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PubMed2026

Breed classification of Lao People's Democratic Republic (Lao PDR) and Thai native chickens using synchrotron radiation-based Fourier transform infrared spectroscopy and genotyping by sequencing.

Lao PDR harbors substantial genetic diversity in native chicken populations, representing an important resource for sustainable production and long-term food security. This study aimed to classify five Lao native chicken breeds-Ou, Black Bone, Horn Chou, Yolk, and Chae-and to discriminate them from a Thai native breed, Leung Hang Khao (LK), using integrative genotype-based approaches. Blood samples were collected from 50 LK and Lao native chickens (32 Ou, 10 Black Bone, 9 Horn Chou, 121 Yolk, and 41 Chae). Genomic DNA was extracted and analyzed using synchrotron radiation-based Fourier-transform infrared (SR-FTIR) spectroscopy to characterize biochemical composition, while genotyping-by-sequencing (GBS) was employed to identify genome-wide single nucleotide polymorphisms (SNPs). SR-FTIR analysis revealed highly significant differences among breeds in nucleotide-associated functional groups, including thymine, adenine, guanine, cytosine, as well as DNA backbone and deoxyribose components (P < 0.001). Multivariate analyses demonstrated that principal component analysis (PCA) of SR-FTIR spectra effectively discriminated chicken breeds, while hierarchical cluster analysis (HCA) further resolved them into two major clusters with distinct sub-clusters, reflecting variation in DNA biochemical composition. In contrast, GBS analysis identified 1484 common SNPs; however, PCA based on SNP data showed limited resolution in clearly separating breeds, despite revealing similar clustering trends. Overall, the results highlight the strong discriminatory power of SR-FTIR spectroscopy for rapid and effective classification of native chicken breeds at the molecular level, outperforming SNP-based differentiation under the current marker density. This study provides novel insights into the application of synchrotron-based spectroscopic techniques in poultry genetics and contributes valuable baseline information for the conservation and utilization of Lao native chicken genetic resources.

Breed classification↗
PubMed1995

Behavior of cholesterol and spin-labeled cholestane in model bile systems studied by electron spin resonance and synchrotron x-ray.

The behavior of mixed bile salt micelles consisting of sodium taurocholate, egg phosphatidylcholine, and cholesterol has been studied by ESR spin labeling and synchrotron x-ray scattering. Consistent with published phase diagrams, pure and mixed bile salt micelles have a limited capacity to incorporate and, hence, solubilize cholesterol. Excess cholesterol crystallizes out, a process that is readily detected both by ESR spin labeling using 3-doxyl-5 alpha-cholestane as a probe for cholesterol and synchrotron x-ray scattering. Both methods yield entirely consistent results. The crystallization of cholesterol from mixed bile salt micelles is indicated by the appearance of a magnetically dilute powder spectrum that is readily detected by visual inspection of the ESR spectra. Both the absence of Heissenberg spin exchange and the observation of a magnetically dilute powder spectrum provide evidence for the spin label co-crystallizing with cholesterol. In mixed bile salt micelles containing egg phosphatidylcholine, the solubility of cholesterol is increased as detected by both methods. With increasing content of phosphatidylcholine and increasing mole ratio cholesterol/phosphatidylcholine, the anisotropy of motion of the spin probe increases. The spin label 3-doxyl-5 alpha-cholestane is a useful substitute for cholesterol provided that it is used in dilute mixtures with excess cholesterol: the cholesterol/spin label mole ratio in these mixtures should be greater than 100. Despite the structural similarity between the two compounds, there are still significant differences in their physico-chemical properties. These differences come to the fore when cholesterol is totally replaced by the spin-label: 3-doxyl-5a-cholestane is significantly less soluble in bile salt and mixed bile salt micelles than cholesterol and, in contrast with cholesterol, it interacts only very weakly, if at all,with phosphatidylcholine. The potential of the ESR method for detecting cholesterol crystal growth in human bile is discussed.

