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Results for “Biological Resolution”

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At least 703 records · Page 39Linked to original sources
PubMed1998

Atomic force microscopy: application to investigation of Escherichia coli morphology before and after exposure to cefodizime.

Atomic force microscopy (AFM) is a recently developed technique that allows for the investigation of the surface morphology of a biological specimen at an unprecedented level of resolution. The aim of the present study was to explore some of the new opportunities offered by AFM by studying the morphological and surface alterations induced in Escherichia coli by supra-MICs and sub-MICs of a beta-lactam antibiotic (cefodizime). The underlying principle of AFM is the scanning and sensing of the topography of a sample by means of near-field microscopy that makes it possible to obtain simultaneous digital measurements of the x, y, and z coordinates of any point on the bacterial surface with great resolution (x and y, approximately 20 A; z, approximately 1 A). Unlike scanning electron microscopy, performance of AFM does not require a vacuum, drying to the critical point, or the coating of the bacterial surface with a metal layer. The digital storage of the information makes it easy to rotate the image, observe the bacterial surface and induced structural alterations from different points of view, and obtain a cross-section at any desired point with precise, automatic measurement of the heights and sizes of normal versus damaged bacteria. Use of the new and outstanding technique of AFM will make it possible for researchers to investigate biological samples immersed in biological fluids and will also make it possible for them to study the morphological alterations of living bacteria exposed to antibiotics as they are taking place.

Cefotaxime↗
PubMed1993

High-resolution electron crystallography of protein molecules.

Electron diffraction data and high-resolution images can now be used to obtain accurate, three-dimensional density maps of biological macromolecules. These density maps can be interpreted by building an atomic-resolution model of the structure into the experimental density. The Cowley-Moodie formalism of dynamical diffraction theory has been used to validate the use of kinematic diffraction theory (strictly, the weak phase object approximation) in producing such 3D density maps. Further improvements in the preparation of very flat (planar) specimens and in the retention of diffraction to a resolution of 0.2 nm or better could result in electron crystallography becoming as important a technique as X-ray crystallography currently is for the field of structural molecular biology.

Crystallography↗
PubMed2005

Novel multiwavelength microscopic scanner for mouse imaging.

Real-time in vivo imaging of molecular targets at (sub)cellular resolution is essential in better understanding complex biology. Confocal microscopy and multiphoton microscopy have been used in the past to achieve this goal, but their true capabilities have often been limited by bulky optics and difficult experimental set-ups requiring exteriorized organs. We describe here the development and validation of a unique near-infrared laser scanning microscope system that uses novel optics with a millimeter footprint. Optimized for use in the far red and near-infrared ranges, the system allows an imaging depth that extends up to 500 microm from a 1.3-mm-diameter stick objective, which is up to 2 cm in length. We show exceptionally high spatial, temporal, and multiwavelength resolutions of the system and show that it can be applied to virtually any internal organ through a keyhole surgical access. We demonstrate that, when combined with novel far red imaging probes, it is possible to image the cellular details of many organs and disease processes. The new optics, coupled with the use of near-infrared probes, should prove immensely valuable for in vivo cancer imaging.

Animals↗
PubMed1995

Atomic force microscopy study of fine structures of the entire surface of red blood cells.

Glutaraldehyde-fixed red blood cells were imaged by tapping mode atomic force microscopy (TMAFM) in air at room temperature. The results show that TMAFM can visualize the morphology of the red blood cell at both cellular and nanometer scales. The scan size covers the range from several hundred nanometers to more than one hundred micrometers. TMAFM not only has a higher resolution than the optical microscope, but also can observe biological samples without precoating as required for scanning electron microscopy (SEM). The AFM images of the entire surface of an uncoated red blood cell with nanometer resolution are successfully reconstructed by 28 AFM images of the preselected subareas on the surface of the red blood cell. These images reveal directly the fine structures of the external surface of uncoated red blood cells in air. The surface exhibits a characteristic structure composed of a large number of closely-packed nanometer particles with a size ranging from a few nanometers to tens of nanometers. These "particulate" components are evenly distributed, and no jumping protrusion or depression structures were found. These particles give rise to a very smooth surface of the red blood cell as shown in a large-scan AFM image. In addition, the 28 AFM images obtained by the continuous scanning over 3 hours indicate that TMAFM can image soft biological samples such as red blood cells stably and reproducibly.

Erythrocytes↗
PubMed2003

Ultrahigh-resolution optical coherence tomography by broadband continuum generation from a photonic crystal fiber.

