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At least 433 records · Page 24Linked to original sources
PubMed2003

Probing cell chemistry with time-of-flight secondary ion mass spectrometry: development and exploitation of instrumentation for studies of frozen-hydrated biological material.

Imaging static secondary ion mass spectrometry (SIMS) offers a powerful method of obtaining molecular information from biological systems with good spatial resolution. However, the technique needs further development to make it suitable for routine analysis of cells. We report here the development of a new freeze-facture device to facilitate the manipulation and analysis of biological cell material, with the cell chemistry preserved intact by rapid freezing. We illustrate performance characteristics with high-contrast images of freeze-fractured, frozen-hydrated liposomes with the drug clofazamine constrained within the lipid bilayer providing a marker to determine the fracture plane across the liposome structure. By monitoring and imaging clofazamine on the surface of yeast cells in the frozen-hydrated state, and demonstrating its absence within molecular information from a cell fractured to reveal the cell ultrastructure, we demonstrate that the molecule does not penetrate the cell wall.

Candida glabrata↗
PubMed1995

Stabilization of biological specimens by the use of plasma polymerized hydrocarbon film for imaging with an atomic force microscope.

An atomic force microscope makes imaging of biological molecules possible at high resolution. To this end all samples have to be fixed securely to a flat solid support so that they cannot be displaced by the scanning tip. We herein describe a new method to fix the biological samples to glass surfaces by depositing a thin layer of plasma polymerized methane gas in a high vacuum chamber. Such samples can thus be imaged repeatedly by an atomic force microscope without any loss of image quality.

Bacteriophage T4↗
PubMed2005

ICP-MS multielemental determination of metals potentially released from dental implants and articular prostheses in human biological fluids.

A sector field high-resolution (HR)-ICP-MS and an octapole reaction system (ORS)-ICP-MS have been compared for the simultaneous determination of traces of metals (Ti, V, Cr, Co, Ni, and Mo) released from dental implants and articular prostheses in human biological fluids. Optimum sample treatments were evaluated to minimize matrix effects in urine and whole blood. Urine samples were diluted tenfold with ultrapure water, whereas whole blood samples were digested with high-purity nitric acid and hydrogen peroxide and finally diluted tenfold with ultrapure water. In both matrices, internal standardization (Ga and Y) was employed to avoid potential matrix interferences and ICP-MS signal drift. Spectral interferences arising from the plasma gases or the major components of urine and whole blood were identified by (HR)-ICP-MS at 3,000 resolving power. The capabilities of (HR)-ICP-MS and (ORS)-ICP-MS for the removal of such spectral interferences were evaluated and compared. Results indicate that polyatomic interferences, which hamper the determination of such metallic elements in these biological samples, could be overcome by using a resolving power of 3,000. Using (ORS)-ICP-MS, all those elements could be quantified except Ti and V (due to the polyatomic ions 31P16O and 35Cl16O, respectively). The accuracy of the proposed methodologies by (HR)- and (ORS)-ICP-MS was checked against two reference materials. Good agreement between the given values and the concentrations obtained for all the analytes under scrutiny was found except for Ti and V when analyzed by (ORS)-ICP-MS.

Cartilage, Articular↗
PubMed2003

Small-scale vertical distribution of bacterial biomass and diversity in biological soil crusts from arid lands in the Colorado plateau.

We characterized, at millimeter resolution, bacterial biomass, diversity, and vertical stratification of biological soil crusts in arid lands from the Colorado Plateau. Microscopic counts, extractable DNA, and plate counts of viable aerobic copiotrophs (VAC) revealed that the top centimeter of crusted soils contained atypically large bacterial populations, tenfold larger than those in uncrusted, deeper soils. The plate counts were not always consistent with more direct estimates of microbial biomass. Bacterial populations peaked at the immediate subsurface (1-2 mm) in light-appearing, young crusts, and at the surface (0-1 mm) in well-developed, dark crusts, which corresponds to the location of cyanobacterial populations. Bacterial abundance decreased with depth below these horizons. Spatially resolved DGGE fingerprints of Bacterial 16S rRNA genes demonstrated the presence of highly diverse natural communities, but we could detect neither trends with depth in bacterial richness or diversity, nor a difference in diversity indices between crust types. Fingerprints, however, revealed the presence of marked stratification in the structure of the microbial communities, probably a result of vertical gradients in physicochemical parameters. Sequencing and phylogenetic analyses indicated that most of the naturally occurring bacteria are novel types, with low sequence similarity (83-93%) to those available in public databases. DGGE analyses of the VAC populations indicated communities of lower diversity, with most types having sequences more than 94% similar to those in public databases. Our study indicates that soil crusts represent small-scale mantles of fertility in arid ecosystems, harboring vertically structured, little-known bacterial populations that are not well represented by standard cultivation methods.

