Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Biological Resolution”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 415 records · Page 23Linked to original sources
PubMed2002

Phage genomics: small is beautiful.

The Age of Genomics dawned only gradually for bacteriophages. It was 1977 when the genome of phage phi X174 was published and 1983 when the "large" genome of phage lambda hit the streets. More recently, the pace has quickened, so that we now have over 100 complete phage genomes and can expect thousands in a very few years. These sequences have been marvelously informative for the biology of the individual phages, but with the advent of high volume sequencing technology, the real excitement for phage biology is that it is now possible to analyze the sequences together and thereby address--for the first time at whole genome resolution--a set of fundamental biological questions related to populations: What is the structure of the global phage population? What are its dynamics? How do phages evolve? This is Comparative Genomics with a capital "C".

Bacteriophages↗
PubMed2005

Towards an inline reconstruction architecture for micro-CT systems.

Recent developments in micro-CT have revolutionized the ability to examine in vivo living experimental animal models such as mouse with a spatial resolution less than 50 microm. The main requirements of in vivo imaging for biological researchers are a good spatial resolution, a low dose induced to the animal during the full examination and a reduced acquisition and reconstruction time for screening purposes. We introduce inline acquisition and reconstruction architecture to obtain in real time the 3D attenuation map of the animal fulfilling the three previous requirements. The micro-CT system is based on commercially available x-ray detector and micro-focus x-ray source. The reconstruction architecture is based on a cluster of PCs where a dedicated communication scheme combining serial and parallel treatments is implemented. In order to obtain high performance transmission rate between the detector and the reconstruction architecture, a dedicated data acquisition system is also developed. With the proposed solution, the time required to filter and backproject a projection of 2048 x 2048 pixels inside a volume of 140 mega voxels using the Feldkamp algorithm is similar to 500 ms, the time needed to acquire the same projection.

Algorithms↗
PubMedDate not supplied

[Problems associated with chronological age estimation of children exploited in child pornography production].

Chronological age assessment of young persons featuring in pornographic pictures and videos is crucial to prove a violation of law. The paper discusses possibilities of and difficulties inherent in age estimation in cases of production and distribution of child pornography. The presented problems were divided into technical and individual development-associated issues. Technical difficulties included lack of a reference system for biological features reconstruction, poor quality and resolution of pictures or movies, pictures retouching and photomontage. The author stressed that biological hindrances in age assessment were the consequences of interpersonal variation of developmental patterns, namely overlapping of ranges typical for feature values at particular ages and biological variations between different human populations. The described problems can render age estimation impossible or far from precise. Developing more accurate methods of estimating age from pictures and videos requires the collaboration of specialists in the field of auxology, anthropology, pediatrics, as well as experts in photography and video techniques.

Age Factors↗
PubMed2004

Improvement of low-level light imaging performance using optical clearing method.

Low-level light-emitting imaging technique often detects the light emerged at the tissue surface that is generated internally from a specific target. However, in most cases, the high scattering nature of biological tissue limits the sensitivity and spatial resolution of this imaging modality. In this paper, we report that a significant improvement of chemiluminescence (CL) imaging performance in terms of both sensitivity and spatial resolution can be achieved by use of the topical application of glycerol solution onto tissue sample, i.e. optical clearing approach. Monte Carlo (MC) simulation of internally-launched point source shows that the decrease of scattering coefficient of turbid medium, which can be achieved by optical tissue clearing approach, causes stronger peak intensity with a narrower full-width at half-maximum (FWHM). The improvement becomes more significant with the source depth increasing from 1 to 5 mm. The experimental results shows that tissue clearing with 50% glycerol solution could largely improve the brightness and the spatial resolution of CL imaging when the target is covered by biological tissue with a thickness of either 1 or 3mm. This method could have potential applications for the in vivo low-level light imaging techniques.

Algorithms↗
PubMed2005

Fluorescence microscopy today.