We have developed an ultrahigh-resolution optical coherence tomographic system in which broadband continuum generation from a photonic crystal fiber is used to produce high longitudinal resolution. Longitudinal resolution of 1.3-microm has been achieved in a biological tissue by use of continuum light from 800 to 1400 nm. The system employed a dynamic-focusing tracking method to maintain high lateral resolution over a large imaging depth. Subcellular imaging is demonstrated.

Animals↗
PubMed1997

The crystal structure of human interferon beta at 2.2-A resolution.

Type I interferons (IFNs) are helical cytokines that have diverse biological activities despite the fact that they appear to interact with the same receptor system. To achieve a better understanding of the structural basis for the different activities of alpha and beta IFNs, we have determined the crystal structure of glycosylated human IFN-beta at 2.2-A resolution by molecular replacement. The molecule adopts a fold similar to that of the previously determined structures of murine IFN-beta and human IFN-alpha2b but displays several distinct structural features. Like human IFN-alpha2b, human IFN-beta contains a zinc-binding site at the interface of the two molecules in the asymmetric unit, raising the question of functional relevance for IFN-beta dimers. However, unlike the human IFN-alpha2b dimer, in which homologous surfaces form the interface, human IFN-beta dimerizes with contact surfaces from opposite sides of the molecule. The relevance of the structure to the effects of point mutations in IFN-beta at specific exposed residues is discussed. A potential role of ligand-ligand interactions in the conformational assembly of IFN receptor components is discussed.

Computer Simulation↗
PubMed2006

Highly parallel genomic assays.

Recent developments in highly parallel genome-wide assays are transforming the study of human health and disease. High-resolution whole-genome association studies of complex diseases are finally being undertaken after much hypothesizing about their merit for finding disease loci. The availability of inexpensive high-density SNP-genotyping arrays has made this feasible. Cancer biology will also be transformed by high-resolution genomic and epigenomic analysis. In the future, most cancers might be staged by high-resolution molecular profiling rather than by gross cytological analysis. Here, we describe the key developments that enable highly parallel genomic assays.

Genome, Human↗
PubMed1980

Ultrastructural and elemental imaging of biological specimens by soft X-ray contact microscopy.

Soft X-ray contact microscopy offers a means of visualizing unstained as well as stained biological materials at better than 6 nm resolution. Unlike light and transmission electron microscopy, which rely on stains to increase specimen contrast, soft X-ray imaging is dependent upon the differential absorption of incident soft (1-10nm wavelength) X-rays by the endogenous elements within the specimen. The advantages of using soft X-rays for imaging are: 1) reduced specimen damage during exposure; 2) ability to image hydrated specimens at atmospheric pressure; 3) ability to image specimens ranging in thickness from less than 40 nm to as much as 10 microns; and 4) ability to map the elemental composition of the specimen through observation of the differential absorption of properly chosen incident x-ray wave lengths. This paper explains the principles of the image formation and demonstrates the use of soft X-ray contact microscopy with biological samples which could not readily be imaged in their natural form using conventional electron microscopy methods.

Animals↗
PubMed2004

Ultrahigh-resolution full-field optical coherence tomography.

We have developed a white-light interference microscope for ultrahigh-resolution full-field optical coherence tomography of biological media. The experimental setup is based on a Linnik-type interferometer illuminated by a tungsten halogen lamp. En face tomographic images are calculated by a combination of interferometric images recorded by a high-speed CCD camera. Spatial resolution of 1.8 microm x 0.9 microm (transverse x axial) is achieved owing to the extremely short coherence length of the source, the compensation of dispersion mismatch in the interferometer arms, and the use of relatively high-numerical-aperture microscope objectives. A shot-noise-limited detection sensitivity of 90 dB is obtained in an acquisition time per image of 4 s. Subcellular-level images of plant, animal, and human tissues are presented.

Animals↗
PubMed2006

Automated interpretation of subcellular patterns in fluorescence microscope images for location proteomics.

Proteomics, the large scale identification and characterization of many or all proteins expressed in a given cell type, has become a major area of biological research. In addition to information on protein sequence, structure and expression levels, knowledge of a protein's subcellular location is essential to a complete understanding of its functions. Currently, subcellular location patterns are routinely determined by visual inspection of fluorescence microscope images. We review here research aimed at creating systems for automated, systematic determination of location. These employ numerical feature extraction from images, feature reduction to identify the most useful features, and various supervised learning (classification) and unsupervised learning (clustering) methods. These methods have been shown to perform significantly better than human interpretation of the same images. When coupled with technologies for tagging large numbers of proteins and high-throughput microscope systems, the computational methods reviewed here enable the new subfield of location proteomics. This subfield will make critical contributions in two related areas. First, it will provide structured, high-resolution information on location to enable Systems Biology efforts to simulate cell behavior from the gene level on up. Second, it will provide tools for Cytomics projects aimed at characterizing the behaviors of all cell types before, during, and after the onset of various diseases.

