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At least 289 records · Page 16Linked to original sources
PubMed1986

Vernier acuity in the cat: its relation to hyperacuity.

Vernier thresholds were measured behaviourally in five cats using offsets in gratings of two spatial frequencies and in single lines. Thresholds ranged from 2.2 to 6.7', and no threshold differences were found across stimuli. These results are discussed in relationships with published spatial resolution data and are related to the optical and neural characteristics of the cat's visual system. It is concluded that if vernier acuity is a hyperacuity in cats, the improvement in grain is not of the same magnitude as it is in humans.

Animals↗
PubMed1989

The application of the maximum entropy method to electron microscopic tomography.

The maximum entropy method has been applied to single axis tilt electron microscopic tomography. Its application requires that the problem be correctly formulated and that the model for the noise in electron micrographs be developed. A suitable noise model was determined empirically. The maximum entropy method was applied to a reconstruction of a test object from projections to which noise had been added. These reconstructions were superior to those obtained by reciprocal space weighted back protection. The method was also robust towards the incorrect specification of the noise, the penalty being an increase in the time required for convergence rather than degradation of the quality of the reconstructed image. In the reconstruction of negatively stained chromatin fibres it was possible to obtain satisfactory images utilizing all the information in the projections, in contrast to conventional methods in which high resolution data are removed by the application of Fourier space filters.

Algorithms↗
PubMed1987

Electron-impact mass spectrometry of diuretic agents.

The mass spectrometric behaviour of nineteen diuretic agents in clinical use under conditions of 70 eV electron impact is analysed from reported and novel mass spectra. The molecular compositions of fragment ions are supported by high resolution data in selected cases, and a scheme presented for the rapid identification by MS of diuretics within the group.

Journal Article↗
PubMed1992

Cryo-electron microscopy of vitrified muscle samples.

A great deal of information on the 3-dimensional structure of the protein assemblies involved in muscle contraction has been obtained using conventional transmission electron microscopy. In recent years, developments in cryo-electron microscopy have facilitated work with fully hydrated, non-chemically fixed specimens. It is shown how this technique can be used to visualize muscle sarcomere filaments in quasi-native conditions, to access hitherto inaccessible states of the crossbridge cycle, and to obtain new high resolution structural information on their 3-dimensional protein structure. A short introduction to the crossbridge cycle and its biochemically accessible states illustrates the problems amenable to studies using the electron microscope, as well as the possibilities offered by cryo-microscopy on vitrified samples. Work on vitrified cryo-sections and myosin filament suspensions demonstrates the accessibility of crossbridge states and gives implications on the gross structural features of myosin filaments. Recent studies on actin filaments and myosin (S1) decorated actin filaments provide the first high resolution data on vitrified samples. The use of photolabile nucleotide precursors allows the trapping of short lived states in the millisecond time range, thereby visualizing intermediate states of the crossbridge cycle.

Animals↗
PubMed2006

High pressure macromolecular crystallography: the 140-MPa crystal structure at 2.3 A resolution of urate oxidase, a 135-kDa tetrameric assembly.

We report the three-dimensional structure determined by high-pressure macromolecular crystallography (HPMX) of a 135-kDa homo-tetrameric enzyme, urate oxidase from Aspergillus flavus complexed with its potent inhibitor 8-azaxanthin. Urate oxidase crystals are quite sensitive to pressure, as three-dimensional order is lost at about 180 MPa. A highly complete 2.3 A resolution data set was collected at 140 MPa, close to the critical pressure. Crystal structures at atmospheric pressure and at high pressure were refined in the orthorhombic space group I222 with final crystallographic R factors 14.1% and 16.1%, respectively. The effect of pressure on temperature factors, ordered water molecules, hydrogen bond lengths, contacts, buried surface areas as well as cavity volume was investigated. Results suggest that the onset of disruption of the tetrameric assembly by pressure has been captured in the crystalline state.

