Structural insights into the GTPase domain of Escherichia coli MnmE protein

The Escherichia coli MnmE protein is a 50-kDa multidomain GTPase involved in tRNA modification. Its homologues in eukaryotes are crucial for mitochondrial respiration and, thus, it is thought that the human protein might be involved in mitochondrial diseases. Unlike Ras, MnmE shows a high intrinsic GTPase activity and requires effective GTP hydrolysis, and not simply GTP binding, to be functionally active. The isolated MnmE G-domain (165 residues) conserves the GTPase activity of the entire protein, suggesting that it contains the catalytic residues for GTP hydrolysis. To explore the GTP hydrolysis mechanism of MnmE, we analyzed the effect of low pH on binding and hydrolysis of GTP, as well…

Stabilization of an ?-helical conformation in an isolated hexapeptide inhibitor of calmodulin

The conformational properties of two hexapeptides, Ac-LWRILW-NH(2) and its D-amino acid counterpart Ac-lwrilw-NH(2), identified as calmodulin inhibitors using mixture-based synthetic combinatorial library approaches, have been characterised by NMR and CD spectroscopy. The peptides fold into an alpha-helical conformation in aqueous solution. The observed short- and medium-range nuclear Overhauser effects were consistent with the formation of an alpha-helical structure and a reasonably well-defined set of structures was obtained by using restraints from the NMR data in simulated annealing calculations. Analysis of glycine-substitution analogues demonstrated that all the amino acids that make …

Solution NMR structure of aD,L-alternating oligonorleucine as a model of ?-helix

beta-Helix structures are of particular interest due to their capacity to form transmembrane channels with different transport properties. However, the relatively large number of beta-helices configurations does not allow a direct conformational analysis of beta-helical oligopeptides. A synthetic alternating D,L-oligopeptide with twelve norleucines (XIIMe) has been used as a model to get insight in the conformational features of beta-helix structures. The spatial configuration of XIIMe in solution has been determined by NMR. An extensive set of distances (nuclear Overhauser effect) and dihedral (J coupling constants) constraints have been included in molecular dynamics calculations. The NMR…

High-resolution solution NMR structure of the Z domain of staphylococcal protein A

Staphylococcal protein A (SpA) is a cell-wall-bound pathogenicity factor from the bacterium Staphylococcus aureus. Because of their small size and immunoglobulin (IgG)-binding activities, domains of protein A are targets for protein engineering efforts and for the development of computational approaches for de novo protein folding. The NMR solution structure of an engineered IgG-binding domain of SpA, the Z domain (an analog of the B domain of SpA), has been determined by simulated annealing with restrained molecular dynamics on the basis of 671 conformational constraints. The Z domain contains three well-defined alpha-helices corresponding to polypeptide segments Lys7 to Leu17 (helix 1), G…

Influence of the hydrophilic face on the folding ability and stability of α-helix bundles: relevance to the peptide catalytic activity

Although not the sole feature responsible, the packing of amino acid side chains in the interior of proteins is known to contribute to protein conformational specificity. While a number of amphipathic peptide sequences with optimized hydrophobic domains has been designed to fold into a desired aggregation state, the contribution of the amino acids located on the hydrophilic side of such peptides to the final packing has not been investigated thoroughly. A set of self-aggregating 18-mer peptides designed previously to adopt a high level of alpha-helical conformation in benign buffer is used here to evaluate the effect of the nature of the amino acids located on the hydrophilic face on the pa…

Metabolic profile of chronic liver disease by NMR spectroscopy of human biopsies.

Among the different processes occurring during the evolution of liver disease, fibrosis has a predominant role. Liver fibrosis mechanisms are fairly constant irrespective of the underlying etiology. Cirrhosis is the end-stage of this reaction. Metabolic profiles, which are affected by many physiological and pathological processes, may provide further insight into the metabolic consequences of this severe liver disease. The aim of this study was to demonstrate the applicability of 1H high resolution magic angle spinning (HR-MAS) NMR spectroscopy in the biochemical profile determination of human liver needle biopsy samples for the characterization of metabolic alterations related to the sever…

Metastasizing anaplastic ependymoma in an adult. Chromosomal imbalances, metabolic and gene expression profiles

NMR and homology modeling studies of copper(II)-halocyanin from Natronobacterium pharaonis bacteria

Abstract Halocyanin from the haloalkaliphilic archaean Natronobacterium pharaonis is a peripheral membrane type 1 blue copper protein with a single polypeptide chain of 163 amino acid residues. Halocyanin participates as putative electron carrier protein associated to an electron acceptor role for a terminal oxidase and has the lowest redox potential value reported to date for a BCP. NMR studies and homology modeling calculations were performed to evaluate the electronic properties of Cu(II)-halocyanin from Natronobacterium pharaonis . The copper coordination site properties of Cu(II)-halocyanin are discussed. The 1 H NMR spectra, isotropic chemical shifts and relaxation times for halocyani…

NMR Solution Conformation of the Proposed Recombin Like Structure D(CCGCGG)2

Long repeated stretches of d(CCG) trinucleotide are the crucial mutation of gen that causes hereditary form of mental retardation (fragile X-syndrome). Moreover, the alternating (CG) dinucleotide is one of the candidates for Z-DNA conformation. Both sequences are part of the hexanucleotide d(CCGCGG)2- d(CCGCGG)2 forms different crystals depending on the crystallisation conditions. In one of these forms, the central alternating tetramer has a Z-DNA conformation, while the initial cytosine swings out and forms a Watson-Crick base-pair with the terminal guanine of a symmetry-related molecule. In this communication a detailed comparison between solid and solution spatial conformation by NMR of …

