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At least 919 records · Page 51Linked to original sources
PubMed2005

The solution structure of the FATC domain of the protein kinase target of rapamycin suggests a role for redox-dependent structural and cellular stability.

The target of rapamycin (TOR) is a highly conserved Ser/Thr kinase that plays a central role in the control of cellular growth. TOR has a characteristic multidomain structure. Only the kinase domain has catalytic function; the other domains are assumed to mediate interactions with TOR substrates and regulators. Except for the rapamycin-binding domain, there are no high-resolution structural data available for TOR. Here, we present a structural, biophysical, and mutagenesis study of the extremely conserved COOH-terminal FATC domain. The importance of this domain for TOR function has been highlighted in several publications. We show that the FATC domain, in its oxidized form, exhibits a novel structural motif consisting of an alpha-helix and a COOH-terminal disulfide-bonded loop between two completely conserved cysteine residues. Upon reduction, the flexibility of the loop region increases dramatically. The structural data, the redox potential of the disulfide bridge, and the biochemical data of a cysteine to serine mutant indicate that the intracellular redox potential can affect the cellular amount of the TOR protein via the FATC domain. Because the amount of TOR mRNA is not changed, the redox state of the FATC disulfide bond is probably influencing the degradation of TOR.

Amino Acid Sequence↗
PubMed2004

Clinical progression and outcome of dysphagia following paediatric traumatic brain injury: a prospective study.

OBJECTIVES: To provide a preliminary clinical profile of the resolution and outcomes of oral-motor impairment and swallowing function in a group of paediatric dysphagia patients post-traumatic brain injury (TBI). To document the level of cognitive impairment parallel to the return to oral intake, and to investigate the correlation between the resolution of impaired swallow function versus the resolution of oral-motor impairment and cognitive impairment. PARTICIPANTS: Thirteen children admitted to an acute care setting for TBI. MAIN OUTCOME MEASURES: A series of oral-motor (Verbal Motor Production Assessment for Children, Frenchay Dysarthria Assessment, Schedule for Oral Motor Assessment) and swallowing (Paramatta Hospital's Assessment for Dysphagia) assessments, an outcome measure for swallowing (Royal Brisbane Hospital's Outcome Measure for Swallowing), and a cognitive rating scale (Rancho Level of Cognitive Functioning Scale). RESULTS: Across the patient group, oral-motor deficits resolved to normal status between 3 and 11 weeks post-referral (and at an average of 12 weeks post-injury) and swallowing function and resolution to normal diet status were achieved by 3-11 weeks post-referral (and at an average of 12 weeks post-injury). The resolution of dysphagia and the resolution of oral-motor impairment and cognitive impairment were all highly correlated. CONCLUSION: The provision of a preliminary profile of oral-motor functioning and dysphagia resolution, and data on the linear relationship between swallowing impairment and cognition, will provide baseline information on the course of rehabilitation of dysphagia in the paediatric population post-TBI. Such data will contribute to more informed service provision and rehabilitation planning for paediatric patients post-TBI.

Adolescent↗
PubMed1989

Structure of the nucleosome core particle at 8 A resolution.

The x-ray crystallographic structure of the nucleosome core particle has been determined using 8 A resolution diffraction data. The particle has a mean diameter of 106 A and a maximum thickness of 65 A in the superhelical axis direction. The longest chord through the histone core measures 85 A and is in a non-axial direction. The 1.87 turn superhelix consists of B-DNA with about 78 base pairs or 7.6 helical repeats per superhelical turn. The mean DNA helical repeat contains 10.2 +/- 0.05 base pairs and spans 35 A, slightly more than standard B-DNA. The superhelix varies several Angstroms in radius and pitch, and has three distinct domains of curvature (with radii of curvature of 60, 45 and 51 A). These regions are separated by localized sharper bends +/- 10 and +/- 40 base pairs from the center of the particle, resulting in an overall radius of curvature about 43 A. Compression of superhelical DNA grooves on the inner surface and expansion on the outer surface can be seen throughout the DNA electron density. This density has been fit with a double helical ribbon model providing groove width estimates of 12 +/- 1 A inside vs. 19 +/- 1 A outside for the major groove, and 8 +/- 1 A inside vs. 13 +/- 1 A outside for the minor groove. The histone core is primarily contained within the bounds defined by the superhelical DNA, contacting the DNA where the phosphate backbone faces in toward the core. Possible extensions of density between the gyres have been located, but these are below the significance level of the electron density map. In cross-section, a tripartite organization of the histone octamer is apparent, with the tetramer occupying the central region and the dimers at the extremes. Several extensions of histone density are present which form contacts between nucleosomes in the crystal, perhaps representing flexible or "tail" histone regions. The radius of gyration of the histone portion of the electron density is calculated to be 30.4 A (in reasonable agreement with solution scattering values), and the histone core volume in the map is 93% of its theoretical volume.

