HIV-1 Nef protein: purification, crystallizations, and preliminary X-ray diffraction studies

Human immunodeficiency virus Nef protein accelerates virulent progression of AIDS by its interaction with specific cellular proteins involved in cellular activation and signal transduction. Here we report the purification and crystallization of the conserved core of HIV-1LAI Nef protein in the unliganded form and in complex with the wild-type SH3 domain of the P59fyn protein-tyrosine kinase. One-dimensional NMR experiments show that full-length protein and truncated fragment corresponding to the product of HIV-1 protease cleavage have a well-folded compact tertiary structure. The ligand-free HIV-1 Nefcore protein forms cubic crystals belonging to space group P23 with unit cell dimensions of a = b = c = 86.4 A. The Nef-Fyn SH3 cocrystals belong to the space group P6(1)22 or its enantiomorph, P6(5)22, with unit cell dimensions of a = b = 108.2 A and c = 223.7 A. Both crystal forms diffract to a resolution limit of 3.0 A resolution using synchrotron radiation, and are thus suitable for X-ray structure determination.     

Feldkamp and circle-and-line cone-beam reconstruction for 3D micro-CT of vascular networks

Detailed morphometric knowledge of the microvascular network is needed for studies relating structure to haemodynamic function in organs like the lung. Clinical volumetric CT is limited to millimetre-order spatial resolution. Since evidence suggests that small arterioles (50 to 300 micrometres) dominate pulmonary haemodynamics, we built a micro-CT scanner, capable of imaging excised lungs in 3D with 100 microm resolution, for basic physiology research. The scanner incorporates a micro-focal (3 microm) x-ray source, an xyz theta stage and a CCD-coupled image intensifier detector. We imaged phantoms and contrast-enhanced rat lungs, reconstructing the data with either the Feldkamp or the circle-and-line cone-beam reconstruction algorithm. We present reconstructions using 180 views over 360 degrees for the circular trajectory, augmented with views from a linear scan for the circle-and-line algorithm. Especially for platelike features perpendicular to the rotation axis and remote from the midplane, the circle-and-line algorithm produces superior reconstructions compared with Feldkamp's algorithm. We conclude that the use of nonplanar source trajectories to perform micro-CT on contrast-enhanced, excised lungs can provide data useful for morphometric analysis of vascular trees, currently down to the 130 microm level.     

Synchrotron Radiation for Detecting Movement of a Volatile Soil Liquid

Heat and volatile liquid transport in soils are physically coupled processes. Soil water movement driven by thermal gradients has received considerable attention both experimentally and via models. This is appropriate since the thermal regime of underground electric power cables, pipelines, agricultural soils, and nuclear-waste repositories influences their ability to function effectively. However, available experimental liquid concentration data are of relatively low resolution, generally about one measurement per cm. By using synchrotron x rays we were able to nondestructively obtain high (50 μm) spatial resolution, time-lapsed data for the thermally driven movement of dibromomethane (DBM) in soil. Under repeated temperature cycling during a 22 h period, DBM movement within a sealed, 25-mm-long quartz sand (D50 = 0.25?mm) soil column was highly repeatable. About four complete scans of the column were completed each hour. Average DBM vol?% within the column as a whole was 4.0 and the porosity was 0.31. Measurements of DBM concentration at the same position and equivalent times during different cycles usually differed by less than 0.2 vol?%. Experimental data of this precision will permit better comparison with detailed model predictions.     

Femtosecond time resolution in x-ray diffraction experiments

This paper presents the theoretical background for a synthesis of femtosecond spectroscopy and x-ray diffraction. When a diffraction quality crystal with 0.1-0.3 mm overall dimensions is photoactivated by a femtosecond laser pulse (physical length = 0.3 microm), the evolution of molecules at separated points in the crystal will not be simultaneous because a finite time is required for the laser pulse to propagate through the body of the crystal. Utilizing this lack of global crystal synchronization, topographic x-ray diffraction may enable femtosecond temporal resolution to be achieved from reflection profiles in the diffraction pattern with x-ray exposures of picosecond or longer duration. Such x-ray pulses are currently available, and could be used to study femtosecond reaction dynamics at atomic resolution on crystals of both small- and macromolecules. A general treatment of excitation and diffraction geometries in relation to spatial and temporal resolution is presented.     

