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PubMed2007

Interactions between peptides containing nucleobase amino acids and T7 phages displaying S. cerevisiae proteins.

The importance of high-throughput analyses of protein abundances and functions is interestingly increasing in genomic/proteomic studies. In such postgenome sequencing era, a protein-detecting chip, in which a large number of molecules specifically capturing target proteins (capturing agents) such as antibodies, recombinant proteins, and small molecules are arrayed onto solid, wet, or semi-wet substrates, enables comprehensive analysis of proteomes by a single experiment. However, whole proteomes are generally complicated for comprehensive analyses so that alternative approaches to subproteome analysis categorized by protein functions and binding properties (focused proteome) would be effective. Approaching the goal of development of designed peptide chip for protein analysis, diversity increases in peptide structures and validation of target proteins are needed. We herein describe design and synthesis of nucleobase amino acid (NBA)-containing peptides, selection of nucleic acid-related proteins derived from S. cerevisiae, and detection of interactions between NBA-containing peptides and T7 phages displaying proteins by both enzyme-linked immunosorbent assays (ELISA) and label-free anomalous reflection of gold (AR) measurements. Twenty-eight phage clones were obtained by the phage-display method and sequenced. Ten of 28 clones were expected to be nucleic acid-related proteins including initiation factor, TYB protein, ribosomal proteins, elongation factor, ATP synthase subunit, GTP-binding protein, and ribonuclease. Other phage clones encoded several classes of enzymes such as reductase, oxidase, aldolase, metalloprotease, and hexokinase. Both ELISA and AR measurements suggested that the methodology of in vitro selection for recognition of the NBA-containing peptide presented in this study was successfully established. Such a combination of NBA and phage display technologies would be potential to efficiently confirm valuable target proteins binding specifically to capturing agents, to be arrayed onto solid surfaces to develop the designed peptide chip.

Bacteriophage T7↗

PubMed2005

Assessment of density functionals for the high-spin/low-spin energy difference in the low-spin iron(II) tris(2,2'-bipyridine) complex.

In the iron(II) low-spin complex [Fe(bpy)3]2+, the zero-point energy difference between the 5T2g(t4(2g)e2g) high-spin and the 1A(1g)(t(6)2g) low-spin states, Delta(E)0HL, is estimated to lie in the range of 2500-5000 cm(-1). This estimate is based on the low-temperature dynamics of the high-spin-->low-spin relaxation following the light-induced population of the high-spin state and on the assumption that the bond-length difference between the two states Delta(r)HL is equal to the average value of approximately 0.2 A, as found experimentally for the spin-crossover system. Calculations based on density functional theory (DFT) validate the structural assumption insofar as the low-spin-state optimised geometries are found to be in very good agreement with the experimental X-ray structure of the complex and the predicted high-spin geometries are all very close to one another for a whole series of common GGA (PB86, PW91, PBE, RPBE) and hybrid (B3LYP, B3LYP*, PBE1PBE) functionals. This confirmation of the structural assumption underlying the estimation of Delta(E)0HL from experimental relaxation rate constants permits us to use this value to assess the ability of the density functionals for the calculation of the energy difference between the HS and LS states. Since the different functionals give values from -1000 to 12000 cm(-1), the comparison of the calculated values with the experimental estimate thus provides a stringent criterion for the performance of a given functional. Based on this comparison the RPBE and B3LYP* functionals give the best agreement with experiment.

Ferrous Compounds↗

PubMed2005

Systematic review of screening instruments for adults at risk of PTSD.

The development of effective methods of screening for posttraumatic stress disorder (PTSD) is important in the context of mass trauma, the geographical dispersion of victims, and the restricted availability of specialists in psychological trauma. The review focused on published English-language screening instruments for civilian PTSD consisting of 30 items or fewer and validated against structured clinical interviews. Thirteen instruments were identified meeting these criteria, all consisting of symptoms of traumatic stress. The review concluded that the performance of some currently available instruments is near to their maximal potential effectiveness, and that instruments with fewer items, simpler response scales, and simpler scoring methods perform as well as if not better than longer and more complex measures.

Humans↗

PubMed2005

Phenomenology and psychological assessment of complex posttraumatic states.

