SEARCH · Search PubMed
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.
Over the past year, insights have been made into the biochemistry and biological effects of p53. The high-resolution three-dimensional structure has been determined for the central core and carboxy-terminal domain of the protein, important p53 target genes (such as WAF1) have been identified, and insight has been gained into the relationship between p53-mediated growth arrest and apoptosis.
Highly photostable and strongly luminescent europium(III) beta-diketonate complexes are presented that can act as new probes for optical sensing of temperature. They can be excited with the light of a 405-nm LED and possess strong brightnesses. The decay times of the probes contained in a poly(vinyl methyl ketone) film and in poly(tert-butyl styrene) microparticles are highly temperature-dependent between 0 and 70 degrees C. The temperature-sensitive microparticles were dispersed, along with oxygen-sensitive microbeads consisting of a palladium porphyrin oxygen indicator in poly(styrene-co-acrylonitrile), in a thin layer of a hydrogel to give a dually sensing material which is excitable by a single light source. The two emissions can be separated by appropriate optical filters. The response to oxygen and temperature is described by 3D plots, and unbiased values can be obtained for temperature and oxygen, respectively, from the two luminescence signals if refined in an iteration step. The sensing scheme is intended for use in temperature-compensated sensing of oxygen, in contactless sensing of oxygen and temperature in (micro)biological and medical applications, in high-resolution oxygen profiling, and for simultaneous imaging of air pressure and temperature in wind tunnels.
Posttranslational glycosylation is critical for biological function of many proteins, but its structural characterization is complicated by natural heterogeneity, multiple glycosylation sites, and different forms. Here, a top-down mass spectrometry (MS) characterization is applied to three constructs of the Fc segment of IgE: Fcepsilon(3-4) (52 kDa) and Fcepsilon(2-3-4)(2) (76 kDa) disulfide-bonded homodimers. Fourier transform MS of a reduced sample of Fcepsilon(2-3-4) gave molecular masses of 37 527, 37 689, 37 851, and 38 014 Da, directly characterizing multiple glycoforms (hexose = 162 Da) without chromatographic separation. Limited proteolysis of the nonreduced Fcepsilon(2-3-4)(2) protein yielded a peptide mixture with molecular weight values that agreed with those expected from the DNA sequence. The single glycosylation site in these constructs was identified, and quantities were determined of five glycoforms that agreed within +/-2% of the molecular ion values. The 2-D mass spectrum of two glycosylated peptides showed these to have high-mannose structures, -GlcNAc-(hex)(n)(), demonstrating that Fcepsilon(2-3-4) has a single such structure of n = 5-9. For a mutated sample of Fcepsilon(3-4), in addition to five glycoforms, MS showed a molecular discrepancy that could be assigned with proteolysis and 2-D mass spectra to the oxidation of two methionines and an additional residue difference.
Despite the fact that the biological processes of chiral pesticides are enantioselective, the biotoxicity of methamidophos with respect to enantioselectivity has so far received limited research. In this study, the enantiomeric separation and biotoxicity of the two enantiomers of methamidophos were investigated. Successful enantioseparation of methamidophos using high-performance liquid chromatography on a Chiralcel OD column was achieved. As indicated by the optical rotation and circular dichroism detection, (+)-methamidophos was eluted prior to (-)-methamidophos. The t test at the 95% level of confidence indicated significant differences between the enantiomers in their in vitro inhibition toward acetylcholinesterases of bovine erythrocytes and Electrophorus electricus and in vivo acute aquatic toxicity to Daphnia magna. The in vitro assays showed that (-)-methamidophos was about 8.0-12.4 times more potent to the enzymes than its (+)-form. In contrast, the (+)-enantiomer was 7.0 times more toxic to D. magna in 48 h tests. The toxicity of racemic methamidophos was intermediate in both in vitro and in vivo bioassays. These results suggest that the biotoxicity of chiral OPs to nontargeted organisms is enantioselective and therefore should be reevaluated with their pure enantiomers.
