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Sample records for sequence specific resonance

  1. Prostate cancer in magnetic resonance imaging: diagnostic utilites of spectroscopic sequences

    International Nuclear Information System (INIS)

    Caivano, Rocchina; Cirillo, Patrizia; Lotumolo, Antonella; Fortunato, Giovanna; Zandolino, Alexis; Cammarota, Aldo; Balestra, Antonio; Macarini, Luca; Vita, Giulia

    2012-01-01

    The aim of our work is to determine the efficacy of a combined study 3 Tesla Magnetic Resonance Imaging (3T MRI), with phased-array coil, for the detection of prostate cancer using magnetic resonance spectroscopy (MRS) and diffusion-weighted images (DWI) in identifying doubt nodules. In this study, we prospectively studied 46 patients who consecutively underwent digital-rectal exploration for high doses of prostate specific antigen (PSA), as well as a MRI examination and a subsequent rectal biopsy. The study of magnetic resonance imaging was performed with a Philips Achieva 3T scanner and phased-array coil. The images were obtained with turbo spin-echo sequences T2-weighted images, T1-weighted before and after the administration of contrast medium, DWI sequences and 3D spectroscopic sequences. The ultrasound-guided prostate biopsy was performed approximately 15 days after the MRI. The data obtained from MR images and spectroscopy were correlated with histological data. MRI revealed sensitivity and specificity of 88% and 61% respectively and positive predictive value (PPV) of 73%, negative predicted value (NPV) of 81% and accuracy of 76%. In identifying the location of prostate cancer, the sensitivity of 3T MRS was 92%, with a specificity of 89%, PPV of 87%, NPV of 88% and accuracy of 87%; DWI showed a sensitivity of 88%, specificity of 61%, PPV of 73%, NPV of 81% and accuracy of 76%. The 3T MR study with phased-array coil and the use of DWI and spectroscopic sequences, in addition to T2-weighted sequences, revealed to be accurate in the diagnosis of prostate cancer and in the identification of nodules to be biopsied. It may be indicated as a resolute way before biopsy in patients with elevated PSA value and can be proposed in the staging and follow-up.

  2. Pulse sequences for contrast-enhanced magnetic resonance imaging

    International Nuclear Information System (INIS)

    Graves, Martin J.

    2007-01-01

    The theory and application of magnetic resonance imaging (MRI) pulse sequences following the administration of an exogenous contrast agent are discussed. Pulse sequences are categorised according to the contrast agent mechanism: changes in proton density, relaxivity, magnetic susceptibility and resonant frequency shift. Applications in morphological imaging, magnetic resonance angiography, dynamic imaging and cell labelling are described. The importance of optimising the pulse sequence for each application is emphasised

  3. Automated sequence-specific protein NMR assignment using the memetic algorithm MATCH

    International Nuclear Information System (INIS)

    Volk, Jochen; Herrmann, Torsten; Wuethrich, Kurt

    2008-01-01

    MATCH (Memetic Algorithm and Combinatorial Optimization Heuristics) is a new memetic algorithm for automated sequence-specific polypeptide backbone NMR assignment of proteins. MATCH employs local optimization for tracing partial sequence-specific assignments within a global, population-based search environment, where the simultaneous application of local and global optimization heuristics guarantees high efficiency and robustness. MATCH thus makes combined use of the two predominant concepts in use for automated NMR assignment of proteins. Dynamic transition and inherent mutation are new techniques that enable automatic adaptation to variable quality of the experimental input data. The concept of dynamic transition is incorporated in all major building blocks of the algorithm, where it enables switching between local and global optimization heuristics at any time during the assignment process. Inherent mutation restricts the intrinsically required randomness of the evolutionary algorithm to those regions of the conformation space that are compatible with the experimental input data. Using intact and artificially deteriorated APSY-NMR input data of proteins, MATCH performed sequence-specific resonance assignment with high efficiency and robustness

  4. Wakefield excitation in plasma resonator by a sequence of relativistic electron bunches

    International Nuclear Information System (INIS)

    Kiselev, V.A.; Linnik, A.F.; Mirny, V.I.; Onishchenko, I.N.; Uskov, V.V.

    2008-01-01

    Wakefield excitation in a plasma resonator by a sequence of relativistic electron bunches with the purpose to increase excited field amplitude in comparison to waveguide case is experimentally investigated. A sequence of short electron bunches is produced by the linear resonant accelerator. Plasma resonator is formed at the beam-plasma discharge in rectangular metal waveguide filled with gas and closed by metal foil at entrance and movable short-circuited plunger at exit. Measurements of wakefield amplitude are performed showing considerably higher wakefield amplitude for resonator case

  5. Measurement of specific heat and specific absorption rate by nuclear magnetic resonance

    Energy Technology Data Exchange (ETDEWEB)

    Gultekin, David H., E-mail: david.gultekin@aya.yale.edu [Department of Electrical Engineering, Yale University, New Haven, CT 06520 (United States); Department of Medical Physics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065 (United States); Department of Radiology, Memorial Sloan-Kettering Cancer Center, New York, NY 10065 (United States); Institute of Imaging Science, Vanderbilt University, Nashville, TN 37232 (United States); Gore, John C. [Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37232 (United States); Department of Radiology and Radiological Sciences, Vanderbilt University, Nashville, TN 37232 (United States); Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232 (United States); Department of Physics and Astronomy, Vanderbilt University, Nashville, TN 37232 (United States); Institute of Imaging Science, Vanderbilt University, Nashville, TN 37232 (United States)

    2010-05-20

    We evaluate a nuclear magnetic resonance (NMR) method of calorimetry for the measurement of specific heat (c{sub p}) and specific absorption rate (SAR) in liquids. The feasibility of NMR calorimetry is demonstrated by experimental measurements of water, ethylene glycol and glycerol using any of three different NMR parameters (chemical shift, spin-spin relaxation rate and equilibrium nuclear magnetization). The method involves heating the sample using a continuous wave laser beam and measuring the temporal variation of the spatially averaged NMR parameter by non-invasive means. The temporal variation of the spatially averaged NMR parameter as a function of thermal power yields the ratio of the heat capacity to the respective nuclear thermal coefficient, from which the specific heat can be determined for the substance. The specific absorption rate is obtained by subjecting the liquid to heating by two types of radiation, radiofrequency (RF) and near-infrared (NIR), and by measuring the change in the nuclear spin phase shift by a gradient echo imaging sequence. These studies suggest NMR may be a useful tool for measurements of the thermal properties of liquids.

  6. Parry-Romberg syndrome: findings in advanced magnetic resonance imaging sequences - case report

    Energy Technology Data Exchange (ETDEWEB)

    Paula, Rafael Alfenas de; Ribeiro, Bruno Niemeyer de Freitas, E-mail: alfenas85@gmail.com [Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ (Brazil). Hospital Universitario Clementino Fraga Filho; Bahia, Paulo Roberto Valle [Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ (Brazil). Dept. de radiologia; Ribeiro, Renato Niemeyer de Freitas [Hospital de Clinica de Jacarepagua, Rio de Janeiro, RJ (Brazil); Carvalho, Lais Balbi de [Universidade Presidente Antonio Carlos (Unipac), Juiz de Fora, MG (Brazil)

    2014-05-15

    Parry-Romberg syndrome is a rare disease characterized by progressive hemifacial atrophy associated with other systemic changes, including neurological symptoms. Currently, there are few studies exploring the utilization of advanced magnetic resonance sequences in the investigation of this disease. The authors report the case of a 45-year-old patient and describe the findings at structural magnetic resonance imaging and at advanced sequences, correlating them with pathophysiological data. (author)

  7. The role of the STIR sequence in magnetic resonance imaging examination of bone tumours

    International Nuclear Information System (INIS)

    Golfieri, R.; Baddeley, H.; Pringle, J.S.; Souhami, R.

    1990-01-01

    Sixty patients with primary bone tumours were evaluated with magnetic resonance imaging (MRI) at 0.5 T with both conventional spin-echo (SE) and short inversion time inversion recovery (STIR) sequences. The STIR sequence with T 1 of 120-130 ms in all cases suppressed the high signal from fatty bone marrow, giving a clear depiction of tumour extent, in both its intramedullary and soft-tissue components, and is superior to conventional SE images. The high sensitivity (100% of our cases) of this technique is counterbalanced by its lack of specificity: on STIR sequences both tumour and peritumorous oedema give an increase of signal intensity, limiting assessment of tumour extent. Peritumoral oedema, only present in this series in malignant neoplasms, may however be differentiated on the basis of the configuration of the abnormal areas, and by comparing STIR images with short repetition time/echo time sequence results. (author)

  8. NOESY-WaterControl: a new NOESY sequence for the observation of under-water protein resonances

    International Nuclear Information System (INIS)

    Torres, Allan M.; Zheng, Gang; Price, William S.

    2017-01-01

    Highly selective and efficient water signal suppression is indispensable in biomolecular 2D nuclear Overhauser effect spectroscopy (NOESY) experiments. However, the application of conventional water suppression schemes can cause a significant or complete loss of the biomolecular resonances at and around the water chemical shift (ω 2 ). In this study, a new sequence, NOESY-WaterControl, was developed to address this issue. The new sequence was tested on lysozyme and bovine pancreatic trypsin inhibitor (BPTI), demonstrating its efficiency in both water suppression and, more excitingly, preserving water-proximate biomolecular resonances in ω 2 . The 2D NOESY maps obtained using the new sequence thus provide more information than the maps obtained with conventional water suppression, thereby lessening the number of experiments needed to complete resonance assignments of biomolecules. The 2D NOESY-WaterControl map of BPTI showed strong bound water and exchangeable proton signals in ω 1 but these signals were absent in ω 2 , indicating the possibility of using the new sequence to discriminate bound water and exchangeable proton resonances from non-labile proton resonances with similar chemical shifts to water.

  9. NOESY-WaterControl: a new NOESY sequence for the observation of under-water protein resonances

    Energy Technology Data Exchange (ETDEWEB)

    Torres, Allan M.; Zheng, Gang, E-mail: g.zheng@westernsydney.edu.au; Price, William S. [Western Sydney University, Nanoscale Organisation and Dynamics Group, School of Science and Health (Australia)

    2017-03-15

    Highly selective and efficient water signal suppression is indispensable in biomolecular 2D nuclear Overhauser effect spectroscopy (NOESY) experiments. However, the application of conventional water suppression schemes can cause a significant or complete loss of the biomolecular resonances at and around the water chemical shift (ω{sub 2}). In this study, a new sequence, NOESY-WaterControl, was developed to address this issue. The new sequence was tested on lysozyme and bovine pancreatic trypsin inhibitor (BPTI), demonstrating its efficiency in both water suppression and, more excitingly, preserving water-proximate biomolecular resonances in ω{sub 2}. The 2D NOESY maps obtained using the new sequence thus provide more information than the maps obtained with conventional water suppression, thereby lessening the number of experiments needed to complete resonance assignments of biomolecules. The 2D NOESY-WaterControl map of BPTI showed strong bound water and exchangeable proton signals in ω{sub 1} but these signals were absent in ω{sub 2}, indicating the possibility of using the new sequence to discriminate bound water and exchangeable proton resonances from non-labile proton resonances with similar chemical shifts to water.

  10. The hydrophobic core of twin-arginine signal sequences orchestrates specific binding to Tat-pathway related chaperones.

    Directory of Open Access Journals (Sweden)

    Anitha Shanmugham

    Full Text Available Redox enzyme maturation proteins (REMPs bind pre-proteins destined for translocation across the bacterial cytoplasmic membrane via the twin-arginine translocation system and enable the enzymatic incorporation of complex cofactors. Most REMPs recognize one specific pre-protein. The recognition site usually resides in the N-terminal signal sequence. REMP binding protects signal peptides against degradation by proteases. REMPs are also believed to prevent binding of immature pre-proteins to the translocon. The main aim of this work was to better understand the interaction between REMPs and substrate signal sequences. Two REMPs were investigated: DmsD (specific for dimethylsulfoxide reductase, DmsA and TorD (specific for trimethylamine N-oxide reductase, TorA. Green fluorescent protein (GFP was genetically fused behind the signal sequences of TorA and DmsA. This ensures native behavior of the respective signal sequence and excludes any effects mediated by the mature domain of the pre-protein. Surface plasmon resonance analysis revealed that these chimeric pre-proteins specifically bind to the cognate REMP. Furthermore, the region of the signal sequence that is responsible for specific binding to the corresponding REMP was identified by creating region-swapped chimeric signal sequences, containing parts of both the TorA and DmsA signal sequences. Surprisingly, specificity is not encoded in the highly variable positively charged N-terminal region of the signal sequence, but in the more similar hydrophobic C-terminal parts. Interestingly, binding of DmsD to its model substrate reduced membrane binding of the pre-protein. This property could link REMP-signal peptide binding to its reported proofreading function.

  11. Optimized, unequal pulse spacing in multiple echo sequences improves refocusing in magnetic resonance.

    Science.gov (United States)

    Jenista, Elizabeth R; Stokes, Ashley M; Branca, Rosa Tamara; Warren, Warren S

    2009-11-28

    A recent quantum computing paper (G. S. Uhrig, Phys. Rev. Lett. 98, 100504 (2007)) analytically derived optimal pulse spacings for a multiple spin echo sequence designed to remove decoherence in a two-level system coupled to a bath. The spacings in what has been called a "Uhrig dynamic decoupling (UDD) sequence" differ dramatically from the conventional, equal pulse spacing of a Carr-Purcell-Meiboom-Gill (CPMG) multiple spin echo sequence. The UDD sequence was derived for a model that is unrelated to magnetic resonance, but was recently shown theoretically to be more general. Here we show that the UDD sequence has theoretical advantages for magnetic resonance imaging of structured materials such as tissue, where diffusion in compartmentalized and microstructured environments leads to fluctuating fields on a range of different time scales. We also show experimentally, both in excised tissue and in a live mouse tumor model, that optimal UDD sequences produce different T(2)-weighted contrast than do CPMG sequences with the same number of pulses and total delay, with substantial enhancements in most regions. This permits improved characterization of low-frequency spectral density functions in a wide range of applications.

  12. Mechanism of sequence-specific template binding by the DNA primase of bacteriophage T7

    KAUST Repository

    Lee, Seung-Joo

    2010-03-28

    DNA primases catalyze the synthesis of the oligoribonucleotides required for the initiation of lagging strand DNA synthesis. Biochemical studies have elucidated the mechanism for the sequence-specific synthesis of primers. However, the physical interactions of the primase with the DNA template to explain the basis of specificity have not been demonstrated. Using a combination of surface plasmon resonance and biochemical assays, we show that T7 DNA primase has only a slightly higher affinity for DNA containing the primase recognition sequence (5\\'-TGGTC-3\\') than for DNA lacking the recognition site. However, this binding is drastically enhanced by the presence of the cognate Nucleoside triphosphates (NTPs), Adenosine triphosphate (ATP) and Cytosine triphosphate (CTP) that are incorporated into the primer, pppACCA. Formation of the dimer, pppAC, the initial step of sequence-specific primer synthesis, is not sufficient for the stable binding. Preformed primers exhibit significantly less selective binding than that observed with ATP and CTP. Alterations in subdomains of the primase result in loss of selective DNA binding. We present a model in which conformational changes induced during primer synthesis facilitate contact between the zinc-binding domain and the polymerase domain. The Author(s) 2010. Published by Oxford University Press.

  13. Sequence-specific 1H-NMR assignments for the aromatic region of several biologically active, monomeric insulins including native human insulin.

    Science.gov (United States)

    Roy, M; Lee, R W; Kaarsholm, N C; Thøgersen, H; Brange, J; Dunn, M F

    1990-06-12

    The aromatic region of the 1H-FT-NMR spectrum of the biologically fully-potent, monomeric human insulin mutant, B9 Ser----Asp, B27 Thr----Glu has been investigated in D2O. At 1 to 5 mM concentrations, this mutant insulin is monomeric above pH 7.5. Coupling and amino acid classification of all aromatic signals is established via a combination of homonuclear one- and two-dimensional methods, including COSY, multiple quantum filters, selective spin decoupling and pH titrations. By comparisons with other insulin mutants and with chemically modified native insulins, all resonances in the aromatic region are given sequence-specific assignments without any reliance on the various crystal structures reported for insulin. These comparisons also give the sequence-specific assignments of most of the aromatic resonances of the mutant insulins B16 Tyr----Glu, B27 Thr----Glu and B25 Phe----Asp and the chemically modified species des-(B23-B30) insulin and monoiodo-Tyr A14 insulin. Chemical dispersion of the assigned resonances, ring current perturbations and comparisons at high pH have made possible the assignment of the aromatic resonances of human insulin, and these studies indicate that the major structural features of the human insulin monomer (including those critical to biological function) are also present in the monomeric mutant.

  14. Molecular design of sequence specific DNA alkylating agents.

    Science.gov (United States)

    Minoshima, Masafumi; Bando, Toshikazu; Shinohara, Ken-ichi; Sugiyama, Hiroshi

    2009-01-01

    Sequence-specific DNA alkylating agents have great interest for novel approach to cancer chemotherapy. We designed the conjugates between pyrrole (Py)-imidazole (Im) polyamides and DNA alkylating chlorambucil moiety possessing at different positions. The sequence-specific DNA alkylation by conjugates was investigated by using high-resolution denaturing polyacrylamide gel electrophoresis (PAGE). The results showed that polyamide chlorambucil conjugates alkylate DNA at flanking adenines in recognition sequences of Py-Im polyamides, however, the reactivities and alkylation sites were influenced by the positions of conjugation. In addition, we synthesized conjugate between Py-Im polyamide and another alkylating agent, 1-(chloromethyl)-5-hydroxy-1,2-dihydro-3H-benz[e]indole (seco-CBI). DNA alkylation reactivies by both alkylating polyamides were almost comparable. In contrast, cytotoxicities against cell lines differed greatly. These comparative studies would promote development of appropriate sequence-specific DNA alkylating polyamides against specific cancer cells.

  15. Acceleration of electrons at wakefield excitation by a sequence of relativistic electron bunches in dielectric resonator

    International Nuclear Information System (INIS)

    Kiselev, V.A.; Linnik, A.F.; Mirnyj, V.I.; Onishchenko, I.N.; Uskov, V.V.

    2009-01-01

    Method is proposed to divide a regular sequence of electron bunches into parts of bunches driving wakefield and witness bunches, which should be accelerated. It allows to avoid the necessity of additional electron accelerator for witness bunches producing and the necessity of precision short time techniques of injection phase adjusting. The idea concludes to the frequency detuning between bunches repetition frequency and the frequency of the fundamental mode of excited wakefield. Experiments were carried out on the linear resonant accelerator 'Almaz-2', which injected in the dielectric resonator a sequence of 6000 short bunches of relativistic electrons with energy 4.5 MeV, charge 0.16 nC and duration 60 psec each, the repetition interval 360 ps. Frequency detuning was entered by change of frequency of the master generator of the klystron within the limits of one percent so that the phase taper on the length of bunches sequence achieved 2π. Energy spectra of electrons of bunches sequence, which have been propagated through the dielectric resonator are measured and analyzed

  16. Study and realisation of a programmable generator of pulse sequences, for nuclear magnetic resonance

    International Nuclear Information System (INIS)

    Lambert, Daniel

    1974-01-01

    After having recalled the operation of pulse-based nuclear magnetic resonance and the use of pulse sequences in NMR-based measurements, and outlined the need for a pulse sequence generator, the author reports the design and realisation of such a device. He describes its general organisation with its base sequence, base clock, sequence start, duration, displays, data transfers, data processing, and signal distribution. He presents the chosen technology (ECL logics), the sequence base set, time bases, multiplexers, comparison sets, the distribution set, the sequence programming, the sampling and output set. He reports tests and the use of the so-designed generator [fr

  17. The sequence specificity of UV-induced DNA damage in a systematically altered DNA sequence.

    Science.gov (United States)

    Khoe, Clairine V; Chung, Long H; Murray, Vincent

    2018-06-01

    The sequence specificity of UV-induced DNA damage was investigated in a specifically designed DNA plasmid using two procedures: end-labelling and linear amplification. Absorption of UV photons by DNA leads to dimerisation of pyrimidine bases and produces two major photoproducts, cyclobutane pyrimidine dimers (CPDs) and pyrimidine(6-4)pyrimidone photoproducts (6-4PPs). A previous study had determined that two hexanucleotide sequences, 5'-GCTC*AC and 5'-TATT*AA, were high intensity UV-induced DNA damage sites. The UV clone plasmid was constructed by systematically altering each nucleotide of these two hexanucleotide sequences. One of the main goals of this study was to determine the influence of single nucleotide alterations on the intensity of UV-induced DNA damage. The sequence 5'-GCTC*AC was designed to examine the sequence specificity of 6-4PPs and the highest intensity 6-4PP damage sites were found at 5'-GTTC*CC nucleotides. The sequence 5'-TATT*AA was devised to investigate the sequence specificity of CPDs and the highest intensity CPD damage sites were found at 5'-TTTT*CG nucleotides. It was proposed that the tetranucleotide DNA sequence, 5'-YTC*Y (where Y is T or C), was the consensus sequence for the highest intensity UV-induced 6-4PP adduct sites; while it was 5'-YTT*C for the highest intensity UV-induced CPD damage sites. These consensus tetranucleotides are composed entirely of consecutive pyrimidines and must have a DNA conformation that is highly productive for the absorption of UV photons. Crown Copyright © 2018. Published by Elsevier B.V. All rights reserved.

  18. Comparison between two.magnetic resonance sequences (spin-echo and gradient-echo) in the analysis of lesions of the knee joint meniscus

    International Nuclear Information System (INIS)

    Marti-Bonati, L.; Casillas, C.

    1999-01-01

    To compare the diagnostic reliability, the proportion of common diagnoses and the degree of agreement between the results of two magnetic resonance (MR) sequences in the diagnosis of lesions of the meniscus of the knee. One hundred consecutive patients were studied prospectively by MR (1,5 Teslas). All of them underwent T1-weighted spin-echo and T1 and T2-weighted gradient-echo sequences. The final diagnosis was based on the combined results of four imaging sequences. The sensitivity, specificity, positive predictive value (PPV) and negative predictive (NPV) in terms of the final diagnosis were calculated for each meniscus and MR technique. The chi.squared test and kappa test were employed for the statistical analysis. There were discrepancies between the final diagnosis and the spin-echo sequence in 4 cases and between the final diagnosis and the gradient-echo sequences in 5 Both spin-echo and gradient-echo sequences showed the same diagnostic reliabilities: sensitivity of 0.98, specificity of 0.99, PPV of 0.98 and NPV of 0.99. The correlation between the two sequences was highly significant (chi-squared, p < 0.001) with a very high rate of agreement (kappa=0.84). The two sequences can be considered equally reliable in the study of meniscal lesions. (Author) 7 refs

  19. A modified strategy for sequence specific assignment of protein NMR spectra based on amino acid type selective experiments

    International Nuclear Information System (INIS)

    Schubert, Mario; Labudde, Dirk; Leitner, Dietmar; Oschkinat, Hartmut; Schmieder, Peter

    2005-01-01

    The determination of the three-dimensional structure of a protein or the study of protein-ligand interactions requires the assignment of all relevant nuclei as an initial step. This is nowadays almost exclusively performed using triple-resonance experiments. The conventional strategy utilizes one or more pairs of three dimensional spectra to obtain redundant information and thus reliable assignments. Here, a modified strategy for obtaining sequence specific assignments based on two dimensional amino acid type selective triple-resonance experiments is proposed. These experiments can be recorded with good resolution in a relatively short time. They provide very specific and redundant information, in particular on sequential connectivities, that drastically increases the ease and reliability of the assignment procedure, done either manually or in an automated fashion. The new strategy is demonstrated with the protein domain PB1 from yeast CDC24p

  20. Sequence-specific DNA alkylation by tandem Py-Im polyamide conjugates.

    Science.gov (United States)

    Taylor, Rhys Dylan; Kawamoto, Yusuke; Hashiya, Kaori; Bando, Toshikazu; Sugiyama, Hiroshi

    2014-09-01

    Tandem N-methylpyrrole-N-methylimidazole (Py-Im) polyamides with good sequence-specific DNA-alkylating activities have been designed and synthesized. Three alkylating tandem Py-Im polyamides with different linkers, which each contained the same moiety for the recognition of a 10 bp DNA sequence, were evaluated for their reactivity and selectivity by DNA alkylation, using high-resolution denaturing gel electrophoresis. All three conjugates displayed high reactivities for the target sequence. In particular, polyamide 1, which contained a β-alanine linker, displayed the most-selective sequence-specific alkylation towards the target 10 bp DNA sequence. The tandem Py-Im polyamide conjugates displayed greater sequence-specific DNA alkylation than conventional hairpin Py-Im polyamide conjugates (4 and 5). For further research, the design of tandem Py-Im polyamide conjugates could play an important role in targeting specific gene sequences. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Adenosine stress cardiovascular magnetic resonance with variable-density spiral pulse sequences accurately detects coronary artery disease: initial clinical evaluation.

    Science.gov (United States)

    Salerno, Michael; Taylor, Angela; Yang, Yang; Kuruvilla, Sujith; Ragosta, Michael; Meyer, Craig H; Kramer, Christopher M

    2014-07-01

    Adenosine stress cardiovascular magnetic resonance perfusion imaging can be limited by motion-induced dark-rim artifacts, which may be mistaken for true perfusion abnormalities. A high-resolution variable-density spiral pulse sequence with a novel density compensation strategy has been shown to reduce dark-rim artifacts in first-pass perfusion imaging. We aimed to assess the clinical performance of adenosine stress cardiovascular magnetic resonance using this new perfusion sequence to detect obstructive coronary artery disease. Cardiovascular magnetic resonance perfusion imaging was performed during adenosine stress (140 μg/kg per minute) and at rest on a Siemens 1.5-T Avanto scanner in 41 subjects with chest pain scheduled for coronary angiography. Perfusion images were acquired during injection of 0.1 mmol/kg Gadolinium-diethylenetriaminepentacetate at 3 short-axis locations using a saturation recovery interleaved variable-density spiral pulse sequence. Significant stenosis was defined as >50% by quantitative coronary angiography. Two blinded reviewers evaluated the perfusion images for the presence of adenosine-induced perfusion abnormalities and assessed image quality using a 5-point scale (1 [poor] to 5 [excellent]). The prevalence of obstructive coronary artery disease by quantitative coronary angiography was 68%. The average sensitivity, specificity, and accuracy were 89%, 85%, and 88%, respectively, with a positive predictive value and negative predictive value of 93% and 79%, respectively. The average image quality score was 4.4±0.7, with only 1 study with more than mild dark-rim artifacts. There was good inter-reader reliability with a κ statistic of 0.67. Spiral adenosine stress cardiovascular magnetic resonance results in high diagnostic accuracy for the detection of obstructive coronary artery disease with excellent image quality and minimal dark-rim artifacts. © 2014 American Heart Association, Inc.

  2. Campbell's monkeys concatenate vocalizations into context-specific call sequences

    Science.gov (United States)

    Ouattara, Karim; Lemasson, Alban; Zuberbühler, Klaus

    2009-01-01

    Primate vocal behavior is often considered irrelevant in modeling human language evolution, mainly because of the caller's limited vocal control and apparent lack of intentional signaling. Here, we present the results of a long-term study on Campbell's monkeys, which has revealed an unrivaled degree of vocal complexity. Adult males produced six different loud call types, which they combined into various sequences in highly context-specific ways. We found stereotyped sequences that were strongly associated with cohesion and travel, falling trees, neighboring groups, nonpredatory animals, unspecific predatory threat, and specific predator classes. Within the responses to predators, we found that crowned eagles triggered four and leopards three different sequences, depending on how the caller learned about their presence. Callers followed a number of principles when concatenating sequences, such as nonrandom transition probabilities of call types, addition of specific calls into an existing sequence to form a different one, or recombination of two sequences to form a third one. We conclude that these primates have overcome some of the constraints of limited vocal control by combinatorial organization. As the different sequences were so tightly linked to specific external events, the Campbell's monkey call system may be the most complex example of ‘proto-syntax’ in animal communication known to date. PMID:20007377

  3. Sequence-specific {sup 1}H, {sup 13}C, and {sup 15}N resonance assignments for intestinal fatty-acid-binding protein complexed with palmitate (15.4 kDA)

    Energy Technology Data Exchange (ETDEWEB)

    Hodsdon, M.E.; Toner, J.J.; Cistola, D.P. [Washington Univ. School of Medicine, St. Louis, MO (United States)

    1994-12-01

    Intestinal fatty-acid-binding protein (I-FABP) belongs to a family of soluble, cytoplasmic proteins that are thought to function in the intracellular transport and trafficking of polar lipids. Individual members of this protein family have distinct specificities and affinities for fatty acids, cholesterol, bile salts, and retinoids. We are comparing several retinol- and fatty-acid-binding proteins from intestine in order to define the factors that control molecular recognition in this family of proteins. We have established sequential resonance assignments for uniformly {sup 13}C/{sup 15}N-enriched I-FABP complexed with perdeuterated palmitate at pH7.2 and 37{degrees}C. The assignment strategy was similar to that introduced for calmodulin. We employed seven three-dimensional NMR experiments to establish scalar couplings between backbone and sidechain atoms. Backbone atoms were correlated using triple-resonance HNCO, HNCA, TOCSY-HMQC, HCACO, and HCA(CO)N experiments. Sidechain atoms were correlated using CC-TOCSY, HCCH-TOCSY, and TOCSY-HMQC. The correlations of peaks between three-dimensional spectra were established in a computer-assisted manner using NMR COMPASS (Molecular Simulations, Inc.) Using this approach, {sup 1}H, {sup 13}C, and {sup 15}N resonance assignments have been established for 120 of the 131 residues of I-FABP. For 18 residues, amide {sup 1}H and {sup 15}N resonances were unobservable, apparently because of the rapid exchange of amide protons with bulk water at pH 7.2. The missing amide protons correspond to distinct amino acid patterns in the protein sequence, which will be discussed. During the assignment process, several sources of ambiguity in spin correlations were observed. To overcome this ambiguity, the additional inter-residue correlations often observed in the HNCA experiment were used as cross-checks for the sequential backbone assignments.

  4. An extended sequence specificity for UV-induced DNA damage.

    Science.gov (United States)

    Chung, Long H; Murray, Vincent

    2018-01-01

    The sequence specificity of UV-induced DNA damage was determined with a higher precision and accuracy than previously reported. UV light induces two major damage adducts: cyclobutane pyrimidine dimers (CPDs) and pyrimidine(6-4)pyrimidone photoproducts (6-4PPs). Employing capillary electrophoresis with laser-induced fluorescence and taking advantages of the distinct properties of the CPDs and 6-4PPs, we studied the sequence specificity of UV-induced DNA damage in a purified DNA sequence using two approaches: end-labelling and a polymerase stop/linear amplification assay. A mitochondrial DNA sequence that contained a random nucleotide composition was employed as the target DNA sequence. With previous methodology, the UV sequence specificity was determined at a dinucleotide or trinucleotide level; however, in this paper, we have extended the UV sequence specificity to a hexanucleotide level. With the end-labelling technique (for 6-4PPs), the consensus sequence was found to be 5'-GCTC*AC (where C* is the breakage site); while with the linear amplification procedure, it was 5'-TCTT*AC. With end-labelling, the dinucleotide frequency of occurrence was highest for 5'-TC*, 5'-TT* and 5'-CC*; whereas it was 5'-TT* for linear amplification. The influence of neighbouring nucleotides on the degree of UV-induced DNA damage was also examined. The core sequences consisted of pyrimidine nucleotides 5'-CTC* and 5'-CTT* while an A at position "1" and C at position "2" enhanced UV-induced DNA damage. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

  5. Sequence-specific procedural learning deficits in children with specific language impairment.

    Science.gov (United States)

    Hsu, Hsinjen Julie; Bishop, Dorothy V M

    2014-05-01

    This study tested the procedural deficit hypothesis of specific language impairment (SLI) by comparing children's performance in two motor procedural learning tasks and an implicit verbal sequence learning task. Participants were 7- to 11-year-old children with SLI (n = 48), typically developing age-matched children (n = 20) and younger typically developing children matched for receptive grammar (n = 28). In a serial reaction time task, the children with SLI performed at the same level as the grammar-matched children, but poorer than age-matched controls in learning motor sequences. When tested with a motor procedural learning task that did not involve learning sequential relationships between discrete elements (i.e. pursuit rotor), the children with SLI performed comparably with age-matched children and better than younger grammar-matched controls. In addition, poor implicit learning of word sequences in a verbal memory task (the Hebb effect) was found in the children with SLI. Together, these findings suggest that SLI might be characterized by deficits in learning sequence-specific information, rather than generally weak procedural learning. © 2014 The Authors. Developmental Science Published by John Wiley & Sons Ltd.