Animals↗
PubMed2005

Eccentric perception of biological motion is unscalably poor.

Accurately perceiving the activities of other people is a crucially important social skill of obvious survival value. Human vision is equipped with highly sensitive mechanisms for recognizing activities performed by others [Johansson, G. (1973). Visual perception of biological motion and a model for its analysis. Perception and Psychophysics, 14, 201; Johansson, G. (1976). Spatio-temporal differentiation and integration in visual motion perception: An experimental and theoretical analysis of calculus-like functions in visual data processing. Psychological Research, 38, 379]. One putative functional role of biological motion perception is to register the presence of biological events anywhere within the visual field, not just within central vision. To assess the salience of biological motion throughout the visual field, we compared the detectability performances of biological motion animations imaged in central vision and in peripheral vision. To compensate for the poorer spatial resolution within the periphery, we spatially magnified the motion tokens defining biological motion. Normal and scrambled biological motion sequences were embedded in motion noise and presented in two successively viewed intervals on each trial (2AFC). Subjects indicated which of the two intervals contained normal biological motion. A staircase procedure varied the number of noise dots to produce a criterion level of discrimination performance. For both foveal and peripheral viewing, performance increased but saturated with stimulus size. Foveal and peripheral performance could not be equated by any magnitude of size scaling. Moreover, the inversion effect--superiority of upright over inverted biological motion [Sumi, S. (1984). Upside-down presentation of the Johansson moving light-spot pattern. Perception, 13, 283]--was found only when animations were viewed within the central visual field. Evidently the neural resource responsible for biological motion perception are embodied within neural mechanisms focused on central vision.

Discrimination, Psychological↗
PubMed2006

A temporal framework for understanding the effects of stressful life events on inflammation in patients with multiple sclerosis.

A growing literature reports that stressful life events are associated with exacerbation and the subsequent development of brain lesions in patients with multiple sclerosis (MS). The evolution an MS exacerbation occurs over a period of many months and involves many different biological processes that change over time. Likewise, the experience of stress also occurs over time, with an onset, a shift from acute to chronic in some cases, and resolution. Each of these phases is associated with unique biological features. Thus, the impact of stress on MS exacerbation may depend on the temporal trajectories of stress and MS exacerbation, and when the intersection between these two trajectories occurs. This paper presents a temporal model, along with three different temporal relationships and associated mechanisms by which stress may impact MS exacerbation. These include the onset of a stressor, which may be mediated by mast cell activation, the point that a stressor begins to become chronic, which may be mediated by glucocorticoid resistance in immune cells, and the resolution of the stressor, which may be mediated by a drop in cortisol. These three hypotheses are not necessarily mutually exclusive. Data on psychosocial mediators and moderators are also briefly reviewed and future research directions are discussed.

Acute Disease↗
PubMed2003

Proteins from bovine tissues and biological fluids: defining a reference electrophoresis map for liver, kidney, muscle, plasma and red blood cells.

A number of high resolution two-dimensional electrophoresis (2-DE) reference maps for bovine tissues and biological fluids have been determined for animals in basal state. Among the 1863 distinct protein features detected in samples of liver, kidney, muscle, plasma and red blood cells, 509 species were identified and associated to 209 different genes. Difficulties in the identification were related to the poorly characterized Bos taurus genome and were solved by a combined matrix-assisted laser desorption/ionisation-mass spectrometry and liquid chromatography-electrospray ionization tandem mass spectrometry approach. The experimental output allowed us to establish a 2-DE database accessible through the World Wide Web network at the URL address (http://www.iabbam.na.cnr.it/Biochem). These reference maps may serve as a tool in future veterinary medical studies aimed at the evaluation of changes in protein repertoire for altered animal physiological conditions and infectious diseases, to the definition of molecular markers for novel diagnostic kits and vaccines, as well as the characterization of protein modifications in bovine materials following technological processes used in the food industry.

Animals↗
PubMed2002

Use of structure comparison methods for the refinement of protein structure predictions. I. Identifying the structural family of a protein from low-resolution models.