Aspergillus flavus↗
PubMed2005

Immunohistochemical study of p47Phox and gp91Phox distributions in rat brain.

NADPH oxidase is multi-component enzyme, which comprises the cytosolic proteins p40Phox, p47Phox, and p67Phox and the two membrane proteins, gp91Phox and p22Phox, and which is well characterized in phagocytic cells. NADPH oxidase is a primary source of reactive oxygen species (ROS), and recent studies indicate that free radicals and ROS might be causative factors of several brain degenerative diseases and dysfunctions. However, though previous studies have shown the presence of NADPH oxidase subunits in cell culture and mouse brain, they have not provided detailed high power resolution data. Therefore, we investigated the distributions of the p47Phox and gp91Phox subunits in rat brain using immunohistochemical approach. Cortex, hippocampus, and Purkinje cells of cerebellum were prominently stained by p47Phox and gp91Phox antibodies. As compared with the distributions of p47Phox, gp91Phox in mouse, some differences in the rat brain were observed in the hippocampus, thalamus, amygdala, reticular nucleus, and basal ganglia. Additionally, at the cellular level, most p47Phox immunoreactivity was largely confined to cell bodies and proximal portions of the dendritic tree. Taken together, the widespread observed distributions of p47Phox and gp91Phox subunits indicate that they are probably needed to maintain normal brain function.

Animals↗
PubMed2006

Discrimination between sediment and soil samples for forensic purposes using elemental data: an investigation of particle size effects.

This paper reports the results of an investigation to quantify variations in elemental concentrations amongst different particle size fractions obtained from a suite of sediment samples collected from the River Avon, UK. Concentrations of 49 elements determined by inductively coupled plasma spectrometry (ICP-AES and ICP-MS) were compared using conventional and multivariate statistical methods in order to assess compositional differences between different size fractions and between different samples. The results showed significant differences between different size fractions and the bulk sediments, but indicated that all of the size fractions considered (<150, 63-150, 20-63 and <20microm) provided an adequate basis on which to identify associations and differences between samples. It was concluded that, while in certain specific circumstances it may be most appropriate to make forensic comparisons based on a very narrowly defined particle size range, for the majority of purposes the <150microm fraction provides the best compromise between sample size requirements and data resolution.

Cluster Analysis↗
PubMed2026

Multiscale Modeling Primer: Focus on Chromatin and Epigenetics.

A central challenge in modern biology is to understand how molecular interactions produce cellular and organismal functions across vast spatiotemporal scales. Nowhere is this challenge more apparent than in the study of chromatin, where meters of DNA compact into a micron-sized nucleus. How this polymer folds is a dynamic process, regulated by epigenetic modifications-chemical changes to DNA and histones that involve only a handful of atoms. These small changes cooperate to produce emergent, higher-order structures that define cellular identity and function. To explain this system, we must integrate static, high-resolution snapshots from techniques like cryo-EM with dynamic, lower-resolution data from microscopy and genomics. Multiscale computational models are essential tools that bridge these experimental gaps and reveal the mechanisms of emergent behavior. However, the communication divide between experimental biologists and quantitative modelers often hampers progress. This primer addresses that gap. It first introduces the fundamental biology of chromatin and epigenetics at an introductory level for non-biologists audiences. We then survey the landscape of computational approaches, from atomistic to systems-level models, and connect them to the experimental data that inform and validate them at an introductory level for non-computationalists. We argue that the next frontier will require us to build integrative models that can predict how molecular perturbations mechanistically alter cellular phenotypes, which will open a new era of chromatin-targeted therapeutics.

Chromatin Dynamics↗
PubMed2004

Crystal structure of aspartic proteinase from Irpex lacteus in complex with inhibitor pepstatin.