Bile Acids and Salts↗
PubMed1996

In situ characterization of beta-amyloid in Alzheimer's diseased tissue by synchrotron Fourier transform infrared microspectroscopy.

We report the first evidence of the structure of beta-amyloid protein as it exists in situ within a slice of human Alzheimer's diseased brain tissue. Using a Fourier transform infrared microspectroscopic technique, areas of interest can be selected for spectral measurements with regions of potential contamination masked. In so doing, it is possible to obtain infrared spectra only of beta-amyloid and not the surrounding grey matter within which it lies. However, to obtain spectra of high-quality signal-to-noise ratio using a conventional infrared source, we were limited to aperture sizes between 24 microns x 24 microns to 50 microns x 50 microns. Markedly improved high-quality spectra were acquired with infrared radiation provided by a synchrotron light source (National Synchrotron Light Source, Brookhaven National Laboratories), using aperture sizes as small as 12 microns x 12 microns. This allowed spectroscopic mapping of brain tissue regions containing amyloid. We observe that in situ protein of grey matter exist predominantly in an alpha-helical and/or unordered conformation, whereas within amyloid deposits a beta-sheet structure predominates. The hydrogen bonding strength of the beta-structure found in situ is different from that reported in the literature for isolated/chemically synthesized beta-amyloid peptides.

Alzheimer Disease↗
PubMed1999

Tetrameric assembly of full-sequence protein zero myelin glycoprotein by synchrotron x-ray scattering.

Highly purified myelin P0 glycoprotein was solubilized to 1-8 mg/ml in 0.1% sodium dodecyl sulfate (SDS), and the solution structure of the P0 assembly was studied using synchrotron x-ray scattering. The full-length P0, which was isolated from bovine intradural roots, included both the extracellular and cytoplasmic domains of the molecule. At the higher concentrations (4, 6, and 8 mg/ml, respectively), an x-ray intensity maximum was observed at 316 A, 245 A, and 240 A Bragg spacing. Because the position of this intensity depended on P0 concentration, it is most likely due to interparticle interference. By contrast, the position of a second intensity maximum, which was at approximately 40 A Bragg spacing, was invariant with P0 concentration. This latter intensity was accounted for by monodispersed, 80 A-diameter particles that are composed of eight, approximately 30 A-diameter spheres. Chemical parameters suggest that the 80 A particles correspond to the size of a tetramer of P0 molecules. Therefore, the approximately 30 A spheres would correspond to the sizes of the extracellular and cytoplasmic domains for each of the P0 monomers. The invariance of the second intensity maximum with P0 concentration indicates that the structure of the 80 A-diameter, tetrameric particles is unaltered. According to the liquid model for interparticle interference from charged spheres, the 80 A-diameter particle has 10 negative surface charges which likely arise from negatively charged SDS molecules bound to the transmembrane domain of P0. This binding, however, apparently does not alter the tetrameric assembly of P0, suggesting that intermolecular interactions involving extracellular domains and cytoplasmic domains likely stabilize this assembly. Some of our results have been published in abstract form (Inouye, H., H. Tsuruta, D. A. Kirschner, J. Sedzik, and K. Uyemura. Abstracts of the 4th International School and Symposium on Synchrotron Radiation in Natural Science, June 15-20, 1998. Ustron-Jaszowiec, Poland. p. 31).

Animals↗
PubMed1998

Microdiffraction studies of bone tissues using synchrotron radiation.

This is the first report on a series of studies of the crystallinity of bone tissues. The measurements were done at the microfocused diffraction beamline at ERSF (European Synchrotron Radiation Facility) as a feasibility test on various aspects on microdiffraction analysis. Beside the crystal structure, crystallite size distribution and preferential orientation were also studied, with a spatial resolution of 7 microm. The experiments were performed at the microfocus beam line 1 at European Synchrotron Radiation Facility (ESRF). The samples were longitudinal and transversal cuts from human femoral shafts. Over 65 diffraction lines from apatite structure could be identified. The results show that the bone crystallites seem to be oriented in two orthogonal directions, one parallel with the Haversian system and the other perpendicular following the lamella's curvature. Peak width analysis shows that the crystallites are about 25-40 nm along the c-axis with a width of about 10 nm. The result also shows that the peak width is somewhat larger close to the haversian canal compared with the outer region of the osteon.