Low-dose phase contrast x-ray medical imaging

Phase contrast x-ray imaging is a powerful technique for the detection of low-contrast details in weakly absorbing objects. This method is of possible relevance in the field of diagnostic radiology. In fact, imaging low-contrast details within soft tissue does not give satisfactory results in conventional x-ray absorption radiology, mammography being a typical example. Nevertheless, up to now all applications of the phase contrast technique, carried out on thin samples, have required radiation doses substantially higher than those delivered in conventional radiological examinations. To demonstrate the applicability of the method to mammography we produced phase contrast images of objects a few centimetres thick while delivering radiation doses lower than or comparable to doses needed in standard mammographic examinations (typically approximately 1 mGy mean glandular dose (MGD)). We show images of a custom mammographic phantom and of two specimens of human breast tissue obtained at the SYRMEP bending magnet beamline at Elettra, the Trieste synchrotron radiation facility. The introduction of an intensifier screen enabled us to obtain phase contrast images of these thick samples with radiation doses comparable to those used in mammography. Low absorbing details such as 50 microm thick nylon wires or thin calcium deposits (approximately 50 microm) within breast tissue, invisible with conventional techniques, are detected by means of the proposed method. We also find that the use of a bending magnet radiation source relaxes the previously reported requirements on source size for phase contrast imaging. Finally, the consistency of the results has been checked by theoretical simulations carried out for the purposes of this experiment.     

Features of Compaction Kinetics for Powder Materials under Nonisothermal Conditions. Part 2. Existence of Critical Specimen Dimensions during the Preparation of Highly Compacted Materials

On the basis of a numerical solution of the problem for nonisothermal compaction and cooling of viscous compressible materials within a cylindrical chamber the effect of thermal factors and specimen geometrical dimensions on the characteristic times for two autonomous processes is analyzed: spatial propagation of a compression zone through a specimen from layer to layer and temporary additional compaction of material within the compression zone itself. It was revealed that the effect of retarding compaction (induction period) increases with distance of a specimen cross section from the moving piston as conditions for thermal insulation of the specimen ends worsen. The previously known experimental result of two critical specimen dimensions that govern conditions for preparing pore-free materials is confirmed and substantiated.     

X-PEEM Study on Surface Orientation of Stylized and Rubbed Polyimides

X-ray photoelectron emission microscopy (X-PEEM) was used to study the surface orientation of stylized and rubbed polyimide thin films. Using soft X-rays produced by a synchrotron light source, this technique combines high spatial resolution imaging with near-edge X-ray absorption fine structure (NEXAFS) spectroscopy to yield information on the surface orientation of the films. Stylizing is an ideal model of the rubbing process since the local stress acting on the polyimide to orient the molecules can be calculated. The minimum normal stress necessary to orient the surface of BPDA-PDA films was found to be 45 MPa much lower than the bulk yield stress of 200-300 MPa. Studies of the polyimide films oriented by the conventional rubbing method showed lateral inhomogeneities in the orientation of the polymer at the surface.     

Crystallization of a 67 kDa fragment of Escherichia coli DNA topoisomerase I

Escherichia coli DNA topoisomerase I is a well-studied type I DNA topoisomerase that catalyzes the breakage and rejoining of one DNA strand to allow passage of the other strand. We have cloned and over-expressed a 67 kDa amino-terminal fragment of the protein, and shown that it retains the ability of the intact enzyme to cleave single-stranded DNA. High-quality crystals of the purified 67 kDa fragment have been obtained. The crystals belong to space group P2(1)2(1)2(1), with cell dimensions a = 64.0 A, b = 79.9 A and c = 142.3 A. They diffract to at least 2.8 A at low temperature and, when cooled to cryogenic temperatures, to at least 1.9 A in a synchrotron source. A complete native data set and two derivative data sets have been collected. A multiple isomorphous replacement map to 3 A resolution shows clear secondary structural elements. Final structure determination is in progress.     