Conformational studies on a series of 1-phenyl-, 4-phenyl-, and 1-benzyl-1,2,3,4-tetrahydroisoquinolines that possess an identical substituent pattern to the prototypical D1 dopamine receptor antagonist SCH23390 [(R)-(+)-7-chloro-8-hydroxy-3-methyl-1-phenyl-2,3,4,5- tetrahydro-1H-3-benzazepine (1)] were performed with use of molecular mechanics calculations [MM2(85), with newly developed aromatic halide bending and torsional parameters that are now incorporated into MM2(87)], single-crystal X-ray analysis, and high-field NMR spectroscopy. The synthesis and biological testing of compounds 2-7 has been previously reported. The test compounds were compared both quantitatively and graphically to compound 1. Calculations on both the free-base and protonated forms of each compound were carried out. To insure that conformation space was adequately sampled, the test compounds were energy minimized from different starting geometries; ring inversion of the heterocycle was employed, as were dihedral driver calculations on the phenyl or benzyl rings. For N-methyl-6-chloro-7-hydroxy-1-phenyl-1,2,3,4-tetrahydroisoquinoline (2), it was determined that the torsion angle tau(C8a-C1-C12-C17) had energy minima at approximately 60 degrees and 240 degrees. This finding was corroborated by NMR studies that indicated a dramatic upfield chemical shift of ArH8 after ring cyclization. The nitrogen lone pair or hydrogen vector was approximately orthogonal to the plane of the substituted aromatic ring in the tetrahydroisoquinolines; this explained the upfield chemical shift of the vicinal chiral proton (H1). In all instances, the 6-membered heterocyclic ring in the energy-minimized structures preferred the half-chair conformation with the phenyl rings pseudo-equatorial. Distance comparisons of the proposed pharmacophoric atoms (Cl, N, O, centroid of the phenyl or benzyl ring) showed that the phenyl or benzyl centroid to ammonium H distance, Cl to N distance, and distance of the nitrogen above or below the plane of the isoquinoline aromatic ring are the distances most highly correlated with biological activity (r = 0.82, 0.75, 0.81, respectively). Resolution and single-crystal X-ray analysis of compound 2 showed the most active enantiomer to possess the S absolute configuration, in contrast to the benzazepine (R)-1. Least-squares fitting of the energy-minimized structures with SYBYL molecular modeling software showed (S)-(+)-2, rather than (R)-(-)-2, gave a better fit to (R)-1. Volume determinations derived from SYBYL multifit analyses aided in receptor mapping to qualitatively describe areas of "active" pharmacophore space as well as areas of "inactive" substituent space.(ABSTRACT TRUNCATED AT 400 WORDS)
Genome damage is a hallmark of human cancer. Efforts at assessing the impact of genome damage on tumor phenotype and patients outcome have focused on measurements of the relative DNA content in tumor cells compared to normal cells and the assessment of allelic loss at single or multiple selected loci that are thought to harbor genes important in cancer biology. We adapted a global, high-resolution genotyping method for determination of global and unbiased allelic loss. We generated a score, termed global genome damage score (GGDS), that is a continuous variable from zero to one and a measure of the extent of damaged DNA in individual tumors. In 71 patients with completely resected non-small-cell lung cancer, the GGDS ranged from 0.0006 to 0.5530 with a median value of 0.0401 indicating that between 0.06 and 55.3% of the genome has allelic loss. Patients with high scores (>0.04) had a significantly worse outcome than those with low scores (median overall survival time 35.5 vs >120.0 months, P=0.006 log-rank test; median disease-free survival 28.3 vs >120.0 months, P=0.003 log-rank test). This suggests that the clinical behavior of lung tumors with low GGDS is relatively benign whereas tumors with high GGDS are aggressive resulting in early death of patients.