Animals↗
PubMed2002

Topography of rodent whisking--I. Two-dimensional monitoring of whisker movements.

During 'active touch' the rodent whiskers scan the environment in a series of repetitive movements ('whisks') generating afferent signals which transform the spatial properties of objects into spatio-temporal patterns of neural activity. Based upon analyses carried out in a single movement plane, it has been generally assumed that these trajectories are essentially uni-dimensional, although more complex movements have been described in some rodents. The present study was designed to examine this assumption and to more precisely characterize whisking topography by monitoring whisking trajectories along both the antero-posterior and dorso-ventral axes. Using optoelectronic monitoring techniques with high-spatio-temporal resolution, movement data were obtained from a population of vibrissae sampled at different locations on the mystacial pad in head-fixed rats isolated from the perturbing effects of contact. For a substantial proportion of the population of whisking movements sampled, the trajectories generated by a single whisker is most accurately described as occupying an expended two-dimensional space in which the A-P component predominates. However, the whisker system exhibits a considerable range of trajectory types, suggesting a high degree of movement flexibility. For each vibrissa position, it was possible to delineate a 'trajectory' domain-that portion of the animal's whisking space which is scanned by the movements of that vibrissa during whisking. Since the 'domains' of adjacent whiskers in the same row tend to overlap, synchronized movements of a subset of whiskers could generate a set of overlapping somatosensory fields analogous to overlapping retinal receptive fields. The organization of such trajectory domains within the rats' whisking space could provide the spatial component of the spatio-temporal integration process required to extract information about environmental features from the inputs generated by its recursive whisking movements.

Animals↗
PubMed1970

Synthesis and renewal of proteins in duck anterior hypophysis in organ culture.

In cultures of duck anterior pituitaries, the synthesis and renewal of the specific secretory protein prolactin and of total newly synthesized tissue proteins were studied. As concerns prolactin, assay of the tissue and culture media hormone content demonstrates de novo synthesis of prolactin in vitro at a constant rate during at least 2 wk. The prolactin content after 1 wk and after 2 wk of culture is the same and is similar to the initial content. The renewal time of this prolactin can be estimated at 28 or 48 hr. As concerns total proteins, the use of a chase after a short pulse of 5 min in the presence of tritiated L-leucine demonstrated that newly synthesized proteins are excreted into the culture medium from 30 min to 1 hr after the beginning of the chase. Therefore, the synthesis and excretion of proteins are two discontinuous phenomena. The migration rate of the total proteins was slower than that of prolactin, indicating that this hormone does not represent more than about half of the newly synthesized proteins. These conclusions are in good agreement with those based on high resolution radioautographic data previously obtained on the same material.

Animals↗
PubMed1997

Total charge movement per channel. The relation between gating charge displacement and the voltage sensitivity of activation.

One measure of the voltage dependence of ion channel conductance is the amount of gating charge that moves during activation and vice versa. The limiting slope method, introduced by Almers (Almers, W. 1978. Rev. Physiol. Biochem. Pharmacol. 82:96-190), exploits the relationship of charge movement and voltage sensitivity, yielding a lower limit to the range of single channel gating charge displacement. In practice, the technique is plagued by low experimental resolution due to the requirement that the logarithmic voltage sensitivity of activation be measured at very low probabilities of opening. In addition, the linear sequential models to which the original theory was restricted needed to be expanded to accommodate the complexity of mechanisms available for the activation of channels. In this communication, we refine the theory by developing a relationship between the mean activation charge displacement (a measure of the voltage sensitivity of activation) and the gating charge displacement (the integral of gating current). We demonstrate that recording the equilibrium gating charge displacement as an adjunct to the limiting slope technique greatly improves accuracy under conditions where the plots of mean activation charge displacement and gross gating charge displacement versus voltage can be superimposed. We explore this relationship for a wide variety of channel models, which include those having a continuous density of states, nonsequential activation pathways, and subconductance states. We introduce new criteria for the appropriate use of the limiting slope procedure and provide a practical example of the theory applied to low resolution simulation data.

Electrophysiology↗
PubMed1996

The high-latitude cloud MBM 7. I. H I and CO observations.