Delta-1 is a regulator of neurogenesis in the vertebrate retina

Controversy exists about the effect of tissue edema on cerebral microcirculation. High spatial resolution is required for observation of extravasation and microcirculation during focal vasogenic edema formation. To study the relationship between tissue edema and perfusion, we developed a technique for simultaneous visualization of extravasation and microvessel perfusion in rats. Focal intracortical microvascular injury was generated with a 1-sec Nd-YAG laser pulse. Evans blue albumin (EBA) was infused 30 min before decapitation to study extravasation and FITC-dextran was injected 30 sec prior to decapitation to examine microvessel perfusion. Computerized scanning laser-excited fluorescence microscopy followed by high resolution image analysis permitted quantitative assessment of both parameters on single fresh-frozen brain sections. Studied at 30 min (3.66 +/- 0.15 mm), 2 hr (4.14 +/- 0.08 mm, P < .05), and 8 hr (4.69 +/- 0.18 mm, P < .01) after injury, the diameter of the circular, sharply demarcated zone of EBA-extravasation increased progressively. At 30 min, microvessels at a zone surrounding the area of EBA-extravasation contained 69 +/- 14% (P < .05) more fluorescent FITC-filling than in the control hemisphere, but the density of perfused microvessels was unchanged. At 2 hr, secondary tissue changes had already occurred in a zone surrounding the initial laser lesion. While severe reduction in the density (-76 +/- 13%, P < .05) of perfused microvessels was observed within 400 to 240 microm inside the border of EBA extravasation, perfusion indexes were normal despite the presence of extravasated plasma constituents within 0-80 microm from the border. In a narrow zone (80 microm) outside the border of extravasation, individual microvessels contained 34 +/- 9% (P < .01) less FITC-fluorescence than those in a homologous area of the uninjured contralateral hemisphere. This report demonstrates the feasibility of simultaneous measurement and high-resolution mapping of indices of microvascular perfusion (density, filling) and extravasated plasma constituents in damaged and intact brain areas. In this model, the presence of extravasated plasma constituents the size of proteins did not immediately influence indices of cortical microcirculation. However, microvascular perfusion may be perturbed surrounding such an area of advancing vasogenic edema formation.     

Synchrotron radiation microradiography of cracks in aluminum alloys

We have investigated the feasibility of using the intense synchrotron X-radiation to microradiographically image both surface and internal cracks in reasonably thick (200 μm) specimens of aluminum base alloys. It is concluded that synchrotron micro-radiography can be successfully used to image such defects as fatigue microcracks, creep induced wedge cracks and notches with a reasonable contrast and within exposure times of about a minute or less. The resolution capability of this technique is about 20 μm which is better than the currently available NDE techniques such as ultrasonics and macroradiography. Means for improving contrast and resolution without sacrificing the short exposure time capability are suggested. Formerly with Henry Krumb School of Mines.     

Crystallization and preliminary crystallographic studies of Gi alpha 1 and mutants of Gi alpha 1 in the GTP and GDP-bound states

Several different crystal forms of Gi alpha 1 have been grown and analyzed. Crystals of native protein containing bound GTP gamma S belong to space group P3(1)2(1) or P3(2)2(1) with cell dimensions a,b = 80.6 A and c = 106.3 A and diffract to a resolution of 1.9 A using synchrotron radiation. Crystals of native protein containing bound GDP belong to space group I4 with cell dimensions a,b = 121.3 A, and c = 67.7 A and diffract to 3.0 A. Data sets from crystals grown using mutant proteins have also been obtained and characterized.     

A theoretical comparison of energy sources--microwave, ultrasound and laser--for interstitial thermal therapy

A number of heating sources are available for minimally invasive thermal therapy of tumours. The purpose of this work was to compare, theoretically, the heating characteristics of interstitial microwave, laser and ultrasound sources in three tissue sites: breast, brain and liver. Using a numerical method, the heating patterns, temperature profiles and expected volumes of thermal damage were calculated during standard treatment times with the condition that tissue temperatures were not permitted to rise above 100 degrees C (to ensure tissue vaporization did not occur). Ideal spherical and cylindrical applicators (200 microm and 800 microm radii respectively) were modelled for each energy source to demonstrate the relative importance of geometry and energy attenuation in determining heating and thermal damage profiles. The theoretical model included the effects of the collapse of perfusion due to heating. Heating patterns were less dependent on the energy source when small spherical applicators were modelled than for larger cylindrical applicators due to the very rapid geometrical decrease in energy with distance for the spherical applicators. For larger cylindrical applicators, the energy source was of greater importance. In this case, the energy source with the lowest attenuation coefficient was predicted to produce the largest volume of thermally coagulated tissue, in each tissue site.     