The authors offer a framework for the assessment of psychological responses associated with exposure to early onset, multiple, or extended traumatic stressors. Six prominent and overlapping symptoms clusters are described: altered self-capacities, cognitive symptoms, mood disturbance, overdeveloped avoidance responses, somatoform distress, and posttraumatic stress. A strategy for the structured, psychometrically valid assessment of these outcomes is introduced, and specific recommendations for use of various generic and trauma-specific child and adult measures are provided. Implications of trauma assessment for treatment planning are discussed.

Adolescent↗

PubMed1996

The effect of concentration on the structure of alpha-crystallin.

Several models have been proposed for arrangement of the subunits in alpha-crystallin. These include the contrasting proposals that subunits are arranged in three layers and that subunits assemble into micelle-like structures. The validity of the micelle model was investigated by examining the effects of variations in protein concentration on the surface tension, conductivity, molecular weight and conformation of alpha-crystallin. The data were compared with those obtained for bovine serum albumin (BSA) and sodium dodecyl sulphate (SDS). Measurements of surface tension were conducted in the range, 10 micrograms ml-1 to 130 mg ml-1, in low and high ionic strength buffers. An apparent point of inflection, independent of ionic strength, was seen in alpha-crystallin's surface tension at around 1.9 mg ml-1 (95 microM). The surface tension did not plateau beyond this point, as is the case with surfactants, but continued to decrease up to 130 mg ml-1. BSA exhibited similar surface tension properties with an apparent inflection at 0.9 mg ml-1 (13 microM). The conductivity of alpha-crystallin and BSA solutions increased smoothly with no sign of any transition up to 96 mg ml-1 and 60 mg ml-1, respectively. In contrast, SDS showed a clear transition in this property at the concentration corresponding to its CMC. The aggregation state of the alpha-crystallin aggregates was examined by comparing molecular masses and Stokes radii. The size of the protein remained uniform over a wide concentration range and was unaffected by variations in ionic strength. Protein conformation, which was monitored by examining the microenvironment of tryptophan residues, was also found to be independent of protein concentration. It is concluded that over the concentration range that was investigated, alpha-crystallin does not exhibit any of the properties associated with classical micelles formed from small amphiphilic molecules.

Animals↗

PubMed2002

Environmental sustainability in an agricultural development project: a system dynamics approach.

Regional agricultural projects based on water resource development have many potential impacts on social and natural environments. In this research, potential long-term environmental problems of the Southeastern Anatolian Project (GAP) related to water resources, land use, land degradation, agricultural pollution and demography are analysed from a systems perspective. The analysis focuses on the totality of environmental, social and economic issues. For this purpose, a system dynamics simulation model (GAPSIM) has been developed as an experimental platform for policy analysis. GAPSIM was validated, first 'structurally', using the tests suggested by the literature and then the model 'behaviour' was tested and calibrated with respect to available data. The reference behaviour of GAPSIM reveals that, as the irrigated lands are developed, GAP faces significant water scarcity because of the increased intensity of cotton, the crop with the highest demands for water. Simulation results also indicate that two key environmental factors, pesticide and fertilizer consumption may reach undesirable levels. Alternative irrigation water release strategies, development rates of irrigated fields and farm rotation practices appear as important policy tools in achieving long-term environmental sustainability. GAPSIM promises to be not only a useful laboratory for policy makers of GAP, but also a useful generic structure applicable to other similar regional development projects.

Agriculture↗

PubMed1999

Influence of internal dynamics on accuracy of protein NMR structures: derivation of realistic model distance data from a long molecular dynamics trajectory.

In order to study the effect of internal dynamics on the accuracy of NMR structures in detail, we generated NOE distance data from a long molecular dynamics trajectory of BPTI. Cross-relaxation rates were calculated from the trajectory by analysis of the appropriate proton-proton vector autocorrelation functions. A criterion for the convergence of correlation functions was developed, and the analysis was restricted to those correlation functions that had converged within the simulation time. Effective distances were determined from the calculated cross-relaxation rates. Internal dynamics affected the derived distances in a realistic way, since they were subject both to radial averaging (which increases the cross-relaxation rate) and angular averaging (which decreases the cross-relaxation rate). The comparison of the effective distances with average distance between the protons during the trajectory showed that for most the effects of angular and distance averaging essentially cancel out. For these distances, the effective distance derived from an NOE is therefore a very good estimate of the average distance, or the distance in the average structure. However, for about 10% of the distances, the effective distance was more than 10% larger than the average distance, while for about 5%, it was more than 10% smaller, in some cases by more than 2 A. Little correlation is observed between the effects on cross-relaxation rates to different protons of the same residue. The results of this analysis have implications for the way structures are calculated from NOE distance data. For many distances, the assumption of a rigid structure is valid, and large error bounds would result in the loss of too much information content. On the other hand, the error bounds very often employed are not wide enough for some of the effects seen in our study.

