Canada

**Effect of Lung Surfactant Protein B Fragment, SP-B1-9 on Model Lipid Bilayer.**
Abinu, MHK, ISV, MRM

Lung surfactant is a mixture of protein and lipid that reduces surface tension at the air-water interface in the lungs and thus reduces the work needed to breathe. Two hydrophobic proteins, SP-B and SP-C, are thought to facilitate the re-spreading of fresh and recycled surfactant material from bilayer and multilayer reservoirs. In an earlier deuterium NMR study of bilayer model membranes containing either the SP-B fragment SP-B(1-25, 63-78) or the fragment SP-B(8-25, 63-78), it was found that lipid acyl chain orientational order was perturbed more strongly by SP-B(1-25, 63-78). Both fragments contain the first and last SP-B helices but differ in whether or not the insertion motif, SP-B1-7, is present, suggesting that the insertion motif might play a role in the capacity of SP-B to promote the bilayer reorganization implicit in lung surfactant function. To gain more insight into the interaction of the insertion motif with surfactant lipids, we have studied the effect of SP-B1-9 on lipid acyl chain order in DPPC-d62 /POPG(7:3) bilayers using deuterium NMR and GROMACS molecular dynamics simulations.
Using deuterium NMR at a peptide: lipid ratio of 0.065, we find that the peptide tends to disorder acyl chains in the liquid crystalline bilayer phase suggesting that it promotes an increase in average lipid headgroup separation. MD simulation of a bilayer model containing SP-B1-9 at a peptide: lipid ratio of 0.031 also shows a decrease in chain orientational order. The MD simulations also provide information about the average peptide orientation and conformation. These findings may provide a better understanding of the extent to which the insertion motif may contribute to the capacity of SP-B to promote reorganization of bilayer surfactant material.

Supported by NSERC Discovery Grants to MRM and ISV.

2021 CAP Virtual Congress

Effect of Lung Surfactant Protein B Fragment, SP-B1-9 on Model Lipid Bilayer.

md simulation

deuterium nmr

lung surfactants

**WELCOME TO THE 2021 CAP VIRTUAL CONGRESS UNDERLINE PLATFORM**

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poster

The Canadian Light Source (CLS) is considering a linear accelerator (LINAC) upgrade. As a result, the radio frequency (RF) structure in the downstream Energy Compression System (ECS) needs to be redesigned. In this paper, we describe the design process followed to determine the geometry of the RF structure cells and coupler. Wakefield simulation results are also presented. The wakefields and input RF fields are applied to beam dynamics simulations.

Energy Compression System Radio Frequency Design at the Canadian Light Source

A key feature of third-generation light sources is their small vertical opening angle, which is difficult to measure experimentally. To reconstruct the vertical phase space, one can scan the beam’s position using X-ray synchrotron radiation (XSR) and a pinhole camera. The XSR diagnostic beamline, operational in the wavelength region of $\lambda$= 0.05 - 0.15 nm, in Canadian Light Source (CLS) is qualified to measure the beam position with X-ray radiation. Using the corrector magnets in CLS lattice made of 12 identical double-bend achromats (DBA) cells, vertical iterations of 100 $\mu$m can be executed parallel to the beam's original orbit. The outcomes of this experiment are: 1) the vertical beam positions that are monitored by BPMs on both sides of the X-ray’s source point, 2) the X-ray image of the beam that is projected through the pinhole and converted to visible light to be captured on the CCD camera. The bumps were simulated using Matlab Middle Layer (MML) for Accelerator control systems to get an insight of the source point's position in the XSR's bending magnet. The simulation shows the position of the source point depends on which corrector sets are chosen. To make a truly parallel bump in the DBA sector and to be able to calculate the source point's actual position, critical in reconstructing the vertical phase space, a particular set of correctors should be chosen.

Vertical phase space measurement at Canadian Light Source

Laser-induced breakdown spectroscopy (LIBS) is a laser-based spectrochemical technique that allows a near-instantaneous measurement of the elemental composition of a target by making time-resolved spectroscopic analyses of laser-induced ablation plasmas. Utilizing nanosecond laser pulses and a broadband high-resolution Echelle spectrometer, high signal-to-noise optical emission spectra can be obtained from almost any desired target.

When the ablation target contains bacterial cells, the inorganic elements present in the bacterial cells (phosphorous, magnesium, calcium, and sodium) can be used to discriminate the bacteria on the basis of their atomic emission spectrum alone. Currently, we deposit bacterial cells onto a nitrocellulose filtration medium by centrifuging very low titer liquid specimens through a custom-fabricated centrifuge tube insert device. Prior to centrifugation, the bacteria cells are obtained by swabbing abiotic surfaces upon which a known number of bacteria cells have been deposited. The cells are then shaken off the disposable pathology swabs into a water suspension in a vortex mixing instrument.