  6. Encoding efficiency of suprathreshold stochastic resonance on stimulus-specific information

    Energy Technology Data Exchange (ETDEWEB)

    Duan, Fabing, E-mail: fabing.duan@gmail.com [Institute of Complexity Science, Qingdao University, Qingdao 266071 (China); Chapeau-Blondeau, François, E-mail: chapeau@univ-angers.fr [Laboratoire Angevin de Recherche en Ingénierie des Systèmes (LARIS), Université d' Angers, 62 avenue Notre Dame du Lac, 49000 Angers (France); Abbott, Derek, E-mail: derek.abbott@adelaide.edu.au [Centre for Biomedical Engineering (CBME) and School of Electrical & Electronic Engineering, The University of Adelaide, Adelaide, SA 5005 (Australia)

    2016-01-08

    In this paper, we evaluate the encoding efficiency of suprathreshold stochastic resonance (SSR) based on a local information-theoretic measure of stimulus-specific information (SSI), which is the average specific information of responses associated with a particular stimulus. The theoretical and numerical analyses of SSIs reveal that noise can improve neuronal coding efficiency for a large population of neurons, which leads to produce increased information-rich responses. The SSI measure, in contrast to the global measure of average mutual information, can characterize the noise benefits in finer detail for describing the enhancement of neuronal encoding efficiency of a particular stimulus, which may be of general utility in the design and implementation of a SSR coding scheme. - Highlights: • Evaluating the noise-enhanced encoding efficiency via stimulus-specific information. • New form of stochastic resonance based on the measure of encoding efficiency. • Analyzing neural encoding schemes from suprathreshold stochastic resonance detailedly.

  7. Predicting tissue-specific expressions based on sequence characteristics

    KAUST Repository

    Paik, Hyojung; Ryu, Tae Woo; Heo, Hyoungsam; Seo, Seungwon; Lee, Doheon; Hur, Cheolgoo

    2011-01-01

    In multicellular organisms, including humans, understanding expression specificity at the tissue level is essential for interpreting protein function, such as tissue differentiation. We developed a prediction approach via generated sequence features from overrepresented patterns in housekeeping (HK) and tissue-specific (TS) genes to classify TS expression in humans. Using TS domains and transcriptional factor binding sites (TFBSs), sequence characteristics were used as indices of expressed tissues in a Random Forest algorithm by scoring exclusive patterns considering the biological intuition; TFBSs regulate gene expression, and the domains reflect the functional specificity of a TS gene. Our proposed approach displayed better performance than previous attempts and was validated using computational and experimental methods.

  8. Predicting tissue-specific expressions based on sequence characteristics

    KAUST Repository

    Paik, Hyojung

    2011-04-30

    In multicellular organisms, including humans, understanding expression specificity at the tissue level is essential for interpreting protein function, such as tissue differentiation. We developed a prediction approach via generated sequence features from overrepresented patterns in housekeeping (HK) and tissue-specific (TS) genes to classify TS expression in humans. Using TS domains and transcriptional factor binding sites (TFBSs), sequence characteristics were used as indices of expressed tissues in a Random Forest algorithm by scoring exclusive patterns considering the biological intuition; TFBSs regulate gene expression, and the domains reflect the functional specificity of a TS gene. Our proposed approach displayed better performance than previous attempts and was validated using computational and experimental methods.

  9. Optimal sequence for magnetic resonance cholangiopancreatography

    Energy Technology Data Exchange (ETDEWEB)

    Kanzaki, Hiroshi; Akata, Soichi; Ozuki, Taizo; Abe, Kimihiko [Tokyo Medical Coll. (Japan)

    2001-09-01

    Magnetic resonance cholangiopancreatography (MRCP) has attracted attention as a useful examination for abnormalities of the pancreaticobiliary system, because it is a simple procedure. Since there are few detailed reports on optimal sequences for MRCP, we attempted to clarify the topic. The magnetic resonance imaging (MRI) equipment we used was a 1.0 Tesla super-conductive type. A fast spin echo (16 echo train) was used, and the echo space was set at 17 msec. TE was changed from 17 msec to 272 msec in 17 msec increments. TR was changed from 1,000 msec to 9,000 msec by 1,000 msec increments. Bile juice which had been collected from the PTCD tube of a patient with common bile duct cancer, was put in a test tube of 10 mm internal diameter. Saline was used as a substitute for pancreatic juice, because collection of pancreatic juice was difficult. Fat was used for contrast. Each signal intensity inside the test tube was measured and evaluated. We attempted to evaluate the signal of gastric juice by adding blueberry juice, making use of its manganese ion (Mn{sup ++}). With longer TR, the signal intensities of bile and pancreas juice increased. As TE became longer, the signal intensities of bile and pancreas juice decreased slightly, while that of fat decreased much more. In MRCP, it is necessary to set up a long TE to increase the relative signal intensity difference of fat in bile and pancreas juice. The signal intensity of gastric juice was made to disappear by the addition of blueberry juice diluted to a ratio of 1:3. (author)

  10. Optimal sequence for magnetic resonance cholangiopancreatography

    International Nuclear Information System (INIS)

    Kanzaki, Hiroshi; Akata, Soichi; Ozuki, Taizo; Abe, Kimihiko

    2001-01-01

    Magnetic resonance cholangiopancreatography (MRCP) has attracted attention as a useful examination for abnormalities of the pancreaticobiliary system, because it is a simple procedure. Since there are few detailed reports on optimal sequences for MRCP, we attempted to clarify the topic. The magnetic resonance imaging (MRI) equipment we used was a 1.0 Tesla super-conductive type. A fast spin echo (16 echo train) was used, and the echo space was set at 17 msec. TE was changed from 17 msec to 272 msec in 17 msec increments. TR was changed from 1,000 msec to 9,000 msec by 1,000 msec increments. Bile juice which had been collected from the PTCD tube of a patient with common bile duct cancer, was put in a test tube of 10 mm internal diameter. Saline was used as a substitute for pancreatic juice, because collection of pancreatic juice was difficult. Fat was used for contrast. Each signal intensity inside the test tube was measured and evaluated. We attempted to evaluate the signal of gastric juice by adding blueberry juice, making use of its manganese ion (Mn ++ ). With longer TR, the signal intensities of bile and pancreas juice increased. As TE became longer, the signal intensities of bile and pancreas juice decreased slightly, while that of fat decreased much more. In MRCP, it is necessary to set up a long TE to increase the relative signal intensity difference of fat in bile and pancreas juice. The signal intensity of gastric juice was made to disappear by the addition of blueberry juice diluted to a ratio of 1:3. (author)

  11. High dimensional and high resolution pulse sequences for backbone resonance assignment of intrinsically disordered proteins

    Energy Technology Data Exchange (ETDEWEB)

    Zawadzka-Kazimierczuk, Anna; Kozminski, Wiktor, E-mail: kozmin@chem.uw.edu.pl [University of Warsaw, Faculty of Chemistry (Poland); Sanderova, Hana; Krasny, Libor [Institute of Microbiology, Academy of Sciences of the Czech Republic, Laboratory of Molecular Genetics of Bacteria, Department of Bacteriology (Czech Republic)

    2012-04-15

    Four novel 5D (HACA(N)CONH, HNCOCACB, (HACA)CON(CA)CONH, (H)NCO(NCA)CONH), and one 6D ((H)NCO(N)CACONH) NMR pulse sequences are proposed. The new experiments employ non-uniform sampling that enables achieving high resolution in indirectly detected dimensions. The experiments facilitate resonance assignment of intrinsically disordered proteins. The novel pulse sequences were successfully tested using {delta} subunit (20 kDa) of Bacillus subtilis RNA polymerase that has an 81-amino acid disordered part containing various repetitive sequences.

  12. Sequence-specific bias correction for RNA-seq data using recurrent neural networks.

    Science.gov (United States)

    Zhang, Yao-Zhong; Yamaguchi, Rui; Imoto, Seiya; Miyano, Satoru

    2017-01-25

    The recent success of deep learning techniques in machine learning and artificial intelligence has stimulated a great deal of interest among bioinformaticians, who now wish to bring the power of deep learning to bare on a host of bioinformatical problems. Deep learning is ideally suited for biological problems that require automatic or hierarchical feature representation for biological data when prior knowledge is limited. In this work, we address the sequence-specific bias correction problem for RNA-seq data redusing Recurrent Neural Networks (RNNs) to model nucleotide sequences without pre-determining sequence structures. The sequence-specific bias of a read is then calculated based on the sequence probabilities estimated by RNNs, and used in the estimation of gene abundance. We explore the application of two popular RNN recurrent units for this task and demonstrate that RNN-based approaches provide a flexible way to model nucleotide sequences without knowledge of predetermined sequence structures. Our experiments show that training a RNN-based nucleotide sequence model is efficient and RNN-based bias correction methods compare well with the-state-of-the-art sequence-specific bias correction method on the commonly used MAQC-III data set. RNNs provides an alternative and flexible way to calculate sequence-specific bias without explicitly pre-determining sequence structures.

  13. Magnetic resonance imaging of anterior cruciate ligament of the knee: a comparison of four sequences

    International Nuclear Information System (INIS)

    Casillas, C.; Marti-Bonmati, L.; Molla, E.; Ferrer, P.; Dosda, R.

    1999-01-01

    To compare the diagnostic efficacy of the four magnetic resonance imaging (MRI) sequences that compose the standard protocol for the study of the knee in our center when employed in the examination of anterior cruciate ligament (ACL). A prospective study was carried out based on MRI findings in the knees of 326 consecutive patients. Sagittal [proton density (PD w eighted turbo-spin-echo and T2*-weighted gradient echo], coronal (PD-weighted turbo-spin-echo with fat suppression) and transverse (T2*-weighted gradient echo with magnetization transfer) images were evaluated. Each sequence was analyzed independently by two radiologists, while another two assessed all the sequences together with the clinical findings. Four categories were established: normal ACL, partially torn, completely torn and synovialized. The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) with respect to the definitive diagnosis were calculated for each sequence. The statistical analysis of the findings for each category was done using the chi-squared test and the Kappa test was employed to assess the degree of agreement. According to the final diagnosis, 263 ACL were normal, 29 were partially torn, 33 were completely torn and there was 1 case of synovialization associated with a completely torn ACL. The relationship between the analysis of the ACL according to each sequence and the definitive diagnosis was very significant (p<0.001) and the agreement was excellent. All the sequences presented similar levels of diagnostic precision. The coronal sequence had least number of diagnostic errors (2.1%). The combinations of imaging techniques that resulted in the lowest error rate with respect to the definitive diagnosis were coronal PD-weighted turbo-spin-echo with fat suppression and sagittal PD-weighted turbo-spin-echo. Coronal images are highly precise in the evaluation of ACL. Sagittal sequences are the most valid for diagnosis of torn ACL. Transverse

  14. Winnowing DNA for rare sequences: highly specific sequence and methylation based enrichment.

    Directory of Open Access Journals (Sweden)

    Jason D Thompson

    Full Text Available Rare mutations in cell populations are known to be hallmarks of many diseases and cancers. Similarly, differential DNA methylation patterns arise in rare cell populations with diagnostic potential such as fetal cells circulating in maternal blood. Unfortunately, the frequency of alleles with diagnostic potential, relative to wild-type background sequence, is often well below the frequency of errors in currently available methods for sequence analysis, including very high throughput DNA sequencing. We demonstrate a DNA preparation and purification method that through non-linear electrophoretic separation in media containing oligonucleotide probes, achieves 10,000 fold enrichment of target DNA with single nucleotide specificity, and 100 fold enrichment of unmodified methylated DNA differing from the background by the methylation of a single cytosine residue.

  15. Winnowing DNA for rare sequences: highly specific sequence and methylation based enrichment.

    Science.gov (United States)

    Thompson, Jason D; Shibahara, Gosuke; Rajan, Sweta; Pel, Joel; Marziali, Andre

    2012-01-01

    Rare mutations in cell populations are known to be hallmarks of many diseases and cancers. Similarly, differential DNA methylation patterns arise in rare cell populations with diagnostic potential such as fetal cells circulating in maternal blood. Unfortunately, the frequency of alleles with diagnostic potential, relative to wild-type background sequence, is often well below the frequency of errors in currently available methods for sequence analysis, including very high throughput DNA sequencing. We demonstrate a DNA preparation and purification method that through non-linear electrophoretic separation in media containing oligonucleotide probes, achieves 10,000 fold enrichment of target DNA with single nucleotide specificity, and 100 fold enrichment of unmodified methylated DNA differing from the background by the methylation of a single cytosine residue.

  16. Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences.

    Directory of Open Access Journals (Sweden)

    Alexander M Sevy

    2015-07-01

    Full Text Available Computational protein design has found great success in engineering proteins for thermodynamic stability, binding specificity, or enzymatic activity in a 'single state' design (SSD paradigm. Multi-specificity design (MSD, on the other hand, involves considering the stability of multiple protein states simultaneously. We have developed a novel MSD algorithm, which we refer to as REstrained CONvergence in multi-specificity design (RECON. The algorithm allows each state to adopt its own sequence throughout the design process rather than enforcing a single sequence on all states. Convergence to a single sequence is encouraged through an incrementally increasing convergence restraint for corresponding positions. Compared to MSD algorithms that enforce (constrain an identical sequence on all states the energy landscape is simplified, which accelerates the search drastically. As a result, RECON can readily be used in simulations with a flexible protein backbone. We have benchmarked RECON on two design tasks. First, we designed antibodies derived from a common germline gene against their diverse targets to assess recovery of the germline, polyspecific sequence. Second, we design "promiscuous", polyspecific proteins against all binding partners and measure recovery of the native sequence. We show that RECON is able to efficiently recover native-like, biologically relevant sequences in this diverse set of protein complexes.

  17. Searching sequences of resonant orbits between a spacecraft and Jupiter

    International Nuclear Information System (INIS)

    Formiga, J K S; Prado, A F B A

    2013-01-01

    This research shows a study of the dynamical behavior of a spacecraft that performs a series of close approaches with the planet Jupiter. The main idea is to find a sequence of resonant orbits that allows the spacecraft to stay in the region of the space near the orbit of Jupiter around the Sun gaining energy from each passage by the planet. The dynamical model considers the existence of only two massive bodies in the systems, which are the Sun and Jupiter. They are assumed to be in circular orbits around their center of mass. Analytical equations are used to obtain the values of the parameters required to get this sequence of close approaches. Those equations are useful, because they show which orbits are physically possible when taking into account that the periapsis distances have to be above the surface of the Sun and that the closest approach distances during the passage by Jupiter have to be above its surface

  18. The diagnostic value of magnetic resonance urography using a balanced turbo field echo sequence

    Energy Technology Data Exchange (ETDEWEB)

    Cifci, Egemen; Coban, Goekcen [Baskent University Faculty of Medicine, Department of Radiology, Konya (Turkey); Cicek, Tufan; Goenuelalan, Umut [Baskent University Faculty of Medicine, Department of Urology, Konya (Turkey)

    2016-12-15

    The aim of the study was to compare the inter-observer variability and the accuracy of magnetic resonance urography (MRU) using a thin sectional balanced-turbo field echo (B-TFE) sequence for detecting ureteral calculi and to determine the effect of additional factors (size, density and location of the calculus) on the sensitivity and specificity of the MRU. MRU and CT images were evaluated independently by two radiologists according to presence, density and localization of calculi. The degrees of inter-rater agreement for categorical items were evaluated by the Kappa coefficient. According to the 1st and 2nd observers, the sensitivity of MRU was 65.9 %, 71.8 % and the specificity of MRU was 95.9 %, 100 %, respectively. Inter-observer agreement was 84.6 % for stone detection. The larger size had a better effect on detectability (p < 0.05). Also, the higher density had a better impact on detectability (p < 0.05). Our study has shown that B-TFE MRU was useful to detect ureteral calculi. However, B-TFE MRU has low sensitivity and high specificity in comparison with CT images. MRU is a reasonable alternative imaging technique for follow-up periods of selective groups like patients with large urinary stones, children or pregnant patients when ionizing radiation is undesirable. (orig.)

  19. Specific detection of proteins using Nanomechanical resonators

    DEFF Research Database (Denmark)

    Fischer, Lee MacKenzie; Wright, V.A.; Guthy, C.

    2008-01-01

    of probes onto their surfaces in order to enable the specificity of the detection. Such nanoresonator-based specific detection of proteins is here reported using streptavidin as target system, and immobilized biotin as probe. Nanomechanical resonators resistant to stiction were first realized from silicon...... carbonitride using a novel fabrication method. Vapor-phase deposition of mercaptopropyl trimethoxysilane was performed, and an added mass of 2.22 +/- 0.07 fg/mu m(2) was measured. This linker molecule was used to attach biotin onto the devices, enabling the specific detection of streptavidin. A mass of 3.6 fg....../mu m(2) was attributed to the added streptavidin, corresponding to one molecule per 27 nm(2). The specificity of this recognition was confirmed by exposing the devices to a solution of streptavidin that was already saturated with biotin. An additional negative control was also performed by also...

  20. Stimulation of Protein Expression Through the Harmonic Resonance of Frequency-Specific Music.

    Science.gov (United States)

    Orhan, Ibrahim Y; Gulbahar, Burak A

    2016-12-01

    The use of specific frequencies for specific individual amino acids may increase the potential energy of protein molecules in the medium [1]. The resonance would also increase the movement of particles in the cytosol, increasing the collisions necessary for the conduction of protein expression. The clash of two waves that share frequencies will exhibit an increase in energy through an increase in amplitude [2]. The increase in energy would in turn increase the number of collisions forming the tRNA-amino acid, increasing the amino acid acquiry for ribosomes to improve intracellular efficiency in gene expression. To test the hypothesis, Red Fluorescent Protein (RFP) in transformated BL-21 strains of E. coli and p53 protein of MCF-7 were examined after exposure to sounds of specific frequencies. Through the exposure of the experimental systems to a sequence of sounds that match the frequencies of specific amino acids, the levels of RFP exhibition respective to the control groups in the bacterial medium increased two-fold in terms of RFU. The experiments that targeted the p53 protein with the 'music' showed a decrease in the cell prevalence in the MCF-7 type breast cancer cells by 28%, by decreasing the speed of tumour formation. Exposure to 'music' that was designed through assigning a musical note for every single one of the twenty unique amino acids, produced both an analytical and a visible shift in protein synthesis, making it as potential tool for reducing procedural time uptake.

  1. Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials.

    Science.gov (United States)

    Bikard, David; Euler, Chad W; Jiang, Wenyan; Nussenzweig, Philip M; Goldberg, Gregory W; Duportet, Xavier; Fischetti, Vincent A; Marraffini, Luciano A

    2014-11-01

    Antibiotics target conserved bacterial cellular pathways or growth functions and therefore cannot selectively kill specific members of a complex microbial population. Here, we develop programmable, sequence-specific antimicrobials using the RNA-guided nuclease Cas9 (refs.1,2) delivered by a bacteriophage. We show that Cas9, reprogrammed to target virulence genes, kills virulent, but not avirulent, Staphylococcus aureus. Reprogramming the nuclease to target antibiotic resistance genes destroys staphylococcal plasmids that harbor antibiotic resistance genes and immunizes avirulent staphylococci to prevent the spread of plasmid-borne resistance genes. We also show that CRISPR-Cas9 antimicrobials function in vivo to kill S. aureus in a mouse skin colonization model. This technology creates opportunities to manipulate complex bacterial populations in a sequence-specific manner.

  2. 1H NMR studies of plastocyanin from Scenedesmus obliquus: Complete sequence-specific assignment, secondary structure analysis, and global fold

    International Nuclear Information System (INIS)

    Moore, J.M.; Chazin, W.J.; Wright, P.E.; Powls, R.

    1988-01-01

    Two-dimensional 1 H NMR methods have been used to make sequence-specific resonance assignments for the 97 amino acid residues of the plastocyanin from the green alga Scenedesmus obliquus. Assignments were obtained for all backbone protons and the majority of the side-chain protons. Spin system identification relied heavily on the observation of relayed connectivities to the backbone amide proton. Sequence-specific assignments were made by using the sequential assignment procedure. During this process, an extra valine residue was identified that had not been detected in the original amino acid sequence. Elements of regular secondary structure were identified from characteristic NOE connectivities between backbone protons, coupling constant values, and the observation of slowly exchanging amide protons. The protein in solution contains eight β-strands, one short segment of helix, five reverse turns, and five loops. The β-strands may be arranged into two βsheets on the basis of extensive cross-strand NOE connectivities. The chain-folding topology determined from the NMR experiments is that of a Greek key β-barrel and is similar to that observed for French bean plastocyanin in solution and poplar plastocyanin in the crystalline state. While the overall structures are similar, several differences in local structure between the S. obliquus and higher plant plastocyanins have been identified

  3. Magnetic resonance imaging in local staging of endometrial carcinoma: diagnostic performance, pitfalls, and literature review.

    Science.gov (United States)

    Zandrino, Franco; La Paglia, Ernesto; Musante, Francesco

    2010-01-01

    To assess the diagnostic accuracy of magnetic resonance imaging in local staging of endometrial carcinoma, and to review the results and pitfalls described in the literature. Thirty women with a histological diagnosis of endometrial carcinoma underwent magnetic resonance imaging. Unenhanced T2-weighted and dynamic contrast-enhanced Ti-weighted sequences were obtained. Hysterectomy and salpingo-oophorectomy was performed in all patients. Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and accuracy were calculated for the detection of deep myometrial and cervical infiltration. For deep myometrial infiltration T2-weighted sequences reached a sensitivity of 85%, specificity of 76%, PPV of 73%, NVP of 87%, and accuracy of 80%, while contrast-enhanced scans reached a sensitivity of 90%, specificity of 80%, PPV of 82%, NPV of 89%, and accuracy of 85%. For cervical infiltration T2-weighted sequences reached a sensitivity of 75%, specificity of 88%, PPV of 50%, NPV of 96%, and accuracy of 87%, while contrast-enhanced scans reached a sensitivity of 100%, specificity of 94%, PPV of 75%, NPV of 100%, and accuracy of 95%. Unenhanced and dynamic gadolinium-enhanced magnetic resonance allows accurate assessment of myometrial and cervical infiltration. Information provided by magnetic resonance imaging can define prognosis and management.

  4. Effect of endorsed body weight on specific absorption rate during magnetic resonance imaging

    International Nuclear Information System (INIS)

    Singh, Harish K.; Gupta, R.K.; Gujral, R.B.; Shukla, A.K.

    2001-01-01

    As a routine safety of the patients undergoing magnetic resonance imaging (MRI), the limits of radiofrequency (RF) specific absorption rate (SAR) are set by the manufacturers of all MRI systems because RF causes thermo genesis of the RF exposed tissue. It has been mandatory practice to endorse body weight and age of the patients required by the MRI systems for the SAR check. The problems arise on those patients who are critically ill, and consequently body weight could not be measured. In such cases, approximate body weight has to be endorsed. In case of underweight and overweight patients, sometimes SAR check does not permit to run the MRI pulse sequences. Also, in such cases, body weight remains the parameter which is being changed to get the MRI done. The purpose of this study is to assess the change of SAR with endorsed body weight. The change of SAR was recorded with the endorsed weight using phantoms and most commonly used T1 and T2 weighted pulse sequence on clinical MRI system. At true endorsed weight, using respective coils and the head and spine coil phantoms, the body averaged and localised SAR were found to be within limits while this was not the case with body coil phantom. Unrealistic endorsed weights are permissible for the adult age cases in all coils while using the routine T1 and T2 weighted pulse sequences. This finding is absolutely new in the field and certainly, will be of great applicability to develop a uniform and standard system of SAR checks in the patient interest. (author)

  5. Structure-Related Roles for the Conservation of the HIV-1 Fusion Peptide Sequence Revealed by Nuclear Magnetic Resonance.

    Science.gov (United States)

    Serrano, Soraya; Huarte, Nerea; Rujas, Edurne; Andreu, David; Nieva, José L; Jiménez, María Angeles

    2017-10-17

    Despite extensive characterization of the human immunodeficiency virus type 1 (HIV-1) hydrophobic fusion peptide (FP), the structure-function relationships underlying its extraordinary degree of conservation remain poorly understood. Specifically, the fact that the tandem repeat of the FLGFLG tripeptide is absolutely conserved suggests that high hydrophobicity may not suffice to unleash FP function. Here, we have compared the nuclear magnetic resonance (NMR) structures adopted in nonpolar media by two FP surrogates, wtFP-tag and scrFP-tag, which had equal hydrophobicity but contained wild-type and scrambled core sequences LFLGFLG and FGLLGFL, respectively. In addition, these peptides were tagged at their C-termini with an epitope sequence that folded independently, thereby allowing Western blot detection without interfering with FP structure. We observed similar α-helical FP conformations for both specimens dissolved in the low-polarity medium 25% (v/v) 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP), but important differences in contact with micelles of the membrane mimetic dodecylphosphocholine (DPC). Thus, whereas wtFP-tag preserved a helix displaying a Gly-rich ridge, the scrambled sequence lost in great part the helical structure upon being solubilized in DPC. Western blot analyses further revealed the capacity of wtFP-tag to assemble trimers in membranes, whereas membrane oligomers were not observed in the case of the scrFP-tag sequence. We conclude that, beyond hydrophobicity, preserving sequence order is an important feature for defining the secondary structures and oligomeric states adopted by the HIV FP in membranes.

  6. Comparison between arthroscopy and 3 dimensional double echo steady state 3D-DESS sequences in magnetic resonance imaging of internal derangements of the knee

    International Nuclear Information System (INIS)

    Dongola, Nagwa A.; Gishen, Philip

    2004-01-01

    This study was performed with the aim of evaluating the usefulness of 3 dimensional double-echo steady state sequences in examining the internal derangements of the knee. Arthroscopy was used as a referral standard. The study was performed in the Radiology and Arthroscopy Departments of Kings College Hospital, London, United Kingdom, during a 6-month period from January 1997 to June 1997. All patients who had knee magnetic resonance imaging within 3 months of arthroscopy were retrospectively studied. Thirty-three patients fulfilled these criteria and were selected. Three dimensional double-echo steady state sequences produced sensitivity for detecting meniscal tears of 87.5% for medial menisci (MM) and 75% for lateral menisci (LM). Specificity was 76% for MM and 96% for LM; positive predictive value (PPV) was 46.1% for MM and 85.7% for LM and negative predictive value (NPV) of 95% for MM and 96% for LM. The sensitivity for the anterior cruciate ligament was 83.3%, specificity was 77.7%, PPV was 45.4% and NPV was 95.4%. Three dimensional double-echo steady state sequences are useful in evaluating internal derangement of the knee, especially in advanced cartilage lesions. (author)

  7. Cell type-specific termination of transcription by transposable element sequences.

    Science.gov (United States)

    Conley, Andrew B; Jordan, I King

    2012-09-30

    Transposable elements (TEs) encode sequences necessary for their own transposition, including signals required for the termination of transcription. TE sequences within the introns of human genes show an antisense orientation bias, which has been proposed to reflect selection against TE sequences in the sense orientation owing to their ability to terminate the transcription of host gene transcripts. While there is evidence in support of this model for some elements, the extent to which TE sequences actually terminate transcription of human gene across the genome remains an open question. Using high-throughput sequencing data, we have characterized over 9,000 distinct TE-derived sequences that provide transcription termination sites for 5,747 human genes across eight different cell types. Rarefaction curve analysis suggests that there may be twice as many TE-derived termination sites (TE-TTS) genome-wide among all human cell types. The local chromatin environment for these TE-TTS is similar to that seen for 3' UTR canonical TTS and distinct from the chromatin environment of other intragenic TE sequences. However, those TE-TTS located within the introns of human genes were found to be far more cell type-specific than the canonical TTS. TE-TTS were much more likely to be found in the sense orientation than other intragenic TE sequences of the same TE family and TE-TTS in the sense orientation terminate transcription more efficiently than those found in the antisense orientation. Alu sequences were found to provide a large number of relatively weak TTS, whereas LTR elements provided a smaller number of much stronger TTS. TE sequences provide numerous termination sites to human genes, and TE-derived TTS are particularly cell type-specific. Thus, TE sequences provide a powerful mechanism for the diversification of transcriptional profiles between cell types and among evolutionary lineages, since most TE-TTS are evolutionarily young. The extent of transcription

  8. Evaluation of Magnetic Resonance Imaging-Compatible Needles and Interactive Sequences for Musculoskeletal Interventions Using an Open High-Field Magnetic Resonance Imaging Scanner

    International Nuclear Information System (INIS)

    Wonneberger, Uta; Schnackenburg, Bernhard; Streitparth, Florian; Walter, Thula; Rump, Jens; Teichgraeber, Ulf K. M.

    2010-01-01

    In this article, we study in vitro evaluation of needle artefacts and image quality for musculoskeletal laser-interventions in an open high-field magnetic resonance imaging (MRI) scanner at 1.0T with vertical field orientation. Five commercially available MRI-compatible puncture needles were assessed based on artefact characteristics in a CuSO4 phantom (0.1%) and in human cadaveric lumbar spines. First, six different interventional sequences were evaluated with varying needle orientation to the main magnetic field B0 (0 o to 90 o ) in a sequence test. Artefact width, needle-tip error, and contrast-to-noise ratio (CNR) were calculated. Second, a gradient-echo sequence used for thermometric monitoring was assessed and in varying echo times, artefact width, tip error, and signal-to-noise ratio (SNR) were measured. Artefact width and needle-tip error correlated with needle material, instrument orientation to B0, and sequence type. Fast spin-echo sequences produced the smallest needle artefacts for all needles, except for the carbon fibre needle (width o to B0. Overall, the proton density-weighted spin-echo sequences had the best CNR (CNR Muscle/Needle >16.8). Concerning the thermometric gradient echo sequence, artefacts remained <5 mm, and the SNR reached its maximum at an echo time of 15 ms. If needle materials and sequences are accordingly combined, guidance and monitoring of musculoskeletal laser interventions may be feasible in a vertical magnetic field at 1.0T.

  9. Paramagnetic contrast media for magnetic resonance imaging of the central nervous system

    International Nuclear Information System (INIS)

    McNamara, M.T.

    1987-01-01

    Presently, a variety of radiofrequency (RF) and magnetic field gradient pulse sequences is used to manipulate magnetic resonance (MR) image contrast. Such manipulation may be performed by altering the RF pulse sequence repetition time (TR), the spin-echo delay time (TE), the inversion-delay time (TI), and the flip angle. The detection and characterization of a lesion or structure may thus be optimized. Although such contrast manipulation is noninvasive, magnetic resonance imaging (MRI) still suffers somewhat from lack of specificity. Also, the use of multiple imaging sequences to locate and characterize a lesion may prolong the imaging time and, thus, might place an economic burden on the system. Paramagnetic pharmaceuticals offer promise in this regard. They shorten tissue relaxation times, thus permitting the use of shorter imaging parameters, and in some circumstances, may obviate additional and more time-consuming pulse sequences. Paramagnetics could expand the sensitivity and specificity of MRI and provide functional information with regard to tissue perfusion, tissue viability, and blood-brain barrier integrity

  10. Sequence-specific RNA Photocleavage by Single-stranded DNA in Presence of Riboflavin

    Science.gov (United States)

    Zhao, Yongyun; Chen, Gangyi; Yuan, Yi; Li, Na; Dong, Juan; Huang, Xin; Cui, Xin; Tang, Zhuo

    2015-10-01

    Constant efforts have been made to develop new method to realize sequence-specific RNA degradation, which could cause inhibition of the expression of targeted gene. Herein, by using an unmodified short DNA oligonucleotide for sequence recognition and endogenic small molecue, vitamin B2 (riboflavin) as photosensitizer, we report a simple strategy to realize the sequence-specific photocleavage of targeted RNA. The DNA strand is complimentary to the target sequence to form DNA/RNA duplex containing a G•U wobble in the middle. The cleavage reaction goes through oxidative elimination mechanism at the nucleoside downstream of U of the G•U wobble in duplex to obtain unnatural RNA terminal, and the whole process is under tight control by using light as switch, which means the cleavage could be carried out according to specific spatial and temporal requirements. The biocompatibility of this method makes the DNA strand in combination with riboflavin a promising molecular tool for RNA manipulation.

  11. Discrimination of the Lactobacillus acidophilus group using sequencing, species-specific PCR and SNaPshot mini-sequencing technology based on the recA gene.