Animals↗

PubMed1995

A local lymph-node assay validation study of a structure-activity relationship model for contact allergens.

A structure-activity relationship model for prediction of contact allergenic potential of chemicals had previously been developed. The model had been shown to be able to classify known allergens and nonallergens using data on physicochemical and reactivity parameters of functional groups by discriminant two-value multiple regression analysis. To investigate the model, six selected chemicals which had not been previously investigated for allergenicity were studied with both the model and a murine local lymph-node assay. The same compounds were predicted to be allergens (3-bromo-2-coumaranone, 1-nitrocyclohexene and alpha-acryloyloxy-beta, beta-dimethyl-beta-butyrolactone) and nonallergens (1-carbethoxy-4-piperidone, 6,7-dimethoxy-2-tetralone and 9-acetylanthracene) by both the model and the local lymph-node assay.

Allergens↗

PubMed1989

Effect of neuroleptics on positive and negative symptoms and the deficit state.

The concept of negative symptoms tries to operationalize a deficit syndrome observed in schizophrenia, but also in other disorders. The instruments for the measurement developed so far are unclear in their dimensional structure and validity. Further methodological development is needed. A new scale for measuring negative symptoms was derived from the AMDP-system and applied to results of drug trials with clozapine, fluperlapine, and haloperidol. The three drugs were equally effective on negative symptoms of acute and chronic schizophrenics.

Antipsychotic Agents↗

PubMed2003

[Opioid therapy in chronic non-malignant pain].

In long-term treatment opioids seem to have only minimal side-effects compared with other analgesics and co-analgesics.Nevertheless, some risks have to be considered. While immunosuppression, neurotoxicity, teratogenity, tolerance and addiction are clinically not relevant or very rare, cognitive impairment, sedation and obstipation may have a clinical impact.However, these symptoms can usually be managed by adjuvant medication and patient education. Treatment of non-malignant pain with opioids can only be considered on an individual basis. Scientific evidence for general treatment with opioids, treatment of specific pain syndromes or treatment with certain opioids is not available. In conclusion, only recommendations regarding opioid treatment for certain chronic pain syndromes can be made. In only a minority of patients can a long-term analgesic effect be expected.Therefore, careful evaluation of alternative options of pain management is necessary before opioid therapy is started. With standardized documentation responders may be distinguished from non-responders. For clinical practice of long-term opioid therapy in non-malignant pain a specialized knowledge in pain management is a prerequisite. Future studies with more sophisticated methodology will be necessary to advocate more precise guidelines.However, the therapeutic recommendations from the DGSS consensus conference allow a safer,well structured and validated use of opioids for chronic non-malignant pain.

Analgesics, Opioid↗

PubMed2005

[The surgeon's role as expert witness in malpractice lawsuits. Purpose and requirements of legal medical opinions].

Even experienced medical advisors need clear guidelines on the extent and form of expert opinions presented to courts of law. The importance of thorough document study, correctly organizing findings, and carefully weighing the various factors influencing an opinion cannot be stressed enough. Presented here is a sample opinion for German civil court trials at the state level. It illustrates how best to combine research and clinical results, personal professional experience, and citations from the literature to structure legally valid evidence in the form of an expert opinion. The importance of cogent response to examiners' and cross-examiners' questions is demonstrated, as are differences between civil and criminal proceedings. An appendix cites the appropriate passages from the German legal code concerning remuneration for expert opinions.

Certification↗

PubMed1999

[Quality of life. Construct validation and the development of a modular system].