Differentiation between Brain Metastasis and Glioblastoma using MRI and two-dimensional Turbo Spectroscopic Imaging data

In this paper we propose a novel technique to differentiate brain metastases from high-grade gliomas, which represent the most aggressive and common brain lesions. In spite of the significant progresses achieved in the field of MRI in the last decades, the differentiation between these two types of tumors is still a challenge as they show a similar appearance on MRI images, but require a completely different therapeutic treatment. Here, we show that such a differentiation is actually possible and can be obtained by making use of MRI as well as of two-dimensional Turbo Spectroscopic Imaging (2D-TSI) information. Specifically, the proposed technique consists of three steps: we first detect th…

Letter to the Editor: Solution structure of hypothetical protein TA1414 from Thermoplasma acidophilum

Amino acid sequence and homology modeling of obtustatin, a novel non-RGD-containing short disintegrin isolated from the venom of Vipera lebetina obtusa

Disintegrins represent a group of cysteine-rich peptides occurring in Crotalidae and Viperidae snake venoms, and are potent antagonists of several integrin receptors. A novel disintegrin, obtustatin, was isolated from the venom of the Vipera lebetina obtusa viper, and represents the first potent and selective inhibitor of the binding of integrin alpha(1)beta(1) to collagen IV. The primary structure of obtustatin contains 41 amino acids and is the shortest disintegrin described to date. Obtustatin shares the pattern of cysteines of other short disintegrins. However, in contrast to known short disintegrins, the integrin-binding loop of obtustatin is two residues shorter and does not express t…

Conformation and concerted dynamics of the integrin-binding site and the C-terminal region of echistatin revealed by homonuclear NMR

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A procedure for predicting sorption equilibrium in ternary polymer systems from Flory–Huggins binary interaction parameters and the inversion point of preferential solvation

A procedure has been developed, based on the Flory–Huggins theory as generalized by Pouchlý, which permits the calculation of preferential (λ) and total (Y) sorption coefficients from previous information on the binary interaction parameters, χ, χ, and g12(ϕ10) and on the mixture composition at which the sign of λ inverts. The expressions obtained were applied to 10 cosolvent polymer systems for which experimental values of λ and Y are known. Practically in all the studied systems, the theoretical predictions are in fair accordance with the experimental data.

Differentiation between brain metastases and glioblastoma multiforme based on MRI, MRS and MRSI

Brain metastases and glioblastoma multiforme are the most aggressive and common brain tumours in adults and they require a different clinical management. Anatomical magnetic resonance imaging (MRI) or clinical history, cannot always clearly distinguish between them. This study describes and verifies the use of magnetic resonance spectroscopy (MRS) and magnetic resonance spectroscopic imaging (MRSI) in combination with MRI for differential diagnosis of glioblastomas and metastases. Feature selection methods are applied to the magnetic resonance (MR) spectra of 121 patients and relevant features are detected. Different classification methods are used to distinguish glioblastoma multiforme and…

A Flory–Huggins thermodynamic approach for predicting sorption equilibrium in ternary polymer systems

The Flory–Huggins theory as modified by Pouchlý has been applied to calculate preferential (λ) and total (Y) sorption coefficients for a ternary polymer system. The ternary interaction function (ϕ1ϕ2ϕ3GT(u1, ϕ3)) is described as the product of three independent binary functions. This expression allows prediction of λ and Y from binary interaction parameters χ, χ, g, g, and g12(ϕ10). Three ternary polymer systems are used to check the validity of the expression. Moreover for polymer systems in which the parameters g and/or g are unknown, a procedure to evaluate them has been developed and verified on systems for which sufficient experimental information is available.

New pattern of EGFR amplification in glioblastoma and the relationship of gene copy number with gene expression profile

Gene amplification is a process that is characterized by an increase in the copy number of a restricted region in a chromosome arm, and is frequently associated with an overexpression of the corresponding amplified gene. Amplified DNA can be organized either as extrachromosomal elements, repeated units at a single locus or scattered throughout the genome. The amplification of the gene for epidermal growth factor receptor (EGFR) is a common finding in glioblastomas and the amplified gene copies appears as double minutes. The aim of this study was to investigate the different patterns of EGFR amplification in 40 cases of glioblastoma using FISH analysis in metaphases and paraffin sections, an…

Letter to the Editor: Backbone1H,13C and15N Resonance Assignments for the 18.7 kDa GTPase Domain of Escherichia Coli MnmE Protein

Snake venom disintegrins: evolution of structure and function.