    Science.gov (United States)

    Huang, Chien-Hsun; Chang, Mu-Tzu; Huang, Mu-Chiou; Wang, Li-Tin; Huang, Lina; Lee, Fwu-Ling

    2012-10-01

    To clearly identify specific species and subspecies of the Lactobacillus acidophilus group using phenotypic and genotypic (16S rDNA sequence analysis) techniques alone is difficult. The aim of this study was to use the recA gene for species discrimination in the L. acidophilus group, as well as to develop a species-specific primer and single nucleotide polymorphism primer based on the recA gene sequence for species and subspecies identification. The average sequence similarity for the recA gene among type strains was 80.0%, and most members of the L. acidophilus group could be clearly distinguished. The species-specific primer was designed according to the recA gene sequencing, which was employed for polymerase chain reaction with the template DNA of Lactobacillus strains. A single 231-bp species-specific band was found only in L. delbrueckii. A SNaPshot mini-sequencing assay using recA as a target gene was also developed. The specificity of the mini-sequencing assay was evaluated using 31 strains of L. delbrueckii species and was able to unambiguously discriminate strains belonging to the subspecies L. delbrueckii subsp. bulgaricus. The phylogenetic relationships of most strains in the L. acidophilus group can be resolved using recA gene sequencing, and a novel method to identify the species and subspecies of the L. delbrueckii and L. delbrueckii subsp. bulgaricus was developed by species-specific polymerase chain reaction combined with SNaPshot mini-sequencing. Copyright © 2012 Society of Chemical Industry.

  12. Magnetic resonance imaging of metal artifact reduction sequences in the assessment of metal-on-metal hip prostheses

    Directory of Open Access Journals (Sweden)

    Aboelmagd SM

    2014-05-01

    Full Text Available Sharief M Aboelmagd, Paul N Malcolm, Andoni P Toms Department of Radiology, Norfolk and Norwich University Hospital National Health Service Trust, Norwich, UK Abstract: Recent developments in metal artifact reduction techniques in magnetic resonance (MR have, in large part, been stimulated by the advent of soft tissue complications associated with modern metal-on-metal total hip replacements. Metallic orthopedic implants can result in severe degradation of MR images because ferromagnetic susceptibility causes signal loss, signal pile-up, geometric distortion, and failure of fat suppression. There are several approaches to controlling these susceptibility artifacts. Standard fast spin echo sequences can be adapted by modifying echo times, matrix, receiver bandwidth, slice thickness, and echo trains to minimize frequency encoding misregistration. Short tau inversion recovery and 2-point Dixon techniques are both more resistant to susceptibility artifacts than spectral fat suppression. A number of dedicated metal artifact reduction sequences are now available commercially. The common approach of these multispectral techniques is to generate three dimensional datasets from which the final images are reconstructed. Frequency encoding misregistration is controlled using a variety of techniques, including specific resonant frequency acquisition, view-angle tilting, and phase encoding. Metal artifact reduction MR imaging has been the key to understanding the prevalence, severity, and prognosis of adverse reactions to metal debris in metal-on-metal hip replacements. Conventional radiographs are typically normal or demonstrate minimal change and are unable to demonstrate the often extensive soft tissue abnormalities, which include necrosis, soft tissue masses and fluid collections, myositis, muscle atrophy, tendon avulsions, and osteonecrosis. These MR findings correlate poorly with clinical and serological measures of disease, and therefore MR imaging is

  13. Magnetic resonance imaging of breast implants.

    Science.gov (United States)

    Shah, Mala; Tanna, Neil; Margolies, Laurie

    2014-12-01

    Silicone breast implants have significantly evolved since their introduction half a century ago, yet implant rupture remains a common and expected complication, especially in patients with earlier-generation implants. Magnetic resonance imaging is the primary modality for assessing the integrity of silicone implants and has excellent sensitivity and specificity, and the Food and Drug Administration currently recommends periodic magnetic resonance imaging screening for silent silicone breast implant rupture. Familiarity with the types of silicone implants and potential complications is essential for the radiologist. Signs of intracapsular rupture include the noose, droplet, subcapsular line, and linguine signs. Signs of extracapsular rupture include herniation of silicone with a capsular defect and extruded silicone material. Specific sequences including water and silicone suppression are essential for distinguishing rupture from other pathologies and artifacts. Magnetic resonance imaging provides valuable information about the integrity of silicone implants and associated complications.

  14. Cell type-specific termination of transcription by transposable element sequences

    Directory of Open Access Journals (Sweden)

    Conley Andrew B

    2012-09-01

    Full Text Available Abstract Background Transposable elements (TEs encode sequences necessary for their own transposition, including signals required for the termination of transcription. TE sequences within the introns of human genes show an antisense orientation bias, which has been proposed to reflect selection against TE sequences in the sense orientation owing to their ability to terminate the transcription of host gene transcripts. While there is evidence in support of this model for some elements, the extent to which TE sequences actually terminate transcription of human gene across the genome remains an open question. Results Using high-throughput sequencing data, we have characterized over 9,000 distinct TE-derived sequences that provide transcription termination sites for 5,747 human genes across eight different cell types. Rarefaction curve analysis suggests that there may be twice as many TE-derived termination sites (TE-TTS genome-wide among all human cell types. The local chromatin environment for these TE-TTS is similar to that seen for 3′ UTR canonical TTS and distinct from the chromatin environment of other intragenic TE sequences. However, those TE-TTS located within the introns of human genes were found to be far more cell type-specific than the canonical TTS. TE-TTS were much more likely to be found in the sense orientation than other intragenic TE sequences of the same TE family and TE-TTS in the sense orientation terminate transcription more efficiently than those found in the antisense orientation. Alu sequences were found to provide a large number of relatively weak TTS, whereas LTR elements provided a smaller number of much stronger TTS. Conclusions TE sequences provide numerous termination sites to human genes, and TE-derived TTS are particularly cell type-specific. Thus, TE sequences provide a powerful mechanism for the diversification of transcriptional profiles between cell types and among evolutionary lineages, since most TE-TTS are

  15. Methods for sequential resonance assignment in solid, uniformly 13C, 15N labelled peptides: Quantification and application to antamanide

    International Nuclear Information System (INIS)

    Detken, Andreas; Hardy, Edme H.; Ernst, Matthias; Kainosho, Masatsune; Kawakami, Toru; Aimoto, Saburo; Meier, Beat H.

    2001-01-01

    The application of adiabatic polarization-transfer experiments to resonance assignment in solid, uniformly 13 C- 15 N-labelled polypeptides is demonstrated for the cyclic decapeptide antamanide. A homonuclear correlation experiment employing the DREAM sequence for adiabatic dipolar transfer yields a complete assignment of the C α and aliphatic side-chain 13 C resonances to amino acid types. The same information can be obtained from a TOBSY experiment using the recently introduced P9 1 12 TOBSY sequence, which employs the J couplings as a transfer mechanism. A comparison of the two methods is presented. Except for some aromatic phenylalanine resonances, a complete sequence-specific assignment of the 13 C and 15 N resonances in antamanide is achieved by a series of selective or broadband adiabatic triple-resonance experiments. Heteronuclear transfer by adiabatic-passage Hartmann-Hahn cross polarization is combined with adiabatic homonuclear transfer by the DREAM and rotational-resonance tickling sequences into two- and three-dimensional experiments. The performance of these experiments is evaluated quantitatively

  16. Whole-genome in-silico subtractive hybridization (WISH - using massive sequencing for the identification of unique and repetitive sex-specific sequences: the example of Schistosoma mansoni

    Directory of Open Access Journals (Sweden)

    Parrinello Hugues

    2010-06-01

    Full Text Available Abstract Background Emerging methods of massive sequencing that allow for rapid re-sequencing of entire genomes at comparably low cost are changing the way biological questions are addressed in many domains. Here we propose a novel method to compare two genomes (genome-to-genome comparison. We used this method to identify sex-specific sequences of the human blood fluke Schistosoma mansoni. Results Genomic DNA was extracted from male and female (heterogametic S. mansoni adults and sequenced with a Genome Analyzer (Illumina. Sequences are available at the NCBI sequence read archive http://www.ncbi.nlm.nih.gov/Traces/sra/ under study accession number SRA012151.6. Sequencing reads were aligned to the genome, and a pseudogenome composed of known repeats. Straightforward comparative bioinformatics analysis was performed to compare male and female schistosome genomes and identify female-specific sequences. We found that the S. mansoni female W chromosome contains only few specific unique sequences (950 Kb i.e. about 0.2% of the genome. The majority of W-specific sequences are repeats (10.5 Mb i.e. about 2.5% of the genome. Arbitrarily selected W-specific sequences were confirmed by PCR. Primers designed for unique and repetitive sequences allowed to reliably identify the sex of both larval and adult stages of the parasite. Conclusion Our genome-to-genome comparison method that we call "whole-genome in-silico subtractive hybridization" (WISH allows for rapid identification of sequences that are specific for a certain genotype (e.g. the heterogametic sex. It can in principle be used for the detection of any sequence differences between isolates (e.g. strains, pathovars or even closely related species.

  17. Importance of the Sequence-Directed DNA Shape for Specific Binding Site Recognition by the Estrogen-Related Receptor

    Directory of Open Access Journals (Sweden)

    Kareem Mohideen-Abdul

    2017-06-01

    Full Text Available Most nuclear receptors (NRs bind DNA as dimers, either as hetero- or as homodimers on DNA sequences organized as two half-sites with specific orientation and spacing. The dimerization of NRs on their cognate response elements (REs involves specific protein–DNA and protein–protein interactions. The estrogen-related receptor (ERR belongs to the steroid hormone nuclear receptor (SHR family and shares strong similarity in its DNA-binding domain (DBD with that of the estrogen receptor (ER. In vitro, ERR binds with high affinity inverted repeat REs with a 3-bps spacing (IR3, but in vivo, it preferentially binds to single half-site REs extended at the 5′-end by 3 bp [estrogen-related response element (ERREs], thus explaining why ERR was often inferred as a purely monomeric receptor. Since its C-terminal ligand-binding domain is known to homodimerize with a strong dimer interface, we investigated the binding behavior of the isolated DBDs to different REs using electrophoretic migration, multi-angle static laser light scattering (MALLS, non-denaturing mass spectrometry, and nuclear magnetic resonance. In contrast to ER DBD, ERR DBD binds as a monomer to EREs (IR3, such as the tff1 ERE-IR3, but we identified a DNA sequence composed of an extended half-site embedded within an IR3 element (embedded ERRE/IR3, where stable dimer binding is observed. Using a series of chimera and mutant DNA sequences of ERREs and IR3 REs, we have found the key determinants for the binding of ERR DBD as a dimer. Our results suggest that the sequence-directed DNA shape is more important than the exact nucleotide sequence for the binding of ERR DBD to DNA as a dimer. Our work underlines the importance of the shape-driven DNA readout mechanisms based on minor groove recognition and electrostatic potential. These conclusions may apply not only to ERR but also to other members of the SHR family, such as androgen or glucocorticoid, for which a strong well-conserved half

  18. Nostoc PCC7524, a cyanobacterium which contains five sequence-specific deoxyribonucleases

    NARCIS (Netherlands)

    Reaston, J.; Duybesteyn, M.G.C.; Waard, Adrian de

    1982-01-01

    Five nucleotide sequence-specific deoxyribonucleases present in cell-free extracts of the filamentous cyanobacterium Nostoc PCC7524 have been purified and characterized. One of these enzymes, designated Nsp(7524)I cleaves at a new kind of nucleotide sequence i.e. 5'-PuCATG λ Py-3'. The other four

  19. Multiphoton resonances

    International Nuclear Information System (INIS)

    Shore, B.W.

    1977-01-01

    The long-time average of level populations in a coherently-excited anharmonic sequence of energy levels (e.g., an anharmonic oscillator) exhibits sharp resonances as a function of laser frequency. For simple linearly-increasing anharmonicity, each resonance is a superposition of various multiphoton resonances (e.g., a superposition of 3, 5, 7, . . . photon resonances), each having its own characteristic width predictable from perturbation theory

  20. Specific Deficit in Implicit Motor Sequence Learning following Spinal Cord Injury.

    Directory of Open Access Journals (Sweden)

    Ayala Bloch

    Full Text Available Physical and psychosocial rehabilitation following spinal cord injury (SCI leans heavily on learning and practicing new skills. However, despite research relating motor sequence learning to spinal cord activity and clinical observations of impeded skill-learning after SCI, implicit procedural learning following spinal cord damage has not been examined.To test the hypothesis that spinal cord injury (SCI in the absence of concomitant brain injury is associated with a specific implicit motor sequence learning deficit that cannot be explained by depression or impairments in other cognitive measures.Ten participants with SCI in T1-T11, unharmed upper limb motor and sensory functioning, and no concomitant brain injury were compared to ten matched control participants on measures derived from the serial reaction time (SRT task, which was used to assess implicit motor sequence learning. Explicit generation of the SRT sequence, depression, and additional measures of learning, memory, and intelligence were included to explore the source and specificity of potential learning deficits.There was no between-group difference in baseline reaction time, indicating that potential differences between the learning curves of the two groups could not be attributed to an overall reduction in response speed in the SCI group. Unlike controls, the SCI group showed no decline in reaction time over the first six blocks of the SRT task and no advantage for the initially presented sequence over the novel interference sequence. Meanwhile, no group differences were found in explicit learning, depression, or any additional cognitive measures.The dissociation between impaired implicit learning and intact declarative memory represents novel empirical evidence of a specific implicit procedural learning deficit following SCI, with broad implications for rehabilitation and adjustment.

  1. First-order and higher order sequence learning in specific language impairment.

    Science.gov (United States)

    Clark, Gillian M; Lum, Jarrad A G

    2017-02-01

    A core claim of the procedural deficit hypothesis of specific language impairment (SLI) is that the disorder is associated with poor implicit sequence learning. This study investigated whether implicit sequence learning problems in SLI are present for first-order conditional (FOC) and higher order conditional (HOC) sequences. Twenty-five children with SLI and 27 age-matched, nonlanguage-impaired children completed 2 serial reaction time tasks. On 1 version, the sequence to be implicitly learnt comprised a FOC sequence and on the other a HOC sequence. Results showed that the SLI group learned the HOC sequence (η p ² = .285, p = .005) but not the FOC sequence (η p ² = .099, p = .118). The control group learned both sequences (FOC η p ² = .497, HOC η p 2= .465, ps < .001). The SLI group's difficulty learning the FOC sequence is consistent with the procedural deficit hypothesis. However, the study provides new evidence that multiple mechanisms may underpin the learning of FOC and HOC sequences. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  2. Magnetic resonance for T-staging of nasopharyngeal carcinoma. The most informative pair of sequences

    International Nuclear Information System (INIS)

    Lau, Kam Y.; Kan, Wai K.; Sze, Wai M.

    2004-01-01

    The objective of this study was to evaluate the most informative pair of sequences in magnetic resonance (MR) for T-staging of nasopharyngeal carcinoma (NPC). The MR images of 134 patients with newly diagnosed NRC, from 1996 to 2002, were retrospectively reviewed. All the patients were scanned using 1.5 Tesla MR systems. The images of the nasopharynx were reviewed by two qualified radiologists to determine the positive findings and the T-stage by Union Internationale Contre le Cancer (UICC) (6th edition) System, using each sequence separately. The T-stage derived from a single MR sequence was then compared with the T-stage based on the five selected sequences to assess the number and percentage of patients who were being understaged. Therefore, the overall percentage accuracy of each single sequence could be determined. A pair of sequences providing information to achieve almost 100% diagnostic accuracy was then derived. The overall percentage accuracy of five individual sequences of the nasopharynx is as follows: contrast-enhanced (CE) fat suppression (FS) axial T1 (94.8%), CE FS coronal T1 (88.1%), FS axial T2 (85.8%), non-contrast enhanced (NE) axial T1 (78.4%) and NE coronal T1 (77.6%). CE FS axial T1 has the best accuracy. All the structures that are missed in CE FS axial T1 which lead to apparent understaging, are appreciated in NE axial T1-weighted images. Individual sequences supplement each other in the NPC staging. CE FS axial T1 is the most informative individual sequence. Combination of CE FS axial T1 and NE axial T1 of the nasopharynx provides sufficient information to achieve almost 100% diagnostic accuracy in T-staging; therefore, both should be included in the MR-staging protocol. (author)

  3. CaMV-35S promoter sequence-specific DNA methylation in lettuce.

    Science.gov (United States)

    Okumura, Azusa; Shimada, Asahi; Yamasaki, Satoshi; Horino, Takuya; Iwata, Yuji; Koizumi, Nozomu; Nishihara, Masahiro; Mishiba, Kei-ichiro

    2016-01-01

    We found 35S promoter sequence-specific DNA methylation in lettuce. Additionally, transgenic lettuce plants having a modified 35S promoter lost methylation, suggesting the modified sequence is subjected to the methylation machinery. We previously reported that cauliflower mosaic virus 35S promoter-specific DNA methylation in transgenic gentian (Gentiana triflora × G. scabra) plants occurs irrespective of the copy number and the genomic location of T-DNA, and causes strong gene silencing. To confirm whether 35S-specific methylation can occur in other plant species, transgenic lettuce (Lactuca sativa L.) plants with a single copy of the 35S promoter-driven sGFP gene were produced and analyzed. Among 10 lines of transgenic plants, 3, 4, and 3 lines showed strong, weak, and no expression of sGFP mRNA, respectively. Bisulfite genomic sequencing of the 35S promoter region showed hypermethylation at CpG and CpWpG (where W is A or T) sites in 9 of 10 lines. Gentian-type de novo methylation pattern, consisting of methylated cytosines at CpHpH (where H is A, C, or T) sites, was also observed in the transgenic lettuce lines, suggesting that lettuce and gentian share similar methylation machinery. Four of five transgenic lettuce lines having a single copy of a modified 35S promoter, which was modified in the proposed core target of de novo methylation in gentian, exhibited 35S hypomethylation, indicating that the modified sequence may be the target of the 35S-specific methylation machinery.

  4. Sequence specificity and biological consequences of drugs that bind covalently in the minor groove of DNA

    International Nuclear Information System (INIS)

    Hurley, L.H.; Needham-VanDevanter, D.R.

    1986-01-01

    DNA ligands which bind within the minor groove of DNA exhibit varying degrees of sequence selectivity. Factors which contribute to nucleotide sequence recognition by minor groove ligands have been extensively investigated. Electrostatic interactions, ligand and DNA dehydration energies, hydrophobic interactions and steric factors all play significant roles in sequence selectivity in the minor groove. Interestingly, ligand recognition of nucleotide sequence in the minor groove does not involve significant hydrogen bonding. This is in sharp contrast to cellular enzyme and protein recognition of nucleotide sequence, which is achieved in the major groove via specific hydrogen bond formation between individual bases and the ligand. The ability to read nucleotide sequence via hydrogen bonding allows precise binding of proteins to specific DNA sequences. Minor groove ligands examined to date exhibit a much lower sequence specificity, generally binding to a subset of possible sequences, rather than a single sequence. 19 refs., 7 figs

  5. Proton nuclear magnetic resonance studies on bulge-containing DNA oligonucleotides from a mutational hot-spot sequence

    International Nuclear Information System (INIS)

    Woodson, S.A.; Crothers, D.M.

    1987-01-01

    A series of bulge-containing and normal double-helical synthetic oligodeoxyribonucleotides, of sequence corresponding to a frame-shift mutational hot spot in the λ C/sub I/ gene, are compared by proton magnetic resonance spectroscopy at 500 MHz. The imino proton resonances are assigned by one-dimensional nuclear Overhauser effect spectroscopy. Nonselective T 1 inversion-recovery experiments are used to determine exchangeable proton lifetimes and to compare helix stability and dynamics of the three duplexes. An extra adenosine flanking the internal G-C base pairs has a strongly localized effect on helix stability, but the destabilizing effect of an extra cytidine in a C tract is delocalized over the entire G-C run. These data lead to the conclusion that the position of the bulge migrates along the run in the fast-exchange limit on the NMR time scale. Rapid migration of the bulge defect in homopolymeric sequences may help rationalize both frame-shift mutagenesis and translational frame shifting. The authors estimate that the unfavorable free energy of a localized bulge defect is 2.9-3.2 kcal/mol, in good agreement with earlier estimates for RNA helices

  6. Cellular specificity of HIV-1 replication can be controlled by LTR sequences

    International Nuclear Information System (INIS)

    Reed-Inderbitzin, Edward; Maury, Wendy

    2003-01-01

    Two well-established determinants of retroviral tropism are envelope sequences that regulate entry and LTR sequences that can regulate viral expression in a cell-specific manner. Studies with human immunodeficiency virus-1 (HIV-1) have demonstrated that tropism of this virus maps primarily to variable envelope sequences. Studies have demonstrated that T cell and macrophage-specific transcription factor binding motifs exist in the upstream region of the LTR U3; however, the ability of the core enhancer/promoter proximal elements (two NF-κB and three Sp1 sites) to function well in macrophages and T cells have led many to conclude that HIV LTR sequences are not primary determinants of HIV tropism. To determine if cellular specificity could be imparted to HIV by the core enhancer elements, the enhancer/promoter proximal region of the HIV LTR was substituted with motifs that control gene expression in a myeloid-specific manner. The enhancer region from equine infectious anemia virus (EIAV) when substituted for the HIV enhancer/promoter proximal region was found to drive expression in a macrophage-specific manner and was responsive to HIV Tat. The addition of a 5' methylation-dependent binding site (MDBP) and a promoter proximal Sp1 motif increased expression without altering cellular specificity. Spacing between the promoter proximal region and the TATA box was also found to influence LTR activity. Infectivity studies using chimeric LTRs within the context of a dual-tropic infectious molecular clone established that these LTRs directed HIV replication and production of infectious virions in macrophages but not primary T cells or T cell lines. This investigation demonstrates that cellular specificity can be imparted onto HIV-1 replication at the level of viral transcription and not entry

  7. Limited-sequence magnetic resonance imaging in the evaluation of the ultrasonographically indeterminate pelvic mass

    International Nuclear Information System (INIS)

    Chang, S.D.; Cooperberg, P.L.; Wong, A.D.; Llewellyn, P.A.; Bilbey, J.H.

    2004-01-01

    To evaluate the usefulness of limited-sequence magnetic resonance imaging (MRI) in the elucidation of ultrasonographically indeterminate pelvic masses. This study focused only on pelvic masses in which the origin of the mass (uterine v. extrauterine) could not be determined by ultrasonography (US). The origin of a pelvic mass has clinical implications. A mass arising from the uterus is most likely to be a leiomyoma, which is a benign lesion, whereas an extrauterine mass will have a higher likelihood of malignancy and usually requires surgery. Eighty-one female patients whose pelvic mass was of indeterminate origin on US also underwent limited-sequence MRI of the pelvis. Most of the MRI examinations were performed on the same day as the US. Limited-sequence MRI sequences included a quick gradient-echoT 1 -weighted localizer and a fast spin-echoT 2 -weighted sequence. Final diagnoses were established by surgical pathology or by clinical and imaging follow-up. Limited-sequence MRI was helpful in 79 of the 81 cases (98%). Fifty-two of the 81 masses (64%) were leiomyomas. One was a leiomyosarcoma. The extrauterine masses (26/81 [32%]) were identified as 14 ovarian malignancies, 4 endometriomas, 3 dermoids, an ovarian fibroma, an infarcted fibrothecoma, an infarcted hemorrhagic cyst, a sigmoid diverticular abscess and a gastrointestinal stromal tumour of the ileum. In the other 2 cases (2/81 [2%]), the origin of the pelvic mass remained indeterminate. Both of these indeterminate masses showed low signal onT 2 -weighted images and were interpreted as probable leiomyomas. They were not surgically removed but were followed clinically and had a stable course. Limited-sequence MRI is a quick and efficient way to further evaluate ultrasonographically indeterminate pelvic masses. Limited-sequence MRI of the pelvis can suffice, in these cases, without requiring a full MRI examination. (author)

  8. Limited-sequence magnetic resonance imaging in the evaluation of the ultrasonographically indeterminate pelvic mass

    Energy Technology Data Exchange (ETDEWEB)

    Chang, S.D. [Univ. of British Columbia, Vancouver Hospital and Helath Services Centre, Dept. of Radiology, Vancouver, British Columbia (Canada)]. E-mail: schang@vanhosp.bc.ca; Cooperberg, P.L.; Wong, A.D. [Univ. of British Columbia, St. Paul' s Hospital, Dept. of Radiology, Vancouver, British Columbia (Canada); Llewellyn, P.A. [Lion' s Gate Hospital, Dept. of Radiology, North Vancouver, British Columbia (Canada); Bilbey, J.H. [Royal Inland Hospital, Dept. of Radiology, Kamloops, British Columbia (Canada)

    2004-04-01

    To evaluate the usefulness of limited-sequence magnetic resonance imaging (MRI) in the elucidation of ultrasonographically indeterminate pelvic masses. This study focused only on pelvic masses in which the origin of the mass (uterine v. extrauterine) could not be determined by ultrasonography (US). The origin of a pelvic mass has clinical implications. A mass arising from the uterus is most likely to be a leiomyoma, which is a benign lesion, whereas an extrauterine mass will have a higher likelihood of malignancy and usually requires surgery. Eighty-one female patients whose pelvic mass was of indeterminate origin on US also underwent limited-sequence MRI of the pelvis. Most of the MRI examinations were performed on the same day as the US. Limited-sequence MRI sequences included a quick gradient-echoT{sub 1}-weighted localizer and a fast spin-echoT{sub 2}-weighted sequence. Final diagnoses were established by surgical pathology or by clinical and imaging follow-up. Limited-sequence MRI was helpful in 79 of the 81 cases (98%). Fifty-two of the 81 masses (64%) were leiomyomas. One was a leiomyosarcoma. The extrauterine masses (26/81 [32%]) were identified as 14 ovarian malignancies, 4 endometriomas, 3 dermoids, an ovarian fibroma, an infarcted fibrothecoma, an infarcted hemorrhagic cyst, a sigmoid diverticular abscess and a gastrointestinal stromal tumour of the ileum. In the other 2 cases (2/81 [2%]), the origin of the pelvic mass remained indeterminate. Both of these indeterminate masses showed low signal onT{sub 2}-weighted images and were interpreted as probable leiomyomas. They were not surgically removed but were followed clinically and had a stable course. Limited-sequence MRI is a quick and efficient way to further evaluate ultrasonographically indeterminate pelvic masses. Limited-sequence MRI of the pelvis can suffice, in these cases, without requiring a full MRI examination. (author)

  9. Flanking sequence determination and specific PCR identification of transgenic wheat B102-1-2.

    Science.gov (United States)

    Cao, Jijuan; Xu, Junyi; Zhao, Tongtong; Cao, Dongmei; Huang, Xin; Zhang, Piqiao; Luan, Fengxia

    2014-01-01

    The exogenous fragment sequence and flanking sequence between the exogenous fragment and recombinant chromosome of transgenic wheat B102-1-2 were successfully acquired using genome walking technology. The newly acquired exogenous fragment encoded the full-length sequence of transformed genes with transformed plasmid and corresponding functional genes including ubi, vector pBANF-bar, vector pUbiGUSPlus, vector HSP, reporter vector pUbiGUSPlus, promoter ubiquitin, and coli DH1. A specific polymerase chain reaction (PCR) identification method for transgenic wheat B102-1-2 was established on the basis of designed primers according to flanking sequence. This established specific PCR strategy was validated by using transgenic wheat, transgenic corn, transgenic soybean, transgenic rice, and non-transgenic wheat. A specifically amplified target band was observed only in transgenic wheat B102-1-2. Therefore, this method is characterized by high specificity, high reproducibility, rapid identification, and excellent accuracy for the identification of transgenic wheat B102-1-2.

  10. Integrated analysis of RNA-binding protein complexes using in vitro selection and high-throughput sequencing and sequence specificity landscapes (SEQRS).

    Science.gov (United States)

    Lou, Tzu-Fang; Weidmann, Chase A; Killingsworth, Jordan; Tanaka Hall, Traci M; Goldstrohm, Aaron C; Campbell, Zachary T

    2017-04-15

    RNA-binding proteins (RBPs) collaborate to control virtually every aspect of RNA function. Tremendous progress has been made in the area of global assessment of RBP specificity using next-generation sequencing approaches both in vivo and in vitro. Understanding how protein-protein interactions enable precise combinatorial regulation of RNA remains a significant problem. Addressing this challenge requires tools that can quantitatively determine the specificities of both individual proteins and multimeric complexes in an unbiased and comprehensive way. One approach utilizes in vitro selection, high-throughput sequencing, and sequence-specificity landscapes (SEQRS). We outline a SEQRS experiment focused on obtaining the specificity of a multi-protein complex between Drosophila RBPs Pumilio (Pum) and Nanos (Nos). We discuss the necessary controls in this type of experiment and examine how the resulting data can be complemented with structural and cell-based reporter assays. Additionally, SEQRS data can be integrated with functional genomics data to uncover biological function. Finally, we propose extensions of the technique that will enhance our understanding of multi-protein regulatory complexes assembled onto RNA. Copyright © 2016 Elsevier Inc. All rights reserved.

  11. Templated Chemistry for Sequence-Specific Fluorogenic Detection of Duplex DNA

    Science.gov (United States)

    Li, Hao; Franzini, Raphael M.; Bruner, Christopher; Kool, Eric T.

    2015-01-01

    We describe the development of templated fluorogenic chemistry for detection of specific sequences of duplex DNA in solution. In this approach, two modified homopyrimidine oligodeoxynucleotide probes are designed to bind by triple helix formation at adjacent positions on a specific purine-rich target sequence of duplex DNA. One fluorescein-labeled probe contains an α-azidoether linker to a fluorescence quencher; the second (trigger) probe carries a triarylphosphine, designed to reduce the azide and cleave the linker. The data showed that at pH 5.6 these probes yielded a strong fluorescence signal within minutes on addition to a complementary homopurine duplex DNA target. The signal increased by a factor of ca. 60, and was completely dependent on the presence of the target DNA. Replacement of cytosine in the probes with pseudoisocytosine allowed the templated chemistry to proceed readily at pH 7. Single nucleotide mismatches in the target oligonucleotide slowed the templated reaction considerably, demonstrating high sequence selectivity. The use of templated fluorogenic chemistry for detection of duplex DNAs has not been previously reported and may allow detection of double stranded DNA, at least for homopurine-homopyrimidine target sites, under native, non-disturbing conditions. PMID:20859985

  12. Targeting and tracing of specific DNA sequences with dTALEs in living cells

    Science.gov (United States)

    Thanisch, Katharina; Schneider, Katrin; Morbitzer, Robert; Solovei, Irina; Lahaye, Thomas; Bultmann, Sebastian; Leonhardt, Heinrich

    2014-01-01

    Epigenetic regulation of gene expression involves, besides DNA and histone modifications, the relative positioning of DNA sequences within the nucleus. To trace specific DNA sequences in living cells, we used programmable sequence-specific DNA binding of designer transcription activator-like effectors (dTALEs). We designed a recombinant dTALE (msTALE) with variable repeat domains to specifically bind a 19-bp target sequence of major satellite DNA. The msTALE was fused with green fluorescent protein (GFP) and stably expressed in mouse embryonic stem cells. Hybridization with a major satellite probe (3D-fluorescent in situ hybridization) and co-staining for known cellular structures confirmed in vivo binding of the GFP-msTALE to major satellite DNA present at nuclear chromocenters. Dual tracing of major satellite DNA and the replication machinery throughout S-phase showed co-localization during mid to late S-phase, directly demonstrating the late replication timing of major satellite DNA. Fluorescence bleaching experiments indicated a relatively stable but still dynamic binding, with mean residence times in the range of minutes. Fluorescently labeled dTALEs open new perspectives to target and trace DNA sequences and to monitor dynamic changes in subnuclear positioning as well as interactions with functional nuclear structures during cell cycle progression and cellular differentiation. PMID:24371265

  13. Targeting and tracing of specific DNA sequences with dTALEs in living cells.

    Science.gov (United States)

    Thanisch, Katharina; Schneider, Katrin; Morbitzer, Robert; Solovei, Irina; Lahaye, Thomas; Bultmann, Sebastian; Leonhardt, Heinrich

    2014-04-01

    Epigenetic regulation of gene expression involves, besides DNA and histone modifications, the relative positioning of DNA sequences within the nucleus. To trace specific DNA sequences in living cells, we used programmable sequence-specific DNA binding of designer transcription activator-like effectors (dTALEs). We designed a recombinant dTALE (msTALE) with variable repeat domains to specifically bind a 19-bp target sequence of major satellite DNA. The msTALE was fused with green fluorescent protein (GFP) and stably expressed in mouse embryonic stem cells. Hybridization with a major satellite probe (3D-fluorescent in situ hybridization) and co-staining for known cellular structures confirmed in vivo binding of the GFP-msTALE to major satellite DNA present at nuclear chromocenters. Dual tracing of major satellite DNA and the replication machinery throughout S-phase showed co-localization during mid to late S-phase, directly demonstrating the late replication timing of major satellite DNA. Fluorescence bleaching experiments indicated a relatively stable but still dynamic binding, with mean residence times in the range of minutes. Fluorescently labeled dTALEs open new perspectives to target and trace DNA sequences and to monitor dynamic changes in subnuclear positioning as well as interactions with functional nuclear structures during cell cycle progression and cellular differentiation.