Fluorescence microscopy has undergone a renaissance in the last decade. The introduction of green fluorescent protein (GFP) and two-photon microscopy has allowed systematic imaging studies of protein localization in living cells and of the structure and function of living tissues. The impact of these and other new imaging methods in biophysics, neuroscience, and developmental and cell biology has been remarkable. Further advances in fluorophore design, molecular biological tools and nonlinear and hyper-resolution microscopies are poised to profoundly transform many fields of biological research.

Animals↗
PubMed2004

[Atomic force microscopy: from cell imaging to molecular manipulation].

The atomic force microscope (AFM) allows to explore the surface of biological samples bathed in physiological solutions, with vertical and horizontal resolutions ranging from nanometers to angströms. Complex biological structures as well as single molecules can be observed and recent examples of the possibilities offered by the AFM in the imaging of intact cells, isolated membranes, membrane model systems and single molecules are discussed in this review. Applications where the AFM tip is used as a nanotool to manipulate biomolecules and to determine intra and intermolecular forces from single molecules are also presented.

Animals↗
PubMed2004

Chemoenzymatic synthesis of (S) and (R)-propranolol and sotalol employing one-pot lipase resolution protocol.

Synthesis of both enantiomers of biologically active propranolol and sotalol has been achieved in high optical purity by one-pot reduction of 3 and 7 followed by in situ lipase resolution of the respective chlorohydrins. Pseudomonas cepacia lipase immobilized on ceramic particles (PS-C) provided the chlorohydrin and acetate, which on nucleophilic substitution with isopropyl amine afforded the target amino alcohols in high enantioselectivity under mild reaction conditions.

Lipase↗
PubMed2005

Progress in analytical imaging of the cell by dynamic secondary ion mass spectrometry (SIMS microscopy).

This paper reviews the most recent methodological advances in the field of biological imaging using dynamic secondary ion mass spectrometry (SIMS). After a short reminder of the basic principle of SIMS imaging, the latest high-resolution dynamic SIMS equipment is briefly described. This new ion nanoprobe (CAMECA NanoSIMS 50) has a lateral resolution of less than 50 nm with primary Cs+ ion, the ability to detect simultaneously 5 different ions from the same micro-volume and a very good transmission even at high mass resolution (60% at M/DeltaM=5000). Basic considerations related to sample preparation, mass resolution and primary ion implantation are given. The decisive capability of this new instrument, and more generally of high-resolution dynamic SIMS imaging in biology, are illustrated with the most recent examples of utilization.

Animals↗
PubMed2004

Hydrogen and hydration in proteins.

Neutron diffraction provides an experimental method of directly locating hydrogen atoms in proteins. High-resolution neutron diffractometers dedicated to biological macromolecules (BIX-type diffractometer) have been constructed at the Japan Atomic Energy Research Institute and they have been used in the 1.5A-resolution crystal structure analyses of several proteins. Interesting topics relevant to hydrogen and hydration in proteins, such as (1) the detailed geometry of hydrogen bonds; (2) information regarding hydrogen/deuterium exchange behavior; (3) the acidities of certain H atoms; (4) the role of hydrogen atoms in enzyme mechanisms and thermostability; (5) the location methyl hydrogen atoms; and (6) dynamical behavior of hydration structures that include H positions have been extracted from these structural results. In addition, a method for the systematic growth of large single crystals based on phase diagrams has been introduced and will be briefly described in this article.

Crystallization↗
PubMed2006

Accurate mass filtering of ion chromatograms for metabolite identification using a unit mass resolution liquid chromatography/mass spectrometry system.