Disintegrins represent a family of polypeptides present in the venoms of various vipers that selectively block the function of integrin receptors. Here, we review our current view and hypothesis on the emergence and the structural and functional diversification of disintegrins by accelerated evolution and the selective loss of disulfide bonds of duplicated genes. Research on disintegrins is relevant for understanding the biology of viper venom toxins, but also provides information on new structural determinants involved in integrin recognition that may be useful in basic and clinical research. The role of the composition, conformation, and dynamics of the integrin inhibitory loop acting in …

Fusingin vivoandex vivoNMR sources of information for brain tumor classification

In this study we classify short echo-time brain magnetic resonance spectroscopic imaging (MRSI) data by applying a model-based canonical correlation analyses algorithm and by using, as prior knowledge, multimodal sources of information coming from high-resolution magic angle spinning (HR-MAS), MRSI and magnetic resonance imaging. The potential and limitations of fusing in vivo and ex vivo nuclear magnetic resonance sources to detect brain tumors is investigated. We present various modalities for multimodal data fusion, study the effect and the impact of using multimodal information for classifying MRSI brain glial tumors data and analyze which parameters influence the classification results…

Deterioro cognitivo: clasificación mediante espectroscopia de resonancia magnética de protón y contribución de la imagen convencional

Objetivo Analizar la eficacia diagnostica de la espectroscopia de resonancia magnetica de proton (1H ERM) en pacientes con deterioro cognitivo y establecer la complementariedad de la informacion de imagen de resonancia magnetica (RM) mediante curvas ROC. Material y metodos Se estudian 64 pacientes con deterioro cognitivo, incluyendo enfermedad de Alzheimer (EA) (N = 31), demencia vascular (N = 6), deterioro cognitivo leve (DCL) (N = 9) y depresion mayor (N = 18). Todos se exploraron con RM cerebral y 1H ERM usando dos tiempos de eco (TE, 31 y 136 ms) con volumen unico en la circonvolucion cingular posterior y lobulo temporal derecho. Los metabolitos analizados fueron N-acetilaspartato (NAA)…

MRS as Endogenous Molecular Imaging for Brain and Prostate Tumors: FP6 Project “eTUMOR“

Molecular imaging has become during the last years in an important tool for supporting cancer diagnosis and prognosis. PET and SPECT are the most common molecular imaging techniques, although very promising and specific biological molecular agent contrast for CT and MRI are being recently developed. However, the above imaging techniques require exogenous contrast agents and usually a sole molecular image can be obtained at once. On the contrary, in vivo magnetic resonance spectroscopy (MRS), in particular 1H MRS can simultaneously provide several molecular images using endogenous metabolites. In addition to biochemical spatial information from molecular imaging spectroscopy, MRS can also pr…

Cognitive impairment: classification by 1H magnetic resonance spectroscopy.

1H magnetic resonance spectroscopy (MRS) allows accurate and non-invasive in vivo metabolic study, and is a useful tool for the diagnosis of different forms of dementias. Cognitive impairment pathologies have been almost exclusively studied with MRS by comparison with healthy without a global comparison amongst Alzheimer disease (AD), vascular dementia, mild cognitive impairment (MCI) and major depression patients with cognitive impairment. Whereas decrease of N-acetylaspartate (NAA) and increase myo-Inositol (mI) at different brain locations by 1H MRS are common features of AD, Choline (Cho) alterations have been inconclusive. In our study, 64 patients with cognitive impairment were evalua…

Development of a three-dimensional cell culture system based on microfluidics for nuclear magnetic resonance and optical monitoring

A new microfluidic cell culture device compatible with real-time nuclear magnetic resonance (NMR) is presented here. The intended application is the long-term monitoring of 3D cell cultures by several techniques. The system has been designed to fit inside commercially available NMR equipment to obtain maximum readout resolution when working with small samples. Moreover, the microfluidic device integrates a fibre-optic-based sensor to monitor parameters such as oxygen, pH, or temperature during NMR monitoring, and it also allows the use of optical microscopy techniques such as confocal fluorescence microscopy. This manuscript reports the initial trials culturing neurospheres inside the micro…

1H and 13C HR-MAS spectroscopy of intact biopsy samples ex vivo and in vivo 1H MRS study of human high grade gliomas.

High-resolution magic angle spinning (HR-MAS) one- and two-dimensional 1H and 13C nuclear magnetic resonance (NMR) spectroscopy has been used to study intact glioblastoma (GBM) brain tumour tissue. The results were compared with in vitro chemical extract and in vivo spectra. The resolution of 1H one-dimensional, 1H TOCSY and 13C HSQC HR-MAS spectra is comparable to that obtained on perchloric extracts. 13C HSQC HR-MAS spectra have been particularly useful for the identification of 37 different metabolites in intact biopsy tumours, excluding water and DSS components. To our knowledge, this is the most detailed assignment of biochemical compounds obtained in intact human tissue, in particular…

On the Implementation of HealthAgents: Agent-Based Brain Tumour Diagnosis

This paper introduces HealthAgents, an EC-funded research project to improve the classification of brain tumours through multi-agent decision support over a secure and distributed network of local databases or Data Marts. HealthAgents will not only develop new pattern recognition methods for distributed classification and analysis of in vivo MRS and ex vivo/in vitro HRMAS and DNA data, but also define a method to assess the quality and usability of a new candidate local database containing a set of new cases, based on a compatibility score. Using its Multi-Agent architecture, HealthAgents intends to apply cutting-edge agent technology to the Biomedical field and develop the HealthAgents net…

Fast nosological imaging using canonical correlation analysis of brain data obtained by two-dimensional turbo spectroscopic imaging.