Predicting the three-dimensional structure of proteins is still one of the most challenging problems in molecular biology. Despite its difficulty, several investigators have started to produce consistently low-resolution predictions for small proteins. However, in most of these cases, the prediction accuracy is still too low to make them useful. In the present article, we address the problem of obtaining better-quality predictions, starting from low-resolution models. To this end, we have devised a new procedure that uses these models, together with structure comparison methods, to identify the structural family of the target protein. This would allow, in a second step not described in the present work, to refine the predictions using conserved features of the identified family. In our approach, the structure database is investigated using predictions, at different accuracy levels, for a given protein. As query structures, we used both low-resolution versions of the native structures, as well as different sets of low accuracy predictions. In general, we found that for predictions with a resolution of > or =5-7 A, structure comparison methods were able to identify the fold of a protein in the top positions.

Databases, Protein↗
PubMed2006

Nonequilibrium self-assembly of linear fibers: microscopic treatment of growth, decay, catastrophe and rescue.

Many of the large structures of cells are constructed from fibers. These fibers self-assemble from individual proteins in a far-from-equilibrium fashion. Nonequilibrium self-assembly results in a highly dynamic process at the subcellular level that can be regulated and tuned to carry out many of the biological functions of the cell: growth, division and locomotion. We construct and analyze a nonequilibrium model of the dynamic end of a biological fiber that possesses site-resolved resolution. We solve for the steady states of this nonequilibrium system using a variational method. The results are compared to exact numerical solutions for systems with modest size. Using an effective reaction coordinate, we construct an effective potential from the steady-state distribution. The stochastic transitions of the system can be analyzed in this representation. We then apply this method to model microtubule systems. Predictions for macroscopic catastrophe, rescue and dynamic instability in the steady states are analyzed. We find that the length of the cap of the microtubule is small. The relations between the catastrophe/rescue rate and the growth rate are also discussed.

Cell Physiological Phenomena↗
PubMed1977

Transmission microscropy of unmodified biological materials: comparative radiation dosages with electrons and ultrasoft x-ray photons.

The minimum radiation dosage in a specimen consistent with transmission microscopy at resolution d and specimen thickness t is calculated for model specimens resembling biological materials in their natural state. The calculations cover 10(4)-10(7) eV electrons and 1.3-90 A photons in a number of microscopy modes. The results indicate that over a considerable part of the (t,d)-plane transmission microscopy on such specimens can be carried out at lower dosage with photons than with electrons. Estimates of the maximum resolutions obtainable with electrons and photons, consistent with structural survival of the specimen, are obtained, as are data on optimal operating conditions for microscopy with the two particles.

Air↗
PubMed1996

Applications of laser microprobe mass spectrometry in biology and medicine.

Laser microprobe mass spectrometry (LMMS) provides spot analysis with a lateral resolution of 1-5 microns. Focused laser ionisation, combined with mass spectrometry, yields information on elements, molecular identification of inorganic substances, and structural characterisation of organic molecules of typically less than 2-3 kDa. Quantification in complex heterogeneous systems, such as biological materials, is not possible at the present state of the art. The strength of the method lies in the qualitative information on the molecular composition of the analyte, not just element detection, with a lateral resolution at the light microscopy level. The applications of this technique in the field of biomedicine and biology are illustrated by examples that demonstrate the use of this qualitative information in practical test cases.

Fourier Analysis↗
PubMed2025

ORCO: Ollivier-Ricci Curvature-Omics-an unsupervised method for analyzing robustness in biological systems.

MOTIVATION: Although recent advanced sequencing technologies have improved the resolution of genomic and proteomic data to better characterize molecular phenotypes, efficient computational tools to analyze and interpret large-scale omic data are still needed. RESULTS: To address this, we have developed a network-based bioinformatic tool called Ollivier-Ricci curvature for omics (ORCO). ORCO incorporates omics data and a network describing biological relationships between the genes or proteins and computes Ollivier-Ricci curvature (ORC) values for individual interactions. ORC is an edge-based measure that assesses network robustness. It captures functional cooperation in gene signaling using a consistent information-passing measure, which can help investigators identify therapeutic targets and key regulatory modules in biological systems. ORC has identified novel insights in multiple cancer types using genomic data and in neurodevelopmental disorders using brain imaging data. This tool is applicable to any data that can be represented as a network. AVAILABILITY AND IMPLEMENTATION: ORCO is an open-source Python package and is publicly available on GitHub at https://github.com/aksimhal/ORC-Omics.

Software↗