Acceleration of liquid chromatography/mass spectrometric (LC/MS) analysis for metabolite identification critically relies on effective data processing since the rate of data acquisition is much faster than the rate of data mining. The rapid and accurate identification of metabolite peaks from complex LC/MS data is a key component to speeding up the process. Current approaches routinely use selected ion chromatograms that can suffer severely from matrix effects. This paper describes a new method to automatically extract and filter metabolite-related information from LC/MS data obtained at unit mass resolution in the presence of complex biological matrices. This approach is illustrated by LC/MS analysis of the metabolites of verapamil from a rat microsome incubation spiked with biological matrix (bile). MS data were acquired in profile mode on a unit mass resolution triple-quadrupole instrument, externally calibrated using a unique procedure that corrects for both mass axis and mass spectral peak shape to facilitate metabolite identification with high mass accuracy. Through the double-filtering effects of accurate mass and isotope profile, conventional extracted ion chromatograms corresponding to the parent drug (verapamil at m/z 455), demethylated verapamil (m/z 441), and dealkylated verapamil (m/z 291), that contained substantial false-positive peaks, were simplified into chromatograms that are substantially free from matrix interferences. These filtered chromatograms approach what would have been obtained by using a radioactivity detector to detect radio-labeled metabolites of interest.

Animals↗
PubMed1988

Studies on the crystal structure of A1-(L-tryptophan) insulin at 2.1 A resolution.

In order to study the biological effect of alterations to the N-terminus of the insulin A-chain, we have determined the crystal structure of A1-(L-Trp) insulin and discovered that it belongs to the trigonal system with space group R3. The parameters of the unit cell are a = b = 80.3A, c = 37.5A. The model was adjusted and refined by using a stereochemically-restrained least squares program, assisted by manual revision of the model based on the difference Fourier map, to a final R-factor of 0.195. The main and side chains of both A1-(L-Trp) residues in the asymmetric unit are well ordered. It was found that the A1-Trp residue of molecule I occupied two distinct positions. We have proposed from the results of the three-dimensional structure that the 4-zinc insulin hexameric form is a stored state of insulin molecules in a conformation of low activity. The structural details of the insulin molecule and its structure and function relationship have also been discussed.

Insulin↗
PubMed1992

Preservation and visualization of molecular structure in detergent-extracted whole mounts of cultured cells.

Today's electron microscopes have a resolution sufficient to resolve supramolecular structures. However, the methods used to prepare biological samples for electron microscopy often limit our ability to achieve the resolution that is theoretically possible. We use whole mounts of detergent-extracted cells grown on Formvar-coated gold grids as a model system to evaluate various steps in the preparation of biological samples for high resolution scanning electron microscopy (SEM). Factors that are important in determining the structure and composition of detergent-extracted cells include the nature of the detergent and the composition of the extraction vehicle. Chelation of calcium is extremely important to stabilize and preserve the cytoskeletal filaments. We have also demonstrated both morphologically and by gel electrophoresis that treatment of cells with bifunctional protein crosslinkers before or during extraction with detergent can significantly enhance the preservation of both proteins and supramolecular structures. The methods used to dry samples are a major determinant of the quality of structural preservation. For cytoskeletons freeze-drying (FD) is superior to critical point-drying (CPD), one reason being that CPD samples have to be dehydrated, thereby causing more shrinkage as compared to FD samples. The high pressures to which samples are exposed during CPD may also cause increased shrinkage, and water contamination during CPD causes severe structural damage. We have obtained the best structural preservation of detergent-extracted and fixed cells by manually plunging them into liquid propane and drying over night in a freeze-dryer. The factor that most limits achievement of high resolution in SEM is the metal coat, which has to be very thin, uniform, and free of grain in order not to hide structures or to create artifactual ones. We have found that sputter-coating with 1-3 nm of tungsten (W) or niobium (Nb) gives extremely fine-grained films as well as satisfactory emission of secondary electrons. These samples can also be examined at high resolution by transmission electron microscopy (TEM) and scanning transmission electron microscopy (STEM). The best preservation and visualization of supramolecular structures have been obtained using cryosputtering, in which the samples are freeze-dried and then sputter-coated within the freeze-dryer while still frozen.