The construct Quality of Life (QoL) is investigated by metaanalysis of eight (inter)nationally validated questionnaires in a multicenter study. Data have been collected in a mentally healthy (n = 479), a depressed (n = 171) and a schizophrenic (n = 139) sample. Conventional psychometric criteria and a facet analytical methodology have been applied. The resulting questionnaire "Modular System for Quality of Life" (MSQoL) consists of a core module with 47 items (one "G-factor" and six subdimensions), which is sufficiently valid for all three samples. Additionally, there are four specific modules (demography, family, partnership, profession). No specific modules can be identified for the psychopathological subgroups. The validated radex structure for subjective QoL offers the opportunity for a cumulative research design and for adaptations to the actual setting.

Adolescent↗

PubMed2006

A parent questionnaire for distinguishing between reactive and proactive aggression in children.

BACKGROUND: Evidence suggests that reactive and proactive aggression can be distinguished on the basis of teacher-rating scales. In this article a newly developed parent-rated questionnaire that aims to distinguish between reactive and proactive aggression is evaluated with regard to its structure and validity. METHOD: In study 1, a confirmatory factor analysis was performed on the data of 442 children aged 6-12 years of a general population. Study 2 examined the relations between the two forms of aggression and hostile intentions, expected outcome of aggression, ADHD symptoms and callous-unemotional traits in a sample of 40 normal and 40 disruptive behaviour disordered boys aged 8-12 years. RESULTS: The confirmatory factor analysis showed that the two-factor model, unlike a singlefactor model, produced a reasonable fit to the data. The results of study 2 showed that the correlations between the different variables and reactive aggression differed from the correlations with proactive aggression in ways that were consistent with theoretical definitions and earlier findings. CONCLUSION: These results, in addition to those of earlier studies using teacher-rating scales, suggest that it is possible to make a valid distinction between reactive and proactive aggression using this newly developed parent-rated questionnaire.

Child↗

PubMed2005

Structure prediction of a multi-domain EF-hand Ca2+ binding protein by PROPAINOR.

PROPAINOR is a new algorithm developed for ab initio prediction of the 3D structures of proteins using knowledge-based nonparametric multivariate statistical methods. This algorithm is found to be most efficient in terms of computational simplicity and prediction accuracy for single-domain proteins as compared to other ab initio methods. In this paper, we have used the algorithm for the atomic structure prediction of a multi-domain (two-domain) calcium-binding protein, whose solution structure has been deposited in the PDB recently (PDB ID: 1JFK). We have studied the sensitivity of the predicted structure to NMR distance restraints with their incorporation as an additional input. Further, we have compared the predicted structures in both these cases with the NMR derived solution structure reported earlier. We have also validated the refined structure for proper stereochemistry and favorable packing environment with good results and elucidated the role of the central linker.

Animals↗

PubMedDate not supplied

Coregistration of magnetic resonance and single photon emission computed tomography images for noninvasive localization of stem cells grafted in the infarcted rat myocardium.

This paper demonstrates the application of mutual information based coregistration of radionuclide and magnetic resonance imaging (MRI) in an effort to use multimodality imaging for noninvasive localization of stem cells grafted in the infarcted myocardium in rats. Radionuclide imaging such as single photon emission computed tomography (SPECT) or positron emission tomography (PET) inherently has high sensitivity and is suitable for tracking of labeled stem cells, while high-resolution MRI is able to provide detailed anatomical and functional information of myocardium. Thus, coregistration of PET or SPECT images with MRI will map the location and distribution of stem cells on detailed myocardium structures. To validate this coregistration method, SPECT data were simulated by using a Monte Carlo-based projector that modeled the pinhole-imaging physics assuming nonzero diameter and photon penetration at the edge. Translational and rotational errors of the coregistration were examined with respect to various SPECT activities, and they are on average about 0.50 mm and 0.82 degrees , respectively. Only the rotational error is dependent on activity of SPECT data. Stem cells were labeled with (111)Indium oxyquinoline and grafted in the ischemic myocardium of a rat model. Dual-tracer small-animal SPECT images were acquired, which allowed simultaneous detection of (111)In-labeled stem cells and of [(99m)Tc]sestamibi to assess myocardial perfusion deficit. The same animals were subjected to cardiac MRI. A mutual-information-based coregistration method was then applied to the SPECT and MRIs. By coregistration, the (111)In signal from labeled cells was mapped into the akinetic region identified on cine MRIs; the regional perfusion deficit on the SPECT images also coincided with the akinetic region on the MR image.