A new fast and accurate tissue typing technique has recently been successfully applied to prostate MR spectroscopic imaging (MRSI) data. This technique is based on canonical correlation analysis (CCA), a statistical method able to simultaneously exploit the spectral and spatial information characterizing the MRSI data. Here, the performance of CCA is further investigated by using brain data obtained by two-dimensional turbo spectroscopic imaging (2DTSI) from patients affected by glioblastoma. The purpose of this study is to investigate the applicability of CCA when typing tissues of heterogeneous tumors. The performance of CCA is also compared with that of ordinary correlation analysis on s…

Static measurements of refractive index increments at 633 nm with a modified refractive index detector

A R 401 Waters Assoc. differential refractometer has been modified to obtain the variation of refractive index increments, dn/dc, of polymer solutions at 633 nm. The introduced modifications were in the sample injection system and in the light source. The performance of the modified refractometer both with aqueous and organic solutions is analyzed. In order to localize a conformational transition in lysozyme, the dependence of dn/dc on temperature for lysozyme solutions in phosphate buffer is studied. Similarly, (dn/dc)k values for the ternary n-alkane/butanone/poly(dimethyl siloxane) systems over the whole composition range of the binary solvent mixtures are evaluated.

NMR Solution Structure of the Non-RGD Disintegrin Obtustatin

The solution structure of obtustatin, a novel non-RGD disintegrin of 41 residues isolated from Vipera lebetina obtusa venom, and a potent and selective inhibitor of the adhesion of integrin alpha(1)beta(1) to collagen IV, has been determined by two-dimensional nuclear magnetic resonance. Almost the whole set of chemical shifts for 1H, 13C and 15N were assigned at natural abundance from 2D homonuclear and heteronuclear 500 MHz, 600 MHz and 800 MHz spectra at pH 3.0 recorded at 298 K and 303 K. Final structural constraints consisted of 302 non-redundant NOE (95 long-range, 60 medium, 91 sequential and 56 intra-residue), four disulfide bond distances, five chi1 dihedral angles and four hydroge…

Ranking of Brain Tumour Classifiers Using a Bayesian Approach

This study presents a ranking for classifers using a Bayesian perspective. This ranking framework is able to evaluate the performance of the models to be compared when they are inferred from different sets of data. It also takes into account the performance obtained on samples not used during the training of the classifiers. Besides, this ranking assigns a prior to each model based on a measure of similarity of the training data to a test case. An evaluation consisting of ranking brain tumour classifiers is presented. These multilayer perceptron classifiers are trained with 1H magnetic resonance spectroscopy (MRS) signals following a multiproject multicenter evaluation approach. We demonstr…

Novel, potent calmodulin antagonists derived from an all-dhexapeptide combinatorial library that inhibitin vivocell proliferation: activity and structural characterization

: Calmodulin is known to bind to various amphipathic helical peptide sequences, and the calmodulin–peptide binding surface has been shown to be remarkably tolerant sterically. d-Amino acid peptides, therefore, represent potential non-hydrolysable intracellular antagonists of calmodulin. In the present study, synthetic combinatorial libraries have been used to develop novel d-amino acid hexapeptide antagonists to calmodulin-regulated phosphodiesterase activity. Five hexapeptides were identified from a library containing over 52 million sequences. These peptides inhibited cell proliferation both in cell culture using normal rat kidney cells and by injection via the femoral vein following part…

Predictability of properties of ternary systems solvent/solvent/polymer from interaction parameters of the binary systems—III. Analysis of binary potential functions forming ternary ones

Abstract The assumption that the ternary parameter, g τ , and its derivative with respect to polymer concentration, ( ∂g τ / ∂φ 3 ) μ 1 , φ 3 → 0 , can be described by three binary interaction parameters, g o i 3 ( i = 1, 2) and g 12 , implies that these must be independent functions. This feature has been demonstrated by using g o i 3 values obtained from A/B/polymer(P) and C/D/P ternary polymer systems to predict the ternary properties, namely preferential solvation (λ), second virial coefficient ( A 2 ) and intrinsic viscosity ([η]), of a A/C/P ternary system. Two distinct polymers, polystyrene(PS) and poly(dimethylsiloxane)(PDMS), have been utilized in three solvent mixtures, benzene(BZ…

Quadrature coils for magnetic resonance spectroscopy in the detection of prostate cancer: Single voxel acquisition does not improve the diagnostic accuracy of multivoxel images

Abstract Objective To determine the viability of quadrature coils for detecting prostate cancer using single voxel and multivoxel spectroscopy images. Material and methods We used a quadrature coil on a 1.5T MR scanner to evaluate 23 patients with suspected prostate cancer and prostate specific antigen levels greater than 4 ng/ml (mean 12 ± 8 ng/ml), independently of findings at digital rectal examination. We acquired T2-weighted images and MR spectroscopy images. We also acquired single voxel studies in areas in which the T2-weighted images or the multivoxel images were altered. We used a citrate solution to verify the spectroscopic calibration. Results Using spectroscopy images and a (Cho…

Incorporating in vivo and ex vivo NMR sources of information for modeling robust brain tumor classifiers

The purpose of this paper is to investigate the potential and limitations of using multimodal sources of information coming from in vivo NMR and ex vivo NMR data for detecting brain tumors. Supervised pattern recognition methods, whose performance directly depends on the prior available observations used in building them, are proposed. We show that high resolution magic angle spinning (HR-MAS) data act as complementary information for classifying magnetic resonance spectroscopic imaging (MRSI) data. In particularly, when considering rare brain tumors, since it is unlikely to acquire sufficient cases to define their metabolite profiles using only in vivo NMR information, HR-MAS can support t…

Concerted motions of the integrin-binding loop and the C-terminal tail of the non-RGD disintegrin obtustatin.