Adult↗
PubMed2000

Synchrotron crystallography.

The past decade has seen an explosive growth in atomic-level structures determined by X-ray crystallography. Synchrotron radiation and a number of technical advances related quite directly to its development have fueled this growth. With the most recent advances coming to be used collectively and new resources being built, the foundation is laid for a dramatic further expansion of synchrotron crystallography in the next decade. Both the high-throughput applications of structural genomics and also the challenging studies of macromolecular machinery are expected to flourish.

Crystallography, X-Ray↗
PubMed2001

Synchrotron radiation circular dichroism spectroscopy of proteins: secondary structure, fold recognition and structural genomics.

Recent developments in instrumentation and bioinformatics show that the technique of synchrotron radiation circular dichroism spectroscopy can provide novel information on protein secondary structures and folding motifs, and has the potential to play an important role in structural genomics studies, both as a means of target selection and as a high-throughput, low-sample-requiring screening method. This is possible because of the additional information content in the low-vacuum ultraviolet wavelength data obtainable with intense synchrotron radiation light sources, compared with that present in spectra from conventional lab-based circular dichroism instruments.

Circular Dichroism↗
PubMed2002

Non-destructive three-dimensional evaluation of a polymer sponge by micro-tomography using synchrotron radiation.

X-ray micro-tomography, a non-destructive technique is used to uncover the complex 3-D micro-architecture of a degradable polymer sponge designed for bone augmentation. The measurements performed at HASYLAB at DESY are based on a synchrotron radiation source resulting in a spatial resolution of about 5.4 microm. In the present communication we report the quantitative analysis of the porosity and of the pore architecture. First, we elucidate that synchrotron radiation at the photon energy of 9 keV has an appropriate cross section for this low-weight material. Modifications in sponge micro-architecture during measurement are not detected. Second, the treatment of the data, an amount of 2.5 Gbyte to generate binary data is described. We compare the 3-D with the 2-D analysis in a quantitative manner. The obtained values for the mean distance to material within the sponge calculated from 2-D and 3-D data of the whole tomogram differ significantly: 12.5 microm for 3-D and 17.6 microm for 2-D analysis. If the pores exhibit a spherical shape as frequently found, the derived mean pore diameter, however, is overestimated only by 6% in the 2-D image analysis with respect to the 3-D evaluation. This approach can be applied to different porous biomaterials and composites even in a hydrated state close to physiological conditions, where any surface preparation artifact is avoided.

Absorbable Implants↗
PubMed2002

New applications of electron diffraction in the pharmaceutical industry: polymorph determination by using a combination of electron diffraction and synchrotron X-ray powder diffraction techniques.

Electron diffraction has been recently used in the pharmaceutical industry to study the polymorphism in crystalline drug substances. While conventional X-ray diffraction patterns could not be used to determine the cell parameters of two forms of the microcrystalline GP IIb/IIIa receptor antagonist roxifiban, a combination of electron single-crystal and synchrotron powder diffraction techniques were able to clearly distinguish the two polymorphs. The unit-cell parameters of the two polymorphs were ultimately determined using new software routines designed to take advantage of each technique's unique capabilities. The combined use of transmission electron microscopy (TEM) and synchrotron patterns appears to be a good general approach for characterizing complex (low-symmetry, large-unit-cell, micron-sized) polymorphic pharmaceutical compounds.

Amidines↗
PubMed2002

Spectrochemical analysis of dental calculus by synchrotron radiation X-ray fluorescence.