Biomass↗
PubMed2005

Global gene annotation analysis and transcriptional profiling identify key biological modules in hypoxic pulmonary hypertension.

Chronic hypoxic pulmonary hypertension is an important clinical disorder causing significant morbidity. Despite recent discoveries, many molecular mechanisms involved in its pathogenesis remain unexplored. We have undertaken a systematic and unbiased approach to gain global insights into this complex process. By combining transcriptional profiling with rigorous statistical methods and cluster analysis, we identified the dominant temporal patterns of gene expression during progression and regression of hypoxic pulmonary hypertension. We next integrated these results with global gene annotation analysis to identify key biological themes involved in the development and resolution of hypoxic pulmonary hypertension and vascular remodeling. This novel approach assigned biological roles to thousands of candidate genes based on their temporal expression profiles and membership in specific biological modules. Our procedure confirmed several molecular pathways and gene products known to be important in hypoxic pulmonary hypertension. Furthermore, we discovered several novel candidates and molecular mechanisms, including IQ motif containing GTPase-activating protein-1 (IQGAP1), decorin, insulin-like growth factor binding protein-3 (IGFBP3), and lactotransferrin, that may play crucial roles in hypoxic pulmonary hypertension and vascular remodeling. Our methodology of integrating transcriptional profiling, cluster analysis, and global gene annotation provides new insights into the pathophysiology of pulmonary hypertension and is applicable to other models of human disease.

Animals↗
PubMed1982

Specificity of stain distribution in electron micrographs of protein molecules contrasted with uranyl acetate.

The mechanism of contrast enhancement of protein molecules by negative staining with uranyl acetate has been investigated by analysing electron micrographs of microcrystals of the human immunoglobulin Dob. Digitally filtered micrographs were compared systematically with idealized reference images which were constructed computationally, starting from knowledge of the primary sequence and three-dimensional crystal structure of this IgG molecule. By separately modelling negative staining as bulk exclusion of heavy metals, and positive staining as the specific decoration of charged amino acid residues, and then combining these simulated images, we were able to assess quantitatively the amount of positive staining present in micrographs of ostensibly 'negatively stained' proteins. At a resolution of 2 nm, we find that the experimental images do indeed exhibit predominantly negative staining, the best matches being obtained by simulations which also include a minor contribution (10-40%) of positive staining. We have also compared two independent measures for the significant resolution present in images of periodic biological specimens: (i) the outermost visible orders of optical diffraction patterns, and (ii) the band-limited resolutions of the idealized simulations when they most closely match the experimental images. These criteria observe close correspondence, thus vindicating the traditional practice of inferring resolution from the optical diffraction spectra of indirectly represented (stained) objects.

Computers↗
PubMed1991

One- and two-dimensional electron paramagnetic resonance imaging in skin.

EPR imaging with modulated field gradients provides the possibility for obtaining an EPR spectrum in a selected volume. We demonstrate the feasibility of X-band (9.5 GHz) electron paramagnetic resonance (EPR) imaging in skin biopsies of hairless mice. One- (1D) and two-dimensional (2D) EPR images of the persistent free radical di-tertiary-butyl-nitroxide are measured. At a microwave frequency of 9.5 GHz (X-band), 2D images are obtained in skin biopsies with an actual point distinction resolution of 25 microns. In a biological model system, 2D images are measured at L-band frequency (2.0 GHz) with a pixel resolution of 61 microns, and a theoretical spatial resolution of 12.5 microns. In combination with the spin labeling and spin trapping technique, EPR imaging is the most direct approach to analyzing spatial distribution of physicochemical properties in skin, such as membrane fluidity and polarity, as well as detection of free radicals.

Animals↗
PubMed2006

Ultrasound elastomicroscopy using water jet and osmosis loading: potentials for assessment for articular cartilage.

