting changes in local chemistry that opens up a wide range of applications from molecular sensing to monitoring water quality. Conventional plasmonics have previously shown great promise as nanoscale chemical sensors through detection of small variations in the local refractive index (RI). The motivation behind using plasmonics for these applications includes the fact that detection is entirely passive and the devices themselves can be readily miniaturized. Previously, a lack of any control over the output of these devices, has fundamentally limited their application to chemicals which produce clearly identifiable resonances within the range of detection. Here it is demonstrated that microfluidic devices, incorporating polarization-controlled plasmonic nanopixels, allow the device response to be tuned to the particular analyte of interest, anywhere within the visible spectrum. This dramatically increases the effective dynamic range and allows local variations in RI to be perceived directly as color changes by the human eye. Active control over the output of the device also enables clear differentiation between a number of different analytes, paving the way for plasmonics to be used for a wide range of real-world chemical sensing applications.

The human eye can distinguish as many as 10,000 different colours but is far less sensitive to variations in intensity1, meaning that colour is highly desirable when interpreting images. However, most biological samples are essentially transparent, and nearly invisible when viewed using a standard optical microscope2. It is therefore highly desirable to be able to produce coloured images without needing to add any stains or dyes, which can alter the sample properties. Here we demonstrate that colorimetric histology images can be generated using full-sized plasmonically active microscope slides. These slides translate subtle changes in the dielectric constant into striking colour contrast when samples are placed upon them. We demonstrate the biomedical potential of this technique, which we term histoplasmonics, by distinguishing neoplastic cells from normal breast epithelium during the earliest stages of tumorigenesis in the mouse MMTV-PyMT mammary tumour model. We then apply this method to human diagnostic tissue and validate its utility in distinguishing normal epithelium, usual ductal hyperplasia, and early-stage breast cancer (ductal carcinoma in situ). The colorimetric output of the image pixels is compared to conventional histopathology. The results we report here support the hypothesis that histoplasmonics can be used as a novel alternative or adjunct to general staining. The widespread availability of this technique and its incorporation into standard laboratory workflows may prove transformative for applications extending well beyond tissue diagnostics. This work also highlights opportunities for improvements to digital pathology that have yet to be explored.

Serial crystallography of membrane proteins often employs high-viscosity injectors (HVIs) to deliver micrometre-sized crystals to the X-ray beam. Typically, the carrier medium is a lipidic cubic phase (LCP) media, which can also be used to nucleate and grow the crystals. However, despite the fact that the LCP is widely used with HVIs, the potential impact of the injection process on the LCP structure has not been reported and hence is not yet well understood. The self-assembled structure of the LCP can be affected by pressure, dehydration and temperature changes, all of which occur during continuous flow injection. These changes to the LCP structure may in turn impact the results of X-ray diffraction measurements from membrane protein crystals. To investigate the influence of HVIs on the structure of the LCP we conducted a study of the phase changes in monoolein/water and monoolein/buffer mixtures during continuous flow injection, at both atmospheric pressure and under vacuum. The reservoir pressure in the HVI was tracked to determine if there is any correlation with the phase behaviour of the LCP. The results indicated that, even though the reservoir pressure underwent (at times) significant variation, this did not appear to correlate with observed phase changes in the sample stream or correspond to shifts in the LCP lattice parameter. During vacuum injection, there was a three-way coexistence of the gyroid cubic phase, diamond cubic phase and lamellar phase. During injection at atmospheric pressure, the coexistence of a cubic phase and lamellar phase in the monoolein/water mixtures was also observed. The degree to which the lamellar phase is formed was found to be strongly dependent on the co-flowing gas conditions used to stabilize the LCP stream. A combination of laboratory-based optical polarization microscopy and simulation studies was used to investigate these observations.

Test

No description supplied

Additional Simulation Results and Fitting Results

Histology Data

Additional simulation results and fitting results

No description supplied

Microfluidic devices which integrate both rapid mixing and liquid jetting for sample delivery are an emerging solution for studying molecular dynamics via X-ray diffraction. Here we use finite element modelling to investigate the efficiency and time-resolution achievable using microfluidic mixers within the parameter range required for producing stable liquid jets. Three-dimensional simulations, validated by experimental data, are used to determine the velocity and concentration distribution within these devices. The results show that by adopting a serpentine geometry, it is possible to induce chaotic mixing, which effectively reduces the time required to achieve a homogeneous mixture for sample delivery. Further, we investigate the effect of flow rate and the mixer microchannel size on the mixing efficiency and minimum time required for complete mixing of the two solutions whilst maintaining a stable jet. In general, we find that the smaller the cross-sectional area of the mixer microchannel, the shorter the time needed to achieve homogeneous mixing for a given flow rate. The results of these simulations will form the basis for optimised designs enabling the study of molecular dynamics occurring on millisecond timescales using integrated mix-and-inject microfluidic devices.