  14. Using the Δ3 statistic to test for missed levels in mixed sequence neutron resonance data

    International Nuclear Information System (INIS)

    Mulhall, Declan

    2009-01-01

    The Δ 3 (L) statistic is studied as a tool to detect missing levels in the neutron resonance data where two sequences are present. These systems are problematic because there is no level repulsion, and the resonances can be too close to resolve. Δ 3 (L) is a measure of the fluctuations in the number of levels in an interval of length L on the energy axis. The method used is tested on ensembles of mixed Gaussian orthogonal ensemble spectra, with a known fraction of levels (x%) randomly depleted, and can accurately return x. The accuracy of the method as a function of spectrum size is established. The method is used on neutron resonance data for 11 isotopes with either s-wave neutrons on odd-A isotopes, or p-wave neutrons on even-A isotopes. The method compares favorably with a maximum likelihood method applied to the level spacing distribution. Nuclear data ensembles were made from 20 isotopes in total, and their Δ 3 (L) statistics are discussed in the context of random matrix theory.

  15. Proton magnetic resonance spectroscopy and perfusion magnetic resonance imaging in the evaluation of musculoskeletal tumors

    International Nuclear Information System (INIS)

    Costa, Flavia Martins; Setti, Marcela; Vianna, Evandro Miguelote; Domingues, Romulo Cortes; Meohas, Walter; Rezende, Jose Francisco; Gasparetto, Emerson Leandro

    2009-01-01

    Objective: To assess the role of proton magnetic resonance spectroscopy and dynamic contrast-enhanced magnetic resonance imaging in the differentiation between malignant and benign musculoskeletal tumors. Materials And Methods: Fifty-five patients with musculoskeletal tumors (27 malignant and 28 benign) were studied. The examinations were performed in a 1.5 T magnetic resonance scanner with standard protocol, and single voxel proton magnetic resonance spectroscopy with 135 msec echo time. The dynamic contrast study was performed using T1-weighted gradient-echo sequence after intravenous gadolinium injection. Time signal intensity curves and slope values were calculated. The statistical analysis was performed with the Levene's test, followed by a Student's t-test, besides the Pearson's chi-squared and Fischer's exact tests. Results: Proton magnetic resonance spectroscopy sensitivity, specificity and accuracy were, respectively, 87.5%, 92.3% and 90.9% (p < 0.0001). Statistically significant difference was observed in the slope (%/min) between benign (mean, 27.5%/min) and malignant (mean, 110.9%/min) lesions (p < 0.0001). Conclusion: The time-intensity curve and slope values using dynamic-enhanced perfusion magnetic resonance imaging in association with the presence of choline peak demonstrated by single voxel magnetic resonance spectroscopy study are useful in the differentiation between malignant and benign musculoskeletal tumors. (author)

  16. Magnetic resonance findings in amyotrophic lateral sclerosis using a spin echo magnetization transfer sequence: preliminary report

    Directory of Open Access Journals (Sweden)

    ROCHA ANTÔNIO JOSÉ DA

    1999-01-01

    Full Text Available We present the magnetic resonance (MR findings of five patients with amyotrophic lateral sclerosis (ALS using a spin-echo sequence with an additional magnetization transfer (MT pulse on T1-weighted images (T1 SE/MT. These findings were absent in the control group and consisted of hyperintensity of the corticospinal tract. Moreover we discuss the principles and the use of this fast but simple MR technique in the diagnosis of ALS

  17. Organism-specific rRNA capture system for application in next-generation sequencing.

    Directory of Open Access Journals (Sweden)

    Sai-Kam Li

    Full Text Available RNA-sequencing is a powerful tool in studying RNomics. However, the highly abundance of ribosomal RNAs (rRNA and transfer RNA (tRNA have predominated in the sequencing reads, thereby hindering the study of lowly expressed genes. Therefore, rRNA depletion prior to sequencing is often performed in order to preserve the subtle alteration in gene expression especially those at relatively low expression levels. One of the commercially available methods is to use DNA or RNA probes to hybridize to the target RNAs. However, there is always a concern with the non-specific binding and unintended removal of messenger RNA (mRNA when the same set of probes is applied to different organisms. The degree of such unintended mRNA removal varies among organisms due to organism-specific genomic variation. We developed a computer-based method to design probes to deplete rRNA in an organism-specific manner. Based on the computation results, biotinylated-RNA-probes were produced by in vitro transcription and were used to perform rRNA depletion with subtractive hybridization. We demonstrated that the designed probes of 16S rRNAs and 23S rRNAs can efficiently remove rRNAs from Mycobacterium smegmatis. In comparison with a commercial subtractive hybridization-based rRNA removal kit, using organism-specific probes is better in preserving the RNA integrity and abundance. We believe the computer-based design approach can be used as a generic method in preparing RNA of any organisms for next-generation sequencing, particularly for the transcriptome analysis of microbes.

  18. Increased sequence diversity coverage improves detection of HIV-Specific T cell responses

    DEFF Research Database (Denmark)

    Frahm, N.; Kaufmann, D.E.; Yusim, K.

    2007-01-01

    The accurate identification of HIV-specific T cell responses is important for determining the relationship between immune response, viral control, and disease progression. HIV-specific immune responses are usually measured using peptide sets based on consensus sequences, which frequently miss res...

  19. Chromatin accessibility data sets show bias due to sequence specificity of the DNase I enzyme.

    Directory of Open Access Journals (Sweden)

    Hashem Koohy

    Full Text Available DNase I is an enzyme which cuts duplex DNA at a rate that depends strongly upon its chromatin environment. In combination with high-throughput sequencing (HTS technology, it can be used to infer genome-wide landscapes of open chromatin regions. Using this technology, systematic identification of hundreds of thousands of DNase I hypersensitive sites (DHS per cell type has been possible, and this in turn has helped to precisely delineate genomic regulatory compartments. However, to date there has been relatively little investigation into possible biases affecting this data.We report a significant degree of sequence preference spanning sites cut by DNase I in a number of published data sets. The two major protocols in current use each show a different pattern, but for a given protocol the pattern of sequence specificity seems to be quite consistent. The patterns are substantially different from biases seen in other types of HTS data sets, and in some cases the most constrained position lies outside the sequenced fragment, implying that this constraint must relate to the digestion process rather than events occurring during library preparation or sequencing.DNase I is a sequence-specific enzyme, with a specificity that may depend on experimental conditions. This sequence specificity is not taken into account by existing pipelines for identifying open chromatin regions. Care must be taken when interpreting DNase I results, especially when looking at the precise locations of the reads. Future studies may be able to improve the sensitivity and precision of chromatin state measurement by compensating for sequence bias.

  20. Comparing an accelerated 3D fast spin-echo sequence (CS-SPACE) for knee 3-T magnetic resonance imaging with traditional 3D fast spin-echo (SPACE) and routine 2D sequences

    Energy Technology Data Exchange (ETDEWEB)

    Altahawi, Faysal F.; Blount, Kevin J.; Omar, Imran M. [Northwestern University Feinberg School of Medicine, Department of Radiology, Chicago, IL (United States); Morley, Nicholas P. [Marshfield Clinic, Department of Radiology, Marshfield, WI (United States); Raithel, Esther [Siemens Healthcare GmbH, Erlangen (Germany)

    2017-01-15

    To compare a faster, new, high-resolution accelerated 3D-fast-spin-echo (3D-FSE) acquisition sequence (CS-SPACE) to traditional 2D and high-resolution 3D sequences for knee 3-T magnetic resonance imaging (MRI). Twenty patients received knee MRIs that included routine 2D (T1, PD ± FS, T2-FS; 0.5 x 0.5 x 3 mm{sup 3}; ∝10 min), traditional 3D FSE (SPACE-PD-FS; 0.5 x 0.5 x 0.5 mm{sup 3}; ∝7.5 min), and accelerated 3D-FSE prototype (CS-SPACE-PD-FS; 0.5 x 0.5 x 0.5 mm{sup 3}; ∝5 min) acquisitions on a 3-T MRI system (Siemens MAGNETOM Skyra). Three musculoskeletal radiologists (MSKRs) prospectively and independently reviewed the studies with graded surveys comparing image and diagnostic quality. Tissue-specific signal-to-noise ratios (SNR) and contrast-to-noise ratios (CNR) were also compared. MSKR-perceived diagnostic quality of cartilage was significantly higher for CS-SPACE than for SPACE and 2D sequences (p < 0.001). Assessment of diagnostic quality of menisci and synovial fluid was higher for CS-SPACE than for SPACE (p < 0.001). CS-SPACE was not significantly different from SPACE but had lower assessments than 2D sequences for evaluation of bones, ligaments, muscles, and fat (p ≤ 0.004). 3D sequences had higher spatial resolution, but lower overall assessed contrast (p < 0.001). Overall image quality from CS-SPACE was assessed as higher than SPACE (p = 0.007), but lower than 2D sequences (p < 0.001). Compared to SPACE, CS-SPACE had higher fluid SNR and CNR against all other tissues (all p < 0.001). The CS-SPACE prototype allows for faster isotropic acquisitions of knee MRIs over currently used protocols. High fluid-to-cartilage CNR and higher spatial resolution over routine 2D sequences may present a valuable role for CS-SPACE in the evaluation of cartilage and menisci. (orig.)

  1. Resonant magnetoelectric response of composite cantilevers: Theory of short vs. open circuit operation and layer sequence effects

    Directory of Open Access Journals (Sweden)

    Matthias C. Krantz

    2015-11-01

    Full Text Available The magnetoelectric effect in layered composite cantilevers consisting of strain coupled layers of magnetostrictive (MS, piezoelectric (PE, and substrate materials is investigated for magnetic field excitation at bending resonance. Analytic theories are derived for the transverse magnetoelectric (ME response in short and open circuit operation for three different layer sequences and results presented and discussed for the FeCoBSi-AlN-Si and the FeCoBSi-PZT-Si composite systems. Response optimized PE-MS layer thickness ratios are found to greatly change with operation mode shifting from near equal MS and PE layer thicknesses in the open circuit mode to near vanishing PE layer thicknesses in short circuit operation for all layer sequences. In addition the substrate layer thickness is found to differently affect the open and short circuit ME response producing shifts and reversal between ME response maxima depending on layer sequence. The observed rich ME response behavior for different layer thicknesses, sequences, operating modes, and PE materials can be explained by common neutral plane effects and different elastic compliance effects in short and open circuit operation.

  2. Multi circular-cavity surface coil for magnetic resonance imaging of monkey's brain at 4 Tesla

    Science.gov (United States)

    Osorio, A. I.; Solis-Najera, S. E.; Vázquez, F.; Wang, R. L.; Tomasi, D.; Rodriguez, A. O.

    2014-11-01

    Animal models in medical research has been used to study humans diseases for several decades. The use of different imaging techniques together with different animal models offers a great advantage due to the possibility to study some human pathologies without the necessity of chirurgical intervention. The employ of magnetic resonance imaging for the acquisition of anatomical and functional images is an excellent tool because its noninvasive nature. Dedicated coils to perform magnetic resonance imaging experiments are obligatory due to the improvement on the signal-to-noise ratio and reduced specific absorption ratio. A specifically designed surface coil for magnetic resonance imaging of monkey's brain is proposed based on the multi circular-slot coil. Numerical simulations of the magnetic and electric fields were also performed using the Finite Integration Method to solve Maxwell's equations for this particular coil design and, to study the behavior of various vector magnetic field configurations and specific absorption ratio. Monkey's brain images were then acquired with a research-dedicated magnetic resonance imaging system at 4T, to evaluate the anatomical images with conventional imaging sequences. This coil showed good quality images of a monkey's brain and full compatibility with standard pulse sequences implemented in research-dedicated imager.

  3. Identification of Bacillus anthracis specific chromosomal sequences by suppressive subtractive hybridization

    Directory of Open Access Journals (Sweden)

    Redkar Rajendra

    2004-02-01

    Full Text Available Abstract Background Bacillus anthracis, Bacillus thuringiensis and Bacillus cereus are closely related members of the B. cereus-group of bacilli. Suppressive subtractive hybridization (SSH was used to identify specific chromosomal sequences unique to B. anthracis. Results Two SSH libraries were generated. Genomic DNA from plasmid-cured B. anthracis was used as the tester DNA in both libraries, while genomic DNA from either B. cereus or B. thuringiensis served as the driver DNA. Progressive screening of the libraries by colony filter and Southern blot analyses identified 29 different clones that were specific for the B. anthracis chromosome relative not only to the respective driver DNAs, but also to seven other different strains of B. cereus and B. thuringiensis included in the process. The nucleotide sequences of the clones were compared with those found in genomic databases, revealing that over half of the clones were located into 2 regions on the B. anthracis chromosome. Conclusions Genes encoding potential cell wall synthesis proteins dominated one region, while bacteriophage-related sequences dominated the other region. The latter supports the hypothesis that acquisition of these bacteriophage sequences occurred during or after speciation of B. anthracis relative to B. cereus and B. thuringiensis. This study provides insight into the chromosomal differences between B. anthracis and its closest phylogenetic relatives.

  4. Flanking sequence determination and event-specific detection of genetically modified wheat B73-6-1.

    Science.gov (United States)

    Xu, Junyi; Cao, Jijuan; Cao, Dongmei; Zhao, Tongtong; Huang, Xin; Zhang, Piqiao; Luan, Fengxia

    2013-05-01

    In order to establish a specific identification method for genetically modified (GM) wheat, exogenous insert DNA and flanking sequence between exogenous fragment and recombinant chromosome of GM wheat B73-6-1 were successfully acquired by means of conventional polymerase chain reaction (PCR) and thermal asymmetric interlaced (TAIL)-PCR strategies. Newly acquired exogenous fragment covered the full-length sequence of transformed genes such as transformed plasmid and corresponding functional genes including marker uidA, herbicide-resistant bar, ubiquitin promoter, and high-molecular-weight gluten subunit. The flanking sequence between insert DNA revealed high similarity with Triticum turgidum A gene (GenBank: AY494981.1). A specific PCR detection method for GM wheat B73-6-1 was established on the basis of primers designed according to the flanking sequence. This specific PCR method was validated by GM wheat, GM corn, GM soybean, GM rice, and non-GM wheat. The specifically amplified target band was observed only in GM wheat B73-6-1. This method is of high specificity, high reproducibility, rapid identification, and excellent accuracy for the identification of GM wheat B73-6-1.

  5. Structural basis for sequence-specific recognition of DNA by TAL effectors

    KAUST Repository

    Deng, Dong; Yan, Chuangye; Pan, Xiaojing; Mahfouz, Magdy M.; Wang, Jiawei; Zhu, Jiankang; Shi, Yi Gong; Yan, Nieng

    2012-01-01

    TAL (transcription activator-like) effectors, secreted by phytopathogenic bacteria, recognize host DNA sequences through a central domain of tandem repeats. Each repeat comprises 33 to 35 conserved amino acids and targets a specific base pair

  6. Analysis of B Cell Repertoire Dynamics Following Hepatitis B Vaccination in Humans, and Enrichment of Vaccine-specific Antibody Sequences.

    Science.gov (United States)

    Galson, Jacob D; Trück, Johannes; Fowler, Anna; Clutterbuck, Elizabeth A; Münz, Márton; Cerundolo, Vincenzo; Reinhard, Claudia; van der Most, Robbert; Pollard, Andrew J; Lunter, Gerton; Kelly, Dominic F

    2015-12-01

    Generating a diverse B cell immunoglobulin repertoire is essential for protection against infection. The repertoire in humans can now be comprehensively measured by high-throughput sequencing. Using hepatitis B vaccination as a model, we determined how the total immunoglobulin sequence repertoire changes following antigen exposure in humans, and compared this to sequences from vaccine-specific sorted cells. Clonal sequence expansions were seen 7 days after vaccination, which correlated with vaccine-specific plasma cell numbers. These expansions caused an increase in mutation, and a decrease in diversity and complementarity-determining region 3 sequence length in the repertoire. We also saw an increase in sequence convergence between participants 14 and 21 days after vaccination, coinciding with an increase of vaccine-specific memory cells. These features allowed development of a model for in silico enrichment of vaccine-specific sequences from the total repertoire. Identifying antigen-specific sequences from total repertoire data could aid our understanding B cell driven immunity, and be used for disease diagnostics and vaccine evaluation.

  7. Specific versus non-specific immune responses in an invertebrate species evidenced by a comparative de novo sequencing study.

    Directory of Open Access Journals (Sweden)

    Emeline Deleury

    Full Text Available Our present understanding of the functioning and evolutionary history of invertebrate innate immunity derives mostly from studies on a few model species belonging to ecdysozoa. In particular, the characterization of signaling pathways dedicated to specific responses towards fungi and Gram-positive or Gram-negative bacteria in Drosophila melanogaster challenged our original view of a non-specific immunity in invertebrates. However, much remains to be elucidated from lophotrochozoan species. To investigate the global specificity of the immune response in the fresh-water snail Biomphalaria glabrata, we used massive Illumina sequencing of 5'-end cDNAs to compare expression profiles after challenge by Gram-positive or Gram-negative bacteria or after a yeast challenge. 5'-end cDNA sequencing of the libraries yielded over 12 millions high quality reads. To link these short reads to expressed genes, we prepared a reference transcriptomic database through automatic assembly and annotation of the 758,510 redundant sequences (ESTs, mRNAs of B. glabrata available in public databases. Computational analysis of Illumina reads followed by multivariate analyses allowed identification of 1685 candidate transcripts differentially expressed after an immune challenge, with a two fold ratio between transcripts showing a challenge-specific expression versus a lower or non-specific differential expression. Differential expression has been validated using quantitative PCR for a subset of randomly selected candidates. Predicted functions of annotated candidates (approx. 700 unisequences belonged to a large extend to similar functional categories or protein types. This work significantly expands upon previous gene discovery and expression studies on B. glabrata and suggests that responses to various pathogens may involve similar immune processes or signaling pathways but different genes belonging to multigenic families. These results raise the question of the importance

  8. [Possibilities in the differential diagnosis of brain neoplasms using the long and short time sequences of proton magnetic resonance spectroscopy

    NARCIS (Netherlands)

    Gajewicz, W.; Goraj, B.M.

    2004-01-01

    Currently to perform proton magnetic resonance spectroscopy (1H MRS) with single voxel spectroscopy (SVS) technique long and/or short echo time sequences are used in order to provide complementary information. PURPOSE: The aim of the study was to compare the usefulness of STEAM (time echo, TE, 20

  9. Sequence motifs in MADS transcription factors responsible for specificity and diversification of protein-protein interaction.

    Directory of Open Access Journals (Sweden)

    Aalt D J van Dijk

    Full Text Available Protein sequences encompass tertiary structures and contain information about specific molecular interactions, which in turn determine biological functions of proteins. Knowledge about how protein sequences define interaction specificity is largely missing, in particular for paralogous protein families with high sequence similarity, such as the plant MADS domain transcription factor family. In comparison to the situation in mammalian species, this important family of transcription regulators has expanded enormously in plant species and contains over 100 members in the model plant species Arabidopsis thaliana. Here, we provide insight into the mechanisms that determine protein-protein interaction specificity for the Arabidopsis MADS domain transcription factor family, using an integrated computational and experimental approach. Plant MADS proteins have highly similar amino acid sequences, but their dimerization patterns vary substantially. Our computational analysis uncovered small sequence regions that explain observed differences in dimerization patterns with reasonable accuracy. Furthermore, we show the usefulness of the method for prediction of MADS domain transcription factor interaction networks in other plant species. Introduction of mutations in the predicted interaction motifs demonstrated that single amino acid mutations can have a large effect and lead to loss or gain of specific interactions. In addition, various performed bioinformatics analyses shed light on the way evolution has shaped MADS domain transcription factor interaction specificity. Identified protein-protein interaction motifs appeared to be strongly conserved among orthologs, indicating their evolutionary importance. We also provide evidence that mutations in these motifs can be a source for sub- or neo-functionalization. The analyses presented here take us a step forward in understanding protein-protein interactions and the interplay between protein sequences and

  10. A survey of the sequence-specific interaction of damaging agents with DNA: emphasis on antitumor agents.

    Science.gov (United States)

    Murray, V

    1999-01-01

    This article reviews the literature concerning the sequence specificity of DNA-damaging agents. DNA-damaging agents are widely used in cancer chemotherapy. It is important to understand fully the determinants of DNA sequence specificity so that more effective DNA-damaging agents can be developed as antitumor drugs. There are five main methods of DNA sequence specificity analysis: cleavage of end-labeled fragments, linear amplification with Taq DNA polymerase, ligation-mediated polymerase chain reaction (PCR), single-strand ligation PCR, and footprinting. The DNA sequence specificity in purified DNA and in intact mammalian cells is reviewed for several classes of DNA-damaging agent. These include agents that form covalent adducts with DNA, free radical generators, topoisomerase inhibitors, intercalators and minor groove binders, enzymes, and electromagnetic radiation. The main sites of adduct formation are at the N-7 of guanine in the major groove of DNA and the N-3 of adenine in the minor groove, whereas free radical generators abstract hydrogen from the deoxyribose sugar and topoisomerase inhibitors cause enzyme-DNA cross-links to form. Several issues involved in the determination of the DNA sequence specificity are discussed. The future directions of the field, with respect to cancer chemotherapy, are also examined.

  11. Analysis of B Cell Repertoire Dynamics Following Hepatitis B Vaccination in Humans, and Enrichment of Vaccine-specific Antibody Sequences

    Directory of Open Access Journals (Sweden)

    Jacob D. Galson

    2015-12-01

    Full Text Available Generating a diverse B cell immunoglobulin repertoire is essential for protection against infection. The repertoire in humans can now be comprehensively measured by high-throughput sequencing. Using hepatitis B vaccination as a model, we determined how the total immunoglobulin sequence repertoire changes following antigen exposure in humans, and compared this to sequences from vaccine-specific sorted cells. Clonal sequence expansions were seen 7 days after vaccination, which correlated with vaccine-specific plasma cell numbers. These expansions caused an increase in mutation, and a decrease in diversity and complementarity-determining region 3 sequence length in the repertoire. We also saw an increase in sequence convergence between participants 14 and 21 days after vaccination, coinciding with an increase of vaccine-specific memory cells. These features allowed development of a model for in silico enrichment of vaccine-specific sequences from the total repertoire. Identifying antigen-specific sequences from total repertoire data could aid our understanding B cell driven immunity, and be used for disease diagnostics and vaccine evaluation.

  12. Rapid detection and purification of sequence specific DNA binding proteins using magnetic separation

    Directory of Open Access Journals (Sweden)

    TIJANA SAVIC

    2006-02-01

    Full Text Available In this paper, a method for the rapid identification and purification of sequence specific DNA binding proteins based on magnetic separation is presented. This method was applied to confirm the binding of the human recombinant USF1 protein to its putative binding site (E-box within the human SOX3 protomer. It has been shown that biotinylated DNA attached to streptavidin magnetic particles specifically binds the USF1 protein in the presence of competitor DNA. It has also been demonstrated that the protein could be successfully eluted from the beads, in high yield and with restored DNA binding activity. The advantage of these procedures is that they could be applied for the identification and purification of any high-affinity sequence-specific DNA binding protein with only minor modifications.

  13. Sequence specific electronic conduction through polyion-stabilized double-stranded DNA in nanoscale break junctions

    International Nuclear Information System (INIS)

    Mahapatro, Ajit K; Jeong, Kyung J; Lee, Gil U; Janes, David B

    2007-01-01

    This paper presents a study of sequence specific electronic conduction through short (15-base-pair) double-stranded (ds) DNA molecules, measured by immobilizing 3 ' -thiol-derivatized DNAs in nanometre scale gaps between gold electrodes. The polycation spermidine was used to stabilize the ds-DNA structure, allowing electrical measurements to be performed in a dry state. For specific sequences, the conductivity was observed to scale with the surface density of immobilized DNA, which can be controlled by the buffer concentration. A series of 15-base DNA oligonucleotide pairs, in which the centre sequence of five base pairs was changed from G:C to A:T pairs, has been studied. The conductivity per molecule is observed to decrease exponentially with the number of adjacent A:T pairs replacing G:C pairs, consistent with a barrier at the A:T sites. Conductance-based devices for short DNA sequences could provide sensing approaches with direct electrical readout, as well as label-free detection

  14. Micropatterning stretched and aligned DNA for sequence-specific nanolithography

    Science.gov (United States)

    Petit, Cecilia Anna Paulette

    Techniques for fabricating nanostructured materials can be categorized as either "top-down" or "bottom-up". Top-down techniques use lithography and contact printing to create patterned surfaces and microfluidic channels that can corral and organize nanoscale structures, such as molecules and nanorods in contrast; bottom-up techniques use self-assembly or molecular recognition to direct the organization of materials. A central goal in nanotechnology is the integration of bottom-up and top-down assembly strategies for materials development, device design; and process integration. With this goal in mind, we have developed strategies that will allow this integration by using DNA as a template for nanofabrication; two top-down approaches allow the placement of these templates, while the bottom-up technique uses the specific sequence of bases to pattern materials along each strand of DNA. Our first top-down approach, termed combing of molecules in microchannels (COMMIC), produces microscopic patterns of stretched and aligned molecules of DNA on surfaces. This process consists of passing an air-water interface over end adsorbed molecules inside microfabricated channels. The geometry of the microchannel directs the placement of the DNA molecules, while the geometry of the airwater interface directs the local orientation and curvature of the molecules. We developed another top-down strategy for creating micropatterns of stretched and aligned DNA using surface chemistry. Because DNA stretching occurs on hydrophobic surfaces, this technique uses photolithography to pattern vinyl-terminated silanes on glass When these surface-, are immersed in DNA solution, molecules adhere preferentially to the silanized areas. This approach has also proven useful in patterning protein for cell adhesion studies. Finally, we describe the use of these stretched and aligned molecules of DNA as templates for the subsequent bottom-up construction of hetero-structures through hybridization

  15. Whole-body magnetic resonance imaging for staging and follow-up of pediatric patients with Hodgkin's lymphoma: comparison of different sequences

    International Nuclear Information System (INIS)

    Nava, Daniel; Oliveira, Heverton Cesar de

    2011-01-01

    Objective: to compare the performance of the T1, T2, STIR and DWIBS (diffusion-weighted whole-body imaging with background body signal suppression) sequences in the staging and follow-up of pediatric patients with Hodgkin's lymphoma in lymph node chains, parenchymal organs and bone marrow, and to evaluate interobserver agreement. Materials and methods: the authors studied 12 patients with confirmed diagnosis of Hodgkin's lymphoma. The patients were referred for whole body magnetic resonance imaging with T1-weighted, T2-weighted, STIR and DWIBS sequences. Results: the number of lymph node sites characterized as affected by the disease on T1- and T2-weighted sequences showed similar results (8 sites for both sequences), but lower than DWIBS and STIR sequences (11 and 12 sites, respectively). The bone marrow involvement by lymphoma showed the same values for the T1-, T2-weighted and DWIBS sequences (17 lesions), higher than the value found on STIR (13 lesions). A high rate of interobserver agreement was observed as the four sequences were analyzed. Conclusion: STIR and DWIBS sequences detected the highest number of lymph node sites characterized as affected by the disease. Similar results were demonstrated by all the sequences in the evaluation of parenchymal organs and bone marrow. A high interobserver agreement was observed as the four sequences were analyzed. (author)

  16. Testing resonating vector strength: Auditory system, electric fish, and noise

    Science.gov (United States)

    Leo van Hemmen, J.; Longtin, André; Vollmayr, Andreas N.

    2011-12-01

    Quite often a response to some input with a specific frequency ν○ can be described through a sequence of discrete events. Here, we study the synchrony vector, whose length stands for the vector strength, and in doing so focus on neuronal response in terms of spike times. The latter are supposed to be given by experiment. Instead of singling out the stimulus frequency ν○ we study the synchrony vector as a function of the real frequency variable ν. Its length turns out to be a resonating vector strength in that it shows clear maxima in the neighborhood of ν○ and multiples thereof, hence, allowing an easy way of determining response frequencies. We study this "resonating" vector strength for two concrete but rather different cases, viz., a specific midbrain neuron in the auditory system of cat and a primary detector neuron belonging to the electric sense of the wave-type electric fish Apteronotus leptorhynchus. We show that the resonating vector strength always performs a clear resonance correlated with the phase locking that it quantifies. We analyze the influence of noise and demonstrate how well the resonance associated with maximal vector strength indicates the dominant stimulus frequency. Furthermore, we exhibit how one can obtain a specific phase associated with, for instance, a delay in auditory analysis.

  17. High-specificity detection of rare alleles with Paired-End Low Error Sequencing (PELE-Seq).

    Science.gov (United States)

    Preston, Jessica L; Royall, Ariel E; Randel, Melissa A; Sikkink, Kristin L; Phillips, Patrick C; Johnson, Eric A

    2016-06-14

    Polymorphic loci exist throughout the genomes of a population and provide the raw genetic material needed for a species to adapt to changes in the environment. The minor allele frequencies of rare Single Nucleotide Polymorphisms (SNPs) within a population have been difficult to track with Next-Generation Sequencing (NGS), due to the high error rate of standard methods such as Illumina sequencing. We have developed a wet-lab protocol and variant-calling method that identifies both sequencing and PCR errors, called Paired-End Low Error Sequencing (PELE-Seq). To test the specificity and sensitivity of the PELE-Seq method, we sequenced control E. coli DNA libraries containing known rare alleles present at frequencies ranging from 0.2-0.4 % of the total reads. PELE-Seq had higher specificity and sensitivity than standard libraries. We then used PELE-Seq to characterize rare alleles in a Caenorhabditis remanei nematode worm population before and after laboratory adaptation, and found that minor and rare alleles can undergo large changes in frequency during lab-adaptation. We have developed a method of rare allele detection that mitigates both sequencing and PCR errors, called PELE-Seq. PELE-Seq was evaluated using control E. coli populations and was then used to compare a wild C. remanei population to a lab-adapted population. The PELE-Seq method is ideal for investigating the dynamics of rare alleles in a broad range of reduced-representation sequencing methods, including targeted amplicon sequencing, RAD-Seq, ddRAD, and GBS. PELE-Seq is also well-suited for whole genome sequencing of mitochondria and viruses, and for high-throughput rare mutation screens.

  18. Sequence specific motor performance gains after memory consolidation in children and adolescents.

    Directory of Open Access Journals (Sweden)

    Shoshi Dorfberger

    Full Text Available Memory consolidation for a trained sequence of finger opposition movements, in 9- and 12-year-old children, was recently found to be significantly less susceptible to interference by a subsequent training experience, compared to that of 17-year-olds. It was suggested that, in children, the experience of training on any sequence of finger movements may affect the performance of the sequence elements, component movements, rather than the sequence as a unit; the latter has been implicated in the learning of the task by adults. This hypothesis implied a possible childhood advantage in the ability to transfer the gains from a trained to the reversed, untrained, sequence of movements. Here we report the results of transfer tests undertaken to test this proposal in 9-, 12-, and 17-year-olds after training in the finger-to-thumb opposition sequence (FOS learning task. Our results show that the performance gains in the trained sequence partially transferred from the left, trained hand, to the untrained hand at 48-hours after a single training session in the three age-groups tested. However, there was very little transfer of the gains from the trained to the untrained, reversed, sequence performed by either hand. The results indicate sequence specific post-training gains in FOS performance, as opposed to a general improvement in performance of the individual, component, movements that comprised both the trained and untrained sequences. These results do not support the proposal that the reduced susceptibility to interference, in children before adolescence, reflects a difference in movement syntax representation after training.

  19. Sequence specific motor performance gains after memory consolidation in children and adolescents.

    Science.gov (United States)

    Dorfberger, Shoshi; Adi-Japha, Esther; Karni, Avi

    2012-01-01

    Memory consolidation for a trained sequence of finger opposition movements, in 9- and 12-year-old children, was recently found to be significantly less susceptible to interference by a subsequent training experience, compared to that of 17-year-olds. It was suggested that, in children, the experience of training on any sequence of finger movements may affect the performance of the sequence elements, component movements, rather than the sequence as a unit; the latter has been implicated in the learning of the task by adults. This hypothesis implied a possible childhood advantage in the ability to transfer the gains from a trained to the reversed, untrained, sequence of movements. Here we report the results of transfer tests undertaken to test this proposal in 9-, 12-, and 17-year-olds after training in the finger-to-thumb opposition sequence (FOS) learning task. Our results show that the performance gains in the trained sequence partially transferred from the left, trained hand, to the untrained hand at 48-hours after a single training session in the three age-groups tested. However, there was very little transfer of the gains from the trained to the untrained, reversed, sequence performed by either hand. The results indicate sequence specific post-training gains in FOS performance, as opposed to a general improvement in performance of the individual, component, movements that comprised both the trained and untrained sequences. These results do not support the proposal that the reduced susceptibility to interference, in children before adolescence, reflects a difference in movement syntax representation after training.

