Biomedical subjects

Chris Jacobsen

Publications and source records attributed to Chris Jacobsen.

12 recordsLinked to original sources

PubMed2006

Comet 81P/Wild 2 under a microscope.

The Stardust spacecraft collected thousands of particles from comet 81P/Wild 2 and returned them to Earth for laboratory study. The preliminary examination of these samples shows that the nonvolatile portion of the comet is an unequilibrated assortment of materials that have both presolar and solar system origin. The comet contains an abundance of silicate grains that are much larger than predictions of interstellar grain models, and many of these are high-temperature minerals that appear to have formed in the inner regions of the solar nebula. Their presence in a comet proves that the formation of the solar system included mixing on the grandest scales.

Journal Article↗

PubMed2006

Organics captured from comet 81P/Wild 2 by the Stardust spacecraft.

Organics found in comet 81P/Wild 2 samples show a heterogeneous and unequilibrated distribution in abundance and composition. Some organics are similar, but not identical, to those in interplanetary dust particles and carbonaceous meteorites. A class of aromatic-poor organic material is also present. The organics are rich in oxygen and nitrogen compared with meteoritic organics. Aromatic compounds are present, but the samples tend to be relatively poorer in aromatics than are meteorites and interplanetary dust particles. The presence of deuterium and nitrogen-15 excesses suggest that some organics have an interstellar/protostellar heritage. Although the variable extent of modification of these materials by impact capture is not yet fully constrained, a diverse suite of organic compounds is present and identifiable within the returned samples.

Carbon↗

PubMed2006

Reconstruction of a yeast cell from X-ray diffraction data.

Details are provided of the algorithm used for the reconstruction of yeast cell images in the recent demonstration of diffraction microscopy by Shapiro, Thibault, Beetz, Elser, Howells, Jacobsen, Kirz, Lima, Miao, Nieman & Sayre [Proc. Natl Acad. Sci. USA (2005), 102, 15343-15346]. Two refinements of the iterative constraint-based scheme are developed to address the current experimental realities of this imaging technique, which include missing central data and noise. A constrained power operator is defined whose eigenmodes allow the identification of a small number of degrees of freedom in the reconstruction that are negligibly constrained as a result of the missing data. To achieve reproducibility in the algorithm's output, a special intervention is required for these modes. Weak incompatibility of the constraints caused by noise in both direct and Fourier space leads to residual phase fluctuations. This problem is addressed by supplementing the algorithm with an averaging method. The effect of averaging may be interpreted in terms of an effective modulation transfer function, as used in optics, to quantify the resolution. The reconstruction details are prefaced with simulations of wave propagation through a model yeast cell. These show that the yeast cell is a strong-phase-contrast object for the conditions in the experiment.

Algorithms↗

PubMed2006

Scanning transmission X-ray microscopic analysis of purified melanosomes of the mouse iris.

Melanosomes are specialized intracellular membrane bound organelles that produce and store melanin pigment. The composition of melanin and distribution of melanosomes determine the color of many mammalian tissues, including the hair, skin, and iris. However, the presence of melanosomes within a tissue carries potentially detrimental risks related to the cytotoxic indole-quinone intermediates produced during melanin synthesis. In order to study melanosomal molecules, including melanin and melanin-related intermediates, we have refined methods allowing spectromicroscopic analysis of purified melanosomes using scanning transmission X-ray microscopy. Here, we present for the first time absorption data for melanosomes at the carbon absorption edge ranging from 284 to 290 eV. High-resolution images of melanosomes at discrete energies demonstrate that fully melanized mature melanosomes are internally non-homogeneous, suggesting the presence of an organized internal sub-structure. Spectra of purified melanosomes are complex, partially described by a predominating absorption band at 288.4 eV with additional contributions from several minor bands. Differences in these spectra were detectable between samples from two strains of inbred mice known to harbor genetically determined melanosomal differences, DBA/2J and C57BL/6J, and are likely to represent signatures arising from biologically relevant and tractable phenomena.

Absorption↗

PubMed2006

High-resolution ab initio three-dimensional x-ray diffraction microscopy.