Animals↗

PubMed1992

Development of a computer application for headache diagnosis: the Headache Diagnostic System.

A computer-assisted decision support system for headache classification and diagnosis is presented. The system provides: structured headache data collection, automated data quality control and management, and automated headache classification. The system is based upon headache classification and diagnostic criteria recently developed by the International Headache Society. Development, logical structure and validation of the system are discussed. The system is shown to provide a general improvement in headache classification reliability and has utility for validation and improvement of present headache classification criteria.

Adult↗

PubMed1996

Heteroligation of a mouse monoclonal IgE antibody (La2) with small molecules, analysed by computer-aided automated docking.

A mouse monoclonal anti-TNP IgE antibody (IgE-La2) was screened by a competitive-binding ELISA with a random pool of over 2000 small molecules, mostly drugs, drug derivatives and metabolites. Thirteen of these (naproxene, beta-carboxy-chi-naphthol, oxolinic acid, hymecromone, 8-aminoquinoline, beta-naphthylamine, chi-nitrilo-cinnamic acid, 1,5-diaminonaphthaline, prolonium iodide, diaspirin, 3,4,5-trimethoxy-cinnamic acid, cycrimine, hemimellitic acid) were found to bind as strongly, or stronger, to the antibody as the immunizing hapten. We have used a Monte Carlo search technique for simulated docking of the DNP and non-DNP ligands to a model of the Fv region of IgE(La2). The validity of structural predictions made by the AutoDock program were tested on IgG(ANO2), the three-dimensional structure of which had been obtained previously by X-ray crystallography and 2D-NMR. The rms differences between the experimentally determined and auto-docked complexes in the energetically most favored binding modes were 0.31-0.44 A. Evaluation of structures of IgE(La2)-ligand complexes [including 2,4-dinitrophenol (DNP), 16 DNP amino acids, and the 13 non-DNP ligands listed above] obtained by computer-aided automated docking, suggested the existence of two subsites within an approximately 12 x 18 A2 groove extending between the H and L CDRs. Some of the ligands (DNP-Glu, 8-aminoquinoline, prolonium-I, beta-naphthylamine) were found to bind exclusively to subsite 1, others (DNP-Ala, chi-nitrilo-cinnamic acid, hemimellitic acid, beta-carboxy-chi-naphthol) to subsite 2. The majority of DNP amino acids and other ligands (oxolinic acid, 3,4,5-trimethoxy-cinnamic acid, diaspirin, [R]-cycrimine) were found to occupy an overlapping area including subsites 1 and 2, while some of the compounds (DNP-Asn, DNP-Pro, hymecromone, 1,5-naphthylenediamine) were predicted to interact with either of these subsites with comparable probabilities. When all of the docked La2-ligand complexes were taken into account, five tyrosine residues (H33, L32, L91, L92, L96) were found to provide the majority (53.4%) of all observed contact points. Thus, a multitude of interactions with aromatic residues, and a combinatorial type of interaction within the binding region, seem to be the major factors to explain the mechanism of heteroligation by IgE(La2).

Amino Acid Sequence↗

PubMed1987

Reconstruction of NOESY maps. A requirement for a reliable conformational analysis of biomolecules using 2D NMR.

The modelling of the conformation of a biomolecule in solution is based mainly on the internuclear distances deduced from measurements of nuclear Overhauser effects (nOe) in NOESY correlation maps. The distances are then used as restraints in the energy minimization procedure, which leads to one or several optimized conformations. A general and safe technique for validating these structures with respect to the experimental data is here proposed: from the internuclear distances, the relaxation matrix can be computed under the assumption of a unique rotational correlation time. By stepwise integration of these relaxation equations, the NOESY maps can be accurately reconstructed for any mixing time. Because multi-spin effects are correctly taken into account, any difference between the experimental and theoretical maps can be easily interpreted in terms of conformation, and possible inconsistencies due to conformational averaging can be pointed out. The technique is illustrated for a bacterial lipopeptide, mycosubtilin, the spectrum of which is completely assigned.

Biopolymers↗