  20. 29 CFR 1926.752 - Site layout, site-specific erection plan and construction sequence.

    Science.gov (United States)

    2010-07-01

    ... 29 Labor 8 2010-07-01 2010-07-01 false Site layout, site-specific erection plan and construction... Steel Erection § 1926.752 Site layout, site-specific erection plan and construction sequence. (a... strength or sufficient strength to support the loads imposed during steel erection. (c) Site layout. The...

  1. Chirality- and sequence-selective successive self-sorting via specific homo- and complementary-duplex formations

    Science.gov (United States)

    Makiguchi, Wataru; Tanabe, Junki; Yamada, Hidekazu; Iida, Hiroki; Taura, Daisuke; Ousaka, Naoki; Yashima, Eiji

    2015-01-01

    Self-recognition and self-discrimination within complex mixtures are of fundamental importance in biological systems, which entirely rely on the preprogrammed monomer sequences and homochirality of biological macromolecules. Here we report artificial chirality- and sequence-selective successive self-sorting of chiral dimeric strands bearing carboxylic acid or amidine groups joined by chiral amide linkers with different sequences through homo- and complementary-duplex formations. A mixture of carboxylic acid dimers linked by racemic-1,2-cyclohexane bis-amides with different amide sequences (NHCO or CONH) self-associate to form homoduplexes in a completely sequence-selective way, the structures of which are different from each other depending on the linker amide sequences. The further addition of an enantiopure amide-linked amidine dimer to a mixture of the racemic carboxylic acid dimers resulted in the formation of a single optically pure complementary duplex with a 100% diastereoselectivity and complete sequence specificity stabilized by the amidinium–carboxylate salt bridges, leading to the perfect chirality- and sequence-selective duplex formation. PMID:26051291

  2. Sequence-specific protection of duplex DNA against restriction and methylation enzymes by pseudocomplementary PNAs

    DEFF Research Database (Denmark)

    Izvolsky, K I; Demidov, V V; Nielsen, P E

    2000-01-01

    I restriction endonuclease and dam methylase. The pcPNA-assisted protection against enzymatic methylation is more efficient when the PNA-binding site embodies the methylase-recognition site rather than overlaps it. We conclude that pcPNAs may provide the robust tools allowing to sequence-specifically manipulate...... DNA duplexes in a virtually sequence-unrestricted manner....

  3. Sequence-specific 1H NMR resonance assignments of Bacillus subtilis HPr: Use of spectra obtained from mutants to resolve spectral overlap

    International Nuclear Information System (INIS)

    Wittekind, M.; Klevit, R.E.; Reizer, J.

    1990-01-01

    On the basis of an analysis of two-dimensional 1 H NMR spectra, the complete sequence-specific 1 H NMR assignments are presented for the phosphocarrier protein HPr from the Gram-positive bacterium Bacillus subtilis. During the assignment procedure, extensive use was made of spectra obtained from point mutants of HPr in order to resolve spectral overlap and to provide verification of assignments. Regions of regular secondary structure were identified by characteristic patterns of sequential backbone proton NOEs and slowly exchanging amide protons. B subtilis HPr contains four β-strands that form a single antiparallel β-sheet and two well-defined α-helices. There are two stretches of extended backbone structure, one of which contains the active site His 15 . The overall fold of the protein is very similar to that of Escherichia coli HPr determined by NMR studies

  4. Diffusion-weighted Imaging Is a Sensitive and Specific Magnetic Resonance Sequence in the Diagnosis of Ankylosing Spondylitis.

    Science.gov (United States)

    Bradbury, Linda A; Hollis, Kelly A; Gautier, Benoît; Shankaranarayana, Sateesh; Robinson, Philip C; Saad, Nivene; Lê Cao, Kim-Anh; Brown, Matthew A

    2018-06-01

    We tested the discriminatory capacity of diffusion-weighted magnetic resonance imaging (DWI) and its potential as an objective measure of treatment response to tumor necrosis factor inhibition in ankylosing spondylitis (AS). Three cohorts were studied prospectively: (1) 18 AS patients with Bath Ankylosing Spondylitis Disease Activity Index > 4, and erythrocyte sedimentation rate > 25 and/or C-reactive protein > 10 meeting the modified New York criteria for AS; (2) 20 cases of nonradiographic axial spondyloarthritis (nr-axSpA) as defined by the Assessment of Spondyloarthritis international Society (ASAS) criteria; and (3) 20 non-AS patients with chronic low back pain, aged between 18 and 45 years, who did not meet the imaging arm of the ASAS criteria for axSpA. Group 1 patients were studied prior to and following adalimumab treatment. Patients were assessed by DWI and conventional magnetic resonance imaging (MRI), and standard nonimaging measures. At baseline, in contrast to standard nonimaging measures, DWI apparent diffusion coefficient (ADC) values showed good discriminatory performance [area under the curve (AUC) > 80% for Group 1 or 2 compared with Group 3]. DWI ADC values were significantly lower posttreatment (0.45 ± 0.433 before, 0.154 ± 0.23 after, p = 0.0017), but had modest discriminating capacity comparing pre- and posttreatment measures (AUC = 68%). This performance was similar to the manual Spondyloarthritis Research Consortium of Canada (SPARCC) scoring system. DWI is informative for diagnosis of AS and nr-axSpA, and has moderate utility in assessment of disease activity or treatment response, with performance similar to that of the SPARCC MRI score.

  5. BrEPS: a flexible and automatic protocol to compute enzyme-specific sequence profiles for functional annotation

    Directory of Open Access Journals (Sweden)

    Schomburg D

    2010-12-01

    Full Text Available Abstract Background Models for the simulation of metabolic networks require the accurate prediction of enzyme function. Based on a genomic sequence, enzymatic functions of gene products are today mainly predicted by sequence database searching and operon analysis. Other methods can support these techniques: We have developed an automatic method "BrEPS" that creates highly specific sequence patterns for the functional annotation of enzymes. Results The enzymes in the UniprotKB are identified and their sequences compared against each other with BLAST. The enzymes are then clustered into a number of trees, where each tree node is associated with a set of EC-numbers. The enzyme sequences in the tree nodes are aligned with ClustalW. The conserved columns of the resulting multiple alignments are used to construct sequence patterns. In the last step, we verify the quality of the patterns by computing their specificity. Patterns with low specificity are omitted and recomputed further down in the tree. The final high-quality patterns can be used for functional annotation. We ran our protocol on a recent Swiss-Prot release and show statistics, as well as a comparison to PRIAM, a probabilistic method that is also specialized on the functional annotation of enzymes. We determine the amount of true positive annotations for five common microorganisms with data from BRENDA and AMENDA serving as standard of truth. BrEPS is almost on par with PRIAM, a fact which we discuss in the context of five manually investigated cases. Conclusions Our protocol computes highly specific sequence patterns that can be used to support the functional annotation of enzymes. The main advantages of our method are that it is automatic and unsupervised, and quite fast once the patterns are evaluated. The results show that BrEPS can be a valuable addition to the reconstruction of metabolic networks.

  6. Differential representation of sunflower ESTs in enriched organ-specific cDNA libraries in a small scale sequencing project

    Directory of Open Access Journals (Sweden)

    Heinz Ruth A

    2003-09-01

    Full Text Available Abstract Background Subtractive hybridization methods are valuable tools for identifying differentially regulated genes in a given tissue avoiding redundant sequencing of clones representing the same expressed genes, maximizing detection of low abundant transcripts and thus, affecting the efficiency and cost effectiveness of small scale cDNA sequencing projects aimed to the specific identification of useful genes for breeding purposes. The objective of this work is to evaluate alternative strategies to high-throughput sequencing projects for the identification of novel genes differentially expressed in sunflower as a source of organ-specific genetic markers that can be functionally associated to important traits. Results Differential organ-specific ESTs were generated from leaf, stem, root and flower bud at two developmental stages (R1 and R4. The use of different sources of RNA as tester and driver cDNA for the construction of differential libraries was evaluated as a tool for detection of rare or low abundant transcripts. Organ-specificity ranged from 75 to 100% of non-redundant sequences in the different cDNA libraries. Sequence redundancy varied according to the target and driver cDNA used in each case. The R4 flower cDNA library was the less redundant library with 62% of unique sequences. Out of a total of 919 sequences that were edited and annotated, 318 were non-redundant sequences. Comparison against sequences in public databases showed that 60% of non-redundant sequences showed significant similarity to known sequences. The number of predicted novel genes varied among the different cDNA libraries, ranging from 56% in the R4 flower to 16 % in the R1 flower bud library. Comparison with sunflower ESTs on public databases showed that 197 of non-redundant sequences (60% did not exhibit significant similarity to previously reported sunflower ESTs. This approach helped to successfully isolate a significant number of new reported sequences

  7. Screening for SNPs with Allele-Specific Methylation based on Next-Generation Sequencing Data

    OpenAIRE

    Hu, Bo; Ji, Yuan; Xu, Yaomin; Ting, Angela H

    2013-01-01

    Allele-specific methylation (ASM) has long been studied but mainly documented in the context of genomic imprinting and X chromosome inactivation. Taking advantage of the next-generation sequencing technology, we conduct a high-throughput sequencing experiment with four prostate cell lines to survey the whole genome and identify single nucleotide polymorphisms (SNPs) with ASM. A Bayesian approach is proposed to model the counts of short reads for each SNP conditional on its genotypes of multip...

  8. Isolation of laccase gene-specific sequences from white rot and brown rot fungi by PCR.

    Science.gov (United States)

    D'Souza, T M; Boominathan, K; Reddy, C A

    1996-01-01

    Degenerate primers corresponding to the consensus sequences of the copper-binding regions in the N-terminal domains of known basidiomycete laccases were used to isolate laccase gene-specific sequences from strains representing nine genera of wood rot fungi. All except three gave the expected PCR product of about 200 bp. Computer searches of the databases identified the sequence of each of the PCR products analyzed as a laccase gene sequence, suggesting the specificity of the primers. PCR products of the white rot fungi Ganoderma lucidum, Phlebia brevispora, and Trametes versicolor showed 65 to 74% nucleotide sequence similarity to each other; the similarity in deduced amino acid sequences was 83 to 91%. The PCR products of Lentinula edodes and Lentinus tigrinus, on the other hand, showed relatively low nucleotide and amino acid similarities (58 to 64 and 62 to 81%, respectively); however, these similarities were still much higher than when compared with the corresponding regions in the laccases of the ascomycete fungi Aspergillus nidulans and Neurospora crassa. A few of the white rot fungi, as well as Gloeophyllum trabeum, a brown rot fungus, gave a 144-bp PCR fragment which had a nucleotide sequence similarity of 60 to 71%. Demonstration of laccase activity in G. trabeum and several other brown rot fungi was of particular interest because these organisms were not previously shown to produce laccases. PMID:8837429

  9. Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method

    Directory of Open Access Journals (Sweden)

    Sette Alessandro

    2005-05-01

    Full Text Available Abstract Background Many processes in molecular biology involve the recognition of short sequences of nucleic-or amino acids, such as the binding of immunogenic peptides to major histocompatibility complex (MHC molecules. From experimental data, a model of the sequence specificity of these processes can be constructed, such as a sequence motif, a scoring matrix or an artificial neural network. The purpose of these models is two-fold. First, they can provide a summary of experimental results, allowing for a deeper understanding of the mechanisms involved in sequence recognition. Second, such models can be used to predict the experimental outcome for yet untested sequences. In the past we reported the development of a method to generate such models called the Stabilized Matrix Method (SMM. This method has been successfully applied to predicting peptide binding to MHC molecules, peptide transport by the transporter associated with antigen presentation (TAP and proteasomal cleavage of protein sequences. Results Herein we report the implementation of the SMM algorithm as a publicly available software package. Specific features determining the type of problems the method is most appropriate for are discussed. Advantageous features of the package are: (1 the output generated is easy to interpret, (2 input and output are both quantitative, (3 specific computational strategies to handle experimental noise are built in, (4 the algorithm is designed to effectively handle bounded experimental data, (5 experimental data from randomized peptide libraries and conventional peptides can easily be combined, and (6 it is possible to incorporate pair interactions between positions of a sequence. Conclusion Making the SMM method publicly available enables bioinformaticians and experimental biologists to easily access it, to compare its performance to other prediction methods, and to extend it to other applications.

  10. Epitopes of human testis-specific lactate dehydrogenase deduced from a cDNA sequence

    International Nuclear Information System (INIS)

    Millan, J.L.; Driscoll, C.E.; LeVan, K.M.; Goldberg, E.

    1987-01-01

    The sequence and structure of human testis-specific L-lactate dehydrogenase [LDHC 4 , LDHX; (L)-lactate:NAD + oxidoreductase, EC 1.1.1.27] has been derived from analysis of a complementary DNA (cDNA) clone comprising the complete protein coding region of the enzyme. From the deduced amino acid sequence, human LDHC 4 is as different from rodent LDHC 4 (73% homology) as it is from human LDHA 4 (76% homology) and porcine LDHB 4 (68% homology). Subunit homologies are consistent with the conclusion that the LDHC gene arose by at least two independent duplication events. Furthermore, the lower degree of homology between mouse and human LDHC 4 and the appearance of this isozyme late in evolution suggests a higher rate of mutation in the mammalian LDHC genes than in the LDHA and -B genes. Comparison of exposed amino acid residues of discrete anti-genic determinants of mouse and human LDHC 4 reveals significant differences. Knowledge of the human LDHC 4 sequence will help design human-specific peptides useful in the development of a contraceptive vaccine

  11. The Optimization of Magnetic Resonance Imaging Pulse Sequences in Order to Better Detection of Multiple Sclerosis Plaques.

    Science.gov (United States)

    Farshidfar, Z; Faeghi, F; Haghighatkhah, H R; Abdolmohammadi, J

    2017-09-01

    Magnetic resonance imaging (MRI) is the most sensitive technique to detect multiple sclerosis (MS) plaques in central nervous system. In some cases, the patients who were suspected to MS, Whereas MRI images are normal, but whether patients don't have MS plaques or MRI images are not enough optimized enough in order to show MS plaques? The aim of the current study is evaluating the efficiency of different MRI sequences in order to better detection of MS plaques. In this cross-sectional study which was performed at Shohada-E Tajrish in Tehran - Iran hospital between October, 2011 to April, 2012, included 20 patients who suspected to MS disease were selected by the method of random sampling and underwent routine brain Pulse sequences (Axial T2w, Axial T1w, Coronal T2w, Sagittal T1w, Axial FLAIR) by Siemens, Avanto, 1.5 Tesla system. If any lesion which is suspected to the MS disease was observed, additional sequences such as: Sagittal FLAIR Fat Sat, Sagittal PDw-fat Sat, Sagittal PDw-water sat was also performed. This study was performed in about 52 lesions and the results in more than 19 lesions showed that, for the Subcortical and Infratentorial areas, PDWw sequence with fat suppression is the best choice, And in nearly 33 plaques located in Periventricular area, FLAIR Fat Sat was the most effective sequence than both PDw fat and water suppression pulse sequences. Although large plaques may visible in all images, but important problem in patients with suspected MS is screening the tiny MS plaques. This study showed that for revealing the MS plaques located in the Subcortical and Infratentorial areas, PDw-fat sat is the most effective sequence, and for MS plaques in the periventricular area, FLAIR fat Sat is the best choice.

  12. Identification of antigen-specific human monoclonal antibodies using high-throughput sequencing of the antibody repertoire.

    Science.gov (United States)

    Liu, Ju; Li, Ruihua; Liu, Kun; Li, Liangliang; Zai, Xiaodong; Chi, Xiangyang; Fu, Ling; Xu, Junjie; Chen, Wei

    2016-04-22

    High-throughput sequencing of the antibody repertoire provides a large number of antibody variable region sequences that can be used to generate human monoclonal antibodies. However, current screening methods for identifying antigen-specific antibodies are inefficient. In the present study, we developed an antibody clone screening strategy based on clone dynamics and relative frequency, and used it to identify antigen-specific human monoclonal antibodies. Enzyme-linked immunosorbent assay showed that at least 52% of putative positive immunoglobulin heavy chains composed antigen-specific antibodies. Combining information on dynamics and relative frequency improved identification of positive clones and elimination of negative clones. and increase the credibility of putative positive clones. Therefore the screening strategy could simplify the subsequent experimental screening and may facilitate the generation of antigen-specific antibodies. Copyright © 2016 Elsevier Inc. All rights reserved.

  13. Antitumor activity of sequence-specific alkylating agents: pyrolle-imidazole CBI conjugates with indole linker.

    Science.gov (United States)

    Shinohara, Ken-ichi; Bando, Toshikazu; Sasaki, Shunta; Sakakibara, Yogo; Minoshima, Masafumi; Sugiyama, Hiroshi

    2006-03-01

    DNA-targeting agents, including cisplatin, bleomycin and mitomycin C, are used routinely in cancer treatments. However, these drugs are extremely toxic, attacking normal cells and causing severe side effects. One important question to consider in designing anticancer agents is whether the introduction of sequence selectivity to DNA-targeting agents can improve their efficacy as anticancer agents. In the present study, the growth inhibition activities of an indole-seco 1,2,9,9a-tetrahydrocyclopropa[1,2-c]benz[1,2-e]indol-4-one (CBI) (1) and five conjugates with hairpin pyrrole-imidazole polyamides (2-6), which have different sequence specificities for DNA alkylation, were compared using 10 different cell lines. The average values of -log GI50 (50% growth inhibition concentration) for compounds 1-6 against the 10 cell lines were 8.33, 8.56, 8.29, 8.04, 8.23 and 8.83, showing that all of these compounds strongly inhibit cell growth. Interestingly, each alkylating agent caused significantly different growth inhibition patterns with each cell line. In particular, the correlation coefficients between the -log GI50 of compound 1 and its conjugates 2-6 showed extremely low values (Ralkylation lead to marked differences in biological activity. Comparison of the correlation coefficients between compounds 6 and 7, with the same sequence specificity as 6, and MS-247, with sequence specificity different from 6, when used against a panel of 37 human cancer cell lines further confirmed the above hypothesis.

  14. Detection of hepatic VX2 carcinomas with ferucarbotran-enhanced magnetic resonance imaging in rabbits: Comparison of nine pulse sequences

    International Nuclear Information System (INIS)

    Kim, Seong Hyun; Choi, Dongil; Lim, Hyo K.; Kim, Min Ju; Jang, Kyung Mi; Kim, Seung Hoon; Lee, Won Jae; Lee, Jongmee; Jeon, Yong Hwan; Lim, Jae Hoon

    2006-01-01

    Objective: To compare the diagnostic performance of a variety of magnetic resonance imaging (MRI) sequences, in order to identify the most effective ferucarbotran-enhanced sequence for the detection of multiple small hepatic VX2 carcinomas in rabbits. Methods: Fifteen rabbits with experimentally induced 135 VX2 carcinomas in the liver underwent ferucarbotran-enhanced MRI using the following nine pulse sequences: a fat-suppressed fast spin-echo (FSE) sequence with two echo times (TE) (proton density- and T2-weighted images), four different T2*-weighted fast multiplanar GRASS (gradient-recalled acquisition in the steady state) (FMPGR) with the combination of three TEs (9, 12, 15 ms, respectively) and two flip angles (20 deg., 80 deg., respectively), T2*-weighted fast multiplanar spoiled GRASS (FMPSPGR), T1-weighted FMPSPGR, and dynamic T1-weighted FMPSPGR. All images were reviewed by three radiologists with quantitative and qualitative analysis. Results: Tumor-to-liver contrast-to-noise ratio of the proton density-weighted FSE sequence was significantly higher than those of the others (p o ) images were superior to those of the others and for the detection of very small hepatic tumors of less than 5 mm, the sensitivities of these sequences were less than 30%. Conclusion: Ferucarbotran-enhanced T2- and proton density-weighted FSE and T2*-weighed FMPGR (TE/flip angle, 12/20 o ) images were found to be the most effective pulse sequences for the detection of multiple small hepatic VX2 carcinomas but these sequences were limited in the detection of very small hepatic tumors of less than 5 mm in size

  15. Luminescence resonance energy transfer (LRET) aptasensor for ochratoxin A detection using upconversion nanoparticles

    Science.gov (United States)

    Jo, Eun-Jung; Byun, Ju-Young; Mun, Hyoyoung; Kim, Min-Gon

    2017-07-01

    We report an aptasensor for homogeneous ochratoxin A (OTA) detection based on luminescence resonance energy transfer (LRET). This system uses upconversion nanoparticles (UCNPs), such as NaYF4:Yb3+, Er 3+, as the donor. The aptamer includes the optimum-length linker (5-mer-length DNA) and OTA-specific aptamer sequences. Black hole quencher 1 (BHQ1), as the acceptor, was modified at the 3' end of the aptamer sequence. BHQ1 plays as a quencher in LRET aptasensor and shows absorption at 543 nm, which overlaps with well the emission of the UCNPs. When OTA is added, the BHQ1-labeled OTA aptamer was folded due to the formation of the G-quadruplex-OTA complex, which induced the BHQ1 close to the UCNPs. Consequently, resonance energy transfer between UCNPs (donor) and BHQ1 (acceptor) enables quenching of upconversion luminescence signals under laser irradiation of 980 nm. Our results showed that the LRET-based aptasensor allows specific OTA analysis with a limit of detection of 0.03 ng/mL. These results demonstrated that the OTA in diverse foods can be detected specifically and sensitively in a homogeneous manner.

  16. Isolation of laccase gene-specific sequences from white rot and brown rot fungi by PCR

    Energy Technology Data Exchange (ETDEWEB)

    D`Souza, T.M.; Boominathan, K.; Reddy, C.A. [Michigan State Univ., East Lansing, MI (United States)

    1996-10-01

    Degenerate primers corresponding to the consensus sequences of the copper-binding regions in the N-terminal domains of known basidiomycete laccases were used to isolate laccase gene-specific sequences from strains representing nine genera of wood rot fungi. All except three gave the expected PCR product of about 200 bp. Computer searches of the databases identified the sequences of each of the PCR product of about 200 bp. Computer searches of the databases identified the sequence of each of the PCR products analyzed as a laccase gene sequence, suggesting the specificity of the primers. PCR products of the white rot fungi Ganoderma lucidum, Phlebia brevispora, and Trametes versicolor showed 65 to 74% nucleotide sequence similarity to each other; the similarity in deduced amino acid sequences was 83 to 91%. The PCR products of Lentinula edodes and Lentinus tigrinus, on the other hand, showed relatively low nucleotide and amino acid similarities (58 to 64 and 62 to 81%, respectively); however, these similarities were still much higher than when compared with the corresponding regions in the laccases of the ascomycete fungi Aspergillus nidulans and Neurospora crassa. A few of the white rot fungi, as well as Gloeophyllum trabeum, a brown rot fungus, gave a 144-bp PCR fragment which had a nucleotide sequence similarity of 60 to 71%. Demonstration of laccase activity in G. trabeum and several other brown rot fungi was of particular interest because these organisms were not previously shown to produce laccases. 36 refs., 6 figs., 2 tabs.

  17. Molecular Simulations of Sequence-Specific Association of Transmembrane Proteins in Lipid Bilayers

    Science.gov (United States)

    Doxastakis, Manolis; Prakash, Anupam; Janosi, Lorant

    2011-03-01

    Association of membrane proteins is central in material and information flow across the cellular membranes. Amino-acid sequence and the membrane environment are two critical factors controlling association, however, quantitative knowledge on such contributions is limited. In this work, we study the dimerization of helices in lipid bilayers using extensive parallel Monte Carlo simulations with recently developed algorithms. The dimerization of Glycophorin A is examined employing a coarse-grain model that retains a level of amino-acid specificity, in three different phospholipid bilayers. Association is driven by a balance of protein-protein and lipid-induced interactions with the latter playing a major role at short separations. Following a different approach, the effect of amino-acid sequence is studied using the four transmembrane domains of the epidermal growth factor receptor family in identical lipid environments. Detailed characterization of dimer formation and estimates of the free energy of association reveal that these helices present significant affinity to self-associate with certain dimers forming non-specific interfaces.

  18. Molecular-Level Thermodynamic Switch Controls Chemical Equilibrium in Sequence-Specific Hydrophobic Interaction of 35 Dipeptide Pairs

    OpenAIRE

    Chun, Paul W.

    2003-01-01

    Applying the Planck-Benzinger methodology, the sequence-specific hydrophobic interactions of 35 dipeptide pairs were examined over a temperature range of 273–333 K, based on data reported by Nemethy and Scheraga in 1962. The hydrophobic interaction in these sequence-specific dipeptide pairs is highly similar in its thermodynamic behavior to that of other biological systems. The results imply that the negative Gibbs free energy change minimum at a well-defined stable temperature, 〈Ts〉, where t...

  19. A fluorescence resonance energy transfer (FRET) biosensor based on graphene quantum dots (GQDs) and gold nanoparticles (AuNPs) for the detection of mecA gene sequence of Staphylococcus aureus.

    Science.gov (United States)

    Shi, Jingyu; Chan, Chunyu; Pang, Yukting; Ye, Weiwei; Tian, Feng; Lyu, Jing; Zhang, Yu; Yang, Mo

    2015-05-15

    In this work, a novel fluorescence resonance energy transfer (FRET) biosensor based on graphene quantum dots (GQDs) and gold nanoparticles (AuNPs) pairs was developed for Staphylococcus aureus specific gene sequence detection. This FRET biosensor platform was realized by immobilization of capture probes on GQDs and conjugation of reporter probes on AuNPs. Target oligos then co-hybridized with capture probes and reporter probes to form a sandwich structure which brought GQDs and AuNPs to close proximity to trigger FRET effect. The fluorescence signals before and after addition of targets were measured and the fluorescence quenching efficiency could reach around 87% with 100 nM target oligo. The limit of detection (LOD) of this FRET biosensor was around 1 nM for S.aureus gene detection. Experiments with both single-base mismatched oligos and double-base mismatched oligos demonstrated the good sequence selectivity of this FRET biosensor. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. Screening for sequence-specific RNA-BPs by comprehensive UV crosslinking

    Directory of Open Access Journals (Sweden)

    Le Meuth-Metzinger Valerie

    2002-06-01

    Full Text Available Abstract Background Specific cis-elements and the associated trans-acting factors have been implicated in the post-transcriptional regulation of gene expression. In the era of genome wide analyses identifying novel trans-acting factors and cis-regulatory elements is a step towards understanding coordinated gene expression. UV-crosslink analysis is a standard method used to identify RNA-binding proteins. Uridine is traditionally used to radiolabel substrate RNAs, however, proteins binding to cis-elments particularly uridine poor will be weakly or not detected. We evaluate here the possibility of using UV-crosslinking with RNA substrates radiolabeled with each of the four ribonucleotides as an approach for screening for novel sequence specific RNA-binding proteins. Results The radiolabeled RNA substrates were derived from the 3'UTRs of the cloned Eg and c-mos Xenopus laevis maternal mRNAs. Specific, but not identical, uv-crosslinking signals were obtained, some of which corresponded to already identified proteins. A signal for a novel 90 kDa protein was observed with the c-mos 3'UTR radiolabeled with both CTP and GTP but not with UTP. The binding site of the 90 kDa RNA-binding protein was localised to a 59-nucleotide portion of the c-mos 3'UTR. Conclusion That the 90 kDa signal was detected with RNAs radiolabeled with CTP or GTP but not UTP illustrates the advantage of radiolabeling all four nucleotides in a UV-crosslink based screen. This method can be used for both long and short RNAs and does not require knowledge of the cis-acting sequence. It should be amenable to high throughput screening for RNA binding proteins.

  1. Resonant vibrations of self-interstitials in fcc metals with application to specific heat and neutron scattering

    International Nuclear Information System (INIS)

    Ram, P.N.; Dederichs, P.H.

    1981-07-01

    Some aspects of resonant vibrations of self-interstitials in the 100-dumbbell configuration in fcc-metals are discussed by extending previous calculations of Zeller et al. and Schober et al. Employing a simple defect model with nearest-neighbour interaction the local frequency spectrum of the defect is calculated showing several localized modes and low-frequency resonant modes. The change in the total density of states due to the defects is expressed as the derivative of a generalized phase shift which is used to calculate the change in the lattic specific heat due to single interstitials. Inelastic neutron scattering away from the one-phonon lines is proposed as a method to observe the resonant modes induced by self-interstitials. The model calculation in Cu shows that the well defined resonant modes due to dumbbell vibrations have appreciable intensity and could presumably be detected in neutron scattering measurements. The effect of di-interstitials on the phonon dispersion in Al is also discussed. (orig./GSCH)

  2. Early Magnetic Resonance Detection of Natalizumab-Related Progressive Multifocal Leukoencephalopathy in a Patient with Multiple Sclerosis

    Directory of Open Access Journals (Sweden)

    Guglielmo Manenti

    2013-01-01

    Full Text Available Diagnosis of progressive multifocal leukoencephalopathy is usually based on the clinical presentation, on the demonstration of the brain lesions at the magnetic resonance imaging examination, and on the detection of the JC virus DNA in the cerebrospinal fluid with high sensitive polymerase chain reaction. The role of magnetic resonance imaging specifically in natalizumab-associated progressive multifocal leukoencephalopathy is strengthening, and it is gaining importance not only as an irreplaceable diagnostic tool but also as a surveillance and risk stratifying tool in treated patients. While other imaging techniques such as computed tomography lack sensitivity and specificity, magnetic resonance performed with morphological and functional sequences offers clinicians the possibility to early identify the stage of the disease and the emergence of an immune reconstitution inflammatory syndrome after natalizumab blood removal plasmapheresis.

  3. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes

    NARCIS (Netherlands)

    Skaletsky, Helen; Kuroda-Kawaguchi, Tomoko; Minx, Patrick J.; Cordum, Holland S.; Hillier, LaDeana; Brown, Laura G.; Repping, Sjoerd; Pyntikova, Tatyana; Ali, Johar; Bieri, Tamberlyn; Chinwalla, Asif; Delehaunty, Andrew; Delehaunty, Kim; Du, Hui; Fewell, Ginger; Fulton, Lucinda; Fulton, Robert; Graves, Tina; Hou, Shun-Fang; Latrielle, Philip; Leonard, Shawn; Mardis, Elaine; Maupin, Rachel; McPherson, John; Miner, Tracie; Nash, William; Nguyen, Christine; Ozersky, Philip; Pepin, Kymberlie; Rock, Susan; Rohlfing, Tracy; Scott, Kelsi; Schultz, Brian; Strong, Cindy; Tin-Wollam, Aye; Yang, Shiaw-Pyng; Waterston, Robert H.; Wilson, Richard K.; Rozen, Steve; Page, David C.

    2003-01-01

    The male-specific region of the Y chromosome, the MSY, differentiates the sexes and comprises 95% of the chromosome's length. Here, we report that the MSY is a mosaic of heterochromatic sequences and three classes of euchromatic sequences: X-transposed, X-degenerate and ampliconic. These classes

  4. Chimeric TALE recombinases with programmable DNA sequence specificity.

    Science.gov (United States)

    Mercer, Andrew C; Gaj, Thomas; Fuller, Roberta P; Barbas, Carlos F

    2012-11-01

    Site-specific recombinases are powerful tools for genome engineering. Hyperactivated variants of the resolvase/invertase family of serine recombinases function without accessory factors, and thus can be re-targeted to sequences of interest by replacing native DNA-binding domains (DBDs) with engineered zinc-finger proteins (ZFPs). However, imperfect modularity with particular domains, lack of high-affinity binding to all DNA triplets, and difficulty in construction has hindered the widespread adoption of ZFPs in unspecialized laboratories. The discovery of a novel type of DBD in transcription activator-like effector (TALE) proteins from Xanthomonas provides an alternative to ZFPs. Here we describe chimeric TALE recombinases (TALERs): engineered fusions between a hyperactivated catalytic domain from the DNA invertase Gin and an optimized TALE architecture. We use a library of incrementally truncated TALE variants to identify TALER fusions that modify DNA with efficiency and specificity comparable to zinc-finger recombinases in bacterial cells. We also show that TALERs recombine DNA in mammalian cells. The TALER architecture described herein provides a platform for insertion of customized TALE domains, thus significantly expanding the targeting capacity of engineered recombinases and their potential applications in biotechnology and medicine.

  5. Implicit sequence-specific motor learning after sub-cortical stroke is associated with increased prefrontal brain activations: An fMRI study

    Science.gov (United States)

    Meehan, Sean K.; Randhawa, Bubblepreet; Wessel, Brenda; Boyd, Lara A.