The high-latitude cloud (HLC) MBM 7 has been observed in the 21 cm H I line and the 12CO(1-0) and 13CO(1-0) lines with similar spatial resolutions. The data reveal a total mass approximately 30 M solar for MBM 7 and a complex morphology. The cloud consists of a cold dense core of 5 M solar surrounded by atomic and molecular gas with about 25 M solar, which is embedded in hotter and more diffuse H I gas. We derive a total column density N(H I + 2H2) of 1 x 10(21) cm-2 toward the center and 1 x 10(20) cm-3 toward the envelope of MBM 7. The CO line indicates the existence of dense cores [n(H2) > or = 2000 cm-3] of size (FWHM) approximately 0.5 pc. The morphology suggests shock compression from the southwest direction, which can form molecular cores along the direction perpendicular to the H I distribution. The H I cloud extends to the northeast, and the velocity gradient appears to be about 2.8 km s-1 pc-1 in this direction, which indicates a systematic outward motion which will disrupt the cloud in approximately 10(6) yr. The observed large line widths of approximately 2 km s-1 for CO suggest that turbulent motions exist in the cloud, and hydrodynamical turbulence may dominate the line broadening. Considering the energy and pressure of MBM 7, the dense cores appear not to be bound by gravity, and the whole cloud including the dense cores seem to be expanding. The distance to HLCs suggest that they belong to the galactic plane, since the scale height of the cloud is < or approximately equal to 100 pc. Compared to the more familiar dense dark clouds, HLCs may differ only in their small mass and low density, with their proximity reducing the filling factor and enhancing the contrast of the core and envelope structure.

Astronomical Phenomena↗
PubMed1994

Non-invasive bone biopsy: a new method to analyse and display the three-dimensional structure of trabecular bone.

Three-dimensional structure is one of the main factors influencing the mechanical behaviour of cancellous bone. To analyse the trabecular bone structure non-destructively we used a peripheral QCT system and applied a special thin-slice technique to create high-resolution volumetric data sets serving as a basis for something we would like to call non-invasive bone biopsy. In order to obtain binary data sets, the mineralized bone in the CT volume was separated from bone marrow and muscle tissue with the help of a sophisticated three-dimensional segmentation algorithm based on the analysis of directional derivatives, which are computed from a locally approximated fit function of the original CT volume. Binary volumes including either a solid representation of trabecular plates and rods or a topological representation of the cancellous bone architecture were acquired. Such volumes can be processed non-destructively and, even more important, repetitively. By using a surface reconstruction algorithm based on interpolating triangulation it was possible to visualize the three-dimensional surface of the trabecular bone structure. The results showed that surface representation and visualization in combination with a multiple thin-slice measuring technique are valuable tools in studying three-dimensional bone architecture. In the future, the non-invasive bone biopsies will be evaluated by means of three-dimensional mechanical analysis incorporating finite element modelling and direct morphological investigations of the cancellous bone architecture for a better prediction of bone strength as an index for fracture risk or osteoporosis.

Biopsy↗
PubMed2000

Measurement of high resolution ECG QT interval during controlled euglycaemia and hypoglycaemia.

During hypoglycaemia, typically there is a change in the surface ECG characterized by a flattened and prolonged T wave, often accompanied by a fused U wave. The QT interval is a useful parameter for quantifying the ECG morphology. However, reliable measurement of QT is not straightforward, particularly for hypoglycaemic ECG morphology. The objective of this study was to compare the ability of two methods of QT measurement to distinguish between ECGs recorded during euglycaemia and hypoglycaemia. The first method involves manually setting the intersection of the isoelectric line and the T wave or, where this is not possible, the nadir between the T and U wave. The second method is semi-automatic and fits a tangent to the point of maximum gradient on the downward slope of the T wave. Two independent observers used both methods to measure the QT for high resolution ECG data recorded during a study of 17 non-diabetic subjects undergoing controlled euglycaemia and hypoglycaemia. Using the mean results of the two observers, the mean +/- SD increase in heart rate corrected QT, QTc, for ECGs recorded during euglycaemia and hypoglycaemia was 32 +/- 25 ms for the non-tangent method and 60 +/- 24 ms for the tangent method. Therefore, the tangent method provides greater distinction between ECGs recorded during euglycaemia and hypoglycaemia than the non-tangent method. A potential clinical application could be the non-invasive detection of impending hypoglycaemia at night, which would be of significant benefit to adults and young children with diabetes.

Adult↗
PubMed2005

Dioxin and furan levels found in tampons.