Multiphoton microscopy relies on nonlinear light-matter interactions to provide contrast and optical sectioning capability for high-resolution imaging. Most multiphoton microscopy studies in biological systems have relied on two-photon excited fluorescence (TPEF) to produce images. With increasing applications of multiphoton microscopy to thick-tissue "intravital" imaging, second-harmonic generation (SHG) from structural proteins has emerged as a potentially important new contrast mechanism. However, SHG is typically detected in transmission mode, thus limiting TPEF/SHG coregistration and its practical utility for in vivo thick-tissue applications. In this study, we use a broad range of excitation wavelengths (730-880 nm) to demonstrate that TPEF/SHG coregistration can easily be achieved in unstained tissues by using a simple backscattering geometry. The combined TPEF/SHG technique was applied to imaging a three-dimensional organotypic tissue model (RAFT). The structural and molecular origin of the image-forming signal from the various tissue constituents was determined by simultaneous spectroscopic measurements and confirming immunofluorescence staining. Our results show that at shorter excitation wavelengths (<800 nm), the signal emitted from the extracellular matrix (ECM) is a combination of SHG and TPEF from collagen, whereas at longer excitation wavelengths the ECM signal is exclusively due to SHG. Endogenous cellular signals are consistent with TPEF spectra of cofactors NAD(P)H and FAD at all excitation wavelengths. The reflected SHG intensity follows a quadratic dependence on the excitation power, decays exponentially with depth, and exhibits a spectral dependence in accordance with previous theoretical studies. The use of SHG and TPEF in combination provides complementary information that allows noninvasive, spatially localized in vivo characterization of cell-ECM interactions in unstained thick tissues.
Biological warfare (BW) threat assessments identify and prioritize BW threats to civilian and military populations. In an ideal world, they provide policymakers with clear and compelling guidance to prioritize biodefense research, development, testing, evaluation, and acquisition of countermeasures. Unfortunately, the biodefense community does not exist in an ideal world. National security professionals responsible for crafting BW threat assessments often are challenged by factors that limit the clarity and/or timeliness of those assessments. Moreover, the potential for life science advances to enhance threats enabled by state programs and the possibility that non-state actors may pursue crude but effective BW methodologies will drastically expand the scope of the perceived threat. Appropriate investment of federal biodefense funds will require some mechanism for validating and prioritizing present and future threats. Ideally, such a mechanism will incorporate empirical data targeted to elucidate actual hazards. In this regard, the Department of Homeland Security's creation of a Biological Threat Characterization Program for the technical validation of threat agents will be a valuable addition to the nation's overall biodefense strategy. This article articulates the need for a coordinated national biological threat characterization program, discusses some of the principal challenges associated with such research, and suggests a few options for their resolution.
BACKGROUND AND PURPOSE: Optical coherence tomography (OCT) is a new modality that allows noninvasive examination of the internal structure of biological tissue in vivo with a spatial resolution of 10 to 15 microm. This study evaluated the clinical application of OCT to determine epithelial and subepithelial anatomic structure and invasiveness of bladder epithelial lesions. MATERIALS AND METHODS: The OCT examination was performed with a 980-nm 10 mW superluminescent diode using a 2.7-mm-diameter optical fiber positioned cystoscopically. A total of 261 scans of 1.5 seconds' duration, which generated 200 x 200-pixel images, were performed on 87 areas in 24 patients at high risk of having transitional-cell carcinoma (TCC). Lesions, visually suspect, and normal areas were photographed, scanned, and biopsied. The scans were evaluated independently before comparison with histopathology findings. RESULTS: Of the 87 areas, 29 of 36 visually suspect areas and 35 of 35 normal areas, were correctly diagnosed with OCT. Of the 16 areas with papillary TCC, all 16 were diagnosed correctly as tumor, and 9 of 10 were diagnosed correctly as invasive, including 6 with lamina propria invasion only. Papillary and flat tumors, carcinoma in situ, inflammation, chronic cystitis, and von Brunn's nests were scanned. Overall, OCT had a sensitivity of 100%, overall specificity of 89%, positive predictive value of 75%, and negative predictive value of 100%. The accuracy was 92%. The positive predictive value for invasion was 90%. CONCLUSION: Optical coherence tomography is a simple, portable, promising modality for evaluation of bladder lesions and depth of tumor penetration. Further refinement of this technology may lead to the development of an optical surrogate for biopsy.
