The effect of optical substrates on micro-FTIR analysis of single mammalian cells

The study of individual cells with infrared (IR) microspectroscopy often requires living cells to be cultured directly onto a suitable substrate. The surface effect of the specific substrates on the cell growth—viability and associated biochemistry—as well as on the IR analysis—spectral interference and optical artifacts—is all too often ignored. Using the IR beamline, MIRIAM (Diamond Light Source, UK), we show the importance of the substrate used for IR absorption spectroscopy by analyzing two different cell lines cultured on a range of seven optical substrates in both transmission and reflection modes. First, cell viability measurements are made to determine the preferable substrates for normal cell growth. Successively, synchrotron radiation IR microspectroscopy is performed on the two cell lines to determine any genuine biochemically induced changes or optical effect in the spectra due to the different substrates. Multivariate analysis of spectral data is applied on each cell line to visualize the spectral changes. The results confirm the advantage of transmission measurements over reflection due to the absence of a strong optical standing wave artifact which amplifies the absorbance spectrum in the high wavenumber regions with respect to low wavenumbers in the mid-IR range. The transmission spectra reveal interference from a more subtle but significant optical artifact related to the reflection losses of the different substrate materials. This means that, for comparative studies of cell biochemistry by IR microspectroscopy, it is crucial that all samples are measured on the same substrate type. [Figure: see text

Fundamental studies on the deposition and characterisation of novel diamond-like materials

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Calculating temperature-dependent X-ray structure factors of α-quartz with an extensible Python 3 package

The design of X-ray optics based on diffraction from crystals depends on the accurate calculation of the structure factors of their Bragg reflections over a wide range of temperatures. In general, the temperature dependence of the lattice parameters, the atomic positions and the atomic thermal vibrations is both anisotropic and nonlinear. Implemented here is a software package for precise and flexible calculation of structure factors for dynamical diffraction. α-Quartz is used as an example because it presents the challenges mentioned above and because it is being considered for use in high-resolution X-ray spectroscopy. The package is designed to be extended easily to other crystals by adding new material files, which are kept separate from the package’s stable core. Python 3 was chosen as the language to allow the easy integration of this code into existing packages. The importance of a correct anisotropic treatment of the atomic thermal vibrations is demonstrated by comparison with an isotropic Debye model. Discrepancies between the two models can be as much as 5% for strong reflections and considerably larger (even to the level of 100%) for weak reflections. A script for finding Bragg reflections that backscatter X-rays of a given energy within a given temperature range is demonstrated. The package and example scripts are available on request. Also discussed, in detail, are the various conventions related to the proper description of chiral quartz

Study of gemcitabine-sensitive/resistant cancer cells by cell cloning and synchrotron FTIR microspectroscopy

Over the last few years, significant scientific insight on the effects of chemotherapy drugs at cellular level using synchrotron-based FTIR (S-FTIR) microspectroscopy has been obtained. The work carried out so far has identified spectral differences in cancer cells before and after the addition of drugs. However, this had to account for the following issues. First, chemotherapy agents cause both chemical and morphological changes in cells, the latter being responsible for changes in the spectral profile not correlated with biochemical characteristics. Second, as the work has been carried out in mixed populations of cells (resistant and sensitive), it is important to distinguish the spectral differences which are due to sensitivity/resistance to those due to cell morphology and/or cell mixture. Here, we successfully cloned resistant and sensitive lung cancer cells to a chemotherapy drug. This allowed us to study a more uniform population and, more important, allowed us to study sensitive and resistant cells prior to the addition of the drug with S-FTIR microscopy. Principal component analysis (PCA) did not detect major differences in resistant cells prior to and after adding the drug. However, PCA separated sensitive cells prior to and after the addition of the drug. This would indicate that the spectral differences between cells prior to and after adding a drug might reside on those more or less sensitive cells that have been able to remain alive when they were collected to be studied with S-FTIR microspectroscopy. This is a proof of concept and a feasibility study showing a methodology that opens a new way to identify the effects of drugs on more homogeneous cell populations using vibrational spectroscopy. © 2014 International Society for Advancement of Cytometr

1200-talet: Ett århundrade för städer

Core Updates: Adds numpy backend for basic (same pattern) processing Framework restructuring to expose local and global slicing methods Allows multiple plugins to process 'raw' data Adds beamline logger for auto-processing Adds 'nprocs' option to previewing Fixes 'File write failed' error caused by ROMIO 2GB read/write limit and h5py create_dataset Replaces h5py create_dataset (with chunking) with direct hdf5 calls, to avoid initialisation of the created file. Updates configurator arg parser to allow negative values in a list Adds beginnings of a GUI for creating plugin templates Plugin Updates: Adds iterative plugin driver Adds iterative vo_centering plugin Adds edfsaver Improves vo_centering Fixes scikitimage to use values from parameters Fixes error in upper and lower bounds for darkandflatfieldcorrection Fixes distortion correction Fixes previewing and parameter tuning at the same time in reconstruction methods Improves all reconstruction wrappers: Improves astra toolbox wrappers Improves base recon and centre/outer padding Padding is now only allowed for suitable methods (e.g. yes for FBP but no for iterative methods

DiamondLightSource/Savu: Version 2.2.1

Core updates: Improves dockerfile for external use Improves HDF5 data chunking, with significant speed increases Plugin updates: Amends DistortionCorrection parameters as agreed and tested with DLS beamline staff Adds 'multiple' frames request with a maximum limit DezingFilter renamed as DezingerSimple Adds Dezinger plugin Adds updated version of Robert Atwood's C-implemented algorithm back in to Savu This is a faster more accurate implementation Updates to DezingerSimple Maximum 8 frames now requested due to memory issues Darks and flats now only processed 8 at a tim