Coherent x-ray diffraction microscopy is a method of imaging nonperiodic isolated objects at resolutions limited, in principle, by only the wavelength and largest scattering angles recorded. We demonstrate x-ray diffraction imaging with high resolution in all three dimensions, as determined by a quantitative analysis of the reconstructed volume images. These images are retrieved from the three-dimensional diffraction data using no a priori knowledge about the shape or composition of the object, which has never before been demonstrated on a nonperiodic object. We also construct two-dimensional images of thick objects with greatly increased depth of focus (without loss of transverse spatial resolution). These methods can be used to image biological and materials science samples at high resolution with x-ray undulator radiation and establishes the techniques to be used in atomic-resolution ultrafast imaging at x-ray free-electron laser sources.

Algorithms↗

PubMed2005

Chemical heterogeneity of organic soil colloids investigated by scanning transmission X-ray microscopy and C-1s NEXAFS microspectroscopy.

Colloid release and deposition in soils and sorption of inorganic and organic pollutants to soil colloids are strongly influenced by the composition and chemical heterogeneity of colloidal soil particles. To investigate the chemical heterogeneity of organic soil colloids at the particle scale, we used synchrotron scanning transmission X-ray microscopy (STXM) and C-1s near-edge X-ray absorption fine structure (NEXAFS) spectroscopy on 49 individual particles isolated from the surface horizons of three forest soils. Stacks of 130 images of each particle were collected at different X-ray energies between 280 and 310 eV. From these image arrays, NEXAFS spectra were obtained for each pixel and analyzed by principle component analysis and cluster analysis (PCA-CA) to characterize the intraparticle heterogeneity of the organic components. The results demonstrate that the organic matter associated with water-dispersible soil colloids is chemically heterogeneous at the single-particle scale. PCA-CA identified at least two distinct regions within single particles. However, the spectral variations between these regions were much smaller than the variations of averaged NEXAFS spectra representing different particles from the same soil horizon, implying that interparticle heterogeneity is much larger than intraparticle heterogeneity. Especially the contents of aromatic and carboxyl carbon exhibited a large variability. Overall, the NEXAFS spectra of water-dispersible soil colloids were similar to the NEXAFS spectrum of the humic acid fraction, but differed clearly from the fulvic acid and dissolved organic matter fractions extracted from the same soil horizon using conventional techniques.

Colloids↗

PubMed2005

Biological imaging by soft x-ray diffraction microscopy.

We have used the method of x-ray diffraction microscopy to image the complex-valued exit wave of an intact and unstained yeast cell. The images of the freeze-dried cell, obtained by using 750-eV x-rays from different angular orientations, portray several of the cell's major internal components to 30-nm resolution. The good agreement among the independently recovered structures demonstrates the accuracy of the imaging technique. To obtain the best possible reconstructions, we have implemented procedures for handling noisy and incomplete diffraction data, and we propose a method for determining the reconstructed resolution. This work represents a previously uncharacterized application of x-ray diffraction microscopy to a specimen of this complexity and provides confidence in the feasibility of the ultimate goal of imaging biological specimens at 10-nm resolution in three dimensions.

Freeze Drying↗

PubMed2004

Evolution of xylem lignification and hydrogel transport regulation.

In vascular plants, the polysaccharide-based walls of water-conducting cells are strengthened by impregnation with the polyphenolic polymer lignin. The fine-scale patterning of lignin deposition in water-conducting cells is shown here to vary phylogenetically across vascular plants. The extent to which water transport in xylem cells can be modified in response to changes in the ionic content of xylem sap also is shown to vary in correlation with variation in lignification patterns, consistent with the proposed mechanism for hydraulic response through size change of middle-lamella pectins. This covariation suggests that the fine-scale distribution of hydrophilic polysaccharides and hydrophobic lignin can affect hydraulic as well as mechanical properties, and that the evolutionary diversification of vascular cells thus reflects biochemical as well as morphological innovations evolved to fulfill opposing cell functions of transport and structural support.

Biological Evolution↗

PubMed2003

Quantifying trace elements in individual aquatic protist cells with a synchrotron X-ray fluorescence microprobe.