BACKGROUND: Human exposure to dioxins and furans through diet and other sources has been of concern for many years. One specific concern, related to exposure in women's health, is the possible link to endometriosis. Although there are differences in opinion about this link, the concern from the public is real. Congressional interest has prompted investigations to determine the amounts of dioxins and furans present in feminine hygiene products available within the United States. METHODS: Tampon samples were analyzed via Gas Chromatography/High Resolution Mass Spectrometry (GC/HRMS) using a Micromass AutoSpec Ultima high resolution mass spectrometer at 10,000 mass resolution. As data were confirmed and quantified using direct isotope dilution, only the 17 2,3,7,8-chlorine-containing dioxin and furan concentrations were calculated from these analyses. RESULTS: A total toxic equivalence (TEQ), using the World Health Organization's toxic equivalency factor (TEF) values, was calculated for each sample. The calculated TEQs for samples were not statistically different from those of the calculated TEQs using the average limit of detection (LOD) values. CONCLUSIONS: Data show results similar to those reported by DeVito and Schecter (Environ Health Perspect 2002;110:23) in that most of the dioxins and furans were below the detection limit or estimated detection limits (EDLs).

Dioxins↗
PubMedDate not supplied

Three-dimensional fractal analysis of the white matter surface from magnetic resonance images of the human brain.

The convolutions of the cerebral cortex are difficult to describe and delineate. Our understanding of the development of the brain and its associated maldevelopment would be assisted by quantitative analysis of the cortex. Volumetric magnetic resonance (MR) imaging provides high-resolution anatomical data from which we can reconstruct the white matter as a three-dimensional object and extract its surface (the grey/white matter interface). Three-dimensional fractal analysis of this surface is a method of quantifying the surface complexity dependent upon the variation of the surface area under different scales of inspection. We estimate the fractal dimension of the white matter surface for each hemisphere and 10 coronal blocks of each hemisphere in 30 normal adult subjects. These values are tightly distributed and have been used to define a normal range of fractal dimensions. Abnormal fractal dimensions were found in 8/16 subjects with epilepsy and a gyral abnormality observed on routine MR imaging; and in 9/23 subjects with epilepsy and normal routine MR imaging. These analytical techniques offer additional information about the structure of the cortex in normal brains and about abnormalities of structure in subjects with suspected but unobserved structural abnormalities.

Adult↗
PubMed2000

The solution structure of the C-terminal domain of the Mu B transposition protein.

Mu B is one of four proteins required for the strand transfer step of bacteriophage Mu DNA transposition and the only one where no high resolution structural data is available. Structural work on Mu B has been hampered primarily by solubility problems and its tendency to aggregate. We have overcome this problem by determination of the three-dimensional structure of the C-terminal domain of Mu B (B(223-312)) in 1.5 M NaCl using NMR spectroscopic methods. The structure of Mu B(223-312) comprises four helices (backbone r.m.s.d. 0.46 A) arranged in a loosely packed bundle and resembles that of the N-terminal region of the replication helicase, DnaB. This structural motif is likely to be involved in the inter-domainal regulation of ATPase activity for both Mu A and DnaB. The approach described here for structural determination in high salt may be generally applicable for proteins that do not crystallize and that are plagued by solubility problems at low ionic strength.

Amino Acid Sequence↗
PubMed1996

Organizational age norms: why is it so hard to know one when you see one?

Scholars believe that age norms, defined here as widely shared judgments of the standard or typical ages of individuals holding a role or status within a given context, circumscribe behavior in all human societies. Admonitions such as "act your age" indicate that we expect older people to conduct themselves differently from younger people. Laws codify society's judgments of when people are old enough to vote and purchase alcoholic beverages. Work organizations have informal rules about typical ages for promotion. Yet, despite the centrality of age norms to human interaction, we know very little about them. Age norms seem easy to observe, but they have proved difficult to define and measure. Moreover, although many scholars consider age norms in a societal context, few examine them in other structured settings, such as communities or work organizations. This article explores theoretical and measurement issues that have impeded age norm studies, and presents one approach to their resolution using data from three work organizations.

Adult↗
PubMed2005

Repetitive interactions observed in the crystal structure of a collagen-model peptide, [(Pro-Pro-Gly)9]3.