MOTIVATION: Several protein function prediction methods employ structural features captured in three-dimensional (3D) descriptors of biologically relevant sites. These methods are successful when applied to high-resolution structures, but their detection ability in lower resolution predicted structures has only been tested for a few cases. RESULTS: A method that automatically generates a library of 3D functional descriptors for the structure-based prediction of enzyme active sites (automated functional templates, 593 in total for 162 different enzymes), based on functional and structural information automatically extracted from public databases, has been developed and evaluated using decoy structures. The applicability to predicted structures was investigated by analyzing decoys of varying quality, derived from enzyme native structures. For 35% of decoy structures, our method identifies the active site in models having 3-4 A coordinate root mean square deviation from the native structure, a quality that is reachable using state of the art protein structure prediction algorithms. AVAILABILITY: See http://www.bioinformatics.buffalo.edu/resources/aft/
How neuronal activity changes cerebral blood flow is of biological and practical importance. The rodent whisker-barrel system has special merits as a model for studies of changes in local cerebral blood flow (LCBF). Stimulus-evoked changes in neural firing and 'intrinsic signals' recorded through a cranial window were used to define regions of interest for repeated flow measurements. Whisker-activated changes in flow were measured with intravascular markers at the pia. LCBF changes were always prompt and localized over the appropriate barrel. Stimulus-related changes in parenchymal flow monitored continuously with H2 electrodes recorded short latency flow changes initiated in middle cortical layers. Activation that increased flow to particular barrels often led to reduced flow to adjacent cortex. Dye was injected into single penetrating arterioles from the pia of the fixed brain and injected into arterioles in slices of cortex where barrels were evident without stains. Arteriolar and venular domains at the surface were not directly related to underlying barrels. Capillary tufts in layer IV were mainly coincident with barrels. The matching between a capillary plexus (a vascular module) and a barrel (a functional neuronal unit) is a spatial organization of neurons and blood vessels that optimizes local interactions between the two. The paths of communication probably include: neurons to neurons, neurons to glia, neurons to vessels, glia to vessels, vessels to vessels and vessels to brain. Matching a functional grouping of neurons with a vascular module is an elegant means of reducing the risk of embarrassment for energy-expensive neuronal activity (ion pumping) while minimizing energy spent for delivery of the energy (cardiac output). For imaging studies this organization sets biological limits to spatial, temporal and magnitude resolution. Reduced flow to nearby inactive cortex enhances local differences.
Chronobiology involves the objective resolution with modern hardware and software of biologic time structure, now known to characterize most, if not all, body functions; it is also the science of timely intervention, a challenge to nutritionists. At all ages, yet the sooner the better, starting preferably in the womb but at least immediately after birth, the application of the principles of chronobiology requires the study of nutrition. In many cases, e.g., in the case of an increased risk of developing high blood pressure later in life, dietary preventive interventions should eventually precede drug treatment. That such intervention should take place at the earliest individualized recognition of risk seems reasonable and is an aim of chronobiologic research. In any event, a mathematical rhythm spectrum becomes evident in any variable measured with sufficient density over an appropriately long span; it constitutes the fabric of all life. In the science and practice of nutrition today, "cherchez le contrôle" (i.e., the provision of a control) requires the assessment of a multifrequency rhythmic structure.