Research in elasticity imaging typically relies on 1-10 MHz ultrasound. Elasticity imaging at these frequencies can provide strain maps with a resolution in the order of millimeters, but this is not sufficient for applications to skin, articular cartilage, or other fine structures. In this paper, we introduced two methods of ultrasound elastomicroscopy using water jet and osmosis loading for imaging the elasticity of biological soft tissues with high resolutions. In the first system, the specimens were compressed using water jet compression. A water jet was used to couple a focused 20 MHz ultrasound beam into the specimen and meanwhile served as a "soft" indenter. Because there was no additional attenuation when propagating from the ultrasound transducer to the specimen, the ultrasound signal with high signal-to-noise ratio could be collected from the specimens simultaneously with compressing process. The compression was achieved by adjusting the water flow. The pressure measured inside the water pipe and that on the specimen surface was calibrated. This system was easily to apply C-scan over sample surfaces. Experiments on the phantoms showed that this water jet indentation method was reliable to map the tissue stiffness distribution. Results of 1D and 2D scanning on phantoms with different stiffness are reported. In the second system, we used osmotic pressure caused by the ion concentration change in the bathing solutions for the articular cartilage to deform them. When bovine articular cartilage specimens were immerged in solutions with different salt concentration, a 50 MHz focused ultrasound beam was used to monitor the dynamic swelling or shrinkage process. Results showed that the system could reliably map the strain distribution induced by the osmotic loading. We extract intrinsic layered material parameters of the articular cartilage using a triphasic model. In addition to biological tissues, these systems have potential applications for the assessment of bioengineered tissues, biomaterials with fine structures, or some engineering materials. Further studies are necessary to fully realize the potentials of these two new methods.

Algorithms↗
PubMed1995

Determination of thiols and disulfides using high-performance liquid chromatography with electrochemical detection.

Low-molecular-mass thiols, such as glutathione (GSH), and their associated disulfides are ubiquitous in nature, and based upon the many known functions of these compounds, their identification and accurate measurement is essential. Our objectives were to develop a simple method for the simultaneous measurement of thiols and disulfides in biological samples using HPLC with dual electrochemical detection (HPLC-DED). Particular emphasis was placed on the applicability to a wide variety of important GSH-related thiols and disulfides, including gamma-Glu-Cys, Cys-Gly, their disulfides, and the mixed disulfide of glutathione and cysteine (CSSG), validation on different types of biological samples, maintenance of chromatographic resolution and reproducibility with routine and extended use, and enhancement of assay sensitivity. To this end, optimal HPLC conditions including mobile phase, column, and electrode polishing procedures were established and the method was applied to, and validated on a variety of biological samples. This improved methodology should prove to be a useful tool in studies on the metabolism of GSH and other thiols and disulfides and their role in cellular homeostasis and disease processes.

Amino Acid Sequence↗
PubMed2001

High resolution scanning force microscopy of cardiac myocytes.

The advent of scanning probe microscopy has introduced a powerful new method of probing the structural features of biological specimens. In this study, high resolution atomic force microscopy micrographs of single, isolated, cardiac myocytes are presented. Significantly, our images show not only the features to be expected of the external sarcolemma, but also resolve sub-surface features, including the striated pattern of the contractile proteins and their associated sarcoplasmic reticulum and mitochondria.

Animals↗
PubMed1988

Resolution as a function of accelerating voltage in electron microscopy of semithick biological specimens.

In the past, biological sections ranging in thickness from 0.10- to 0.50-micron have usually been examined with high-voltage (greater than 500 kV) electron microscopes (HVEM). Now investigators are increasingly using intermediate voltage (200-500 kV) electron microscopes (IVEM), which are more readily available and demand less maintenance. In a study of "typical" plastic-embedded, stained sections of mouse liver ranging from 0.10 to 1.0 micron thick, we determined the resolution obtainable at 100, 200, and 1000 kV. At all three accelerating voltages the resolution (2.7 nm) for 0.10-micron sections was limited only by the sections stain granularity. For 0.25-micron thickness the resolutions were 5.8, 3.1, and 3.1 nm at 100, 200, and 1000 kV, respectively. The maximum usable thickness at 200 kV with resolution sufficient to resolve membranes clearly was between 0.75 and 1.0 micron, depending on the magnification. Resolution at 100 kV was adequate for screening sections up to 1.0-micron thick for preparation defects prior to examination with an IVEM or HVEM.

Animals↗
PubMed1975

Scanning transmission ion microscope with a field ion source.

Experiments with a low-resolution scanning transmission ion microscope, using hydrogen ions from a field ionization source, indicate that it will be feasible by this approach to aim at high-resolution ion microscopy. Micrographs of unstained biological specimens have been obtained by critical range absorption of a 55 keV hydrogen ion beam at a resolution of 2000 A.

Animals↗
PubMed2004

Long live structural biology.

Two camps continue to evolve in the field of structural biology--a 'systems-oriented' camp, which studies proteins or complexes carefully one system at a time, and a 'discovery-oriented' one, which studies proteins of entire families, pathways or genomes. The end goals of both camps are the same: to decipher the atomic-resolution structures and mechanisms of biological macromolecules and understand them in the context of the living cell.