Cholesterol is believed to induce the formation of membrane domains, "rafts", which are implicated in a range of natural and pathologic membrane processes. Therefore, it is important to understand the role that cholesterol plays in the formation of these structures. Here, we use label-free spectroscopic imaging to investigate cholesterol fractioning in supported bilayer membranes at nanoscale. Scattering-Type scanning near-field optical microscopy (s-SNOM) was used to visualize the formation of cholesterol-induced domains in 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) membranes. Our results revealed the coexistence of phase separated domains in DMPC lipids with 10 mol % cholesterol content, whereas a mostly homogeneous bilayer was found at low (5 mol %) and high (15 mol %) cholesterol content. Near-field nano-FTIR spectroscopy was used to identify the cholesterol-rich domains based on their qualitative chemical compositions. It was determined that cholesterol binds to phosphodiester and alkyl glycerol ester moieties, likely via hydrogen bonding of the alcohol to either of the ester oxygens. The results also confirm the existence of an ideal cholesterol-lipid mixture ratio (â 15:85) with a geometrically defined packing. At lower cholesterol content there is phase separation between liquid ordered and almost neat DMPC domains. Thus, the liquid ordered phase exists at an energy minimum at a given lipid-cholesterol ratio.

Article in AOS News

Structural dynamics 6(6), 064702 - (2019). doi:10.1063/1.5124387, Published by AIP Publishing LLC, Melville, NY

The new European X-ray Free-Electron Laser is the first X-ray free-electron laser capable of delivering X-ray pulses with a megahertz inter-pulse spacing, more than four orders of magnitude higher than previously possible. However, to date, it has been unclear whether it would indeed be possible to measure high-quality diffraction data at megahertz pulse repetition rates. Here, we show that high-quality structures can indeed be obtained using currently available operating conditions at the European XFEL. We present two complete data sets, one from the well-known model system lysozyme and the other from a so far unknown complex of a β-lactamase from K. pneumoniae involved in antibiotic resistance. This result opens up megahertz serial femtosecond crystallography (SFX) as a tool for reliable structure determination, substrate screening and the efficient measurement of the evolution and dynamics of molecular structures using megahertz repetition rate pulses available at this new class of X-ray laser source.

The new European X-ray Free-Electron Laser is the first X-ray free-electron laser capable of delivering X-ray pulses with a megahertz inter-pulse spacing, more than four orders of magnitude higher than previously possible. However, to date, it has been unclear whether it would indeed be possible to measure high-quality diffraction data at megahertz pulse repetition rates. Here, we show that high-quality structures can indeed be obtained using currently available operating conditions at the European XFEL. We present two complete data sets, one from the well-known model system lysozyme and the other from a so far unknown complex of a β-lactamase from K. pneumoniae involved in antibiotic resistance. This result opens up megahertz serial femtosecond crystallography (SFX) as a tool for reliable structure determination, substrate screening and the efficient measurement of the evolution and dynamics of molecular structures using megahertz repetition rate pulses available at this new class of X-ray laser source., The new European X-Ray Free-Electron Laser (EuXFEL) is the first XFEL that generates X-ray pulses with a megahertz inter-pulse spacing. Here the authors demonstrate that high-quality and damage-free protein structures can be obtained with the currently available 1.1 MHz repetition rate pulses using lysozyme as a test case and furthermore present a β-lactamase structure.