Magnetic Resonance (MR), which has no known biological hazard, is capable of producing high resolution thin tomographic images in any plane and blocks of 3-dimensional information. It can be used to study blood flow and to gain information about the composition of important materials seen and quantified on dimensionally accurate images. The MR image is a thin tomographic slice or a true three dimensional block of data which can be reconstructed in any desired way rather than a shadowgram of all the structures in the beam. It is the only imaging technique which can acquire data in a 3-dimensional format. CT images can be reconstructed to form a pseudo 3-D image or a hologram but the flexibility conferred by acquiring the data as a true 3-D block gives many advantages. The spatial resolution of MR images are theoretically those of low powered microscopy, the practical limits with the present generation of equipment are voxel sizes of one third by one third by two millimetres. The term Magnetic Resonance Imaging (MRI) is used commonly, particularly in the USA, avoiding association with the term, nuclear, and emphasizing the imaging potential of the technique. The terms Nuclear Magnetic Resonance (NMR) or Magnetic Resonance (MR) more correctly describe the most powerful diagnostic instrument yet devised. The simplified description of the phenomena involved in MR which follows is intended to be comprehensive and does not require foreknowledge of classical physics, quantum mechanics, fluency with mathematical formulae or an understanding of image reconstruction. There are many explanations of MR, some omitting the more difficult concepts. An accurate, comprehensive description is found on the textbook on MR by Gadian, Nuclear Magnetic Resonance and its Applications for Living Systems (Oxford University Press, 1982).
Healing or successful intervention usually leads to the resolution of pain. However, in some patients biologic or psychologic symptoms associated with pain persist despite treatment or apparent healing. In cases in which the etiology is not known, persistent pain is categorized as a clinical syndrome known as "chronic pain." Organic, psychologic, and socioenvironmental factors contribute to the development of chronic pain. Major organic illnesses leading to chronic pain include headaches, back problems, arthritis, and cancer. Significant psychological reactions occur in many pain patients, with depression being the most common. Pain is often seen in patients with psychiatric disorders such as depression, anxiety, and somatization, as well as in substance abusers. Before successful management can begin, the major etiologic factors and sequelae of the chronic pain syndrome must be understood. Antidepressants, neuroleptics, anticonvulsants, nonsteroidal anti-inflammatory drugs, and hydroxyzine have been proven effective in the treatment of pain syndromes. The treatment of patients who present with chronic pain must be individualized based on a comprehensive understanding of the factors underlying the chronic pain syndrome of each patient.
A recently established facility for interactive image processing is described, primarily from the point of view of the system's hardware organization and the special purpose software provided to support it. The performance of more general software (the 'Semper' system) in the new environment has been measured carefully, and found to be about 10 times its performance on our previous PDP 8/E computer; particular attention is given to the data management techniques crucial to the system's efficiency. Some current applications are illustrated, including high resolution image interpretation and image averaging of biological crystals.
An analytical SEM equipped with an above-the-lens detector, an in-the-lens specimen stage and a high brightness LaB6 emitter was used to produce a specimen-specific, secondary electron-I (SE-I) signal for recording edge brightness contrast with high intensity on small particles at high magnification (200,000). The SE-I edge brightness contrast produced from 20-40 nm colloidal gold on silicon wafers was useful for estimating instrument resolution since the edge brightness is the sum of the SE-I signal range (approximately equal to 1 nm) and the beam diameter. LaB6 crystal saturation and gun conditions were determined in order to minimize the probe diameter at the first cross-over position. Ferritin particles also on the silicon wafers were imaged by adjustments of the gun bias voltage conditions. Establishment of these conditions was useful for high resolution SEM studies of appropriately coated bulk biological specimens.
We present a novel tomographer for three-dimensional reconstructions of fluorochromes in diffuse media. Photon detection is based on charge-coupled device technology that allows the implementation of a large parallel array of detection channels with high sensitivity. Using this instrument we studied the response and detection limits of near-infrared fluorochromes in diffuse media as a function of light intensity and for a wide range of biologically relevant concentrations. We further examined the resolution of the scanner and the reconstruction linearity achieved. We demonstrate that the instrument attains better than 3 mm resolution, is linear within more than two orders of magnitude of fluorochrome concentration, and can detect fluorescent objects at femto-mole quantities in small animal-like geometries. These measurements delineate detection and reconstruction characteristics associated with imaging of novel classes of fluorescent probes developed for in vivo molecular and functional probing of tissues.
X-ray micrographs of biological objects have been obtained with a resolution better than 1000 angstroms by using poly(methyl methacrylate) x-ray resist and carbon Kalpha or synchrotron radiation. Synchrotron radiation allows short exposure times; storage rings especially designed as radiation sources and improved x-ray resists would make exposure times under 1 second possible.