Slow conduction in cardiac tissue, I: effects of a reduction of excitability versus a reduction of electrical coupling on microconduction

It was the aim of this study to characterize the spread of activation at the cellular level in cardiac tissue during conduction slowing, a key element of reentrant arrhythmias; therefore, activation patterns were assessed at high spatiotemporal resolution in narrow (70 to 80 microm) and wide (230 to 270 microm) linear strands of cultured neonatal rat ventricular myocytes, using multiple site optical recording of transmembrane voltage. Slow conduction was induced by graded elevation of [K+]o, by applying tetrodotoxin, or by exposing the preparations to the gap junctional uncouplers palmitoleic acid or 1-octanol. The main findings of the study are 4-fold: (1) gap junctional uncoupling reduced conduction velocity (range, 37 to 47 cm/s under control conditions) to a substantially larger extent before block (相似文献   

Synapse specificity of long-term potentiation breaks down at short distances

Long-term potentiation (LTP), the long-lasting increase in synaptic transmission, has been proposed to be a cellular mechanism essential for learning and memory, neuronal development, and circuit reorganization. In the original theoretical and experimental work it was assumed that only synapses that had experienced concurrent pre- and postsynaptic activity are subject to synaptic modification. It has since been shown, however, that LTP is also expressed in synapses on neighbouring neurons that have not undergone the induction procedure. Yet, it is still believed that this spread of LTP is limited to adjacent postsynaptic cells, and does not occur for synapses on neighbouring input fibres. However, for technical reasons, tests for 'input specificity' were always done for synapses relatively far apart. Here we have used a new local superfusion technique, which allowed us to assess the synaptic specificity of LTP with a spatial resolution of approximately 30 microm. Our results indicate that there is no input specificity at a distance of less than 70 microm. Synapses in close proximity to a site of potentiation are also potentiated regardless of their own history of activation, whereas synapses far away show no potentiation.     

Transfer of noncorresponding spatial associations to the auditory Simon task.

Four experiments examined transfer of noncorresponding spatial stimulus-response associations to an auditory Simon task for which stimulus location was irrelevant. Experiment 1 established that, for a horizontal auditory Simon task, transfer of spatial associations occurs after 300 trials of practice with an incompatible mapping of auditory stimuli to keypress responses. Experiments 2-4 examined transfer effects within the auditory modality when the stimuli and responses were varied along vertical and horizontal dimensions. Transfer occurred when the stimuli and responses were arrayed along the same dimension in practice and transfer but not when they were arrayed along orthogonal dimensions. These findings indicate that prior task-defined associations have less influence on the auditory Simon effect than on the visual Simon effect, possibly because of the stronger tendency for an auditory stimulus to activate its corresponding response. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Long-latency event-related potentials in asymptomatic human immunodeficiency virus type 1 infection

An ideal technique for following the development of the vertebrate nervous system would allow cells to be followed at the resolution of light microscopy at depths of several millimeters into the tissue. This would permit critical events to be followed at cellular or sub-cellular resolution even deep within the developing organism. To date, no technique has emerged with all of the needed properties. Light microscopy can follow a cell and its descendants after they have been labeled by either the infection of embryonic cells with a recombinant retrovirus or the microinjection of individual precursor cells with enzymes or fluorescent dyes. However, light microscopy cannot image events deeper than a few hundred micrometers within an embryo due to light scattering and aberrations in the objective lenses and other optics. Magnetic resonance imaging (MRI) does not suffer from these limitations, routinely being used to image in 3 dimensions through specimens as large as adult humans. However, it is relatively slow and, as implemented to date, it cannot routinely achieve cellular resolution. Here, we present our attempts to meet the technical challenges posed by in vivo MRI microscopy. As an example of both the progress and the future challenges, we present images of cells within the developing frog embryo over a several day time course.     

Transfer of magnitude and spatial mappings to the SNARC effect for parity judgments.

Left–right keypresses to numerals are faster for pairings of small numbers to left response and large numbers to right response than for the opposite pairings. This spatial numerical association of response codes (SNARC) effect has been attributed to numbers being represented on a mental number line. We examined this issue in 3 experiments using a transfer paradigm. Participants practiced a number magnitude-judgment task or spatial stimulus–response compatibility task with parallel or orthogonal stimulus–response dimensions prior to performing a parity-judgment task. The SNARC effect was enhanced following a small–left/large–right magnitude mapping but reversed following a small–right/large–left mapping, indicating that associations between magnitude and response defined for the magnitude-judgment task were maintained for the parity-judgment task. The SNARC effect was unaffected by practice with compatible or incompatible spatial mapping for the parallel spatial task but was larger following up–right/down–left mapping than up–left/down–right mapping for the orthogonal spatial task. These results are inconsistent with the SNARC effect being due to a horizontal number line representation but consistent with a view that correspondence of stimulus and response code polarities contributes to the effect. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Purification and crystallization of the CDK-associated protein phosphatase KAP expressed in Escherichia coli