[Extract] Since the early-to-middle 1980s there has been significant change and major reform on all these fronts, leading to the emergence of a more coherent and streamlined national approach. This chapter describes those changes and discusses where they are leading the industry and the aged people who do or will depend on it for care in their later years. Residential aged care, once of interest only to a narrow range of health professionals and those members of the public directly concerned with their own or a relative's circumstances, is now a major topic of discussion in the media and the wider community. Undoubtedly the three major factors driving this change are, first, the occurrence of another phase in the community's awakening to the implications of Australia's changing demographic profile. Second, there have been consequential concerns, especially in government circles, over the budgetary impact of funding the future provision of aged care in the quantities likely to be needed. Third, the first and second factors have prompted a renewed questioning of when and how far community-based and home-delivered services can be substituted for full-time residential care, a question this chapter briefly returns to in closing. Australia's changing demographic profile and the projected future costs of aged care provide our starting point. The chapter then briefly traces the confused course of residential care provision between about 1950 and 1980, a picture of abundant effort with little direction. We shall see how the ill-planned developments of that period caused problems necessitating successive waves of reforms culminating in the aged-care structural reforms of the mid-1980s and early 1990s, and the Aged Care Act 1997. The chapter closes by examining how far those reforms achieved their objectives and what problems can be expected to command our attention in the next ten or so years.

The new European X-ray Free-Electron Laser is the first X-ray free-electron laser capable of delivering X-ray pulses with a megahertz inter-pulse spacing, more than four orders of magnitude higher than previously possible. However, to date, it has been unclear whether it would indeed be possible to measure high-quality diffraction data at megahertz pulse repetition rates. Here, we show that high-quality structures can indeed be obtained using currently available operating conditions at the European XFEL. We present two complete data sets, one from the well-known model system lysozyme and the other from a so far unknown complex of a ��-lactamase from K. pneumoniae involved in antibiotic resistance. This result opens up megahertz serial femtosecond crystallography (SFX) as a tool for reliable structure determination, substrate screening and the efficient measurement of the evolution and dynamics of molecular structures using megahertz repetition rate pulses available at this new class of X-ray laser source.

A peak-finding algorithm for serial crystallography (SX) data analysis based on the principle of `robust statistics' has been developed. Methods which are statistically robust are generally more insensitive to any departures from model assumptions and are particularly effective when analysing mixtures of probability distributions. For example, these methods enable the discretization of data into a group comprising inliers (i.e. the background noise) and another group comprising outliers (i.e. Bragg peaks). Our robust statistics algorithm has two key advantages, which are demonstrated through testing using multiple SX data sets. First, it is relatively insensitive to the exact value of the input parameters and hence requires minimal optimization. This is critical for the algorithm to be able to run unsupervised, allowing for automated selection or `vetoing' of SX diffraction data. Secondly, the processing of individual diffraction patterns can be easily parallelized. This means that it can analyse data from multiple detector modules simultaneously, making it ideally suited to real-time data processing. These characteristics mean that the robust peak finder (RPF) algorithm will be particularly beneficial for the new class of MHz X-ray free-electron laser sources, which generate large amounts of data in a short period of time.

© 2020, This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply. Single Particle Imaging (SPI) with intense coherent X-ray pulses from X-ray free-electron lasers (XFELs) has the potential to produce molecular structures without the need for crystallization or freezing. Here we present a dataset of 285,944 diffraction patterns from aerosolized Coliphage PR772 virus particles injected into the femtosecond X-ray pulses of the Linac Coherent Light Source (LCLS). Additional exposures with background information are also deposited. The diffraction data were collected at the Atomic, Molecular and Optical Science Instrument (AMO) of the LCLS in 4 experimental beam times during a period of four years. The photon energy was either 1.2 or 1.7 keV and the pulse energy was between 2 and 4 mJ in a focal spot of about 1.3 μm x 1.7 μm full width at half maximum (FWHM). The X-ray laser pulses captured the particles in random orientations. The data offer insight into aerosolised virus particles in the gas phase, contain information relevant to improving experimental parameters, and provide a basis for developing algorithms for image analysis and reconstruction.

Nature Communications 12(1), 2578 (2021). doi:10.1038/s41467-021-22590-6, MyD88 and MAL are Toll-like receptor (TLR) adaptors that signal to induce pro-inflammatory cytokine production. We previously observed that the TIR domain of MAL (MALTIR) forms filaments in vitro and induces formation of crystalline higher-order assemblies of the MyD88$^{TIR}$ domain (MyD88$^{TIR}$). These crystals are too small for conventional X-ray crystallography, but are ideally suited to structure determination by microcrystal electron diffraction (MicroED) and serial femtosecond crystallography (SFX). Here, we present MicroED and SFX structures of the MyD88$^{TIR}$ assembly, which reveal a two-stranded higher-order assembly arrangement of TIR domains analogous to that seen previously for MAL$^{TIR}$. We demonstrate via mutagenesis that the MyD88$^{TIR}$ assembly interfaces are critical for TLR4 signaling in vivo, and we show that MAL promotes unidirectional assembly of MyD88$^{TIR}$R. Collectively, our studies provide structural and mechanistic insight into TLR signal transduction and allow a direct comparison of the MicroED and SFX techniques., Published by Nature Publishing Group UK, [London]