Animals↗
PubMed1995

A technical problem in the calculation of laminar flow near irregular surfaces described by sampled geometric data.

The numerical simulation of fluid flow and transport near biological surfaces must take into account the natural irregularity of these surfaces if the influence of the surface geometry on the near-wall flow field is to be modeled. If the geometric description of a biological surface has a limited resolution, what impact will this have on the accuracy of a computational simulation of the near-wall flow field? It is important to emphasize here that the problem arises from the limited number of data points describing the geometry and not from any limit on the number of mesh points in any subsequent calculation. In this note we show that if every point in a geometric data set describing an axisymmetric model of a diseased coronary artery is taken as a mesh point, then a well converged and otherwise accurately calculated wall shear stress distribution contains a degree of uncertainty which is attributable wholly to the limited resolution of the original geometric model. The approach taken is to repeat the numerical calculation on a reduced resolution version of the original geometric data set, comparing the wall shear stress distribution with that obtained originally. We conclude that accurate computational modeling and simulation of transport processes near irregular biological surfaces will be highly dependent on the availability of well-resolved geometric data describing the surface under study.

Blood Pressure↗
PubMed1997

The development of field-emission scanning electron microscopy for imaging biological surfaces.

This article traces the important milestones in the development of high-resolution, field-emission, scanning electron microscopes (SEM). Such instruments are now capable of producing images of the surfaces of biological specimens that rival, in terms of resolution and contrast, those produced by conventional transmission electron microscopy (TEM). Even though one of the first instruments to produce a useful transmission electron microscope image was, in fact, an early scanning microscope, TEM reached its full potential for biological imaging almost 30 years sooner than did SEM. The main reason for this slow rate of development is the dependence of any scanning technique on source brightness. The only suitable electron source was the field-emission source, originally developed in the 1930's. Making this into a stable and reliable electron source for microscopy required many technical barriers to be overcome. An additional delay may have been caused by the great success that attended the introduction of early SEM instruments. These instruments which employed heated, tungsten hairpin cathodes, were inexpensive and reliable, but they that were also far from optimal in terms of optical performance. Their market success may have engendered the sense of inertia and complacency that further delayed the introduction of low aberrations objective lenses and field-emission sources for almost 20 years after they were first introduced to electron microscopy. In addition, the fact that these early SEMs accustomed users to operating with a much higher beam voltage than was either necessary or wise, lead many to assume that the SEM was incapable of producing high-resolution images of biological surfaces. This left them open to fascination with newer ahd slower techniques that, on balance, were less suitable than optimized SEM for most of their imaging needs. In parallel to these developments in instrumentation, major improvements were also made in the way that the specimen surface was prepared before placing it into the vacuum and radiation environment of the microscope.

Cell Membrane↗
PubMed1999

Electrochemical monitoring of biogenic amine neurotransmission in real time.

Three techniques, constant-potential amperometry, high-speed chronoamperometry, and fast-scan cyclic voltammetry, have been used extensively to investigate the rapid events associated with neurotransmission. These techniques vary in sensitivity, chemical resolution and temporal resolution. Amperometry provides the best temporal resolution but little chemical resolution. Fast-scan cyclic voltammetry provides both good temporal and chemical resolution, while high-speed chronoamperometry offers good temporal resolution and moderate chemical resolution. The amount of chemical information which is needed for a neurochemical measurement depends upon the sample. For single cells, secondary methods, such as HPLC and capillary electrophoresis, offer extensive chemical information about the contents of a cell. With this information, chemical information is not needed during the electrochemical measurement. Therefore, amperometry is employed to obtain the greatest temporal resolution. However, when using more complex biological samples, such as brain slices or in vivo implantation, there is a greater demand for chemical resolution provided by the electrochemical measurement. To bolster results, further confirmation is sought from anatomical, physiological and pharmaceutical evidence. Within this review, the three electrochemical techniques are outlined and compared. Examples are then provided of measurements which have been made in the three predominant biological samples which have been studied: single cells, brain slices and intact animals.