Spectra from five different bacterial pathogens and pathogen surrogates (Staphylococcus epidermidis, Escherichia coli, Mycobacterium smegmatis, Pseudomonas aeruginosa, and Enterococcus faecalis) and sterile water control specimens have been obtained along with spectra from sterile deionized water control specimens. 

This presentation will detail our efforts to identify and optimize chemometric algorithms for the autonomous classification of unknown spectra. Algorithms such as principal component analysis (PCA), discriminant function analysis (DFA), partial least squares discriminant analysis (PLSDA), and artificial neural networks (ANN) have been investigated. Rates of sensitivity and specificity have been determined and will be presented for the various techniques. Efforts to use chemometric algorithms to discriminate low-titer suspensions from blank water specimens and thus calculate limits of detection and limits of identification will also be discussed.

Quantification of Sensitivity and Specificity in a Laser-Induced Breakdown Spectroscopy Diagnostic Assay for Pathogenic Bacteria Detection and Classification

The Canadian Light Source (CLS) synchrotron uses four fast kicker magnets to inject electrons into the storage ring from a 2.9 GeV booster ring. The injection occurs over several turns of the stored beam, which is also perturbed by the injection kickers. The resultant oscillations of the stored beam can negatively affect the quality of beamline experiments, so it is desirable to implement an injection scheme which does not disturb the stored beam. Injection schemes of this type allow for transparent injection and are very desirable for the planned top-up operations of the CLS storage ring. Many alternative injection techniques have been presented in recent years and we have examined several of these techniques as they apply to the CLS storage ring. Pulsed multipole magnets and a non-linear kicker are the most viable alternatives for integration with the current ring. Non-linear kicker designs are also being considered for the proposed CLS 2.0 and studying this injection method in the limitations of the current machine provides additional insight to guide the work on the new machine. Simulation with the accelerator code ELEGANT shows the viability of the non-linear kicker design as developed at BESSY, MAX IV and SOLEIL (other synchrotron facilities) for transparent injection at the CLS.

Design and Simulation of Transparent Injection Upgrade for the CLS Storage Ring

Sea spray icing is created by wind/wave-induced spray in harsh arctic and antarctic environments. It is reported that sea spray icing causes hazardous conditions and operational problems for vessels and offshore structures. Nuclear Magnetic Resonance (NMR) is a powerful tool that can provide information about local environment, diffusion, and structure of a sample containing NMR-sensitive nuclei. NMR studies of sea ice are well-known for investigating seawater brine properties and structure. However, typical NMR instruments are big, expensive, and they cannot be moved outside a scientific laboratory. Also, seaspray icing hasn’t been studied with NMR until very recently (Wilbur et al, JMR, 2020). This study was focused on how to measure freezing of a sea-water spray with a portable, unilateral NMR instrument consisting of a handheld 3-magnet array.
For our instrument, the 1H NMR signal was generated approx. 1 cm away from the magnet surface, in the presence of a constant 250 G/cm magnetic field gradient. The pulse sequence used in this study was a combination of the Hahn and CPMG sequences (the CPMG echoes could be either added to increase the SNR, or used for obtaining T2 information). An optimum quality factor for a desired slice thickness was chosen to increase the sensitive volume. Additionally, we explored 1D-imaging with a unilateral NMR by performing Fourier Transform of the echoes acquired in the presence of the constant gradient.
The following parameters of NMR signal from freezing seawater accumulating on a cold surface inside the sensitive volume were measured and analyzed: signal intensity (proportional to the brine concentration), T2 relaxation, and diffusion for a range of temperatures (from-6oCto-14oC) and for two different surface orientations (horizontal and vertical). Results showed differences in signal intensity caused by ice growth rates at different temperatures. The diffusion was highly dependent on temperatures and surface orientations. This study shows that portable NMR devices can be useful for studies of seawater freezing, and freezing in general.

Studies of seawater spray icing phenomena with unilateral NMR

The DC gas discharge is a non-thermal laboratory plasma that is initiated by an applied electric field. It serves as a useful apparatus for studying fundamental phenomena in plasma physics and has found several applications in materials science and engineering. In contrast to thermally ionized plasma, the distribution function of a gas discharge deviates from Maxwellian at low pressures. It is affected by a high-energy tail due to accelerated electrons and is truncated by inelastic collisions. To have a good understanding of particle kinetics within the plasma, measurements of the distribution function are important. Fortunately, this is made possible with the Langmuir probe diagnostic. In addition to measurement of the distribution function, Langmuir probes can also directly measure several important plasma properties including the electron temperature and plasma density. Furthermore, spatially separated probes can measure gradients in potential that can be used to infer an electric field. To investigate properties of gas discharges and to evaluate the design and implementation of a Langmuir probe diagnostic, an array of several probes was designed and inserted into an intermediate pressure DC gas discharge. Before the Langmuir probe experiments, measurements of the discharge were performed including obtaining IV characteristics and determining breakdown voltages for several gases. Images of the discharges were recorded using a USB camera and emission spectra were obtained using a visible light spectrometer. Langmuir probe measurements were then taken of the electric field in the cathode region and IV characteristics were obtained to determine plasma properties: both by a graphical method and by the calculation of the electron energy distribution function (EEDF) from the second derivative.