This work presents elemental composition studies of human dental calculus by X-ray fluorescence analysis using synchrotron radiation. The intrinsic characteristics of synchrotron light allow for a quantitative analysis of major, minor, and trace elements of very small samples in a single measurement. At present, several theories of calculus formation exist, but none of them can describe completely all the complicated mechanisms involved in the mineralization processes. For this reason, and taking into account that experimental data are long overdue, several calculi with certain degrees of formation were collected from adult patients for analysis. The ratio of calcium/phosphorus was used as an indicator of the major crystalline structure and the state of formation of the calculus. The results demonstrate a clear correlation between the concentrations of certain elements and the type of calculus (supra- or sub-gingival). In addition, the possible correlation between the elements was analyzed.

Calcium↗
PubMed2002

Mapping the G-actin binding surface of cofilin using synchrotron protein footprinting.

Cofilin is an actin regulatory protein that binds to both monomeric and filamentous actin, and has filament severing activity. Although crystal structures for the monomeric forms of both G-actin and cofilin have been described, the structure of the binary cofilin-G-actin complex is not available. Synchrotron protein footprinting is used to identify specific side chain residues on the cofilin surface that are buried in the formation of the cofilin-G-actin binary complex. Exposure to synchrotron X-rays results in stable oxidative modifications of aromatic, aliphatic, and sulfur-containing side chains, with the rate of modification for a particular residue being dependent on its intrinsic reactivity and solvent accessibility. The rates of modification were monitored for a number of peptides generated by digestion of oxidized cofilin, both in isolation and in its binary complex with G-actin. After binding to G-actin takes place, a significant decrease in modification rates, indicating protection of side chain groups, is seen for cofilin peptides corresponding to residues 4-20, 10-17, 83-96, 91-105, and 106-117. A number of other peptides show no change in reactivity, and are presumed to represent regions distal to the binding site. Tandem mass spectrometry demonstrates that residues Leu 13, Pro 94, Met 99, and Leu 108 and 112 directly participate in the binding interface. These results are generally consistent with, and complementary to, the results of previous site-directed mutagenesis studies and extend our understanding of the G-actin binding surface of cofilin.

Actin Depolymerizing Factors↗
PubMed2005

Pore-scale characterization of organic immiscible-liquid morphology in natural porous media using synchrotron X-ray microtomography.

The objective of this study was to quantitatively characterize the pore-scale morphology of organic immiscible liquid residing within natural porous media. Synchrotron X-ray microtomography was used to obtain high-resolution, three-dimensional images of solid and liquid phases in packed columns. The image data were processed to generate quantitative measurements of organic-liquid blob morphology. Three porous media, comprising a range of particle-size distributions, were used to evaluate the impact of porous-medium texture on blob morphology. The sizes and shapes of the organic-liquid blobs varied greatly, ranging from small spherical singlets (> or = 0.03 mm in diameter) to large, amorphous ganglia with mean lengths of 4-5 mm. The smaller blobs were composed primarily of singlets, which comprised approximately half of all blobs for all three media. Conversely, large, complex blobs comprising four or more bodies composed 11-24% of the total number of blobs. However, the majority of the total organic-liquid surface area and volume was associated with the largest blobs. The ratio of median blob size to median grain size was close to unity for all three systems. The distribution of blob sizes was greatest for the porous medium with the broadest particle-size and pore-size distributions. These results illustrate the utility of synchrotron X-ray microtomography for characterizing fluid distributions at the pore scale in natural porous media.

Synchrotrons↗
PubMed2002

Crystal structure and hydrogen-bonding system in cellulose Ibeta from synchrotron X-ray and neutron fiber diffraction.