Obtustatin is a potent and selective inhibitor of the alpha1beta1 integrin in vitro and of angiogenesis in vivo. It possesses an integrin recognition loop that harbors, in a lateral position, the inhibitory 21KTS23 motif. We report an analysis of the dynamics of the backbone and side-chain atoms of obtustatin by homonuclear NMR methods. Angular mobility has been calculated for 90 assigned cross-peaks from 22 off-resonance rotating frame nuclear Overhauser effect spectroscopy spectra recorded at three magnetic fields. Our results suggest that the integrin binding loop and the C-terminal tail display concerted motions, which can be interpreted by hinge effects. Among the integrin-binding moti…

Spectroscopic metabolomic abnormalities in the thalamus related to auditory hallucinations in patients with schizophrenia

Abstract Objective Previous studies have found neurochemical abnormalities in thalamic nuclei in patients with schizophrenia. These abnormalities have been associated with information processing deficiencies and symptom formation. There are no metabolic spectroscopy studies in patients with schizophrenia attending to auditory hallucinations. The aim of the present study is to explore metabolic Magnetic Resonance Spectroscopy (MRS) ratio differences in the thalamus between schizophrenic patients with and without auditory hallucinations and control subjects. Methods MRS studies (MRI 1.5 T unit) were performed in 49 patients with schizophrenia (30 with auditory hallucinations and 19 without au…

Metabolite profiling of fecal water extracts from human colorectal cancer.

Colorectal cancer is the second leading cause of cancer death in developed countries. There is a need for better preventive strategies to improve the outcome of this disease. The increasing availability of high-throughput methodologies opens up new possibilities for screening new markers. The application of NMR metabolic profiling to fecal water extracts has interesting potential as a diagnostic tool for detecting colorectal cancer. We obtained NMR metabolic profiles of fecal water extracts from patients with colorectal cancer and healthy individuals, to characterize possible differences between them and to identify potential diagnostic markers. Our results show that metabolic profiling of …

Total Correlation Spectroscopy (TOCSY) of Proteins Using Coaddition of Spectra Recorded with Several Mixing Times

Metabolite identification in human liver needle biopsies by high-resolution magic angle spinning1H NMR spectroscopy

High-resolution magic angle spinning (HR-MAS) 1 H NMR spectroscopy of intact human liver needle biopsies has not been previously reported. HR-MAS NMR spectra collected on 17 specimens with tissue amounts between � 0.5 and 12 mg showed very good spectral resolution and signal-to-noise ratios. One-dimensional 1 H spectra revealed many intense signals corresponding to cellular metabolites. In addition, some high molecular weight metabolites, such as glycogen and mobile fatty acids, could be observed in some spectra. Resonance assignments for 22 metabolites were obtained by combining the analysis of three different types of 1D 1 H spectral editing, such as T2 filtering or the nuclear Overhauser…

Deviations in the determination of the unperturbed dimensions of polymers arising in ternary polymer systems (solvent (1)/solvent (2)/polymer) can be explained by the inaccurate use of an interaction parameter independent of polymer molecular weight. On this basis, a new formalism for the calculation of the second virial coefficient from intrinsic viscosity is proposed. This formalism was tested (and compared with well established formalisms) for all ternary polymer systems with simultaneous intrinsic viscosity and second virial coefficient data in the literature.

Combining HR-MAS and In Vivo MRI and MRSI Information for Robust Brain Tumor Recognition

In this study we propose to classify short echotime brain MRSI data by using multimodal information coming from magnetic resonance imaging (MRI), magnetic resonance spectroscopic imaging (MRSI) and high resolution magic angle spinning (HR-MAS), and to develop an advanced pattern recognition method that could help clinicians in diagnosing brain tumors. We study the impact of using HR-MAS information in combination with in vivo information for classifying brain tumors and we investigate which parameters influence our classification results.

The unperturbed dimensions parameter KΘ is one of the most important characteristics of a polymer chain. For binary systems (polymer/solvent) and mostly for ternary systems (polymer/solvent(1)/solvent(2)) the KΘ values show large discrepancies with respect to those under thetaconditions in a single solvent. These discrepancies can be explained by considering that the interaction parameter χ (and consequently the coil dimensions or the number of intramolecular contacts between polymer segments) changes with molecular weight M. Assuming this dependency, a modified Stockmayer-Fixman equation is proposed from which a unique value of KΘ for a given polymer, independent of M, is obtained. The use…

Incremental Gaussian Discriminant Analysis based on Graybill and Deal weighted combination of estimators for brain tumour diagnosis

In the last decade, machine learning (ML) techniques have been used for developing classifiers for automatic brain tumour diagnosis. However, the development of these ML models rely on a unique training set and learning stops once this set has been processed. Training these classifiers requires a representative amount of data, but the gathering, preprocess, and validation of samples is expensive and time-consuming. Therefore, for a classical, non-incremental approach to ML, it is necessary to wait long enough to collect all the required data. In contrast, an incremental learning approach may allow us to build an initial classifier with a smaller number of samples and update it incrementally…

Strategies for annotation and curation of translational databases: the eTUMOUR project

Altres ajuts: LSHC/CT2004-503094 The eTUMOUR (eT) multi-centre project gathered in vivo and ex vivo magnetic resonance (MR) data, as well as transcriptomic and clinical information from brain tumour patients, with the purpose of improving the diagnostic and prognostic evaluation of future patients. In order to carry this out, among other work, a database-the eTDB-was developed. In addition to complex permission rules and software and management quality control (QC), it was necessary to develop anonymization, processing and data visualization tools for the data uploaded. It was also necessary to develop sophisticated curation strategies that involved on one hand, dedicated fields for QC-gene…

Ex vivo high resolution magic angle spinning metabolic profiles describe intratumoral histopathological tissue properties in adult human gliomas.