Measurements of a DC Gas Discharge

The Transverse Feedback system at the Canadian Light Source can identify, categorize, and mitigate against periodic instabilities that arise in the storage ring beam. By quickly opening and closing the feedback loop, previously mitigated instabilities will be allowed to grow briefly before being damped by the system. The resulting growth in the beam oscillation amplitude curve can be analyzed to determine growth/damp rates and modes of the coupled bunch oscillations. Grow/damp curves will be collected and analyzed for various storage ring beam properties, including beam profile density, beam energy, machine chromaticity, injection instability, insertion device gap width, or bunch fill patterns. These results will be used to characterize the known instability growth rates, and search for unknown instability modes that may cause stability problems in the future. The instability analysis in the CLS will also impact the design of future insertion devices that might be added for new beamlines and the design of the CLS2 ring which is being planned.

Analyzing Growth/Damp curves in the Canadian Light Source storage ring

The Hyper-Kamiokande (Hyper-K) experiment is the next generation of the Super-Kamiokande (Super-K) and T2K experiments investigating a breadth of physics topics including neutrino oscillation. The Hyper-K far-distance detector will contain ~40,000 20” photomultiplier tubes (PMTs), while the Intermediate-distance Water Cherenkov detector (IWCD) will contain ~500 multi-PMTs (each containing 19 3” PMTs). To minimize systematic errors in their measurements, a precise understanding of the PMTs’ intrinsic parameters, such as their detection efficiency and timing as a function of the incident photon position and angle, as well as their response to variations in magnetic field, is required.
These parameters can be measured at TRIUMF’s photosensor test facility (PTF). This facility characterizes PMTs by emitting a laser beam from robotic arms that enable fine control of the beam’s 3D position and orientation. The light wavelength and polarization can also be varied to mimic Cherenkov light. Additionally, the facility uses 6 Helmholtz coils to create and control the magnetic field.
Currently, the PTF is being recommissioned in a new location, farther from the magnetic interference of the on-site cyclotron. This poster will outline the software, hardware, and mechanical upgrades being implemented to improve the facilities robustness and the stability and accuracy of the measurements. These upgrades include mechanical modifications to simplify the process of inserting and removing the PMTs as well as the implementation of motor encoders, environmental sensors, and software to prevent collisions of the robotic arms during reflectivity measurements. Moreover, this poster will cover the modelling and measurement of the environmental magnetic field in the facility to reduce the time required to complete the magnetic field compensation process.

Hyper-Kamiokande Photosensor Test Facility Recommissioning and System Upgrades.

The Canadian Light Source (CLS) is a 3rd generation synchrotron in Saskatoon that is used to produce extremely bright synchrotron light that can be used for research. The light at the CLS is produced by an electron storage ring which has an emmitance of 20 nm. A 4th generation synchrotron (CLS2) is planned which will reduce the emmitance to less than 1 nm and thus reduce the transverse beam size significantly, making it very challenging to measure. A doubleslit interferometer can be used to measure small transverse beamsizes. An x-ray doubleslit interferometer will be designed and manufactured for the current CLS with the goal of using this setup at CLS2. Various constraints require the doubleslit to have dimensions on the micrometer scale, making the manufacturing very difficult.

X-ray Doubleslit Interferometer Progress at CLS

Development of portable X-ray fluorescence devices has made it easier to quickly assess trace elements such as zinc in human tissue. Zinc deficiency can have serious implications on growth and development of the human body. From recent studies zinc content in nail clippings has been suggested to be an effective biomarker for zinc status. In this study, a simulation approach was used to investigate the use of a portable X-ray fluorescence system for detecting the variation of zinc signal with respect to nail thickness and was compared with the experimental results. The portable X-ray device was modelled using the available information from the manufacturer using the TOPAS Monte Carlo code (Geant4 simulation software).The simulations were carried out for varying nail phantom thickness (0.2 mm – 1.2 mm) with concentration of 1000 ppm zinc. Each simulation was run for 10^9 histories and the statistical uncertainty was less than 3.5%. The obtained energy spectra from different measurements were analyzed and three different normalization techniques (Coherent, Compton and Entire) spectrum were investigated to account for the variation of sample interrogated by the X-ray beam. Close agreement between simulation and experimental trends were observed indicating successful benchmarking of the simulation. Compton and Coherent normalization followed a slightly negative trend. One other important observation was coherent normalization can be a robust normalization procedure to improve the accuracy of elemental quantification in order to reduce the variability in nail thickness by ~8%. Overall the simulation approach can provide additional insights into elemental analysis in keratin based nail phantoms.

Effect of Lung Surfactant Protein B Fragment, SP-B1-9 on Model Lipid Bilayer.

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Energy Compression System Radio Frequency Design at the Canadian Light Source

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