The study of trace metal cycling by aquatic protists is limited by current analytical techniques. Standard "bulk" element analysis techniques that rely on physical separations to concentrate cells for analysis cannot separate cells from co-occurring detrital material or other cells of differing taxonomy or trophic function. Here we demonstrate the ability of a synchrotron-based X-ray fluorescence (SXRF) microprobe to quantify the elements Si, Mn, Fe, Ni, and Zn in individual aquatic protist cells. This technique distinguishes between different types of cells in an assemblage and between cells and other particulate matter. Under typical operating conditions, the minimum detection limits are 7.0 x 10(-16) mol microm(-2) for Si and between 5.0 x 10(-20) and 3.9 x 10(-19) mol microm(-2) for Mn, Fe, Ni, and Zn; this sensitivity is sufficient to detect these elements in cells from even the most pristine waters as demonstrated in phytoplankton cells collected from remote areas of the Southern Ocean. Replicate analyses of single cells produced variations of <5% for Si, Mn, Fe, and Zn and <10% for Ni. Comparative analyses of cultured phytoplankton cells generally show no significant differences in cellular metal concentrations measured with SXRF and standard bulk techniques (spectrophotometry and graphite furnace atomic absorption spectrometry). SXRF also produces two-dimensional maps of element distributions in cells, thereby providing information not available with other analytical approaches. This technique enables the accurate and precise measurement of trace metals in individual aquatic protists collected from natural environments.

Calibration↗

PubMed2003

Achromatic Fresnel optics for wideband extreme-ultraviolet and X-ray imaging.

Advances in extreme-ultraviolet (EUV) and X-ray optics are providing powerful new capabilities in high-resolution imaging and trace-element analysis of microscopic specimens, and the potential for fabricating devices of smaller critical dimensions in next-generation integrated circuit lithography. However, achieving the highest resolution with such optics usually requires the illuminating EUV or X-ray beam to be highly monochromatic. It would therefore be highly desirable to have large-field-of-view, sub-100-nm resolution optics that are achromatic to a significant degree, allowing more light to be utilized from broader bandwidth sources such as laser-produced plasmas. Here we report an achromatic Fresnel optical system for EUV or X-ray radiation that combines a Fresnel zone plate with a refractive lens with opposite chromatic aberration. We use the large anomalous dispersion property of the refractive lens material near an absorption edge to make its fabrication practical. The resulting structure can deliver a resolution comparable to that of the Fresnel zone plates that have achieved the highest resolution (25 nm; ref. 3) in the entire electromagnetic spectrum, but with an improvement of two or more orders of magnitude in spectral bandwidth.

Journal Article↗

PubMed2003

Soft X-ray radiation-damage studies in PMMA using a cryo-STXM.

Radiation damage sets a fundamental limit for studies with ionizing radiation; cryo-methods are known to ease these limits. Here, measurements on mass loss and the decrease in the C=O bond density as measured by oxygen-edge XANES (NEXAFS) spectroscopy in thin films of poly(methylmethacrylate) (PMMA), studied in a vacuum, are reported. While cryo-methods allow more than 95% of the mass to remain at doses up to 10(7) Gy, there is little difference in C=O bond density versus dose between 298 K and 113 K sample temperatures. At both temperatures the critical dose for bond breaking is approximately 15 x 10(6) Gy.

Crystallography, X-Ray↗

PubMed2002

AGTR2 mutations in X-linked mental retardation.

Two angiotensin II (Ang II)-specific receptors, AGTR1 and AGTR2, are expressed in the mammalian brain. Ang II actions on blood pressure regulation, water electrolyte balance, and hormone secretion are primarily mediated by AGTR1. The function of AGTR2 remains unclear. Here, we show that expression of the AGTR2 gene was absent in a female patient with mental retardation (MR) who had a balanced X;7 chromosomal translocation. Additionally, 8 of 590 unrelated male patients with MR were found to have sequence changes in the AGTR2 gene, including one frameshift and three missense mutations. These findings indicate a role for AGTR2 in brain development and cognitive function.

Amino Acid Sequence↗