Biochemistry↗
PubMed2003

Preparation and X-ray crystallographic analysis of rubredoxin crystals from Desulfovibrio gigas to beyond ultra-high 0.68 A resolution.

Rubredoxin (D.g. Rd), a small non-heme iron-sulfur protein shown to function as a redox coupling protein from the sulfate reducing bacteria Desulfovibrio gigas, has been crystallized using the hanging-drop vapor diffusion method and macroseeding method. Rubredoxin crystals diffract to an ultra-high resolution 0.68 A using synchrotron radiation X-ray, and belong to the space group P2(1) with unit-cell parameters a=19.44 A, b=41.24 A, c=24.10 A, and beta=108.46 degrees. The data set of single-wavelength anomalous dispersion signal of iron in the native crystal was also collected for ab initio structure re-determination. Preliminary analysis indicates that there is one monomer with a [Fe-4S] cluster in each asymmetric unit. The crystal structure at this ultra-high resolution will reveal the details of its biological function. The crystal character and data collection strategy for ultra-high resolution will also be discussed.

Crystallography, X-Ray↗
PubMed2004

Mapping molecular landscapes inside cells.

Cryoelectron tomography opens a window into the inner space of cells. It combines the potential of three-dimensional imaging with a close-to-life preservation of biological samples. Tomograms with molecular resolution are essentially images of the cellular proteome and, in conjunction with advanced pattern recognition techniques, they can be used to map the molecular landscape inside organelles and cells.

Animals↗
PubMed1998

Reduction of charging in protein electron cryomicroscopy.

Charging causes a loss of resolution in electron cryomicroscopy with biological specimens prepared without a continuous carbon support film. Thin conductive films were deposited onto catalase crystals prepared across holes using ion-beam sputtering and thermal evaporation and evaluated for the effectiveness of charge reduction. Deposits applied by ion-beam sputtering reduced charging but concurrently resulted in structural damage. Coatings applied by thermal evaporation also reduced charging, and preserved the specimen structure beyond 5 A resolution as judged from electron diffraction patterns and images of glucose-embedded catalase crystals tilted to 45 degrees in the microscope. This study demonstrates for the first time the feasibility of obtaining high-resolution data from unstained, unsupported protein crystals with a conductive surface coating.

Catalase↗
PubMed2001

Purification of fibrinogen and virus removal using preparative electrophoresis.

The Gradiflow is a novel, scalable preparative electrophoresis technique that uses the dual characteristics of size and charge to isolate target macro- and micromolecules from complex biological solutions. It does this with high resolution and in rapid time. The mild buffers are used to assist in retaining biological activity of the isolated protein. Gradiflow technology employs a sandwich of three polyacrylamide membranes configured to allow passage of macromolecules ranging in size from 10 kDa to 1,500 kDa. Fibrinogen was isolated from cryoprecipitate 1 using a single phase process. This separation was achieved within three hours with yields of 85%. Purified fibrinogen was then characterized using biophysical characterization of fibrin clot structure and compared with clots derived from a commercially available product and human plasma. Significantly, clots developed from Gradiflow fibrinogen had characteristics closer to human plasma. Viral removal characteristics of the Gradiflow were investigated by spiking the source material (cryoprecipitate 1) with canine parvovirus and testing for its presence in the isolated fibrinogen using PCR. Parvo removal was found to be greater than 4 logs and was achieved during the purification process. The Gradiflow offers the advantage of large-scale separation of macromolecules and provides a new approach to fibrinogen separation that is quite distinct from other present-day technologies. The technology is capable of isolating protein with high purity, recovery, and functionality in combination with the removal of viruses during the purification. Furthermore, it is capable of integrating into present production systems, significantly improving yield and functionality of target molecules.

Base Sequence↗
PubMed1983

Quantitative profiling of prostaglandins and thromboxane by high-resolution gas chromatography-selected--ion monitoring.

The development and biological application of a rapid method for quantitative profiling of prostaglandins and thromboxane using high-resolution gas chromatography (HRGC) coupled with mass spectrometry in the selected-ion monitoring technique (SIM) are described. The method is based on the single-step extraction of prostaglandins from biological samples on C18 reversed-phase cartridges after addition of deuterated analogues as internal standards, followed by derivatization of functional groups and final analysis by HRGC-SIM with wall-coated open tubular persilanized capillary columns. Biological applications include the determination of endogenous arachidonic acid cascade profiles in rat tissue homogenates and thromboxane synthetase inhibition studies in human serum.

6-Ketoprostaglandin F1 alpha↗