The kinase associated phosphatase (KAP) is a human dual specificity protein phosphatase that dephosphorylates the cell cycle control protein, cyclin dependent kinase-2 on Thr 160 in a cyclin dependent manner (Poon & Hunter, 1995). We report here the over-expression of KAP in Escherichia coli as an N-terminal His-tagged protein using a modified pET-28a T7-expression vector. The recombinant protein was purified to homogeneity and crystallized. The crystals diffract to 2.3 A resolution when exposed to synchrotron radiation and belong to space group P6(1)22, or its enantiomorph P6(5)22, with unit cell dimensions a = b = 74.5 A, c = 139.5 A.     

Endothelium-dependent relaxation of collateral microvessels after intramuscular gene transfer of vascular endothelial growth factor in a rat model of hindlimb ischemia

BACKGROUND: Recent investigations have demonstrated the ability of vascular endothelial growth factor (VEGF) to augment the development of collateral arteries in vivo. In vitro studies have suggested that the use of VEGF also improves the endothelium-dependent relaxation of collaterals at the microvascular level. The purpose of this study was to determine in vivo the extent to which vasomotor responses of collateral microvessels are altered after VEGF treatment. METHODS AND RESULTS:Ischemia was induced in the hindlimb of 35 rats by excision of the femoral artery. Immediately thereafter, 400 microg of a plasmid encoding VEGF or ss-galactosidase (control) was transfected into limb muscles. Four weeks later, synchrotron radiation microangiography, with a spatial resolution of 30 microm, was performed to document the reactivity of collateral microvessels. Administration of the endothelium-dependent vasodilator acetylcholine failed to induce dilation of collateral microvessels in control animals. By contrast, profound dilation of collaterals was observed after acetylcholine in VEGF-treated animals. This response was evident in vessels with a linear appearance but not in those with an undulating appearance. The resulting blood flow in the ischemic limb after administration of acetylcholine in the control animals was only 64.6+/-17.0% of that of the contralateral normal limb, whereas blood flow was augmented to 106.1+/-8.4% in VEGF-treated animals (P<0.05). CONCLUSIONS: These results demonstrate in vivo that the use of VEGF restores impaired vasomotor responses in some types of collateral microvessels, which may help to provide a basis for understanding the microcirculation after therapeutic angiogenesis with VEGF.     

Glucocorticoid-induced apoptosis of dendritic cells in the rat tracheal mucosa

The results of two previous studies have shown that implant porosity can be used to increase both the measured diffusion coefficients and the vascularity within the tissue encapsulating long-term subcutaneous implants. This study investigates the hypothesis that the analyte concentrations within the tissue surrounding porous implants will respond more quickly to changes in plasma levels than does the densely packed, avascular fibrous capsule surrounding nonporous implants. The average concentration of lissamine-rhodamine was measured in tissue within 100 microm of the following implants at four different times following injection of the tracer: PVA-skin, PVA-5, PVA-60, PVA-700 (polyvinyl alcohol nonporous, 5 microm, 60 microm, and 700 microm mean pore sizes, respectively) and PTFE-0.5 and PTFE-5 (polytetrafluoroethylene 0.5 microm and 5 microm mean pore sizes, respectively). The results were compared to those of unimplanted subcutaneous tissue (SQ). In addition, the data were analyzed with a simple two-compartment model in which a tissue response time constant (taup) was extracted. As in the case of vascular density, the cellular dimension of the PVA-60 pore sizes produced surrounding tissue with the optimum response times to changes in plasma concentrations. The concentrations of rhodamine within the tissue surrounding the PVA-60 implant were the highest at all time points and responded to the change in plasma rhodamine concentration approximately three times more quickly (taup = 764 s) than the fibrous tissue encapsulating the nonporous PVA-skin (taup = 2058 s) and more than twice as quickly as SQ (taup = 1627 s). The overall mass transfer rate between plasma and the tissue surrounding the different implants calculated from the permeability and density of vessels from the previous study correlated very well (r2 = 0.7, p < .02, slope of 0.98) with the reciprocal of the tissue response time constant (taup).