The crystal structure of Irpex lacteus aspartic proteinase (ILAP) in complex with pepstatin (a six amino acid residue peptide-like inhibitor) was determined at 1.3A resolution. ILAP is a pepsin-like enzyme, widely distributed in nature, with high milk-clotting activity relative to proteolytic activity. The overall structure was in good topological agreement with pepsin and other aspartic proteases. The structure and interaction pattern around the catalytic site were conserved, in agreement with the other aspartic proteinase/inhibitor complex structures reported previously. The high-resolution data also supported the transition state model, as proposed previously for the catalytic mechanism of aspartic proteinase. Unlike the other aspartic proteinases, ILAP was found to require hydrophobic residues either in the P(1) or P(1') site, and also in the P(4) and/or P(3) site(s) for secondary interactions. The inhibitor complex structure also revealed the substrate binding mechanism of ILAP at the P(3) and P(4) site of the substrate, where the inserted loop built up the unique hydrophobic pocket at the P(4) site.

Amino Acid Sequence↗
PubMed2006

Microdialysis coupled on-line to capillary liquid chromatography with tandem mass spectrometry for monitoring acetylcholine in vivo.

Capillary liquid chromatography-mass spectrometry (cLC-MS) was coupled on-line to microdialysis sampling to monitor endogenous acetylcholine (ACh) from the rodent brain. In vivo microdialysate sampled at 0.6 microL/min from the striatum of ketamine or chloral hydrate anesthetized rats was loaded onto a sample loop and then injected onto a approximately 5 cm long strong cation exchange (SCX) capillary column. A step gradient was used to separate the analyte from ionization suppressing salts contained in dialysate in 2.4 min. Sampling coupled on-line with cLC-MS allowed for high temporal resolution (data points at 2.4 min intervals), good reproducibility (10-15% relative standard deviation, R.S.D.), and sensitive limits of detection (0.04 nM or 8 amol injected). The method successfully monitored basal and stimulated levels (induced by increased K+ concentrations) of ACh from the anesthetized rat without necessitating perfusion of an acetylcholinesterase (AChE) inhibitor. Absolute and percent basal levels of ACh from rats receiving different anesthetics were also compared.

Acetylcholine↗
PubMed2026

Digital pathology, image analysis, and artificial intelligence in liver disease.

Advances in digital pathology, image analysis, and artificial intelligence (AI) are rapidly transforming how pathologists and researchers interact with tissue samples and enable the development of diagnostic tools that harness high-resolution whole-slide images; these advances are in turn creating new opportunities for research, education, and routine clinical care globally. Liver disease is no exception, and digital pathology and AI have many applications in the diagnosis of liver cancer and liver diseases and in the assessment and management of transplantation. Although quantitative image analysis techniques have been applied to liver disease in research settings for over 50 years, recent improvements in image resolution, data storage, and the availability of advanced AI methods such as deep learning have driven multiple exciting developments. In this Review, we summarise the advancements in digital pathology, image analysis, and AI in liver disease. Key challenges such as access to and the logistics of using digital solutions, quality issues, and appropriate guidance in research and clinical use are reviewed, along with potential solutions to these challenges in the context of liver pathology and liver disease. Digital technologies are well established in liver pathology research, and access in clinical practice is increasing, with potential to address current laboratory challenges. Further evaluation is required to assess real-world effectiveness, clinical safety, and implementation of AI tools in liver pathology.

Journal Article↗
PubMed2004

A sensitivity study for the visualisation of bacterial weathering of concrete and stone with computerised X-ray microtomography.

Geologists and engineers recently have adopted computerised X-ray microtomography (microCT), a radiological imaging technique, for geological and petrophysical applications such as the assessment of sediment characteristics, CT-measurement of compressibility and compaction, multiphase flow studies, measurement of bulk density and moisture content, and of porosity and permeability. This study focuses on another application: the monitoring of biological weathering of natural building stones and concrete. Microbial activity as a determining factor in the deterioration process of building materials has a major economic impact. Because of its non-destructive character, microCT could be the ideal monitoring technique. With this technique, three-dimensional (3D) images of the entire inner structure of the material can be obtained, together with quantitative data. In depth changes of porosity of concrete and stone specimens due to bacterial weathering were assessed in this work. Also, porosity was visualised based on 3D data with homemade software. Scanning electron microscopy (SEM) images provided additional information and supported conclusions drawn from the X-ray microCT data. Resolution improvement will make the study of petrophysical aspects of physical weathering and/or biological deterioration processes of natural building stones and concrete a promising subject for further microCT-application.