Scientific data 7(1), 404 (2020). doi:10.1038/s41597-020-00745-2, Single Particle Imaging (SPI) with intense coherent X-ray pulses from X-ray free-electron lasers (XFELs) has the potential to produce molecular structures without the need for crystallization or freezing. Here we present a dataset of 285,944 diffraction patterns from aerosolized Coliphage PR772 virus particles injected into the femtosecond X-ray pulses of the Linac Coherent Light Source (LCLS). Additional exposures with background information are also deposited. The diffraction data were collected at the Atomic, Molecular and Optical Science Instrument (AMO) of the LCLS in 4 experimental beam times during a period of four years. The photon energy was either 1.2 or 1.7 keV and the pulse energy was between 2 and 4 mJ in a focal spot of about 1.3 ��m x 1.7 ��m full width at half maximum (FWHM). The X-ray laser pulses captured the particles in random orientations. The data offer insight into aerosolised virus particles in the gas phase, contain information relevant to improving experimental parameters, and provide a basis for developing algorithms for image analysis and reconstruction., Published by Nature Publ. Group, London

MyD88 and MAL are Toll-like receptor (TLR) adaptors that signal to induce pro-inflammatory cytokine production. We previously observed that the TIR domain of MAL (MALTIR) forms filaments in vitro and induces formation of crystalline higher-order assemblies of the MyD88 TIR domain (MyD88TIR). These crystals are too small for conventional X-ray crystallography, but are ideally suited to structure determination by microcrystal electron diffraction (MicroED) and serial femtosecond crystallography (SFX). Here, we present MicroED and SFX structures of the MyD88TIR assembly, which reveal a two-stranded higher-order assembly arrangement of TIR domains analogous to that seen previously for MALTIR. We demonstrate via mutagenesis that the MyD88TIR assembly interfaces are critical for TLR4 signaling in vivo, and we show that MAL promotes unidirectional assembly of MyD88TIR. Collectively, our studies provide structural and mechanistic insight into TLR signal transduction and allow a direct comparison of the MicroED and SFX techniques.

Nature Communications 9(1), 4025 (2018). doi:doi.org/10.1038/s41467-018-06156-7, The new European X-ray Free-Electron Laser is the first X-ray free-electron laser capable of delivering X-ray pulses with a megahertz inter-pulse spacing, more than four orders of magnitude higher than previously possible. However, to date, it has been unclear whether it would indeed be possible to measure high-quality diffraction data at megahertz pulse repetition rates. Here, we show that high-quality structures can indeed be obtained using currently available operating conditions at the European XFEL. We present two complete data sets, one from the well-known model system lysozyme and the other from a so far unknown complex of a β-lactamase from K. pneumoniae involved in antibiotic resistance. This result opens up megahertz serial femtosecond crystallography (SFX) as a tool for reliable structure determination, substrate screening and the efficient measurement of the evolution and dynamics of molecular structures using megahertz repetition rate pulses available at this new class of X-ray laser source., Published by Nature Publishing Group, London

Nature Communications 9(1), 4025 (2018). doi:10.1038/s41467-018-06156-7, The new European X-ray Free-Electron Laser is the first X-ray free-electron laser capable of delivering X-ray pulses with a megahertz inter-pulse spacing, more than four orders of magnitude higher than previously possible. However, to date, it has been unclear whether it would indeed be possible to measure high-quality diffraction data at megahertz pulse repetition rates. Here, we show that high-quality structures can indeed be obtained using currently available operating conditions at the European XFEL. We present two complete data sets, one from the well-known model system lysozyme and the other from a so far unknown complex of a β-lactamase from K. pneumoniae involved in antibiotic resistance. This result opens up megahertz serial femtosecond crystallography (SFX) as a tool for reli- able structure determination, substrate screening and the efficient measurement of the evolution and dynamics of molecular structures using megahertz repetition rate pulses available at this new class of X-ray laser source., Published by Nature Publishing Group, London