    2010-01-01

    Implicit motor learning is preserved after stroke, but how the brain compensates for damage to facilitate learning is unclear. We used a random effects analysis to determine how stroke alters patterns of brain activity during implicit sequence-specific motor learning as compared to general improvements in motor control. Nine healthy participants and 9 individuals with chronic, right focal sub-cortical stroke performed a continuous joystick-based tracking task during an initial fMRI session, over 5 days of practice, and a retention test during a separate fMRI session. Sequence-specific implicit motor learning was differentiated from general improvements in motor control by comparing tracking performance on a novel, repeated tracking sequences during early practice and again at the retention test. Both groups demonstrated implicit sequence-specific motor learning at the retention test, yet substantial differences were apparent. At retention, healthy control participants demonstrated increased BOLD response in left dorsal premotor cortex (BA 6) but decreased BOLD response left dorsolateral prefrontal cortex (DLPFC; BA 9) during repeated sequence tracking. In contrast, at retention individuals with stroke did not show this reduction in DLPFC during repeated tracking. Instead implicit sequence-specific motor learning and general improvements in motor control were associated with increased BOLD response in the left middle frontal gyrus BA 8, regardless of sequence type after stroke. These data emphasize the potential importance of a prefrontal-based attentional network for implicit motor learning after stroke. The present study is the first to highlight the importance of the prefrontal cortex for implicit sequence-specific motor learning after stroke. PMID:20725908

  6. Resonance lines in the Ag I and Pd I isoelectronic sequences: Cs IX through Sm XVI and Cs X through Nd XV

    International Nuclear Information System (INIS)

    Sugar, J.

    1977-01-01

    Spectra of Cs, Ba, La, Ce, Pr, Nd, and Sm ions were obtained with a low-temperature triggered spark produced with a 14.2 μF capacitor charged to voltages of 3--15 KV. They were photographed with a 10.7 m grazing incidence spectrograph in the range of 60--600 A. Resonance lines in the Pd I isolectronic sequences 4d 10 --4d 9 5p and 4d 10 --4d 9 4f were identified. In the Ag I sequences, spectral lines arising from 5s--5p, 5p--5d, 4f--5d, and 4f--5g transitions were identified

  7. Complications after liver transplantation: evaluation with magnetic resonance imaging, magnetic resonance cholangiography, and 3-dimensional contrast-enhanced magnetic resonance angiography in a single session

    International Nuclear Information System (INIS)

    Boraschi, P.; Donati, F.; Gigoni, R.; Salemi, S.; Urbani, L.; Filipponi, F.; Falaschi, F.; Bartolozzi, C.

    2008-01-01

    To evaluate a comprehensive magnetic resonance imaging (MRI) protocol as noninvasive diagnostic modality for simultaneous detection of parenchymal, biliary, and vascular complications after liver transplantation. Fifty-two liver transplant recipients suspected to have parenchymal, biliary, and (or) vascular complications underwent our MRI protocol at 1.5T unit using a phased array coil. After preliminary acquisition of axial T 1 w and T 2 w sequences, magnetic resonance cholangiography (MRC) was performed through a breath-hold, thin- and thick-slab, single-shot T 2 w sequence in the coronal plane. Contrast-enhanced magnetic resonance angiography (CEMRA) was obtained using a 3-dimensional coronal spoiled gradient-echo sequence, which enabled acquisition of 32 partitions 2.0 mm thick. A fixed dose of 20 ml gadobenate dimeglumine was administered at 2 mL/s. A post-contrast T 1 w sequence was also performed. Two observers in conference reviewed source images and 3-dimensional reconstructions to determine the presence of parenchymal, biliary, and vascular complications. MRI findings were correlated with surgery, endoscopic retrograde cholangiography (ERC), biopsy, digital subtraction angiography (DSA), and imaging follow-up. MRI revealed abnormal findings in 32 out of 52 patients (61%), including biliary complications (anastomotic and nonanastomotic strictures, and lithiasis) in 31, vascular disease (hepatic artery stenosis and thrombosis) in 9, and evidence of hepatic abscess and hematoma in 2. ERC confirmed findings of MRC in 30 cases, but suggested disease underestimation in 2. DSA confirmed 7 magnetic resonance angiogram (MRA) findings, but suggested disease overestimation in 2. MRI combined with MRC and CEMRA can provide a comprehensive assessment of parenchymal, biliary, and vascular complications in most recipients of liver transplantation. (author)

  8. Isolation and sequencing analysis on the seed-specific promoter from soybean

    Institute of Scientific and Technical Information of China (English)

    CAIYIN Qinggele; LI Mingchun; WEI Dongsheng; CAI Yi; XING Laijun

    2007-01-01

    The low level of foreign genes' expression in transgenic plants is a key factor that limits plant genetic engineering.Because of the critical regulatory activity of the promoters on gene transcription,they are studied extensively to improve the efficiency of the plant transgenic system.The constitutive promoters,such as CaMV 35S promoter,are usually used in plant genetic engineering.But those constitutive promoters continuously express their downstream genes during the whole life span in all the tissues of the host plants.This is not only wasteful to host plant's energy,but also harmful to host plants and usually affects their agronomic characteristics.In contrast,the seed-specific promoter only expresses its downstream genes from mid to late stage of seed maturation,and there is no expression or much lower expression in other tissues.So the seed-specific promoters are distinguished for their improvement and what they have brought to plant quality engineering.The aim of this article is to characterize a new seed-specific promoter and improve grain quality.The promoter region of β-conglycinin α-subunit gene was isolated from the genomic DNA of soybean Jilin 43 by PCR method,and successfully extended this fragment by TAIL PCR method and obtained the promoter fragment BCSP666.Sequencing analysis showed that the cloned fragment BCSP666 contained all of the motifs,such as RY repeat element,AG/CCCCA motif,TACACAT motif,ACGTmotif,A/T rich motif and E-box etc.,which constituted the seed-specific promoter activity.Based on this sequencing analysis,the seed-specific promoter activity of the fragment BCSP666 was predicted.And then the seed-specific expression vector pBI121-666,which contained GUS reporter gene,was constructed with the fragment BCSP666.Transformation of Arabidopsis thaliana plants by Agrobacterium-mediated floral-dip method with the recombined vector pBI121-666was conducted.The transgenic plants were selected on the kanamycin-resistant MS medium

  9. Automatic Sequences and Zip-Specifications

    NARCIS (Netherlands)

    Grabmayer, C.A.; Endrullis, J.; Hendriks, D.; Klop, J.W.; Moss, L.S.

    2012-01-01

    We consider infinite sequences of symbols, also known as streams, and the decidability question for equality of streams defined in a restricted format. This restricted format consists of prefixing a symbol at the head of a stream, of the stream function `zip', and recursion variables. Here `zip'

  10. Mechanism of sequence-specific template binding by the DNA primase of bacteriophage T7

    KAUST Repository

    Lee, Seung-Joo; Zhu, Bin; Hamdan, Samir; Richardson, Charles C.

    2010-01-01

    DNA primases catalyze the synthesis of the oligoribonucleotides required for the initiation of lagging strand DNA synthesis. Biochemical studies have elucidated the mechanism for the sequence-specific synthesis of primers. However, the physical

  11. Sequence-specific inhibition of Dicer measured with a force-based microarray for RNA ligands.

    Science.gov (United States)

    Limmer, Katja; Aschenbrenner, Daniela; Gaub, Hermann E

    2013-04-01

    Malfunction of protein translation causes many severe diseases, and suitable correction strategies may become the basis of effective therapies. One major regulatory element of protein translation is the nuclease Dicer that cuts double-stranded RNA independently of the sequence into pieces of 19-22 base pairs starting the RNA interference pathway and activating miRNAs. Inhibiting Dicer is not desirable owing to its multifunctional influence on the cell's gene regulation. Blocking specific RNA sequences by small-molecule binding, however, is a promising approach to affect the cell's condition in a controlled manner. A label-free assay for the screening of site-specific interference of small molecules with Dicer activity is thus needed. We used the Molecular Force Assay (MFA), recently developed in our lab, to measure the activity of Dicer. As a model system, we used an RNA sequence that forms an aptamer-binding site for paromomycin, a 615-dalton aminoglycoside. We show that Dicer activity is modulated as a function of concentration and incubation time: the addition of paromomycin leads to a decrease of Dicer activity according to the amount of ligand. The measured dissociation constant of paromomycin to its aptamer was found to agree well with literature values. The parallel format of the MFA allows a large-scale search and analysis for ligands for any RNA sequence.

  12. Sequence dependent structure and thermodynamics of DNA oligonucleotides and polynucleotides: uv melting and NMR (nuclear magnetic resonance) studies

    International Nuclear Information System (INIS)

    Aboul-ela, F.M.

    1987-12-01

    Thermodynamic parameters for double strand formation have been measured for the twenty-five DNA double helices made by mixing deoxyoligonucleotides of the sequence dCA 3 XA 3 G with the complement dCT 3 YT 3 G. Each of the bases A, C, G, T, and I (I = hypoxanthine) have been substituted at the positions labeled X and Y. The results are analyzed in terms of nearest neighbors. At higher temperatures the sequences containing a G/center dot/C base pair become more stable than those containing only A/center dot/T. All molecules containing mismatcher are destabilized with respect to those with only Watson-Crick pairing, but there is a wide range of destabilization. Large neighboring base effects upon stability were observed. For example, when (X, Y) = (I, A), the duplex is eightfold more stable than when (X, Y) = (A, I). Independent of sequence effects the order of stabilities is: I/center dot/C /succ/ I/center dot/ A/succ/ I/center dot/T ∼ I/center dot/G. All of these results are discussed within the context of models for sequence dependent DNA secondary structure, replication fidelity and mechanisms of mismatch repair, and implications for probe design. The duplex deoxyoligonucleotide d(GGATGGGAG)/center dot/d(CTCCCATCC) is a portion of the gene recognition sequence of the protein transcription factor IIIA. The crystal structure of this oligonucleotide was shown to be A-form The present study employs Nuclear Magnetic Resonance, optical, chemical and enzymatic techniques to investigate the solution structure of this DNA 9-mer. (157 refs., 19 figs., 10 tabs.)

  13. Complete sequence-specific 1H NMR assignments for human insulin

    International Nuclear Information System (INIS)

    Kline, A.D.; Justice, R.M. Jr.

    1990-01-01

    Solvent conditions where human insulin could be studied by high-resolution NMR were determined. Both low pH and addition of acetonitrile were required to overcome the protein's self-association and to obtain useful spectra. Two hundred eighty-six 1 H resonances were located and assigned to specific sites on the protein by using two-dimensional NMR methods. The presence and position of numerous d NN sequential NOE's indicate that the insulin conformation seen in crystallographic studies is largely retained under these solution conditions. Slowly exchanging protons were observed for seven backbone amide protons and were assigned to positions A15 and A16 and to positions B15-B19. These amides all occur within helical regions of the protein

  14. Multi-Criteria Decision-Making Model for the Material Flow of Resonant Wood Production

    Directory of Open Access Journals (Sweden)

    Patrik Aláč

    2017-03-01

    Full Text Available This paper proposes a multi-criteria decision-making model, for the selection and evaluation of the most valuable wooden input—resonant wood. Application of a given model can improve the process of input valuation as well as impact and improve particular economic indicators for the resonant wood manufacturer. We have tried to describe and evaluate the supply chain of resonant wood manufacturing and production of musical instruments. Particular value-added and non-value-added activities have been chosen according to the logical sequence of technology. Then, concrete criteria were specified and their significance weightings. Another important part of our paper is the description of resonant wood, specifications, and demands on log and wood species. There are some important physical and mechanical properties which should be taken into account and evaluated during the production of musical instruments. By the application of this model, a particular enterprise can reach an enhanced tool for the continuous evaluation of the product flowing through the supply chain. Visibility of particular operations and their logical sequence, presented by Petri nets, can lead to easier detection of possible defects in these operations and their origin. So, the main purpose of the paper lies in the suggestion of an objective and quantified managerial tool for the decision making.

  15. Meniscal tear evaluation. Comparison of a conventional spin-echo proton density sequence with a fast spin-echo sequence utilizing a 512x358 matrix size

    International Nuclear Information System (INIS)

    Hopper, M.A.; Robinson, P.; Grainger, A.J.

    2011-01-01

    Aim: To determine the sensitivities, specificities, and receiver-operating characteristics (ROCs) for sagittal conventional spin-echo proton density (SE-PD) and fast spin-echo proton density (FSE-PD) sequences in the diagnosis of meniscal tears when compared to arthroscopic findings utilizing increased FSE matrix acquisition size. Method and materials: Magnetic resonance imaging (MRI) studies of 97 knees (194 menisci) were independently and prospectively interpreted by two experienced musculoskeletal radiologists over four separate readings at least 3 weeks apart. Readings 1 and 2 included images in all three planes in accordance with the standard protocol with either a SE or FSE sagittal PD, at readings 3 and 4 just the SE or FSE sagittal PD sequences were reported. The FSE sequence was acquired with an increased matrix size, compared to the SE sequence, to provide increased resolution. Menisci were graded for the presence of a tear and statistical analysis to calculate sensitivity and specificity was performed comparing to arthroscopy as the reference standard. ROC analysis for the diagnosis of meniscal tears on the SE and FSE sagittal sequences was also evaluated. Reader concordance for the SE and FSE sequences was calculated. Results: Sixty-seven tears were noted at arthroscopy; 60 were detected on SE and 56 on FSE. The sensitivity and specificity for SE was 90 and 90%, and for FSE was 84 and 94%, respectively, with no significant difference. ROC analysis showed no significant difference between the two sequences and kappa values demonstrated a higher level of reader agreement for the FSE than for the SE reading. Conclusion: Use of a FSE sagittal PD sequence with an increased matrix size provides comparable performance to conventional SE sagittal PD when evaluating meniscal disease with a modern system. The present study indicates an increased level of concordance between readers for the FSE sagittal sequence compared to the conventional SE.

  16. Meniscal tear evaluation. Comparison of a conventional spin-echo proton density sequence with a fast spin-echo sequence utilizing a 512x358 matrix size

    Energy Technology Data Exchange (ETDEWEB)

    Hopper, M.A.; Robinson, P. [Leeds Teaching Hospitals NHS Trust, Leeds (United Kingdom); Grainger, A.J., E-mail: andrew.grainger@leedsth.nhs.u [Leeds Teaching Hospitals NHS Trust, Leeds (United Kingdom)

    2011-04-15

    Aim: To determine the sensitivities, specificities, and receiver-operating characteristics (ROCs) for sagittal conventional spin-echo proton density (SE-PD) and fast spin-echo proton density (FSE-PD) sequences in the diagnosis of meniscal tears when compared to arthroscopic findings utilizing increased FSE matrix acquisition size. Method and materials: Magnetic resonance imaging (MRI) studies of 97 knees (194 menisci) were independently and prospectively interpreted by two experienced musculoskeletal radiologists over four separate readings at least 3 weeks apart. Readings 1 and 2 included images in all three planes in accordance with the standard protocol with either a SE or FSE sagittal PD, at readings 3 and 4 just the SE or FSE sagittal PD sequences were reported. The FSE sequence was acquired with an increased matrix size, compared to the SE sequence, to provide increased resolution. Menisci were graded for the presence of a tear and statistical analysis to calculate sensitivity and specificity was performed comparing to arthroscopy as the reference standard. ROC analysis for the diagnosis of meniscal tears on the SE and FSE sagittal sequences was also evaluated. Reader concordance for the SE and FSE sequences was calculated. Results: Sixty-seven tears were noted at arthroscopy; 60 were detected on SE and 56 on FSE. The sensitivity and specificity for SE was 90 and 90%, and for FSE was 84 and 94%, respectively, with no significant difference. ROC analysis showed no significant difference between the two sequences and kappa values demonstrated a higher level of reader agreement for the FSE than for the SE reading. Conclusion: Use of a FSE sagittal PD sequence with an increased matrix size provides comparable performance to conventional SE sagittal PD when evaluating meniscal disease with a modern system. The present study indicates an increased level of concordance between readers for the FSE sagittal sequence compared to the conventional SE.

  17. How to analyze a nuclear magnetic resonance image. Application to the pelvis

    International Nuclear Information System (INIS)

    Parienty, R.; Lavayssiere, R.

    1983-01-01

    Nuclear magnetic resonance (NMR) is based on the behaviour of some atomic nuclei when they are placed in a magnetic field and subjected to radiofrequency waves of a specific length. The resonance signals they emit under such conditions are collected as localized digital data which are used to construct an image. The signals vary according to multiple tissue characteristics, notably proton density, relaxation times T1 and T2 and, where applicable, blood flow direction and velocity. The relative influences exerted by these tissue factors on resonance signals can be evaluated by altering the technical parameters of the examination, that is practically the radiofrequency wave sequence. Special formulae make it possible to predict signal variations and to increase, decrease or even reverse contrast, thus obtaining as many morphological or functional images of the different media in the body. NMR semiology therefore is copious, complex and variable, but a diagrammatic description of the interplay between parameters provides a key to elementary analysis. Images of pelvic structures taken as examples illustrate the necessity to select the exploratory procedure according to the purpose of the exploration or to manipulate sequences with greater safety [fr

  18. Contrast-enhanced Magnetic Resonance Imaging of Pelvic Bone Metastases at 3.0 T: Comparison Between 3-dimensional T1-weighted CAIPIRINHA-VIBE Sequence and 2-dimensional T1-weighted Turbo Spin-Echo Sequence.

    Science.gov (United States)

    Yoon, Min A; Hong, Suk-Joo; Lee, Kyu-Chong; Lee, Chang Hee

    2018-06-12

    This study aimed to compare 3-dimensional T1-weighted gradient-echo sequence (CAIPIRINHA-volumetric interpolated breath-hold examination [VIBE]) with 2-dimensional T1-weighted turbo spin-echo sequence for contrast-enhanced magnetic resonance imaging (MRI) of pelvic bone metastases at 3.0 T. Thirty-one contrast-enhanced MRIs of pelvic bone metastases were included. Two contrast-enhanced sequences were evaluated for the following parameters: overall image quality, sharpness of pelvic bone, iliac vessel clarity, artifact severity, and conspicuity and edge sharpness of the smallest metastases. Quantitative analysis was performed by calculating signal-to-noise ratio and contrast-to-noise ratio of the smallest metastases. Significant differences between the 2 sequences were assessed. CAIPIRINHA-VIBE had higher scores for overall image quality, pelvic bone sharpness, iliac vessel clarity, and edge sharpness of the metastatic lesions, and had less artifacts (all P 0.05). Our results suggest that CAIPIRINHA-VIBE may be superior to turbo spin-echo for contrast-enhanced MRI of pelvic bone metastases at 3.0 T.

  19. Magnetic resonance urography in pediatrics: utilization of ultrafast single-shot spin echo sequences

    International Nuclear Information System (INIS)

    Martin, C.; Martin, J.; Duran, C.; Rigol, S.; Rojo, J. C.

    1999-01-01

    To determine the value of magnetic resonance urography (MRU) using ultrafast single-shot (SS) rapid acquisition with relaxation enhancement (RARE) and half-Fourier (HF) SS-RARE (SS-HF-RARE or HASTE) in the evaluation of congenital urinary tract anomalies in pediatric patients, and their possible application as alternatives to intravenous urography (IVU). Eighteen children (11 boys and 7 girls) aged 2 months to 15 years (mean: 5 years) with a total of 19 congenital urinary tract anomalies were studies by MU using SS-RARE and HASTE sequences in a 1 Tesla scanner. All the patients had previously been studies by ultrasound (US) and IVU. Twelve patients required anesthesia. The images were acquired by means of a HASTE sequence with multisection technique (TR, infinite; TE e f, 87 msec; echo train, 128; interval between echoes, 10.9 msec; total acquisition time, 13 sections/12 seconds), and SS-RARE (TR, infinite; TE e f, 1.100 msec; echo train, 240, and acquisition time, 7 seconds). Four radiologists evaluated the images independently; two who reviewed the IV images in consensus and two who reviewed the MRU images in consensus. The images were evaluated to assess the dilatation of the urinary tract and their utility in detecting the level and cause of the obstruction. MRU images revealed the urinary tract dilation, the level of the obstruction and the type of anomaly in 18 patients (100%), while IVU provided this information in only 10 [ sensitivity, 53%, 95% confidence interval (29%, 76%)]. The mean time required for MRU was 20 minutes (range: 7 to 30 minutes), while that of IVU was 1,242 minutes (range: 45 to 1,440 minutes). MRU using ultrafast single-short spin echo sequences is a rapid and effective technique that permits and excellent evaluation of congenital urinary tract anomalies in pediatric patients and does not require the administration of contrast media or ionizing radiation. (Author) 10 refs

  20. Simultaneous discrimination of species and strains in Lactobacillus rhamnosus using species-specific PCR combined with multiplex mini-sequencing technology.

    Science.gov (United States)

    Huang, Chien-Hsun; Chang, Mu-Tzu; Huang, Lina; Chu, Wen-Shen

    2015-12-01

    This study described the use of species-specific PCR in combination with SNaPshot mini-sequencing to achieve species identification and strain differentiation in Lactobacillus rhamnosus. To develop species-specific PCR and strain subtyping primers, the dnaJ gene was used as a target, and its corresponding sequences were analyzed both in Lb. rhamnosus and in a subset of its phylogenetically closest species. The results indicated that the species-specific primer pair was indeed specific for Lb. rhamnosus, and the mini-sequencing assay was able to unambiguously distinguish Lb. rhamnosus strains into different haplotypes. In conclusion, we have successfully developed a rapid, accurate and cost-effective assay for inter- and intraspecies discrimination of Lb. rhamnosus, which can be applied to achieve efficient quality control of probiotic products. Copyright © 2015 Elsevier Ltd. All rights reserved.

  1. The minimum information about a genome sequence (MIGS) specification

    DEFF Research Database (Denmark)

    Field, D; Garrity, G; Gray, T

    2008-01-01

    With the quantity of genomic data increasing at an exponential rate, it is imperative that these data be captured electronically, in a standard format. Standardization activities must proceed within the auspices of open-access and international working bodies. To tackle the issues surrounding the...... that will be required to develop improved mechanisms of metadata capture and exchange. As part of its wider goals, the GSC also supports improving the 'transparency' of the information contained in existing genomic databases....... the development of better descriptions of genomic investigations, we have formed the Genomic Standards Consortium (GSC). Here, we introduce the minimum information about a genome sequence (MIGS) specification with the intent of promoting participation in its development and discussing the resources...

  2. Magnetic resonance, a phenomenon with a great potential in medicine, but with a complex physical background – Part 2: The basics of magnetic resonance

    Directory of Open Access Journals (Sweden)

    Bojan Božič

    2014-01-01

    Full Text Available Magnetic resonance imaging is a very complex diagnostic technique. Therefore, both practical experiences and theoretical understanding is needed for effective diagnostics. It is therefore important that physicians are sufficiently familiar with the basic physical principles of magnetic resonance. In the interpretation of physical concepts, we will rely both on the classical as well as on the quantum-mechanical view of the signal formation in magnetic resonance, which are to some extent complementary. The signal appearance in magnetic resonance imaging will be discussed. A special emphasis will be put on the role of the resonance frequency and the pulse sequences. Furthermore, the spin echo as one of the most used classical signal sequences in diagnostic investigations will be described.

  3. Basic concepts from magnetic resonance imaging

    International Nuclear Information System (INIS)

    Rodriguez Arroyo, Diego

    2011-01-01

    The use of magnetic resonance imaging (MRI) has grown exponentially, due in part to excellent anatomic and pathologic detail provided by the modality, as recent technological advances that have led to more rapid acquisition times. Radiology residents in different parts of the world now receive training in MR images from their first year of residence, included the pulse sequences training spin-echo, gradient-echo, inversion-recovery, echo-planar image and MR angiographic sequences, commonly used in medical imaging. However, to optimize the use of this type of study, it has been necessary to understand the basic concepts of physics, included the concepts of recovery T1, degradation T2* and T2, repetition time, echo time, and the effects of chemical shift. Additionally, it has been important to understand the contrast weighting for better representation of specific tissues and thus perform an appropriate differential diagnosis of various pathological processes. (author) [es

  4. Development of taxon-specific sequence characterized amplified region (SCAR) markers based on actin sequences and DNA amplification fingerprinting (DAF): a case study in the Phoma exigua species complex.

    Science.gov (United States)

    Aveskamp, Maikel M; Woudenberg, Joyce H C; de Gruyter, Johannes; Turco, Elena; Groenewald, Johannes Z; Crous, Pedro W

    2009-05-01

    Phoma exigua is considered to be an assemblage of at least nine varieties that are mainly distinguished on the basis of host specificity and pathogenicity. However, these varieties are also reported to be weak pathogens and secondary invaders on non-host tissue. In practice, it is difficult to distinguish P. exigua from its close relatives and to correctly identify isolates up to the variety level, because of their low genetic variation and high morphological similarity. Because of quarantine issues and phytosanitary measures, a robust DNA-based tool is required for accurate and rapid identification of the separate taxa in this species complex. The present study therefore aims to develop such a tool based on unique nucleotide sequence identifiers. More than 60 strains of P. exigua and related species were compared in terms of partial actin gene sequences, or analysed using DNA amplification fingerprinting (DAF) with short, arbitrary, mini-hairpin primers. Fragments in the fingerprint unique to a single taxon were identified, purified and sequenced. Alignment of the sequence data and subsequent primer trials led to the identification of taxon-specific sequence characterized amplified regions (SCARs), and to a set of specific oligonucleotide combinations that can be used to identify these organisms in plant quarantine inspections.

  5. Sequence specificity of mutagenesis in the cI gene of bacteriophage lambda

    International Nuclear Information System (INIS)

    Skopek, T.R.; Wood, R.D.; Hutchinson, F.

    1985-01-01

    Studies of DNA base sequence alterations have shown that for every agent the mutagenic process is specific with respect to the types of base changes induced and the location of the changes in the DNA. Analysis of the types of mutations produced by mutagenic agents can provide insight into the mechanism of mutation and can suggest which DNA lesions may be involved in the actual mutagenic event. We have developed a system for the analysis of chemically induced base sequence alterations in the cI repressor gene of bacteriophage lambda using DNA sequencing techniques. To illustrate the utility of this type of analysis, we present the results obtained with ultraviolet light (UV). Irradiation of target DNA with UV alone, or UV followed by photoreactivating light (which removes dimers), produces mostly transitions at pyrimidine-pyrimidine sites. Conversely, irradiation with 313 nm light plus acetophenone (which produces only thymine dimers) produces mostly transversions at low efficiency. This and other evidence suggests that the actual premutagenic UV lesion in E. coli may not be pyrimidine-pyrimidine dimers, but rather pyr(6-4)pyo photoproducts

  6. Magnetic resonance visualization of conductive structures by sequence-triggered direct currents and spin-echo phase imaging

    Energy Technology Data Exchange (ETDEWEB)

    Eibofner, Frank; Wojtczyk, Hanne; Graf, Hansjörg, E-mail: hansjoerg.graf@med.uni-tuebingen.de, E-mail: drGraf@t-online.de [Section on Experimental Radiology, University Hospital Tübingen, Tübingen D-72076 (Germany); Clasen, Stephan [Department of Diagnostic and Interventional Radiology, University Hospital Tübingen, Tübingen D-72076 (Germany)

    2014-06-15

    Purpose: Instrument visualization in interventional magnetic resonance imaging (MRI) is commonly performed via susceptibility artifacts. Unfortunately, this approach suffers from limited conspicuity in inhomogeneous tissue and disturbed spatial encoding. Also, susceptibility artifacts are controllable only by sequence parameters. This work presents the basics of a new visualization method overcoming such problems by applying sequence-triggered direct current (DC) pulses in spin-echo (SE) imaging. SE phase images allow for background free current path localization. Methods: Application of a sequence-triggered DC pulse in SE imaging, e.g., during a time period between radiofrequency excitation and refocusing, results in transient field inhomogeneities. Dependent on the additional z-magnetic field from the DC, a phase offset results despite the refocusing pulse. False spatial encoding is avoided by DC application during periods when read-out or slice-encoding gradients are inactive. A water phantom containing a brass conductor (water equivalent susceptibility) and a titanium needle (serving as susceptibility source) was used to demonstrate the feasibility. Artifact dependence on current strength and orientation was examined. Results: Without DC, the brass conductor was only visible due to its water displacement. The titanium needle showed typical susceptibility artifacts. Applying triggered DC pulses, the phase offset of spins near the conductor appeared. Because SE phase images are homogenous also in regions of persistent field inhomogeneities, the position of the conductor could be determined with high reliability. Artifact characteristic could be easily controlled by amperage leaving sequence parameters unchanged. For an angle of 30° between current and static field visualization was still possible. Conclusions: SE phase images display the position of a conductor carrying pulsed DC free from artifacts caused by persistent field inhomogeneities. Magnitude and phase

  7. Two-dimensional NMR studies of squash family inhibitors. Sequence-specific proton assignments and secondary structure of reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor III

    Energy Technology Data Exchange (ETDEWEB)

    Krisnamoorthi, R.; Yuxi Gong; Chanlan Sun Lin (Kansas State Univ., Manhattan (United States)); VanderVelde, D. (Univ. of Kansas, Lawrence (United States))

    1992-01-28

    The solution structure of reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor III (CMTI-III*) was investigated by two-dimensional proton nuclear magnetic resonance (2D NMR) spectroscopy. CMTI-III*, prepared by reacting CMTI-III with trypsin which cleaved the Arg5-Ile6 peptide bond, had the two fragments held together by a disulfide linkage. Sequence-specific {sup 1}H NMR resonance assignments were made for all the 29 amino acid residues of the protein. The secondary structure of CMTI-III*, as deduced from NOESY cross peaks and identification of slowly exchanging hydrogens, contains two turns, a 3{sub 10}-helix, and a triple-stranded {beta}-sheet. Sequential proton assignments were also made for the virgin inhibitor, CMTI-III, at pH 4.71, 30C. Comparison of backbone hydrogen chemical shifts of CMTI-III and CMTI-III* revealed significant changes for residues located far away from the reactive-site region as well as for those located near it, indicating tertiary structural changes that are transmitted through most of the 29 residues of the inhibitor protein. These chemical shift changes were relatively small compared to changes that occurred upon hydrolysis of the reactive-site peptide bond between Arg 5 and Ile6 in CMTI-III.

  8. Sequence dependent structure and thermodynamics of DNA oligonucleotides and polynucleotides: uv melting and NMR (nuclear magnetic resonance) studies

    Energy Technology Data Exchange (ETDEWEB)

    Aboul-ela, F.M.

    1987-12-01

    Thermodynamic parameters for double strand formation have been measured for the twenty-five DNA double helices made by mixing deoxyoligonucleotides of the sequence dCA/sub 3/XA/sub 3/G with the complement dCT/sub 3/YT/sub 3/G. Each of the bases A, C, G, T, and I (I = hypoxanthine) have been substituted at the positions labeled X and Y. The results are analyzed in terms of nearest neighbors. At higher temperatures the sequences containing a G)centerreverse arrowdot)C base pair become more stable than those containing only A)centerreverse arrowdot)T. All molecules containing mismatcher are destabilized with respect to those with only Watson-Crick pairing, but there is a wide range of destabilization. Large neighboring base effects upon stability were observed. For example, when (X, Y) = (I, A), the duplex is eightfold more stable than when (X, Y) = (A, I). Independent of sequence effects the order of stabilities is: I)centerreverse arrowdot)C )succ) I)centerreverse arrowdot) A)succ) I)centerreverse arrowdot)T approx. I)centerreverse arrowdot)G. All of these results are discussed within the context of models for sequence dependent DNA secondary structure, replication fidelity and mechanisms of mismatch repair, and implications for probe design. The duplex deoxyoligonucleotide d(GGATGGGAG))centerreverse arrowdot)d(CTCCCATCC) is a portion of the gene recognition sequence of the protein transcription factor IIIA. The crystal structure of this oligonucleotide was shown to be A-form The present study employs Nuclear Magnetic Resonance, optical, chemical and enzymatic techniques to investigate the solution structure of this DNA 9-mer. (157 refs., 19 figs., 10 tabs.

  9. Stem loop sequences specific to transposable element IS605 are found linked to lipoprotein genes in Borrelia plasmids.