Biodegradation, Environmental↗
PubMed2004

Protein folding studied by real-time NMR spectroscopy.

Real-time NMR spectroscopy developed to a generally applicable method to follow protein folding reactions. It combines the access to high resolution data with kinetic experiments allowing very detailed insights into the development of the protein structure during different steps of folding. The present review concentrates mainly on the progress of real-time NMR during the last 5 years. Starting from simple 1D experiments, mainly changes of the chemical shifts and line widths of the resonances have been used to analyze the different states populated during the folding reactions. Today, we have a broad spectrum of 1D, 2D, and even 3D NMR methods focusing on different characteristics of the folding polypeptide chains. More than 20 proteins have been investigated so far by these time-resolved experiments and the main results and conclusions are discussed in this report. Real-time NMR provides comprehensive contributions for joining experiment and theory within the 'new view' of protein folding.

Animals↗
PubMed2003

Crystal structure of human purine nucleoside phosphorylase at 2.3A resolution.

Purine nucleoside phosphorylase (PNP) catalyzes the phosphorolysis of the N-ribosidic bonds of purine nucleosides and deoxynucleosides. In human, PNP is the only route for degradation of deoxyguanosine and genetic deficiency of this enzyme leads to profound T-cell mediated immunosuppression. PNP is therefore a target for inhibitor development aiming at T-cell immune response modulation and its low resolution structure has been used for drug design. Here we report the structure of human PNP solved to 2.3A resolution using synchrotron radiation and cryocrystallographic techniques. This structure allowed a more precise analysis of the active site, generating a more reliable model for substrate binding. The higher resolution data allowed the identification of water molecules in the active site, which suggests binding partners for potential ligands. Furthermore, the present structure may be used in the new structure-based design of PNP inhibitors.

Amino Acid Sequence↗
PubMed1988

Enhancement and simplification of macromolecular images.

Computer graphics programs have been devised to display selected atomic features and to simplify images of complex macromolecular structures. By using boundary outlines, adjustment of size and shape of the molecular components, color coding, shading, and selective omission of obscuring detail, attention can be focused on specific interactions which determine higher levels of organization. A balanced color table has been constructed in which different hues have equal steps in brightness; this table has facilitated distinction of atom types and sequence coding together with representation of an optimum range of depth cueing and surface shading. The graphics system has been used with the atomic coordinates of the tobacco mosaic virus structure to simplify images of the protein subunit, to illustrate intermolecular interactions, and to relate subunit packing arrangements in different assemblies to the underlying atomic structure. The system has also been used to construct a schematic representation of the polyomavirus capsid, based on low resolution data. Application of artistic methods contributes to the effective presentation and interpretation of detailed scientific information about complex macromolecular structures.

Computer Graphics↗
PubMed2002

DNA-repair by photolyase reveals dynamic properties of nucleosome positioning in vivo.

Nucleosomes exert a repressive influence on the biological functions of DNA by restricting the access of proteins to DNA. To investigate how intrinsic properties of nucleosomes modulate DNA-accessibility in vivo, we studied DNA repair by photolyase in the yeast URA3 gene. Formation of DNA lesions (cyclobutane pyrimidine dimers, CPDs) and photolyase activity are controlled precisely by light. Preceding work revealed that photolyase repairs nucleosome-free DNA rapidly, while repair of nucleosomes is inhibited severely. The high-resolution data presented here show slow repair in the center of nucleosomes and a gradual increase towards the periphery. This pattern was observed in all nucleosomes and demonstrates that dynamic properties facilitate DNA accessibility. Since the URA3 nucleosomes can occupy alternate positions, the repair data are most consistent with nucleosome mobility that moves CPDs in linker DNA where they are repaired rapidly. A partial and transient unfolding or disruption of nucleosomes, however, may not be excluded. In addition, repair heterogeneity was found between closely spaced sites, indicating that structural properties of nucleosomes contribute to damage processing. Moreover, nucleosome-specific modulation of photolyase was found on the transcribed and non-transcribed strand. This is in contrast to homogeneous repair of the transcribed strand by nucleotide excision repair, and reveals fundamental differences in how both repair systems interact with nucleosomes and transcription.