The crystal and molecular structure together with the hydrogen-bonding system in cellulose Ibeta has been determined using synchrotron and neutron diffraction data recorded from oriented fibrous samples prepared by aligning cellulose microcrystals from tunicin. These samples diffracted both synchrotron X-rays and neutrons to better than 1A resolution (>300 unique reflections; P2(1)). The X-ray data were used to determine the C and O atom positions. The resulting structure consisted of two parallel chains having slightly different conformations and organized in sheets packed in a "parallel-up" fashion, with all hydroxymethyl groups adopting the tg conformation. The positions of hydrogen atoms involved in hydrogen-bonding were determined from a Fourier-difference analysis using neutron diffraction data collected from hydrogenated and deuterated samples. The hydrogen atoms involved in the intramolecular O3...O5 hydrogen bonds have well-defined positions, whereas those corresponding to O2 and O6 covered a wider volume, indicative of multiple geometry with partial occupation. The observation of this disorder substantiates a recent infrared analysis and indicates that, despite their high crystallinity, crystals of cellulose Ibeta have an inherent disorganization of the intermolecular H-bond network that maintains the cellulose chains in sheets.

Cellulose↗
PubMed2005

Synthesis, physical properties, multitemperature crystal structure, and 20 K synchrotron X-ray charge density of a magnetic metal organic framework structure, Mn3(C8O4H4)3(C5H11ON)2.

A new magnetic metal organic framework material has been synthesized, Mn3(C8O4H4)3(C5H11ON)2, 1. Magnetic susceptibility measurements from 2 to 400 K reveal anti-ferromagnetic ordering at approximately 4 K and a total magnetic moment of 6.0 micro(B). The magnetic phase transition is confirmed by heat capacity data (2-300 K). The crystal structure is studied by conventional single-crystal X-ray diffraction data at 300, 275, 250, 225, 200, 175, 150, 125, and 100 K, and synchrotron data at 20 K. There is a phase transition between 100 and 20 K due to ordering of the diethylformamide molecules. The X-ray charge density is determined based on multipole modeling of a second 20 K single-crystal synchrotron radiation data set. The electron distributions around the two unique Mn centers are different, and both have substantial anisotropy. Orbital population analysis reveals large electron donation (1.7 e) to each Mn atom and the maximum possible number of unpaired electrons is 3.2 for both Mn sites. Thus, there is a considerable orbital component to the magnetic moment. Bader topological analysis shows an absence of Mn-Mn bonding, and the magnetic ordering is via super-exchange through the oxygen bridges. Formal electron counting suggests Mn2+ sites, but this is not supported by the Bader atomic charges, Mn1 = +0.11 e, Mn2 = +0.17 e. The topological measures show the dominant metal-ligand interactions to be electrostatic, and a simple exponential correlation is derived between Mn-O bond lengths and the values of nabla2rho at the bond critical points.

Magnetics↗
PubMed2006

Characterizing challenging microcrystalline solids with solid-state NMR shift tensor and synchrotron X-ray powder diffraction data: structural analysis of ambuic acid.

Synchrotron X-ray powder diffraction and solid-state (13)C NMR shift tensor data are combined to provide a unique path to structure in microcrystalline organic solids. Analysis is demonstrated on ambuic acid powder, a widely occurring natural product, to provide the complete crystal structure. The NMR data verify phase purity, specify one molecule per asymmetric unit, and provide an initial structural model including relative stereochemistry and molecular conformation. A refinement of X-ray data from the initial model establishes that ambuic acid crystallizes in the P2(1) space group with unit cell parameters a = 15.5047(7), b = 4.3904(2), and c = 14.1933(4) A and beta = 110.3134(3) degrees . This combined analysis yields structural improvements at two dihedral angles over prior NMR predictions with differences of 103 degrees and 37 degrees found. Only minor differences of +/-5.5 degrees , on average, are observed at all remaining dihedral angles. Predicted hydroxyl hydrogen-bonding orientations also fit NMR predictions within +/-6.9 degrees . This refinement corrects chemical shift assignments at two carbons and reduces the NMR error by approximately 16%. This work demonstrates that the combination of long-range order information from synchrotron powder diffraction data together with the accurate shorter range structure given by solid-state NMR measurements is a powerful tool for studying challenging organic solids.