In gliomas one can observe distinct histopathological tissue properties, such as viable tumor cells, necrotic tissue or regions where the tumor infiltrates normal brain. A first screening between the different intratumoral histopathological tissue properties would greatly assist in correctly diagnosing and prognosing gliomas. The potential of ex vivo high resolution magic angle spinning spectroscopy in characterizing these properties is analyzed and the biochemical differences between necrosis, high cellularity and border tumor regions in adult human gliomas are investigated. Statistical studies applied on sets of metabolite concentrations and metabolite ratios extracted from 52 high resolu…

Magnetic Resonance Microscopy Contribution to Interpret High-Resolution Magic Angle Spinning Metabolomic Data of Human Tumor Tissue

[EN] HRMAS NMR is considered a valuable technique to obtain detailed metabolic profile of unprocessed tissues. To properly interpret the HRMAS metabolomic results, detailed information of the actual state of the sample inside the rotor is needed. MRM (Magnetic Resonance Microscopy) was applied for obtaining structural and spatially localized metabolic information of the samples inside the HRMAS rotors. The tissue was observed stuck to the rotor wall under the effect of HRMAS spinning. MRM spectroscopy showed a transference of metabolites from the tissue to the medium. The sample shape and the metabolite transfer after HRMAS indicated that tissue had undergone alterations and it can not be s…

NMR structure of hypothetical protein TA0938 from Thermoplasma acidophilum.

Study of electrostatic potential surface distribution of wild-type plastocyaninSynechocystissolution structure determined by homonuclear NMR

Plastocyanin is a small (∼10 kDa), type I blue copper protein that works as an electron donor to photosystem I from cytochrome f in both chloroplast systems and in some strains of cyanobacteria. Comparative studies of the kinetic mechanisms of plastocyanins in different organisms show that the electron transfer from photosystem I happens by simple collision in cyanobacteria but through a intermediate transition complex in green algae and superior plants. Previous work has proved that this effect cannot be explained by structural variations across the different plastocyanins but it can be explained by differences in the electrostatic potential distribution at the protein surface. In that cas…

Evidence of Wallerian degeneration in normal appearing white matter in the early stages of relapsing-remitting multiple sclerosis

Objective: Wallerian degeneration in normal appearing white matter in early relapsing-remitting multiple sclerosis (RRMS), and its correlation with the number of relapses and disease duration. Background Recent pathological studies have demonstrated Wallerian degeneration in normal appearing white matter (NAWM) in multiple sclerosis (MS), in established RRMS, and in chronic MS. However, the presence of Wallerian degeneration early in the disease and its correlation with relapse and with disease duration has not been studied. Methods: We performed proton magnetic resonance spectroscopic imaging in 21 MS patients, and 4 healthy controls, age and gender matched, aged under 45 years, with a max…

Quantifying brain tumor tissue abundance in HR-MAS spectra using non-negative blind source separation techniques

Given high-resolution magic angle spinning (HR-MAS) spectra from several glial tumor subjects, our goal is to differentiate between tumor tissue types by separating the different sources that contribute to the profile of each spectrum. Blind source separation techniques are applied for obtaining characteristic profiles for necrosis, highly cellular tumor and border tumor tissue and providing the contribution (abundance) of each of these tumor tissue types to the profile of each spectrum. The problem is formulated as a non-negative source separation problem. Non-negative matrix factorization, convex analysis of non-negative sources and non-negative independent component analysis methods are …

NMR metabolic profile of human follicular fluid.

The environment of the oocyte during its in vivo maturation consists of follicular fluid (FF) and is surrounded by granulosa cells. The FF is derived from the sanguineous plasma and secretions, synthesised in the follicle wall, that contain a large variety of growth factors, cytokines, amino acids, and other metabolites. These metabolites are presumably involved in the physiology of the oocyte. The identification, quantification and study of FF metabolites can provide additional information about the oocyte state which can be helpful in distinguishing those oocytes that have a greater capacity to be fertilised and to develop properly. The aim of this work is to identify the metabolic profil…

Non-negative blind source separation techniques for tumor tissue typing using HR-MAS signals.