    Directory of Open Access Journals (Sweden)

    Nicholas Delihas

    Full Text Available BACKGROUND: Plasmids of Borrelia species are dynamic structures that contain a large number of repetitive genes, gene fragments, and gene fusions. In addition, the transposable element IS605/200 family, as well as degenerate forms of this IS element, are prevalent. In Helicobacter pylori, flanking regions of the IS605 transposase gene contain sequences that fold into identical small stem loops. These function in transposition at the single-stranded DNA level. METHODOLOGY/PRINCIPAL FINDINGS: In work reported here, bioinformatics techniques were used to scan Borrelia plasmid genomes for IS605 transposable element specific stem loop sequences. Two variant stem loop motifs are found in the left and right flanking regions of the transposase gene. Both motifs appear to have dispersed in plasmid genomes and are found "free-standing" and phylogenetically conserved without the associated IS605 transposase gene or the adjacent flanking sequence. Importantly, IS605 specific stem loop sequences are also found at the 3' ends of lipoprotein genes (PFam12 and PFam60, however the left and right sequences appear to develop their own evolutionary patterns. The lipoprotein gene-linked left stem loop sequences maintain the IS605 stem loop motif in orthologs but only at the RNA level. These show mutations whereby variants fold into phylogenetically conserved RNA-type stem loops that contain the wobble non-Watson-Crick G-U base-pairing. The right flanking sequence is associated with the family lipoprotein-1 genes. A comparison of homologs shows that the IS605 stem loop motif rapidly dissipates, but a more elaborate secondary structure appears to develop in its place. CONCLUSIONS/SIGNIFICANCE: Stem loop sequences specific to the transposable element IS605 are present in plasmid regions devoid of a transposase gene and significantly, are found linked to lipoprotein genes in Borrelia plasmids. These sequences are evolutionarily conserved and/or structurally developed in

  10. Linking maternal and somatic 5S rRNA types with different sequence-specific non-LTR retrotransposons.

    Science.gov (United States)

    Locati, Mauro D; Pagano, Johanna F B; Ensink, Wim A; van Olst, Marina; van Leeuwen, Selina; Nehrdich, Ulrike; Zhu, Kongju; Spaink, Herman P; Girard, Geneviève; Rauwerda, Han; Jonker, Martijs J; Dekker, Rob J; Breit, Timo M

    2017-04-01

    5S rRNA is a ribosomal core component, transcribed from many gene copies organized in genomic repeats. Some eukaryotic species have two 5S rRNA types defined by their predominant expression in oogenesis or adult tissue. Our next-generation sequencing study on zebrafish egg, embryo, and adult tissue identified maternal-type 5S rRNA that is exclusively accumulated during oogenesis, replaced throughout the embryogenesis by a somatic-type, and thus virtually absent in adult somatic tissue. The maternal-type 5S rDNA contains several thousands of gene copies on chromosome 4 in tandem repeats with small intergenic regions, whereas the somatic-type is present in only 12 gene copies on chromosome 18 with large intergenic regions. The nine-nucleotide variation between the two 5S rRNA types likely affects TFIII binding and riboprotein L5 binding, probably leading to storage of maternal-type rRNA. Remarkably, these sequence differences are located exactly at the sequence-specific target site for genome integration by the 5S rRNA-specific Mutsu retrotransposon family. Thus, we could define maternal- and somatic-type MutsuDr subfamilies. Furthermore, we identified four additional maternal-type and two new somatic-type MutsuDr subfamilies, each with their own target sequence. This target-site specificity, frequently intact maternal-type retrotransposon elements, plus specific presence of Mutsu retrotransposon RNA and piRNA in egg and adult tissue, suggest an involvement of retrotransposons in achieving the differential copy number of the two types of 5S rDNA loci. © 2017 Locati et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  11. The minimum information about a genome sequence (MIGS) specification

    Science.gov (United States)

    Field, Dawn; Garrity, George; Gray, Tanya; Morrison, Norman; Selengut, Jeremy; Sterk, Peter; Tatusova, Tatiana; Thomson, Nicholas; Allen, Michael J; Angiuoli, Samuel V; Ashburner, Michael; Axelrod, Nelson; Baldauf, Sandra; Ballard, Stuart; Boore, Jeffrey; Cochrane, Guy; Cole, James; Dawyndt, Peter; De Vos, Paul; dePamphilis, Claude; Edwards, Robert; Faruque, Nadeem; Feldman, Robert; Gilbert, Jack; Gilna, Paul; Glöckner, Frank Oliver; Goldstein, Philip; Guralnick, Robert; Haft, Dan; Hancock, David; Hermjakob, Henning; Hertz-Fowler, Christiane; Hugenholtz, Phil; Joint, Ian; Kagan, Leonid; Kane, Matthew; Kennedy, Jessie; Kowalchuk, George; Kottmann, Renzo; Kolker, Eugene; Kravitz, Saul; Kyrpides, Nikos; Leebens-Mack, Jim; Lewis, Suzanna E; Li, Kelvin; Lister, Allyson L; Lord, Phillip; Maltsev, Natalia; Markowitz, Victor; Martiny, Jennifer; Methe, Barbara; Mizrachi, Ilene; Moxon, Richard; Nelson, Karen; Parkhill, Julian; Proctor, Lita; White, Owen; Sansone, Susanna-Assunta; Spiers, Andrew; Stevens, Robert; Swift, Paul; Taylor, Chris; Tateno, Yoshio; Tett, Adrian; Turner, Sarah; Ussery, David; Vaughan, Bob; Ward, Naomi; Whetzel, Trish; Gil, Ingio San; Wilson, Gareth; Wipat, Anil

    2008-01-01

    With the quantity of genomic data increasing at an exponential rate, it is imperative that these data be captured electronically, in a standard format. Standardization activities must proceed within the auspices of open-access and international working bodies. To tackle the issues surrounding the development of better descriptions of genomic investigations, we have formed the Genomic Standards Consortium (GSC). Here, we introduce the minimum information about a genome sequence (MIGS) specification with the intent of promoting participation in its development and discussing the resources that will be required to develop improved mechanisms of metadata capture and exchange. As part of its wider goals, the GSC also supports improving the ‘transparency’ of the information contained in existing genomic databases. PMID:18464787

  12. Segment-specific terminal sequences of Bunyamwera bunyavirus regulate genome replication

    International Nuclear Information System (INIS)

    Barr, John N.; Elliott, Richard M.; Dunn, Ewan F.; Wertz, Gail W.

    2003-01-01

    Bunyamwera virus (BUNV) is the prototype of both the Orthobunyavirus genus and the Bunyaviridae family of segmented negative sense RNA viruses. The tripartite BUNV genome consists of small (S), medium (M), and large (L) segments that are transcribed to give a single mRNA and replicated to generate an antigenome that is the template for synthesis of further genomic RNA strands. We modified an existing cDNA-derived RNA synthesis system to allow identification of BUNV RNA replication and transcription products by direct metabolic labeling. Direct RNA analysis allowed us to distinguish between template activities that affected either RNA replication or mRNA transcription, an ability that was not possible using previous reporter gene expression assays. We generated genome analogs containing the entire nontranslated terminal sequences of the S, M, and L BUNV segments surrounding a common sequence. Analysis of RNAs synthesized from these templates revealed that the relative abilities of BUNV segments to perform RNA replication was M > L > S. Exchange of segment-specific terminal nucleotides identified a 12-nt region located within both the 3' and 5' termini of the M segment that correlated with its high replication ability

  13. Sequence-specific DNA binding by MYC/MAX to low-affinity non-E-box motifs.

    Directory of Open Access Journals (Sweden)

    Michael Allevato

    Full Text Available The MYC oncoprotein regulates transcription of a large fraction of the genome as an obligatory heterodimer with the transcription factor MAX. The MYC:MAX heterodimer and MAX:MAX homodimer (hereafter MYC/MAX bind Enhancer box (E-box DNA elements (CANNTG and have the greatest affinity for the canonical MYC E-box (CME CACGTG. However, MYC:MAX also recognizes E-box variants and was reported to bind DNA in a "non-specific" fashion in vitro and in vivo. Here, in order to identify potential additional non-canonical binding sites for MYC/MAX, we employed high throughput in vitro protein-binding microarrays, along with electrophoretic mobility-shift assays and bioinformatic analyses of MYC-bound genomic loci in vivo. We identified all hexameric motifs preferentially bound by MYC/MAX in vitro, which include the low-affinity non-E-box sequence AACGTT, and found that the vast majority (87% of MYC-bound genomic sites in a human B cell line contain at least one of the top 21 motifs bound by MYC:MAX in vitro. We further show that high MYC/MAX concentrations are needed for specific binding to the low-affinity sequence AACGTT in vitro and that elevated MYC levels in vivo more markedly increase the occupancy of AACGTT sites relative to CME sites, especially at distal intergenic and intragenic loci. Hence, MYC binds diverse DNA motifs with a broad range of affinities in a sequence-specific and dose-dependent manner, suggesting that MYC overexpression has more selective effects on the tumor transcriptome than previously thought.

  14. Characterization of shark complement factor I gene(s): genomic analysis of a novel shark-specific sequence.

    Science.gov (United States)

    Shin, Dong-Ho; Webb, Barbara M; Nakao, Miki; Smith, Sylvia L

    2009-07-01

    Complement factor I is a crucial regulator of mammalian complement activity. Very little is known of complement regulators in non-mammalian species. We isolated and sequenced four highly similar complement factor I cDNAs from the liver of the nurse shark (Ginglymostoma cirratum), designated as GcIf-1, GcIf-2, GcIf-3 and GcIf-4 (previously referred to as nsFI-a, -b, -c and -d) which encode 689, 673, 673 and 657 amino acid residues, respectively. They share 95% (shark-specific sequence between the leader peptide (LP) and the factor I membrane attack complex (FIMAC) domain. The cDNA sequences differ only in the size and composition of the shark-specific region (SSR). Sequence analysis of each SSR has identified within the region two novel short sequences (SS1 and SS2) and three repeat sequences (RS1-3). Genomic analysis has revealed the existence of three introns between the leader peptide and the FIMAC domain, tentatively designated intron 1, intron 2, and intron 3 which span 4067, 2293 and 2082bp, respectively. Southern blot analysis suggests the presence of a single gene copy for each cDNA type. Phylogenetic analysis suggests that complement factor I of cartilaginous fish diverged prior to the emergence of mammals. All four GcIf cDNA species are expressed in four different tissues and the liver is the main tissue in which expression level of all four is high. This suggests that the expression of GcIf isotypes is tissue-dependent.

  15. Detection and Characterization of Focal Hepatic lesions using Magnetic resonance Imaging

    International Nuclear Information System (INIS)

    Pulgarin, Luis G; Delgado, Jorge Andres; Toro Nancy

    2008-01-01

    A retrospective one year study was performed from June 2006 to June 2007. A total of ten focal liver lesions in 60 patients were examined, describing their magnetic resonance (MR) characteristics, using T1, T2 and dynamic Gd-enhanced T1 weighted sequences with and without fat suppression. Lesions were classified into benign or malignant tumors and a diagnosis was proposed. Specific diagnoses such as simple cyst, abscess, hemangioma, focal nodular hyperplasia, hepatocellular carcinoma, and cholangiocarcinoma were reported.

  16. Sequences of 12 monoclonal anti-dinitrophenyl spin-label antibodies for NMR studies

    International Nuclear Information System (INIS)

    Leahy, D.J.; Rule, G.S.; Whittaker, M.M.; McConnell, H.M.

    1988-01-01

    Eleven monoclonal antibodies specific for a spin-labeled dinitrophenyl hapten (DNP-SL) have been produces for use in NMR studies. They have been named AN01 and ANO3-AN12. The stability constants for the association of these antibodies with DNP-SL and related haptens were measured by fluorescence quenching. cDNA clones coding for the heavy and light chains of each antibody and of an additional anti-DNP-SL monoclonal antibody, ANO2, have been isolated. The nucleic acid sequence of the 5' end of each clone has been determined, and the amino acid sequence of the variable regions of each antibody has been deduced from the cDNA sequence. The sequences are relatively heterogeneous, but both the heavy and the light chains of ANO1 and ANO3 are derived from the same variable-region gene families as those of the ANO2 antibody. ANO7 has a heavy chain that is related to that of ANO2, and ANO9 has a related light chain. ANO5 and ANO6 are unrelated to ANO2 but share virtually identical heavy and light chains. Preliminary NMR difference spectra comparing related antibodies show that sequence-specific assignment of resonances is possible. Such spectra also provide a measure of structural relatedness

  17. Nuclear magnetic resonance method and apparatus

    International Nuclear Information System (INIS)

    Burl, M.; Young, I.R.

    1984-01-01

    A method and apparatus for determining the rate of flow of a liquid in a selected region of a body by nuclear magnetic resonance techniques are described. The method includes a sequence of applying a first magnetic pulse effective to excite nuclear magnetic resonance of a chosen nucleus within the liquid preferentially in a slice of the body which includes the selected region. A period of time (tsub(D)) is waited and then a second magnetic pulse is applied which is effective to excite nuclear magnetic resonance of the nuclei preferentially in the slice, and the free induction decay signal is measured. The whole sequence is repeated for different values of the period of time (tsub(D)). The variation in the value of the measured signal with tsub(D) is then related to the rate of flow of the liquid through the slice. (author)

  18. Magnetic resonance imaging in cadaver dogs with metallic vertebral implants at 3 Tesla: evaluation of the WARP-turbo spin echo sequence.

    Science.gov (United States)

    Griffin, John F; Archambault, Nicholas S; Mankin, Joseph M; Wall, Corey R; Thompson, James A; Padua, Abraham; Purdy, David; Kerwin, Sharon C

    2013-11-15

    Laboratory investigation, ex vivo. Postoperative complications are common after spinal implantation procedures, and magnetic resonance imaging (MRI) would be the ideal modality to image these patients. Unfortunately, the implants cause artifacts that can render MRI nondiagnostic. The WARP-turbo spin echo (TSE) sequence has been developed to mitigate artifacts caused by metal. The objective of this investigation was to evaluate the performance of the WARP-TSE sequence in canine cadaver specimens after implantation with metallic vertebral implants. Magnetic field strength, implant type, and MRI acquisition technique all play a role in the severity of susceptibility artifacts. The WARP-TSE sequence uses increased bandwidth, view angle tilting, and SEMAC (slice-encoding metal artifact correction) to correct for susceptibility artifact. The WARP-TSE technique has outperformed conventional techniques in patients, after total hip arthroplasty. However, published reports of its application in subjects with vertebral column implants are lacking. Ex vivo anterior stabilization of the atlantoaxial joint was performed on 6 adult small breed (implantation with stainless steel implants. N/A.

  19. Cholangiocarcinoma in Cirrhosis: Value of Hepatocyte Specific Magnetic Resonance Imaging.

    Science.gov (United States)

    Piscaglia, Fabio; Iavarone, Massimo; Galassi, Marzia; Vavassori, Sara; Renzulli, Matteo; Forzenigo, Laura Virginia; Granito, Alessandro; Salvatore, Veronica; Sangiovanni, Angelo; Golfieri, Rita; Colombo, Massimo; Bolondi, Luigi

    2015-10-01

    The diagnosis of intrahepatic cholangiocellular carcinoma (ICC) remains elusive at imaging, which is a critical issue in cirrhotic patients in whom a diagnosis of hepatocellular carcinoma (HCC) can be established only by imaging. The aim of the study was to evaluate the potential of MRI in the diagnosis of ICC in cirrhosis using 'hepatocyte-specific' Gadolinium (Gd)-based contrast agents. Sixteen histologically proven and retrospectively identified ICCs on cirrhosis were investigated with hepatocyte-specific magnetic resonance contrast agents (6 in Bologna with Gd-EOB-DTPA and 10 in Milan with Gd-BOPTA). The control group consisted of 41 consecutively and prospectively collected nodules (31 HCCs) imaged with Gd-EOB-DTPA. Fifteen ICC nodules (94%) displayed hypointensity in the hepatobiliary phase, suggesting malignancy. Thirteen cholangiocarcinomas (81%) showed hyperenhancement in the venous phase. Only 2 cholangiocarcinoma nodules showed hypoenhancement in the venous phase, corresponding to washout, in both cases preceded by rim enhancement in arterial phase. All the hepatocarcinomas showed hypointensity in hepatobiliary phase, but was always preceded by hypointensity in the venous phase; arterial rim enhancement was never observed in any hepatocarcinoma or regenerative nodule. MRI with hepatocyte-specific Gd-based contrast agents showed a pattern of malignancy in almost all the ICCs, concurrently avoiding misdiagnosis with hepatocarcinoma. These findings suggest a greater diagnostic capacity for this technique compared with the results of MRI with conventional contrast agents reported in the literature in this setting. © 2015 S. Karger AG, Basel.

  20. Ability of preoperative 3.0-Tesla magnetic resonance imaging to predict the absence of side-specific extracapsular extension of prostate cancer.

    Science.gov (United States)

    Hara, Tomohiko; Nakanishi, Hiroyuki; Nakagawa, Tohru; Komiyama, Motokiyo; Kawahara, Takashi; Manabe, Tomoko; Miyake, Mototaka; Arai, Eri; Kanai, Yae; Fujimoto, Hiroyuki

    2013-10-01

    Recent studies have shown an improvement in prostate cancer diagnosis with the use of 3.0-Tesla magnetic resonance imaging. We retrospectively assessed the ability of this imaging technique to predict side-specific extracapsular extension of prostate cancer. From October 2007 to August 2011, prostatectomy was carried out in 396 patients after preoperative 3.0-Tesla magnetic resonance imaging. Among these, 132 (primary sample) and 134 patients (validation sample) underwent 12-core prostate biopsy at the National Cancer Center Hospital of Tokyo, Japan, and at other institutions, respectively. In the primary dataset, univariate and multivariate analyses were carried out to predict side-specific extracapsular extension using variables determined preoperatively, including 3.0-Tesla magnetic resonance imaging findings (T2-weighted and diffusion-weighted imaging). A prediction model was then constructed and applied to the validation study sample. Multivariate analysis identified four significant independent predictors (P Tesla diffusion-weighted magnetic resonance imaging findings, ≥2 positive biopsy cores on each side and a maximum percentage of positive cores ≥31% on each side. The negative predictive value was 93.9% in the combination model with these four predictors, meanwhile the positive predictive value was 33.8%. Good reproducibility of these four significant predictors and the combination model was observed in the validation study sample. The side-specific extracapsular extension prediction by the biopsy Gleason score and factors associated with tumor location, including a positive 3.0-Tesla diffusion-weighted magnetic resonance imaging finding, have a high negative predictive value, but a low positive predictive value. © 2013 The Japanese Urological Association.

  1. High-resolution whole-genome sequencing reveals that specific chromatin domains from most human chromosomes associate with nucleoli.

    Science.gov (United States)

    van Koningsbruggen, Silvana; Gierlinski, Marek; Schofield, Pietá; Martin, David; Barton, Geoffey J; Ariyurek, Yavuz; den Dunnen, Johan T; Lamond, Angus I

    2010-11-01

    The nuclear space is mostly occupied by chromosome territories and nuclear bodies. Although this organization of chromosomes affects gene function, relatively little is known about the role of nuclear bodies in the organization of chromosomal regions. The nucleolus is the best-studied subnuclear structure and forms around the rRNA repeat gene clusters on the acrocentric chromosomes. In addition to rDNA, other chromatin sequences also surround the nucleolar surface and may even loop into the nucleolus. These additional nucleolar-associated domains (NADs) have not been well characterized. We present here a whole-genome, high-resolution analysis of chromatin endogenously associated with nucleoli. We have used a combination of three complementary approaches, namely fluorescence comparative genome hybridization, high-throughput deep DNA sequencing and photoactivation combined with time-lapse fluorescence microscopy. The data show that specific sequences from most human chromosomes, in addition to the rDNA repeat units, associate with nucleoli in a reproducible and heritable manner. NADs have in common a high density of AT-rich sequence elements, low gene density and a statistically significant enrichment in transcriptionally repressed genes. Unexpectedly, both the direct DNA sequencing and fluorescence photoactivation data show that certain chromatin loci can specifically associate with either the nucleolus, or the nuclear envelope.

  2. C-terminal sequences of hsp70 and hsp90 as non-specific anchors for tetratricopeptide repeat (TPR) proteins.

    Science.gov (United States)

    Ramsey, Andrew J; Russell, Lance C; Chinkers, Michael

    2009-10-12

    Steroid-hormone-receptor maturation is a multi-step process that involves several TPR (tetratricopeptide repeat) proteins that bind to the maturation complex via the C-termini of hsp70 (heat-shock protein 70) and hsp90 (heat-shock protein 90). We produced a random T7 peptide library to investigate the roles played by the C-termini of the two heat-shock proteins in the TPR-hsp interactions. Surprisingly, phages with the MEEVD sequence, found at the C-terminus of hsp90, were not recovered from our biopanning experiments. However, two groups of phages were isolated that bound relatively tightly to HsPP5 (Homo sapiens protein phosphatase 5) TPR. Multiple copies of phages with a C-terminal sequence of LFG were isolated. These phages bound specifically to the TPR domain of HsPP5, although mutation studies produced no evidence that they bound to the domain's hsp90-binding groove. However, the most abundant family obtained in the initial screen had an aspartate residue at the C-terminus. Two members of this family with a C-terminal sequence of VD appeared to bind with approximately the same affinity as the hsp90 C-12 control. A second generation pseudo-random phage library produced a large number of phages with an LD C-terminus. These sequences acted as hsp70 analogues and had relatively low affinities for hsp90-specific TPR domains. Unfortunately, we failed to identify residues near hsp90's C-terminus that impart binding specificity to individual hsp90-TPR interactions. The results suggest that the C-terminal sequences of hsp70 and hsp90 act primarily as non-specific anchors for TPR proteins.

  3. MRCP. Magnetic resonance cholangiopancreatography; MRCP. Magnetresonanzcholangiopankreatografie

    Energy Technology Data Exchange (ETDEWEB)

    Kinner, Sonja [Wisconsin-Madison Univ., Madison, WI (United States). Dept. of Radiology; Lauenstein, Thomas [Evangelisches Krankenhaus Duesseldorf (Germany). Radiologie

    2016-06-15

    Magnetic resonance cholangiopancreatography (MRCP) is a special MR technique to display and analyze the biliary tract and pancreatic ducts. MRCP sequences are equivalent to endoscopic retrograde cholangiopancreatography (ERCP) for diagnostic purposes due to technical developments of the classical T2 weighted MRCP sequences and the availability of contrast enhanced T1 weighted sequences. Therefore, MRCP plays a fundamental role in the diagnoses of hepatobliary and pancreatic diseases, which are presented in this review article as are technical details of sequence acquisitions and the underlying anatomy.

  4. Extreme sequence divergence but conserved ligand-binding specificity in Streptococcus pyogenes M protein.

    Directory of Open Access Journals (Sweden)

    2006-05-01

    Full Text Available Many pathogenic microorganisms evade host immunity through extensive sequence variability in a protein region targeted by protective antibodies. In spite of the sequence variability, a variable region commonly retains an important ligand-binding function, reflected in the presence of a highly conserved sequence motif. Here, we analyze the limits of sequence divergence in a ligand-binding region by characterizing the hypervariable region (HVR of Streptococcus pyogenes M protein. Our studies were focused on HVRs that bind the human complement regulator C4b-binding protein (C4BP, a ligand that confers phagocytosis resistance. A previous comparison of C4BP-binding HVRs identified residue identities that could be part of a binding motif, but the extended analysis reported here shows that no residue identities remain when additional C4BP-binding HVRs are included. Characterization of the HVR in the M22 protein indicated that two relatively conserved Leu residues are essential for C4BP binding, but these residues are probably core residues in a coiled-coil, implying that they do not directly contribute to binding. In contrast, substitution of either of two relatively conserved Glu residues, predicted to be solvent-exposed, had no effect on C4BP binding, although each of these changes had a major effect on the antigenic properties of the HVR. Together, these findings show that HVRs of M proteins have an extraordinary capacity for sequence divergence and antigenic variability while retaining a specific ligand-binding function.

  5. Stator Current Harmonic Control with Resonant Controller for Doubly Fed Induction Generator

    DEFF Research Database (Denmark)

    Liu, Changjin; Blaabjerg, Frede; Chen, Wenjie

    2012-01-01

    rotor current control loop for harmonic suppression. The overall control scheme is implemented in dq frame. Based on a mathematical model of the DFIG control system, the effects on system stability using the resonant controller, an analysis of the steady-state error, and the dynamic performance......, are discussed in this paper. Taking these effects into account, the parameters of the resonant controller can be designed and effectively damp the influence from the grid voltage harmonics. As a result, the impacts of the negative sequence fifth- and positive sequence seventh-order voltage harmonics...... harmonics, especially low-order harmonics. This paper proposes a stator current harmonic suppression method using a sixth-order resonant controller to eliminate negative sequence fifth- and positive sequence seventh-order current harmonics. A stator current harmonic control loop is added to the conventional...

  6. Putative and unique gene sequence utilization for the design of species specific probes as modeled by Lactobacillus plantarum

    Science.gov (United States)

    The concept of utilizing putative and unique gene sequences for the design of species specific probes was tested. The abundance profile of assigned functions within the Lactobacillus plantarum genome was used for the identification of the putative and unique gene sequence, csh. The targeted gene (cs...

  7. Prediction of membrane transport proteins and their substrate specificities using primary sequence information.

    Directory of Open Access Journals (Sweden)

    Nitish K Mishra

    Full Text Available Membrane transport proteins (transporters move hydrophilic substrates across hydrophobic membranes and play vital roles in most cellular functions. Transporters represent a diverse group of proteins that differ in topology, energy coupling mechanism, and substrate specificity as well as sequence similarity. Among the functional annotations of transporters, information about their transporting substrates is especially important. The experimental identification and characterization of transporters is currently costly and time-consuming. The development of robust bioinformatics-based methods for the prediction of membrane transport proteins and their substrate specificities is therefore an important and urgent task.Support vector machine (SVM-based computational models, which comprehensively utilize integrative protein sequence features such as amino acid composition, dipeptide composition, physico-chemical composition, biochemical composition, and position-specific scoring matrices (PSSM, were developed to predict the substrate specificity of seven transporter classes: amino acid, anion, cation, electron, protein/mRNA, sugar, and other transporters. An additional model to differentiate transporters from non-transporters was also developed. Among the developed models, the biochemical composition and PSSM hybrid model outperformed other models and achieved an overall average prediction accuracy of 76.69% with a Mathews correlation coefficient (MCC of 0.49 and a receiver operating characteristic area under the curve (AUC of 0.833 on our main dataset. This model also achieved an overall average prediction accuracy of 78.88% and MCC of 0.41 on an independent dataset.Our analyses suggest that evolutionary information (i.e., the PSSM and the AAIndex are key features for the substrate specificity prediction of transport proteins. In comparison, similarity-based methods such as BLAST, PSI-BLAST, and hidden Markov models do not provide accurate predictions

  8. Magnetic resonance imaging: effects of magnetic field strength

    International Nuclear Information System (INIS)

    Crooks, L.E.; Arakawa, M.; Hoenninger, J.; McCarten, B.; Watts, J.; Kaufman, L.

    1984-01-01

    Magnetic resonance images of the head, abdomen, and pelvis of normal adult men were obtained using varying magnetic field strength, and measurements of T1 and T2 relaxations and of signal-to-noise (SN) ratios were determined. For any one spin echo sequence, gray/white matter contrast decreases and muscle/fat contrast increases with field. SN levels rise rapidly up to 3.0 kgauss and then change more slowly, actually dropping for muscle. The optimum field for magnetic resonance imaging depends on tissue type, body part, and imaging sequence, so that it does not have a unique value. Magnetic resonance systems that operate in the 3.0-5.0 kgauss range achieve most or all of the gains that can be achieved by higher magnetic fields

  9. Isolation and characterization of antigen-specific alpaca (Lama pacos) VHH antibodies by biopanning followed by high-throughput sequencing.

    Science.gov (United States)

    Miyazaki, Nobuo; Kiyose, Norihiko; Akazawa, Yoko; Takashima, Mizuki; Hagihara, Yosihisa; Inoue, Naokazu; Matsuda, Tomonari; Ogawa, Ryu; Inoue, Seiya; Ito, Yuji

    2015-09-01

    The antigen-binding domain of camelid dimeric heavy chain antibodies, known as VHH or Nanobody, has much potential in pharmaceutical and industrial applications. To establish the isolation process of antigen-specific VHH, a VHH phage library was constructed with a diversity of 8.4 × 10(7) from cDNA of peripheral blood mononuclear cells of an alpaca (Lama pacos) immunized with a fragment of IZUMO1 (IZUMO1PFF) as a model antigen. By conventional biopanning, 13 antigen-specific VHHs were isolated. The amino acid sequences of these VHHs, designated as N-group VHHs, were very similar to each other (>93% identity). To find more diverse antibodies, we performed high-throughput sequencing (HTS) of VHH genes. By comparing the frequencies of each sequence between before and after biopanning, we found the sequences whose frequencies were increased by biopanning. The top 100 sequences of them were supplied for phylogenic tree analysis. In total 75% of them belonged to N-group VHHs, but the other were phylogenically apart from N-group VHHs (Non N-group). Two of three VHHs selected from non N-group VHHs showed sufficient antigen binding ability. These results suggested that biopanning followed by HTS provided a useful method for finding minor and diverse antigen-specific clones that could not be identified by conventional biopanning. © The Authors 2015. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

  10. Virus-specific DNA sequences present in cells which carry the herpes simplex virus thymidine kinase gene.

    Science.gov (United States)

    Minson, A C; Darby, G K; Wildy, P

    1979-11-01

    Two independently derived cell lines which carry the herpes simplex type 2 thymidine kinase gene have been examined for the presence of HSV-2-specific DNA sequences. Both cell lines contained 1 to 3 copies per cell of a sequence lying within map co-ordinates 0.2 to 0.4 of the HSV-2 genome. Revertant cells, which contained no detectable thymidine kinase, did not contain this DNA sequence. The failure of EcoR1-restricted HSV-2 DNA to act as a donor of the thymidine kinase gene in transformation experiments suggests that the gene lies close to the EcoR1 restriction site within this sequence at a map position of approx. 0.3. The HSV-2 kinase gene is therefore approximately co-linear with the HSV-1 gene.

  11. Detection of herpes simplex virus-specific DNA sequences in latently infected mice and in humans.

    Science.gov (United States)

    Efstathiou, S; Minson, A C; Field, H J; Anderson, J R; Wildy, P

    1986-02-01

    Herpes simplex virus-specific DNA sequences have been detected by Southern hybridization analysis in both central and peripheral nervous system tissues of latently infected mice. We have detected virus-specific sequences corresponding to the junction fragment but not the genomic termini, an observation first made by Rock and Fraser (Nature [London] 302:523-525, 1983). This "endless" herpes simplex virus DNA is both qualitatively and quantitatively stable in mouse neural tissue analyzed over a 4-month period. In addition, examination of DNA extracted from human trigeminal ganglia has shown herpes simplex virus DNA to be present in an "endless" form similar to that found in the mouse model system. Further restriction enzyme analysis of latently infected mouse brainstem and human trigeminal DNA has shown that this "endless" herpes simplex virus DNA is present in all four isomeric configurations.

  12. Using sequence-specific chemical and structural properties of DNA to predict transcription factor binding sites.

    Directory of Open Access Journals (Sweden)

    Amy L Bauer

    2010-11-01

    Full Text Available An important step in understanding gene regulation is to identify the DNA binding sites recognized by each transcription factor (TF. Conventional approaches to prediction of TF binding sites involve the definition of consensus sequences or position-specific weight matrices and rely on statistical analysis of DNA sequences of known binding sites. Here, we present a method called SiteSleuth in which DNA structure prediction, computational chemistry, and machine learning are applied to develop models for TF binding sites. In this approach, binary classifiers are trained to discriminate between true and false binding sites based on the sequence-specific chemical and structural features of DNA. These features are determined via molecular dynamics calculations in which we consider each base in different local neighborhoods. For each of 54 TFs in Escherichia coli, for which at least five DNA binding sites are documented in RegulonDB, the TF binding sites and portions of the non-coding genome sequence are mapped to feature vectors and used in training. According to cross-validation analysis and a comparison of computational predictions against ChIP-chip data available for the TF Fis, SiteSleuth outperforms three conventional approaches: Match, MATRIX SEARCH, and the method of Berg and von Hippel. SiteSleuth also outperforms QPMEME, a method similar to SiteSleuth in that it involves a learning algorithm. The main advantage of SiteSleuth is a lower false positive rate.

  13. Whole body sodium MRI at 3T using an asymmetric birdcage resonator and short echo time sequence: first images of a male volunteer

    Science.gov (United States)

    Wetterling, Friedrich; Corteville, Dominique M.; Kalayciyan, Raffi; Rennings, Andreas; Konstandin, Simon; Nagel, Armin M.; Stark, Helmut; Schad, Lothar R.

