Biological specimen | EPFL Graph Search

A biological specimen (also called a biospecimen) is a biological laboratory specimen held by a biorepository for research. Such a specimen would be taken by sampling so as to be representative of any other specimen taken from the source of the specimen. When biological specimens are stored, ideally they remain equivalent to freshly-collected specimens for the purposes of research. Human biological specimens are stored in a type of biorepository called a biobank, and the science of preserving biological specimens is most active in the field of biobanking. Quality control Setting broad standards for quality of biological specimens was initially an underdeveloped aspect of biobank growth. There is currently discussion on what standards should be in place and who should manage those standards. Since many organizations set their own standards and since biobanks are necessarily used by multiple organizations and typically are driven towards expansion, the harmonization of stand

Phase-contrast and fluorescence X-ray imaging of soft and bio matter

Vincent Gajdosik

The high brightness and coherence of X-ray synchrotron sources and steady development in X-ray optics are critical ingredients in novel imaging techniques for a variety of domains. We employed several different approaches and a wide energy spectrum of radiation to demonstrate the applicability of synchrotron X-ray imaging in soft granular matter and life science. We applied refraction-enhanced contrast tomography to the Distinct Element Method (DEM) to predict instant granular jamming in an hourglass. The validation of numerical simulations as a DEM is mostly confined to global properties. We present a stringent microscopic test in the case of instant flow jamming in hourglasses: synchrotron X-ray microtomography coupled to advanced image analysis. The results show that DEM is amazingly successful in predicting the actual microscopic position of individual particles from given initial conditions through to the end of the instant jamming process. We further report refraction-enhanced radiology employed in the study of Drosophila Melanogaster wing development. The objective of the study was to reveal the morphological difference between two different phenotypes of fruit flies. Refraction-enhanced radiology is highly sensitive to morphological information, whereas fluorescent X-ray microanalysis techniques can reveal the distribution of heavy elements containing molecules. Here we report the design of a fast fluorescence detection system coupled to an existing radiology setup at the B01A beamline, NSRRC, Taiwan and the successful test on cartilage samples. Since its invention in 1930, Zernike phase contrast has been a pillar in visible microscopy – and more recently in X-ray microscopy – of low-absorption-contrast objects such as biological specimens. We experimentally demonstrated hard-X-ray Zernike microscopy with lateral resolution beyond 30 nm, opening up many new research opportunities in biomedicine and materials science. In the soft X-ray regime we show that synchrotron X-ray fluorescence microscopy can map molecules with fluorine-containing labels and quantitatively measure the fluorine concentration with micrometer spatial resolution. This is an important result for life science since fluorine is a very widely used molecule label for a variety of investigations such as metabolic processes or therapeutic agents. Our results specifically concern Fluorodeoxyglucose and are therefore directly relevant to the crucial neurobiology issue of glucose metabolism.

EPFL2009

Biological samples studied by optical nanospectroscopy

Johanna Generosi

The different parts of the electromagnetic spectrum result in diverse effects upon interaction with matter: according to the wavelength, the radiation has energy appropriate for the excitation of a specific physical process. X-rays can be used as a tool to analyze the structure of matter since their wavelength is comparable with the interatomic distances. Infrared light is in the spectral region that excites molecular vibrations and is employed to investigate the chemical composition of a material. Visible radiation can study the optical properties of a sample, such as the fluorescence and the absorbance, and provide a chemical fingerprint when the inelastically scattered light is detected. In this thesis work these light sources are used in diverse experimental approaches to study structured biological specimens, resulting in a detailed chemical and physical characterization at the atomic and molecular scale. Conventional spectroscopy is often not enough sensitive and spatially resolved to detect specific elements or domains in a sample. The need of imaging objects on increasingly finer scales and spatially localize specific molecules, brought to combine infrared, visible and Raman spectroscopy with scanning near-field microscopy giving rise to a powerful nanospectroscopic tool used to perform simultaneous topographical measurements and optical/chemical characterizations with subwavelength resolution, overcoming the diffraction limit of light. Our study combines X-ray diffraction and reflectivity with optical nanospectroscopy to investigate the order and clustering of lipid bilayers, the interaction between solid-supported membranes and embedded alamethicin peptides, the optical and chemical properties of hippocampal neuron cells and the trafficking mechanism of specific neuron receptors.

EPFL2009

Phase-contrast and fluorescence X-ray imaging of soft and bio matter

Vincent Gajdosik

EPFL2009