Given High Resolution Magic Angle Spinning (HR-MAS) signals from several glioblastoma tumor subjects, the goal is to differentiate between tumor tissue types by separating the different sources that contribute to the profile of each spectrum. Blind source separation techniques are applied for obtaining characteristic profiles for necrosis, high cellular tumor and border tumor tissue, and providing the contribution (abundance) of each tumor tissue to the profile of the spectra. The problem is formulated as a non-negative source separation problem. We illustrate the effectiveness of the proposed methods and we analyze to which extent the dimension of the input space could influence the perfor…

cDNA Cloning and Functional Expression of Jerdostatin, a Novel RTS-disintegrin from Trimeresurus jerdonii and a Specific Antagonist of the α1β1 Integrin

Jerdostatin represents a novel RTS-containing short disintegrin cloned by reverse transcriptase-PCR from the venom gland mRNA of the Chinese Jerdons pit viper Trimeresurus jerdonii. The jerdostatins precursor cDNA contained a 333-bp open reading frame encoding a signal peptide, a pre-peptide, and a 43-amino acid disintegrin domain, whose amino acid sequence displayed 80% identity with that of the KTS-disintegrins obtustatin and viperistatin. The jerdostatin cDNA structure represents the first complete open reading frame of a short disintegrin and points to the emergence of jerdostatin from a short-coding gene. The different residues between jerdostatin and obtustatin/viperistatin are segreg…

Spectroscopic axonal damage of the right locus coeruleus relates to selective attention impairment in early stage relapsing-remitting multiple sclerosis

Summary Lower levels of N-acetylaspartate (NAA), a marker of axonal damage, have been found in the normal-appearing white matter (NAWM) of relapsing-remitting multiple sclerosis (RRMS) patients with low physical disability. However, its relation to the clinical status of these patients remains unclear. We explored the association between NAA levels [normalized to creatine (Cr), NAA/Cr] and a cognitive feature that is not measured by the standard scales that address functional disability [e.g. Expanded Disability Scale Score (EDSS)] in early RRMS. Given that a considerable number of RRMS patients present attentional dysfunction early in the disease and assuming a functional-anatomical orient…

Benign and Atypical Meningioma Metabolic Signatures by High-Resolution Magic-Angle Spinning Molecular Profiling

Meningiomas are neoplasms that arise from the leptomeningeal covering of the brain and spinal cord, accounting for 15%-20% of CNS tumors. The WHO classifies meningiomas into three histological grades: benign, atypical, and anaplasic in accordance with the clinical prognosis. Atypical and anaplasic meningiomas tend to recur. Sometimes, meningiomas with histological diagnosis of benign meningioma show clinical characteristics of atypical meningioma. In this context, high-resolution magic-angle spinning (HR-MAS) spectroscopy of intact tissue from brain tumor biopsies has shown great potential as a support diagnostic tool. In this work, we show differences between benign and atypical meningioma…

Multiproject–multicenter evaluation of automatic brain tumor classification by magnetic resonance spectroscopy

[EN] Automatic brain tumor classification by MRS has been under development for more than a decade. Nonetheless, to our knowledge, there are no published evaluations of predictive models with unseen cases that are subsequently acquired in different centers. The multicenter eTUMOUR project (2004-2009), which builds upon previous expertise from the INTERPRET project (2000-2002) has allowed such an evaluation to take place. A total of 253 pairwise classifiers for glioblastoma, meningioma, metastasis, and low-grade glial diagnosis were inferred based on 211 SV short TE INTERPRET MR spectra obtained at 1.5 T (PRESS or STEAM, 20-32 ms) and automatically pre-processed. Afterwards, the classifiers …

Structural characterization in solution of multifunctional nucleotide coordination systems

The interaction in aqueous solution of the cyclophane receptors 2,6,10,13,17,21-hexaaza[22]orthocyclophane (L11) and 2,6,10,13,17,21-hexaaza[22]paracyclophane (L22) with the nucleotides ATP, ADP and AMP has been studied by pH titration and NMR. The obtained results are compared with those previously reported for the analogous meta-substituted receptor 2,6,10,13,17,21-hexaaza[22]metacyclophane (L). All the experimental data support the actuation of these cyclophane molecules as multi-point binders of nucleotides through electrostatic, hydrogen bonding and π-stacking interactions. The combined use of NMR and molecular dynamics permits us to get a rather reliable picture of the way in which th…

Conformational and structural analysis of the equilibrium between single- and double-strand ?-helix of aD,L-alternating oligonorleucine

Alternating sequences of D and L residues in peptides are directly related to the formation of several kinds of regular helical conformations usually called beta-helices. The major feature of these structures is that they can be associated with the transmembrane ion-conducting channel activity in some natural antibacterial peptides. The study of alternating D,L synthetic peptides is critical to understand how factors such as surrounding media, main chain length, type of side chain and terminal groups, among others, can determine the adoption of a specific kind of beta-helix. Early studies pointed out that the peptides Boc-(D-NLeu-L-NLeu)(6)-D-MeNLe-L-Nl-D-Nl-L-Nl-OMe (Boc: tert-butyloxycarb…

Combined use of 13C chemical shift and 1H alpha-13C alpha heteronuclear NOE data in monitoring a protein NMR structure refinement.

A large portion of the 13C resonance assignments for murine epidermal growth factor (mEGF) at pH 3.1 and 28 degrees C has been determined at natural isotope abundance. Sequence-specific 13C assignments are reported for 100% of the assignable C alpha, 96% of the C beta, 86% of the aromatic and 70% of the remaining peripheral aliphatic resonances of mEGF. A good correlation was observed between experimental and back-calculated C alpha chemical shifts for regions of regular beta-sheet structure. These assignments also provide the basis for interpreting 1H alpha-13C alpha heteronuclear NOE (HNOE) values in mEGF at natural isotope abundance. Some of the backbone polypeptide segments with high in…

Quantification and classification of high-resolution magic angle spinning data for brain tumor diagnosis.