Cyclohexanones↗
PubMed2003

Chemical imaging of microstructures of plant tissues within cellular dimension using synchrotron infrared microspectroscopy.

Synchrotron radiation-based Fourier transform infrared microspectroscopy (SR-FTIR) is an advanced bioanalytical technique capable of exploring the chemistry within microstructures of plant and animal tissues with a high signal to noise ratio at high ultraspatial resolutions (3-10 microm) without destruction of the intrinsic structures of a tissue. This technique is able to provide information relating to the quantity, composition, structure, and distribution of chemical constituents and functional groups in a tissue. The objective of this study was to illustrate how the SR-FTIR technique can be used to image inherent structures of plant tissues on a cellular level (pixel size, approximately 10 microm x 10 microm). The results showed that with the extremely bright synchrotron light, spectra with high signal to noise ratios were obtained from areas as small as 10 microm x 10 microm in the plant tissue, which allowed us to "see" plant tissue in a chemical sense on a cellular level. The ultraspatial resolved imaging of plant tissues by stepping in pixel-sized increments was obtained. Chemical distributions of plant tissues such as lignin, cellulose, protein, lipid, and total carbohydrate could be mapped. These images revealed the chemical information of plant intrinsic structure. In conclusion, SR-FTIR can provide chemical and functional characteristics of plant tissue at high ultraspatial resolutions. The SR-FTIR microspectroscopic images can generate spatially localized functional group and chemical information within cellular dimensions.

Hordeum↗
PubMed2004

Using synchrotron transmission FTIR microspectroscopy as a rapid, direct, and nondestructive analytical technique to reveal molecular microstructural-chemical features within tissue in grain barley.

The objective of this study was to use synchrotron transmission FTIR microspectroscopy as a rapid, direct, and nondestructive analytical technique to reveal molecular microstructural-chemical features within tissue in grain barley. The results showed that synchrotron transmission FTIR microspectroscopy could provide spectral, chemical, and functional group characteristics of grain barley tissue at ultrahigh spatial resolutions. The spatially localized structural-chemical distributions of biological components (lignin, cellulose, protein, lipid, and carbohydrates) and biological component ratios could be imaged. Such information on molecular microstructural-chemical features within the tissue can be used for plant breeding programs for selecting superior varieties of barley for special purposes and for prediction of grain barley quality and nutritive value for humans and animals.

Carbohydrates↗
PubMed2005

Light scattering of ultrafine silica particles by VUV synchrotron radiation.

Vacuum ultraviolet (VUV) light scattering from ultrafine silica particles is studied with an aerosol instrument recently established at the Advanced Light Source (ALS) in Berkeley. Silica particles, size-selected by a differential mobility analyzer, are introduced into vacuum through a set of aerodynamic lenses to form a particle beam. The scattered photons from the crossing area of the VUV synchrotron beam and particle beam are detected with a rotatable VUV photon detector. The angular distributions of scattered photons (ADSP) originating from 70, 100, 200 nm diameter silica particles are measured with 145.9 and 118.1 nm synchrotron radiation. These angular distributions show strong forward scattering. The measured ADSPs are consistent with simulation of Mie scattering. The refractive indices of silica particles, 2.6 + 1.1i and 1.6 + 0.0001i for 118.1 and 145.9 nm, respectively, are obtained by fitting the measured ADSPs; the least average percentage deviations are 18% and 6%, respectively. The scattered fluxes at widely different wavelengths (visible versus VUV) also exhibit clear size sensitivity. Under comparable experimental conditions of photon fluxes and detection efficiencies, limits of particle size detection of 70 and 250 nm are obtained, respectively, when using 118.1 and 532 nm illumination. As anticipated, VUV scattering is a more sensitive probe for ultrafine particles, which will find application in detection of these ubiquitous species beyond the confines of a laboratory.

Light↗