Journal of applied crystallography 54(5), 1360 - 1378 (2021). doi:10.1107/S1600576721007317, A peak-finding algorithm for serial crystallography (SX) data analysis based on the principle of `robust statistics' has been developed. Methods which are statistically robust are generally more insensitive to any departures from model assumptions and are particularly effective when analysing mixtures of probability distributions. For example, these methods enable the discretization of data into a group comprising inliers (i.e. the background noise) and another group comprising outliers (i.e. Bragg peaks). Our robust statistics algorithm has two key advantages, which are demonstrated through testing using multiple SX data sets. First, it is relatively insensitive to the exact value of the input parameters and hence requires minimal optimization. This is critical for the algorithm to be able to run unsupervised, allowing for automated selection or `vetoing' of SX diffraction data. Secondly, the processing of individual diffraction patterns can be easily parallelized. This means that it can analyse data from multiple detector modules simultaneously, making it ideally suited to real-time data processing. These characteristics mean that the robust peak finder (RPF) algorithm will be particularly beneficial for the new class of MHz X-ray free-electron laser sources, which generate large amounts of data in a short period of time., Published by Wiley-Blackwell, [S.l.]

MyD88 and MAL are Toll-like receptor (TLR) adaptors that signal to induce pro-inflammatory cytokine production. We previously observed that the TIR domain of MAL (MALTIR) forms filaments in vitro and induces formation of crystalline higher-order assemblies of the MyD88 TIR domain (MyD88TIR). These crystals are too small for conventional X-ray crystallography, but are ideally suited to structure determination by microcrystal electron diffraction (MicroED) and serial femtosecond crystallography (SFX). Here, we present MicroED and SFX structures of the MyD88TIR assembly, which reveal a two-stranded higher-order assembly arrangement of TIR domains analogous to that seen previously for MALTIR. We demonstrate via mutagenesis that the MyD88TIR assembly interfaces are critical for TLR4 signaling in vivo, and we show that MAL promotes unidirectional assembly of MyD88TIR. Collectively, our studies provide structural and mechanistic insight into TLR signal transduction and allow a direct comparison of the MicroED and SFX techniques., MAL and MyD88 are downstream adaptors of Toll-like receptors (TLR) and the MAL TIR domain forms filaments in vitro, which in turn nucleate the assembly of crystalline arrays of the MyD88 TIR domain. Here, the authors present the structure of these MyD88 TIR crystalline arrays solved by both microcrystal electron diffraction and serial femtosecond crystallography, and they show with mutagenesis experiments that MyD88 interface residues are important for TLR4 signaling in vivo.

Plasmonic devices offer the possibility of passively detecting changes in local chemistry that opens up a wide range of applications from molecular sensing to monitoring water quality. Conventional plasmonics have previously shown great promise as nanoscale chemical sensors through detection of small variations in the local refractive index (RI). The motivation behind using plasmonics for these applications includes the fact that detection is entirely passive and the devices themselves can be readily miniaturized. Previously, a lack of any control over the output of these devices, has fundamentally limited their application to chemicals which produce clearly identifiable resonances within the range of detection. Here it is demonstrated that microfluidic devices, incorporating polarization-controlled plasmonic nanopixels, allow the device response to be tuned to the particular analyte of interest, anywhere within the visible spectrum. This dramatically increases the effective dynamic range and allows local variations in RI to be perceived directly as color changes by the human eye. Active control over the output of the device also enables clear differentiation between a number of different analytes, paving the way for plasmonics to be used for a wide range of real-world chemical sensing applications.

Undergraduate nursing students rate residential aged care an unattractive career option. Some likely causes are beyond the control of the sector, others within or partly within its control. Addressing the problem - the aim of the modelling connections project - is important and urgent.This paper, derived from that project, profiles the characteristics of 12 residential aged care facilities across four Australian states, 66 of their staff and 53 student nurses undertaking clinical placements. Staff and student responses to a 30-item orientation experience survey are compared. Two-thirds of the items - including manual handling, fire and emergency drills, teaching resources, communications and workplace arrangements - reveal a statistically significant inter-group divergence of opinion, with staff consistently more confident of the orientation's effectiveness. More than half the students were unsure on arrival as to whether the staff were expecting them. Two-thirds said they had not been told, or were unsure if they had been told, what to do if upset or anxious.Staff satisfaction with the orientation's quality was greater than student data warranted. Substantial institutional, procedural and behavioural changes seem necessary if student expectations of their clinical placements are to be met and a positive, attractive image of the sector conveyed Refereed/Peer-reviewed