The goal of this work is to propose a complete protocol (preprocessing, processing and classification) for classifying brain tumors with proton high-resolution magic-angle spinning ((1)H HR-MAS) data. The different steps of the procedure are detailed and discussed. Feature extraction techniques such as peak integration, including also the automated quantitation method AQSES, were combined with linear (LDA) and non-linear (least-squares support vector machine or LS-SVM) classifiers. Classification accuracy was assessed using a stratified random sampling scheme. The results suggest that LS-SVM performs better than LDA while AQSES performs better than the standard peak integration feature extr…

Automated quality control protocol for MR spectra of brain tumors.

Item does not contain fulltext eTUMOUR (http://www.etumour.net/) is acquiring a large database of brain tumor (1)H MR spectra to develop automated pattern recognition methods and decision support system (DSS) for tumor diagnosis. Development of accurate pattern-recognition algorithms requires spectra undistorted by artifacts, low signal-to-noise, or broad lines. eTUMOUR currently uses panels of expert spectroscopists to subjectively grade spectra as being acceptable or unacceptable. Automated quality control (QC) would be more satisfactory for several reasons: 1) to provide a reproducible objective classification of spectrum quality; 2) for use within the future DSS to prevent misdiagnosis …

High Resolution Solution NMR Structure of the Z Domain of Staphylococcal Protein A. Analysis of Secondary Structure for Free Z Domain and Bounded to IgG Antibody

Staphylococcal protein A (SpA) is a cell-wall-bound pathogenicity factor from the bacterium Staphylcoccus aureus. It exhibits tight binding to many IgG, IgA and IgM molecules at site(s) different from antigen-combining site. Because of their small size and immunoglobulin (IgG)-binding activities, domains of protein A are important targets for protein engineering efforts and for the development of computational approaches for de novo protein folding.

NMR study of hexanucleotide d(CCGCGG)2 containing two triplet repeats of fragile X syndrome

Abstract Long repeated stretches of d(CCG) and tri-nucleotide are crucial mutations that cause hereditary forms of mental retardation (fragile X-syndrome). Moreover, the alternating (CG) di-nucleotide is one of the candidates for Z-DNA conformation. Solution NMR structure of d(CCGCGG) 2 has been solved and is discussed. The determined NMR solution structure is a distorted highly bent B-DNA conformation with increased flexibility in both terminal residues. This conformation differs significantly from the Z-DNA tetramer structure reported for the same hexamer in the crystal state at similar ionic strength by Malinina and co-workers. Crystal structure of d(CCGCGG) 2 at high salt concentration …

Solution structure of aD,L-alternating oligonorleucine as a model of double-stranded antiparallel ?-helix

Conformational characteristics of alternating D,L linear peptides are of particular interest because of their capacity to form transmembrane channels with different transport properties, as some natural antibiotics do. Single- and double-stranded beta-helical structures are common for alternating D,L peptides. The stability of the beta-helix depends on several structural factors, such as the backbone peptide length, type and position of side chains, and nature of terminal groups. The NMR and molecular dynamics solution conformation of a synthetic alternating D,L-oligopeptide with 15 norleucines (XVMe) has been used as a model to get insight in to the conformational features of double-strand…

Determination of metabolite concentrations in human brain tumour biopsy samples using HR-MAS and ERETIC measurements.

Accurate determination of the concentration of the metabolites contained in intact human biopsies of 10 glioblastoma multiforme samples was achieved using one-dimensional 1H high-resolution magic angle spinning (HR-MAS) NMR combined with ERETIC™ (electronic reference to in vivo concentrations) measurements. The amount of sample used ranged from 6.8 to 12.9 mg. Metabolite concentrations were measured in each sample using two methods: with DSS (2,2-dimethyl-2-silapentane-5-sulfonate sodium salt) as an internal reference and with ERETIC™ as an external electronically generated reference. The ERETIC™ signal was shown to be highly reproducible and did not affect the spectral quality. The concent…

Accurate classification of childhood brain tumours by in vivo H-1 MRS - A multi-centre study

Aims: To evaluate the accuracy of single-voxel Magnetic Resonance Spectroscopy (1H-MRS) as a non-invasive diagnostic aid for pediatric brain tumours in a multi-national study. Our hypotheses are (1) that automated classification based on 1H-MRS provides an accurate non-invasive diagnosis in multi-centre datasets and (2) using a protocol which increases the metabolite information improves the diagnostic accuracy. Methods: 78 patients under 16 years old with histologically proven brain tumours from 10 international centres were investigated. Discrimination of 29 medulloblastomas, 11 ependymomas and 38 pilocytic astrocytomas was evaluated. Single-voxel MRS was undertaken prior to diagnosis (1.…

The intrinsic viscosities, [η], for the ternary systems alkane (1)/2-butanone (2)/poly(dimethylsiloxane) (PDMS)(3), with the alkanes decane, dodecane and hexadecane, are determined at 20,0°C. The constants a of the Mark-Houwink equation and the constant of the unperturbed dimensions, KΘ, of the polymer are evaluated over the whole composition range of the binary solvent mixture. [η] shows a pronounced maximum at intermediate compositions as found in cosolvent mixtures. In these cosolvent mixtures, the numerical values of KΘ are higher than in the single-component solvents, because the cosolvent mixtures correspond to a mixed solvent with an excess free energy, GE ≥ 0, the increase in KΘ bei…