The crystal structure of a collagen-model peptide [(Pro-Pro-Gly)(9)](3) has been determined at 1.33 A resolution. Diffraction data were collected at 100 K using synchrotron radiation, which led to the first structural study of [(Pro-Pro-Gly)(n)](3) under cryogenic conditions. The crystals belong to the P2(1) space group with cell parameters of a = 25.95, b = 26.56, c = 80.14 Angstroms and beta = 90.0 degrees. The overall molecular conformation was consistent with the left-handed 7/2-helical model with an axial repeat of 20 A for native collagen. A total of 332 water molecules were found in an asymmetric unit. Proline residues in adjacent triple-helices exhibited three types of hydrophobic interactions. Furthermore, three types of hydrogen-bonding networks mediated by water molecules were observed between adjacent triple-helices. These hydrophobic interactions and hydrogen-bonding networks occurred at intervals of 20 Angstroms along the c-axis based on the previous sub-cell structures [(Pro-Pro-Gly)(n)](3) (n = 9, 10), which were also seen in the full-cell structure of [(Pro-Pro-Gly)(10)](3). Five proline residues at the Y position in the X-Y-Gly triplet were found in a down-puckering conformation, this being inconsistent with the recently proposed propensity-based hypothesis. These proline residues were forced to adopt opposing puckering because of the prevailing hydrophobic interaction between triple-helices compared with the Pro:Pro stacking interaction within a triple-helix.

Collagen↗
PubMed1999

Unusual nucleotide conformations in GNRA and UNCG type tetraloop hairpins: evidence from Raman markers assignments.

High resolution NMR data on UNCG and GNRA tetraloops (where N is any of the four nucleotides and R is a purine) have shown that they contain ribonucleosides with unusual 2'-endo/anti and 3'-endo/syn conformations, in addition to the 3'-endo/anti ones which are regularly encountered in RNA chains. In the current study, Raman spectroscopy has been used to probe these nucleoside conformations and follow the order (hairpin) to disorder (random chain) structural transitions in aqueous phase in the 5-80 degreesC temperature range. Spectral evolution of GCAA and GAAA tetraloops, as formed in very short hairpins with only three G.C base pairs in their stems (T m >60 degreesC), are reported and compared with those previously published on UUCG and UACG tetraloops, for which the syn orientation of the terminal guanine as well as the 2'-endo/anti conformation of the third rC residue have been confirmed by means of vibrational marker bands. Raman data obtained as a function of temperature show that the first uracil in the UUCG tetraloop is stacked and the two middle residues (rU and rC) are in the 2'-endo/anti conformation, in agreement with the previously published NMR results. As far as the new data concerning the GNRA type tetraloops are concerned, they lead us to conclude that: (i) in both cases (GCAA and GAAA tetraloops) the adenine bases are stacked; (ii) the second rC residue in the GCAA tetraloop has a 3'-endo/anti conformation; (iii) the sugar pucker associated with the third rA residue in both tetraloops possibly undergoes a 3'-endo/2'-endo interconversion as predicted by NMR results; (iv) the stem adopts a regular A-form structure; (v) all other nucleosides of these two GNRA tetraloops possess the usual 3'-endo/anti conformation.

Molecular Probes↗
PubMed2005

H++: a server for estimating pKas and adding missing hydrogens to macromolecules.

The structure and function of macromolecules depend critically on the ionization (protonation) states of their acidic and basic groups. A number of existing practical methods predict protonation equilibrium pK constants of macromolecules based upon their atomic resolution Protein Data Bank (PDB) structures; the calculations are often performed within the framework of the continuum electrostatics model. Unfortunately, these methodologies are complex, involve multiple steps and require considerable investment of effort. Our web server http://biophysics.cs.vt.edu/H++ provides access to a tool that automates this process, allowing both experts and novices to quickly obtain estimates of pKs as well as other related characteristics of biomolecules such as isoelectric points, titration curves and energies of protonation microstates. Protons are added to the input structure according to the calculated ionization states of its titratable groups at the user-specified pH; the output is in the PQR (PDB + charges + radii) format. In addition, corresponding coordinate and topology files are generated in the format supported by the molecular modeling package AMBER. The server is intended for a broad community of biochemists, molecular modelers, structural biologists and drug designers; it can also be used as an educational tool in biochemistry courses.

Databases, Protein↗
PubMed2005

Complicated water orientations in the minor groove of the B-DNA decamer d(CCATTAATGG)2 observed by neutron diffraction measurements.

It has long been suspected that the structure and function of a DNA duplex can be strongly dependent on its degree of hydration. By neutron diffraction experiments, we have succeeded in determining most of the hydrogen (H) and deuterium (D) atomic positions in the decameric d(CCATTAATGG)2 duplex. Moreover, the D positions in 27 D2O molecules have been determined. In particular, the complex water network in the minor groove has been observed in detail. By a combined structural analysis using 2.0 A resolution X-ray and 3.0 A resolution neutron data, it is clear that the spine of hydration is built up, not only by a simple hexagonal hydration pattern (as reported in earlier X-ray studies), but also by many other water bridges hydrogen-bonded to the DNA strands. The complexity of the hydration pattern in the minor groove is derived from an extraordinary variety of orientations displayed by the water molecules.

Base Sequence↗