Base Sequence↗
PubMed2003

The structure and thermal motion of the B800-850 LH2 complex from Rps.acidophila at 2.0A resolution and 100K: new structural features and functionally relevant motions.

The structure at 100K of integral membrane light-harvesting complex II (LH2) from Rhodopseudomonas acidophila strain 10050 has been refined to 2.0A resolution. The electron density has been significantly improved, compared to the 2.5A resolution map, by high resolution data, cryo-cooling and translation, libration, screw (TLS) refinement. The electron density reveals a second carotenoid molecule, the last five C-terminal residues of the alpha-chain and a carboxy modified alpha-Met1 which forms the ligand of the B800 bacteriochlorophyll. TLS refinement has enabled the characterisation of displacements between molecules in the complex. B850 bacteriochlorophyll molecules are arranged in a ring of 18 pigments composed of nine approximate dimers. These pigments are strongly coupled and at their equilibrium positions the excited state dipole interaction energies, within and between dimers, are approximately 370cm(-1) and 280cm(-1), respectively. This difference in coupling energy is similar in magnitude to changes in interaction energies arising from the pigment displacements described by TLS tensors. The displacements appear to be non-random in nature and appear to be designed to optimise the modulation of pigment energy interactions. This is the first time that LH2 pigment displacements have been quantified experimentally. The calculated energy changes indicate that there may be significant contributions to inter-pigment energy interactions from molecular displacements and these may be of importance to photosynthetic energy transfer.

Bacterial Proteins↗
PubMed2003

Crystal structure of thermostable aspartase from Bacillus sp. YM55-1: structure-based exploration of functional sites in the aspartase family.

The crystal structure of the thermostable aspartase from Bacillus sp. YM55-1 has been solved and refined for 2.5A resolution data with an R-factor of 22.1%. The present enzyme is a homotetramer with subunits composed of three domains. It exhibits no allosteric effects, in contrast to the Escherichia coli aspartase, which is activated by divalent metal cation and L-aspartate, but is four-times more active than the E.coli enzyme. The overall folding of the present enzyme subunit is similar to those of the E.coli aspartase and the E.coli fumarase C, both of which belong to the same superfamily as the present enzyme. A local structural comparison of these three enzymes revealed seven structurally different regions. Five of the regions were located around putative functional sites, suggesting the involvement of these regions into the functions characteristic of the enzymes. Of these regions, the region of Gln96-Gly100 is proposed as a part of the recognition site of the alpha-amino group in L-aspartate for aspartase and the hydroxyl group in L-malate for fumarase. The region of Gln315-Gly323 is a flexible loop with a well-conserved sequence that is suggested to be involved in the catalytic reaction. The region of Lys123-Lys128 corresponds to a part of the putative activator-binding site in the E.coli fumarase C. The region in the Bacillus aspartase, however, adopts a main-chain conformation that prevents the activator binding. The regions of Gly228-Glu241 and Val265-Asp272, which form a part of the active-site wall, are suggested to be involved in the allosteric activation of the E.coli aspartase by the binding of the metal ion and the activator. Moreover, an increase in the numbers of intersubunit hydrogen bonds and salt-bridges is observed in the Bacillus aspartase relative to those of the E.coli enzyme, implying a contribution to the thermostability of the present aspartase.

Allosteric Site↗