Animals↗
PubMed1992

[1H, 13C 15N and 31P NMR spectroscopy of plant seeds: possible applications].

We review here the recent achievements in high resolution NMR spectroscopy of four biologically most important nuclei (1H, 13C, 15N, 31P) applied on plant seeds in vivo or on extracts from the same tissue. Most often used nuclei in NMR analysis of seeds were protons (1H). The application of low resolution NMR for nondestructive analysis of moisture and oil in seeds had a long history--this was actually the only true nondestructive chemical analysis of genetic material. The combination of high resolution 1H NMR with magic angle sample spinning (MAS) enabled some authors to obtain a method for in vivo study of fatty acids composition of seed lipids. A promising technique for in vivo studies of biochemical composition and physiological processes in seeds is 13C NMR, particularly 1H-13C cross-polarization NMR combined with MAS technique. This enabled analysis of lipids in intact seeds, but also obtaining of high resolution spectra from the solid components of the seed matrix (starch, sugars, proteins). An interesting application of 13C NMR was monitoring the biochemical events following seed germination in vivo. Low natural ability of the NMR accessible 15N nucleus restricts the application of 15N NMR for in vivo seed analysis. Nevertheless, some sophisticated experiments combining double cross-polarization 15N/13C with the MAS technique were reviewed. 31P NMR is a promising technique in biological studies. Some recent achievements included detection of energetically important molecules of cells (ADP; ATP, oligosaccharides) as well as compartmentation of the inorganic phosphate (cytoplasmic, vacuolar). There were some indications of the studies made on intact seeds, but most of the 31P NMR work has been done on the extracts from seed material.

Magnetic Resonance Spectroscopy↗
PubMed1993

Glucose alone does not completely hydrate bacteriorhodopsin in glucose-embedded purple membrane.

Glucose embedding is a simple and highly effective method for preparing biological macromolecules for high-resolution electron microscopy. The investigation of conditions that can trap the M-state intermediate in the bacteriorhodopsin (bR) photocycle has revealed, however, that when glucose-embedded bR is prepared at ambient humidity, it does not fully retain the capability to execute a proper photocycle. However, 'native' photocycle properties are returned after glucose-embedded samples are equilibrated at 81% relative humidity. Equilibration at relative humidities significantly higher than 81% causes glucose to dissolve in its own water of hydration, resulting in samples that may be too thick to be suitable for electron microscopy. The results obtained with bR indicate that caution should be taken with other biological specimens, and it cannot be assumed that glucose-embedded biological macromolecules retain completely their native, hydrated structure, even when high-resolution electron diffraction patterns are obtained. Equilibration of such samples at high humidity may generally be a worthwhile precaution when using the glucose-embedding technique.

Bacteriorhodopsins↗
PubMedDate not supplied

Dynamic force microscopy imaging of native membranes.

We employed magnetic ACmode atomic force microscopy (MACmode AFM) as a novel dynamic force microscopy method to image surfaces of biological membranes in their native environments. The lateral resolution achieved under optimized imaging conditions was in the nanometer range, even when the sample was only weakly attached to the support. Purple membranes (PM) from Halobacterium salinarum were used as a test standard for topographical imaging. The hexagonal arrangement of the bacteriorhodopsin trimers on the cytoplasmic side of PM was resolved with 1.5nm lateral accuracy, a resolution similar to images obtained in contact and tapping-mode AFM. Human rhinovirus 2 (HRV2) particles were attached to mica surfaces via nonspecific interactions. The capsid structure and 2nm sized protein loops of HRV2 were routinely obtained without any displacement of the virus. Globular and filamentous structures on living and fixed endothelial cells were observed with a resolution of 5-20nm. These examples show that MACmode AFM is a favorable method in studying the topography of soft and weakly attached biological samples with high resolution under physiological conditions.

Capsid↗