    2012-07-01

    Sodium magnetic resonance imaging (23Na MRI) is a non-invasive technique which allows spatial resolution of the tissue sodium concentration (TSC) in the human body. TSC measurements could potentially serve to monitor early treatment success of chemotherapy on patients who suffer from whole body metastases. Yet, the acquisition of whole body sodium (23Na) images has been hampered so far by the lack of large resonators and the extremely low signal-to-noise ratio (SNR) achieved with existing resonator systems. In this study, a 23Na resonator was constructed for whole body 23Na MRI at 3T comprising of a 16-leg, asymmetrical birdcage structure with 34 cm height, 47.5 cm width and 50 cm length. The resonator was driven in quadrature mode and could be used either as a transceiver resonator or, since active decoupling was included, as a transmit-only resonator in conjunction with a receive-only (RO) surface resonator. The relative B1-field profile was simulated and measured on phantoms, and 3D whole body 23Na MRI data of a healthy male volunteer were acquired in five segments with a nominal isotropic resolution of (6 × 6 × 6) mm3 and a 10 min acquisition time per scan. The measured SNR values in the 23Na-MR images varied from 9 ± 2 in calf muscle, 15 ± 2 in brain tissue, 23 ± 2 in the prostate and up to 42 ± 5 in the vertebral discs. Arms, legs, knees and hands could also be resolved with applied resonator and short time-to-echo (TE) (0.5 ms) radial sequence. Up to fivefold SNR improvement was achieved through combining the birdcage with local RO surface coil. In conclusion, 23Na MRI of the entire human body provides sub-cm spatial resolution, which allows resolution of all major human body parts with a scan time of less than 60 min.

  14. Magnetic resonance imaging of anterior cruciate ligament of the knee: a comparison of four sequences; Valoracion del ligamento cruzado anterior de la rodilla con RM: comparacion de cuatro secuencias

    Energy Technology Data Exchange (ETDEWEB)

    Casillas, C.; Marti-Bonmati, L.; Molla, E.; Ferrer, P.; Dosda, R. [Clinical Quiron-ATQ. Valencia (Spain)

    1999-07-01

    To compare the diagnostic efficacy of the four magnetic resonance imaging (MRI) sequences that compose the standard protocol for the study of the knee in our center when employed in the examination of anterior cruciate ligament (ACL). A prospective study was carried out based on MRI findings in the knees of 326 consecutive patients. Sagittal [proton density (PD{sub w}eighted turbo-spin-echo and T2*-weighted gradient echo], coronal (PD-weighted turbo-spin-echo with fat suppression) and transverse (T2*-weighted gradient echo with magnetization transfer) images were evaluated. Each sequence was analyzed independently by two radiologists, while another two assessed all the sequences together with the clinical findings. Four categories were established: normal ACL, partially torn, completely torn and synovialized. The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) with respect to the definitive diagnosis were calculated for each sequence. The statistical analysis of the findings for each category was done using the chi-squared test and the Kappa test was employed to assess the degree of agreement. According to the final diagnosis, 263 ACL were normal, 29 were partially torn, 33 were completely torn and there was 1 case of synovialization associated with a completely torn ACL. The relationship between the analysis of the ACL according to each sequence and the definitive diagnosis was very significant (p<0.001) and the agreement was excellent. All the sequences presented similar levels of diagnostic precision. The coronal sequence had least number of diagnostic errors (2.1%). The combinations of imaging techniques that resulted in the lowest error rate with respect to the definitive diagnosis were coronal PD-weighted turbo-spin-echo with fat suppression and sagittal PD-weighted turbo-spin-echo. Coronal images are highly precise in the evaluation of ACL. Sagittal sequences are the most valid for diagnosis of torn ACL

  15. Characterization of upstream sequences of the LIM2 gene that bind developmentally regulated and lens-specific proteins

    Institute of Scientific and Technical Information of China (English)

    HSU Heng; Robert L. CHURCH

    2004-01-01

    During lens development, lens epithelial cells differentiate into fiber cells. To date, four major lens fiber cell intrinsic membrane proteins (MIP) ranging in size from 70 kD to 19 kD have been characterized. The second most abundant lens fiber cell intrinsic membrane protein is MP19. This protein probably is involved with lens cell communication and relates with cataractogenesis. The aim of this research is to characterize upstream sequences of the MP19 (also called LIM2) gene that bind developmentally regulated and lens-specific proteins. We have used the gel mobility assays and corresponding competition experiments to identify and characterize cis elements within approximately 500 bases of LIM2 upstream sequences. Our studies locate the positions of some cis elements, including a "CA" repeat, a methylation Hha I island, an FnuD II site, an Ap1 and an Ap2 consensus sequences, and identify some specific cis elements which relate to lens-specific transcription of LIM2. Our experiments also preliminarily identify trans factors which bind to specific cis elements of the LIM2 promoter and/or regulate transcription of LIM2. We conclude that developmental regulation and coordination of the MP 19 gene in ocular lens fiber cells is controlled by the presence of specific cis elements that bind regulatory trans factors that affect LIM2 gene expression. DNA methylation is one mechanism of controlling LIM2 gene expression during lens development.

  16. Molecular Design of Antifouling Polymer Brushes Using Sequence-Specific Peptoids.

    Science.gov (United States)

    Lau, King Hang Aaron; Sileika, Tadas S; Park, Sung Hyun; Sousa, Ana Maria Leal; Burch, Patrick; Szleifer, Igal; Messersmith, Phillip B

    2015-01-07

    Material systems that can be used to flexibly and precisely define the chemical nature and molecular arrangement of a surface would be invaluable for the control of complex biointerfacial interactions. For example, progress in antifouling polymer biointerfaces that prevent non-specific protein adsorption and cell attachment, which can significantly improve the performance of an array of biomedical and industrial applications, is hampered by a lack of chemical models to identify the molecular features conferring their properties. Poly(N-substituted glycine) "peptoids" are peptidomimetic polymers that can be conveniently synthesized with specific monomer sequences and chain lengths, and are presented as a versatile platform for investigating the molecular design of antifouling polymer brushes. Zwitterionic antifouling polymer brushes have captured significant recent attention, and a targeted library of zwitterionic peptoid brushes with a different charge densities, hydration, separations between charged groups, chain lengths, and grafted chain densities, is quantitatively evaluated for their antifouling properties through a range of protein adsorption and cell attachment assays. Specific zwitterionic brush designs were found to give rise to distinct but subtle differences in properties. The results also point to the dominant roles of the grafted chain density and chain length in determining the performance of antifouling polymer brushes.

  17. 3D double-echo steady-state sequence assessment of hip joint cartilage and labrum at 3 Tesla: comparative analysis of magnetic resonance imaging and intraoperative data

    Energy Technology Data Exchange (ETDEWEB)

    Schleich, Christoph; Antoch, Gerald [University of Dusseldorf, Department of Diagnostic and Interventional Radiology, Medical Faculty, Duesseldorf (Germany); Hesper, Tobias; Rettegi, Fanni; Zilkens, Christoph; Krauspe, Ruediger; Bittersohl, Bernd [University of Dusseldorf, Department of Orthopedic Surgery, Medical Faculty, Duesseldorf (Germany); Hosalkar, Harish S. [Paradise Valley Hospital, Joint Preservation and Deformity Correction, San Diego, CA (United States); Tri-city Medical Center, Hip Preservation, San Diego, CA (United States)

    2017-10-15

    To assess the diagnostic accuracy of a high-resolution, three-dimensional (3D) double-echo steady-state (DESS) sequence with radial imaging at 3 Tesla (T) for evaluating cartilage and labral alterations in the hip. Magnetic resonance imaging (MRI) data obtained at 3 T, including radially reformatted DESS images and intraoperative data of 45 patients (mean age 42 ± 13.7 years) who underwent hip arthroscopy, were compared. The acetabular cartilage and labrum of the upper hemisphere of the acetabulum and the central femoral head cartilage were evaluated. Sensitivity, specificity, accuracy, and negative and positive predictive values were determined. Sensitivity, specificity and accuracy of the DESS technique were 96.7%, 75% and 93.7% for detecting cartilage lesions and 98%, 76.2% and 95.9% for detecting labral lesions. The positive and negative predictive values for detecting or ruling out cartilage lesions were 96% and 78.9%. For labral lesions, the positive and negative predictive values were 97.5% and 80%. A high-resolution, 3D DESS technique with radial imaging at 3 T demonstrated high accuracy for detecting hip cartilage and labral lesions with excellent interobserver agreement and moderate correlation between MRI and intraoperative assessment. (orig.)

  18. A framework for establishing predictive relationships between specific bacterial 16S rRNA sequence abundances and biotransformation rates.

    Science.gov (United States)

    Helbling, Damian E; Johnson, David R; Lee, Tae Kwon; Scheidegger, Andreas; Fenner, Kathrin

    2015-03-01

    The rates at which wastewater treatment plant (WWTP) microbial communities biotransform specific substrates can differ by orders of magnitude among WWTP communities. Differences in taxonomic compositions among WWTP communities may predict differences in the rates of some types of biotransformations. In this work, we present a novel framework for establishing predictive relationships between specific bacterial 16S rRNA sequence abundances and biotransformation rates. We selected ten WWTPs with substantial variation in their environmental and operational metrics and measured the in situ ammonia biotransformation rate constants in nine of them. We isolated total RNA from samples from each WWTP and analyzed 16S rRNA sequence reads. We then developed multivariate models between the measured abundances of specific bacterial 16S rRNA sequence reads and the ammonia biotransformation rate constants. We constructed model scenarios that systematically explored the effects of model regularization, model linearity and non-linearity, and aggregation of 16S rRNA sequences into operational taxonomic units (OTUs) as a function of sequence dissimilarity threshold (SDT). A large percentage (greater than 80%) of model scenarios resulted in well-performing and significant models at intermediate SDTs of 0.13-0.14 and 0.26. The 16S rRNA sequences consistently selected into the well-performing and significant models at those SDTs were classified as Nitrosomonas and Nitrospira groups. We then extend the framework by applying it to the biotransformation rate constants of ten micropollutants measured in batch reactors seeded with the ten WWTP communities. We identified phylogenetic groups that were robustly selected into all well-performing and significant models constructed with biotransformation rates of isoproturon, propachlor, ranitidine, and venlafaxine. These phylogenetic groups can be used as predictive biomarkers of WWTP microbial community activity towards these specific

  19. Multi-frequency interpolation in spiral magnetic resonance fingerprinting for correction of off-resonance blurring.

    Science.gov (United States)

    Ostenson, Jason; Robison, Ryan K; Zwart, Nicholas R; Welch, E Brian

    2017-09-01

    Magnetic resonance fingerprinting (MRF) pulse sequences often employ spiral trajectories for data readout. Spiral k-space acquisitions are vulnerable to blurring in the spatial domain in the presence of static field off-resonance. This work describes a blurring correction algorithm for use in spiral MRF and demonstrates its effectiveness in phantom and in vivo experiments. Results show that image quality of T1 and T2 parametric maps is improved by application of this correction. This MRF correction has negligible effect on the concordance correlation coefficient and improves coefficient of variation in regions of off-resonance relative to uncorrected measurements. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. High resolution spectroscopy in solids by nuclear magnetic resonance

    International Nuclear Information System (INIS)

    Bonagamba, T.J.

    1991-07-01

    The nuclear magnetic resonance (NMR) techniques for High Resolution Spectroscopy in Solids are described. Also the construction project of a partially home made spectrometer and its applications in the characterization of solid samples are shown in detail. The high resolution spectrometer used is implemented with the double resonance multiple pulses sequences and magic angle spinning (MAS) and can be used with solid and liquid samples. The maximum spinning frequency for the MAS experiment is in excess of 5 Khz, the double resonance sequences can be performed with any type of nucleus, in the variable temperature operating range with nitrogen gas: -120 0 C to +160 0 C, and is fully controlled by a Macintosh IIci microcomputer. (author)

  1. Radioimmunotherapy of human lymphoma in athymic, nude mice as monitored by 31P nuclear magnetic resonance

    International Nuclear Information System (INIS)

    Adams, D.A.; DeNardo, G.L.; DeNardo, S.J.; Matson, G.B.; Epstein, A.L.; Bradbury, E.M.

    1985-01-01

    Human B cell lymphoma (Raji) growing in athymic, nude mice has been successfully treated with a single pulse dose of 131 I-labeled monoclonal antibody (Lym-1) specific for this tumor. Sequential in vivo measurements of phosphate metabolites in the tumors by 31 P surface coil nuclear magnetic resonance showed a significant initial decrease of phosphocreatine following radioimmunotherapy. Diminution of relative ATP to Pi peak area ratio suggesting tissue damage occurred within 3-4 days. The sequence of alterations of nuclear magnetic resonance spectra from tumors of treated mice were strikingly different from sequential nuclear magnetic resonance spectra obtained from tumors of control mice. These observations lead us to conclude that 31 P surface coil nuclear magnetic resonance is a promising non-invasive method for assessing and predicting the efficacy of radioimmunotherapy. Further spatial discrimination of the region of tissue observed by the surface coil nuclear magnetic resonance experiment is under exploration in an effort to increase the utility of these methods

  2. ATRX mutation in two adult brothers with non-specific moderate intellectual disability identified by exome sequencing.

    Science.gov (United States)

    Moncini, S; Bedeschi, M F; Castronovo, P; Crippa, M; Calvello, M; Garghentino, R R; Scuvera, G; Finelli, P; Venturin, M

    2013-12-01

    In this report, we describe two adult brothers affected by moderate non-specific intellectual disability (ID). They showed minor facial anomalies, not clearly ascribable to any specific syndromic patterns, microcephaly, brachydactyly and broad toes. Both brothers presented seizures. Karyotype, subtelomeric and FMR1 analysis were normal in both cases. We performed array-CGH analysis that revealed no copy-number variations potentially associated with ID. Subsequent exome sequence analysis allowed the identification of the ATRX c.109C>T (p.R37X) mutation in both the affected brothers. Sanger sequencing confirmed the presence of the mutation in the brothers and showed that the mother is a healthy carrier. Mutations in the ATRX gene cause the X-linked alpha thalassemia/mental retardation (ATR-X) syndrome (MIM #301040), a severe clinical condition usually associated with profound ID, facial dysmorphism and alpha thalassemia. However, the syndrome is clinically heterogeneous and some mutations, including the c.109C>T, are associated with a broad phenotypic spectrum, with patients displaying a less severe phenotype with only mild-moderate ID. In the case presented here, exome sequencing provided an effective strategy to achieve the molecular diagnosis of ATR-X syndrome, which otherwise would have been difficult to consider due to the mild non-specific phenotype and the absence of a family history with typical severe cases.

  3. Structural basis for sequence-specific recognition of DNA by TAL effectors

    KAUST Repository

    Deng, Dong

    2012-01-05

    TAL (transcription activator-like) effectors, secreted by phytopathogenic bacteria, recognize host DNA sequences through a central domain of tandem repeats. Each repeat comprises 33 to 35 conserved amino acids and targets a specific base pair by using two hypervariable residues [known as repeat variable diresidues (RVDs)] at positions 12 and 13. Here, we report the crystal structures of an 11.5-repeat TAL effector in both DNA-free and DNA-bound states. Each TAL repeat comprises two helices connected by a short RVD-containing loop. The 11.5 repeats form a right-handed, superhelical structure that tracks along the sense strand of DNA duplex, with RVDs contacting the major groove. The 12th residue stabilizes the RVD loop, whereas the 13th residue makes a base-specific contact. Understanding DNA recognition by TAL effectors may facilitate rational design of DNA-binding proteins with biotechnological applications.

  4. Low-Field Magnetic Resonance Imaging of Canine Hydrocephalus

    Directory of Open Access Journals (Sweden)

    Z. Adamiak* and M. Jaskólska and A. Pomianowski1

    2012-01-01

    Full Text Available The aim of presented study was to evaluate selected surface spine coil, and low-field magnetic resonance (MR selected sequences in diagnosing hydrocephalus in dogs. This paper discusses 19 dogs (14 canine patients with hydrocephalus and 5 healthy dogs, of five breeds, subjected to low-field magnetic resonance imaging (MRI of hydrocephalus. Area of the lateral ventricles and brain were examined in dogs with hydrocephalus using low-field MRI (at 0.25 Tesla. The MRI of FSE REL, SE, FLAIR, STIR, 3D HYCE, T3DT1, GE STIR 3D and 3D SHARC sequences with an indication of the most effective sequences are described. Additionally, coils for MR were compared, and models for infusion anesthesia were described. As a result of performed study all estimated sequences were diagnostically useful. However, spinal coil No. 2 (ESAOTE was the most optimal for examining and positioning the cranium.

  5. Assignment of methyl NMR resonances of a 52 kDa protein with residue-specific 4D correlation maps

    International Nuclear Information System (INIS)

    Mishra, Subrata H.; Frueh, Dominique P.

    2015-01-01

    Methyl groups have become key probes for structural and functional studies by nuclear magnetic resonance. However, their NMR signals cluster in a small spectral region and assigning their resonances can be a tedious process. Here, we present a method that facilitates assignment of methyl resonances from assigned amide groups. Calculating the covariance between sensitive methyl and amide 3D spectra, each providing correlations to C α and C β separately, produces 4D correlation maps directly correlating methyl groups to amide groups. Optimal correlation maps are obtained by extracting residue-specific regions, applying derivative to the dimensions subject to covariance, and multiplying 4D maps stemming from different 3D spectra. The latter procedure rescues weak signals that may be missed in traditional assignment procedures. Using these covariance correlation maps, nearly all assigned isoleucine, leucine, and valine amide resonances of a 52 kDa nonribosomal peptide synthetase cyclization domain were paired with their corresponding methyl groups

  6. Magnetic resonance annual, 1988

    International Nuclear Information System (INIS)

    Kressel, H.Y.

    1987-01-01

    This book features reviews of high-resolution MRI of the knee, MRI of the normal and ischmeic hip, MRI of the heart, and temporomandibular joint imaging, as well as thorough discussion on artifacts in magnetic resonance imaging. Contributors consider the clinical applications of gadolinium-DTPA in magnetic resonance imaging and the clinical use of partial saturation and saturation recovery sequences. Timely reports assess the current status of rapid MRI and describe a new rapid gated cine MRI technique. Also included is an analysis of cerebrospinal fluid flow effects during MRI of the central nervous system

  7. Value of Perineural Edema/Inflammation Detected by Fat Saturation Sequences in Lumbar Magnetic Resonance Imaging of Patients with Unilateral Sciatica

    Energy Technology Data Exchange (ETDEWEB)

    Sirvanci, M.; Duran, C. (Dept. of Radiology, Faculty of Medicine, Istanbul Bilim Univ., Istanbul (Turkey)); Kara, B.; Onat, L.; Ulusoy, O.L.; Mutlu, A. (Dept. of Radiology of Florence Nightingale Hospital, Istanbul (Turkey)); Ozturk, E. (Dept. of Radiology, GATA Haydarpasa Teaching Hospital, Istanbul (Turkey)); Karatoprak, O. (Dept. of Orthopeadic Surgery, Kadikoy Florence Nightingale Hospital, Istanbul (Turkey))

    2009-02-15

    Background: Routine lumbar spine magnetic resonance imaging (MRI) may not show any evidence of the cause of sciatica in some cases. The relationship between nerve root compression detected on lumbar MRI and sciatica is also sometimes uncertain. Purpose: To ascertain whether axial (and, when necessary, sagittal and coronal) short-tau inversion recovery or fat-saturated T2-weighted MRI findings can be used to study the level of sciatica in patients with a non-yielding routine MRI examination. Material and Methods: A total of 215 patients with unilateral sciatica underwent MRI. All patients were asked to complete pain drawing forms describing their pain dermatomal distributions. Perineural edema/inflammation corresponding to the pain location indicated by the pain drawings was sought on short-tau inversion recovery or fat-saturated T2-weighted images. Results: Routine MRI findings revealed that 110 of the 215 patients had nerve root compromise related to the patients' symptoms. Routine MRI could not ascertain the cause of these symptoms in the remaining 105 patients. In 31 (29.5%) of these 105 patients, short-tau inversion recovery or fat-saturated T2-weighted magnetic resonance images revealed perineural edema/inflammation surrounding the nerve roots related to the pain locations indicated in the pain drawings. Conclusion: Axial (and, when required, sagittal and coronal) short-tau inversion recovery or fat-saturated T2-weighted magnetic resonance images may be helpful for revealing additional findings in cases of unexplained sciatica in standard magnetic resonance imaging. However, the value of this imaging may be not great enough to justify routine use of these additional sequences to study the level of sciatica

  8. Value of Perineural Edema/Inflammation Detected by Fat Saturation Sequences in Lumbar Magnetic Resonance Imaging of Patients with Unilateral Sciatica

    International Nuclear Information System (INIS)

    Sirvanci, M.; Duran, C.; Kara, B.; Onat, L.; Ulusoy, O.L.; Mutlu, A.; Ozturk, E.; Karatoprak, O.

    2009-01-01

    Background: Routine lumbar spine magnetic resonance imaging (MRI) may not show any evidence of the cause of sciatica in some cases. The relationship between nerve root compression detected on lumbar MRI and sciatica is also sometimes uncertain. Purpose: To ascertain whether axial (and, when necessary, sagittal and coronal) short-tau inversion recovery or fat-saturated T2-weighted MRI findings can be used to study the level of sciatica in patients with a non-yielding routine MRI examination. Material and Methods: A total of 215 patients with unilateral sciatica underwent MRI. All patients were asked to complete pain drawing forms describing their pain dermatomal distributions. Perineural edema/inflammation corresponding to the pain location indicated by the pain drawings was sought on short-tau inversion recovery or fat-saturated T2-weighted images. Results: Routine MRI findings revealed that 110 of the 215 patients had nerve root compromise related to the patients' symptoms. Routine MRI could not ascertain the cause of these symptoms in the remaining 105 patients. In 31 (29.5%) of these 105 patients, short-tau inversion recovery or fat-saturated T2-weighted magnetic resonance images revealed perineural edema/inflammation surrounding the nerve roots related to the pain locations indicated in the pain drawings. Conclusion: Axial (and, when required, sagittal and coronal) short-tau inversion recovery or fat-saturated T2-weighted magnetic resonance images may be helpful for revealing additional findings in cases of unexplained sciatica in standard magnetic resonance imaging. However, the value of this imaging may be not great enough to justify routine use of these additional sequences to study the level of sciatica

  9. An algorithm and program for finding sequence specific oligo-nucleotide probes for species identification

    Directory of Open Access Journals (Sweden)

    Tautz Diethard

    2002-03-01

    Full Text Available Abstract Background The identification of species or species groups with specific oligo-nucleotides as molecular signatures is becoming increasingly popular for bacterial samples. However, it shows also great promise for other small organisms that are taxonomically difficult to tract. Results We have devised here an algorithm that aims to find the optimal probes for any given set of sequences. The program requires only a crude alignment of these sequences as input and is optimized for performance to deal also with very large datasets. The algorithm is designed such that the position of mismatches in the probes influences the selection and makes provision of single nucleotide outloops. Program implementations are available for Linux and Windows.

  10. Identification of threshold prostate specific antigen levels to optimize the detection of clinically significant prostate cancer by magnetic resonance imaging/ultrasound fusion guided biopsy.

    Science.gov (United States)

    Shakir, Nabeel A; George, Arvin K; Siddiqui, M Minhaj; Rothwax, Jason T; Rais-Bahrami, Soroush; Stamatakis, Lambros; Su, Daniel; Okoro, Chinonyerem; Raskolnikov, Dima; Walton-Diaz, Annerleim; Simon, Richard; Turkbey, Baris; Choyke, Peter L; Merino, Maria J; Wood, Bradford J; Pinto, Peter A

    2014-12-01

    Prostate specific antigen sensitivity increases with lower threshold values but with a corresponding decrease in specificity. Magnetic resonance imaging/ultrasound targeted biopsy detects prostate cancer more efficiently and of higher grade than standard 12-core transrectal ultrasound biopsy but the optimal population for its use is not well defined. We evaluated the performance of magnetic resonance imaging/ultrasound targeted biopsy vs 12-core biopsy across a prostate specific antigen continuum. We reviewed the records of all patients enrolled in a prospective trial who underwent 12-core transrectal ultrasound and magnetic resonance imaging/ultrasound targeted biopsies from August 2007 through February 2014. Patients were stratified by each of 4 prostate specific antigen cutoffs. The greatest Gleason score using either biopsy method was compared in and across groups as well as across the population prostate specific antigen range. Clinically significant prostate cancer was defined as Gleason 7 (4 + 3) or greater. Univariate and multivariate analyses were performed. A total of 1,003 targeted and 12-core transrectal ultrasound biopsies were performed, of which 564 diagnosed prostate cancer for a 56.2% detection rate. Targeted biopsy led to significantly more upgrading to clinically significant disease compared to 12-core biopsy. This trend increased more with increasing prostate specific antigen, specifically in patients with prostate specific antigen 4 to 10 and greater than 10 ng/ml. Prostate specific antigen 5.2 ng/ml or greater captured 90% of upgrading by targeted biopsy, corresponding to 64% of patients who underwent multiparametric magnetic resonance imaging and subsequent fusion biopsy. Conversely a greater proportion of clinically insignificant disease was detected by 12-core vs targeted biopsy overall. These differences persisted when controlling for potential confounders on multivariate analysis. Prostate cancer upgrading with targeted biopsy increases

  11. The specificity of memory for a highly trained finger movement sequence: Change the ending, change all.

    Science.gov (United States)

    Rozanov, Simon; Keren, Ofer; Karni, Avi

    2010-05-17

    How are highly trained movement sequences represented in long-term memory? Here we show that the gains attained in the performance of a well-trained sequence of finger movements can be expressed only when the order of the movements is exactly as practiced. Ten young adults were trained to perform a given 5-element sequence of finger-to-thumb opposition movements with their left hand. Movements were analyzed using video based tracking. Three weeks of training resulted, along with improved accuracy, in robustly shortened movement times as well as shorter finger-to-thumb touch times. However, there was little transfer of these gains in speed to the execution of the same component movements arranged in a new order. Moreover, even when the only change was the omission of the one before final movement of the trained sequence (Omit sequence), the initial movements of the sequence were significantly slowed down, although these movements were identical to the initial movements of the trained sequence. Our results support the notion that a well-trained sequence of finger movements can be represented, in the adult motor system, as a singular, co-articulated, unit of movement, in which even the initial component movements are contingent on the subsequent, anticipated, ones. Because of co-articulation related anticipatory effects, gains in fluency and accuracy acquired in training on a specific movement sequence cannot be expressed in full in the execution of the trained component movements or of a full segment of the trained sequence, if followed by a different ending segment. Copyright 2010. Published by Elsevier B.V.

  12. Versatile Gene-Specific Sequence Tags for Arabidopsis Functional Genomics: Transcript Profiling and Reverse Genetics Applications

    Science.gov (United States)

    Hilson, Pierre; Allemeersch, Joke; Altmann, Thomas; Aubourg, Sébastien; Avon, Alexandra; Beynon, Jim; Bhalerao, Rishikesh P.; Bitton, Frédérique; Caboche, Michel; Cannoot, Bernard; Chardakov, Vasil; Cognet-Holliger, Cécile; Colot, Vincent; Crowe, Mark; Darimont, Caroline; Durinck, Steffen; Eickhoff, Holger; de Longevialle, Andéol Falcon; Farmer, Edward E.; Grant, Murray; Kuiper, Martin T.R.; Lehrach, Hans; Léon, Céline; Leyva, Antonio; Lundeberg, Joakim; Lurin, Claire; Moreau, Yves; Nietfeld, Wilfried; Paz-Ares, Javier; Reymond, Philippe; Rouzé, Pierre; Sandberg, Goran; Segura, Maria Dolores; Serizet, Carine; Tabrett, Alexandra; Taconnat, Ludivine; Thareau, Vincent; Van Hummelen, Paul; Vercruysse, Steven; Vuylsteke, Marnik; Weingartner, Magdalena; Weisbeek, Peter J.; Wirta, Valtteri; Wittink, Floyd R.A.; Zabeau, Marc; Small, Ian

    2004-01-01

    Microarray transcript profiling and RNA interference are two new technologies crucial for large-scale gene function studies in multicellular eukaryotes. Both rely on sequence-specific hybridization between complementary nucleic acid strands, inciting us to create a collection of gene-specific sequence tags (GSTs) representing at least 21,500 Arabidopsis genes and which are compatible with both approaches. The GSTs were carefully selected to ensure that each of them shared no significant similarity with any other region in the Arabidopsis genome. They were synthesized by PCR amplification from genomic DNA. Spotted microarrays fabricated from the GSTs show good dynamic range, specificity, and sensitivity in transcript profiling experiments. The GSTs have also been transferred to bacterial plasmid vectors via recombinational cloning protocols. These cloned GSTs constitute the ideal starting point for a variety of functional approaches, including reverse genetics. We have subcloned GSTs on a large scale into vectors designed for gene silencing in plant cells. We show that in planta expression of GST hairpin RNA results in the expected phenotypes in silenced Arabidopsis lines. These versatile GST resources provide novel and powerful tools for functional genomics. PMID:15489341

  13. Interspecies hybridization on DNA resequencing microarrays: efficiency of sequence recovery and accuracy of SNP detection in human, ape, and codfish mitochondrial DNA genomes sequenced on a human-specific MitoChip

    Directory of Open Access Journals (Sweden)

    Carr Steven M

    2007-09-01

    Full Text Available Abstract Background Iterative DNA "resequencing" on oligonucleotide microarrays offers a high-throughput method to measure intraspecific biodiversity, one that is especially suited to SNP-dense gene regions such as vertebrate mitochondrial (mtDNA genomes. However, costs of single-species design and microarray fabrication are prohibitive. A cost-effective, multi-species strategy is to hybridize experimental DNAs from diverse species to a common microarray that is tiled with oligonucleotide sets from multiple, homologous reference genomes. Such a strategy requires that cross-hybridization between the experimental DNAs and reference oligos from the different species not interfere with the accurate recovery of species-specific data. To determine the pattern and limits of such interspecific hybridization, we compared the efficiency of sequence recovery and accuracy of SNP identification by a 15,452-base human-specific microarray challenged with human, chimpanzee, gorilla, and codfish mtDNA genomes. Results In the human genome, 99.67% of the sequence was recovered with 100.0% accuracy. Accuracy of SNP identification declines log-linearly with sequence divergence from the reference, from 0.067 to 0.247 errors per SNP in the chimpanzee and gorilla genomes, respectively. Efficiency of sequence recovery declines with the increase of the number of interspecific SNPs in the 25b interval tiled by the reference oligonucleotides. In the gorilla genome, which differs from the human reference by 10%, and in which 46% of these 25b regions contain 3 or more SNP differences from the reference, only 88% of the sequence is recoverable. In the codfish genome, which differs from the reference by > 30%, less than 4% of the sequence is recoverable, in short islands ≥ 12b that are conserved between primates and fish. Conclusion Experimental DNAs bind inefficiently to homologous reference oligonucleotide sets on a re-sequencing microarray when their sequences differ by

  14. Myocardial late gadolinium enhancement in specific cardiomyopathies by cardiovascular magnetic resonance: a preliminary experience.

    Science.gov (United States)

    Silva, Caterina; Moon, James C; Elkington, Andrew G; John, Anna S; Mohiaddin, Raad H; Pennell, Dudley J

    2007-12-01

    Late gadolinium enhancement cardiovascular magnetic resonance (CMR) can visualize myocardial interstitial abnormalities. The aim of this study was to assess whether regions of abnormal myocardium can also be visualized by late enhancement gadolinium CMR in the specific cardiomyopathies. A retrospective review of all referrals for gadolinium CMR with specific cardiomyopathy over 20 months. Nine patients with different specific cardiomyopathies were identified. Late enhancement was demonstrated in all patients, with a mean signal intensity of 390 +/- 220% compared with normal regions. The distribution pattern of late enhancement was unlike the subendocardial late enhancement related to coronary territories found in myocardial infarction. The affected areas included papillary muscles (sarcoid), the mid-myocardium (Anderson-Fabry disease, glycogen storage disease, myocarditis, Becker muscular dystrophy) and the global sub-endocardium (systemic sclerosis, Loeffler's endocarditis, amyloid, Churg-Strauss). Focal myocardial late gadolinium enhancement is found in the specific cardiomyopathies, and the pattern is distinct from that seen in infarction. Further systematic studies are warranted to assess whether the pattern and extent of late enhancement may aid diagnosis and prognostic assessment.

  15. Generalized min-max bound-based MRI pulse sequence design framework for wide-range T1 relaxometry: A case study on the tissue specific imaging sequence.

    Directory of Open Access Journals (Sweden)

    Yang Liu

    Full Text Available This paper proposes a new design strategy for optimizing MRI pulse sequences for T1 relaxometry. The design strategy optimizes the pulse sequence parameters to minimize the maximum variance of unbiased T1 estimates over a range of T1 values using the Cramér-Rao bound. In contrast to prior sequences optimized for a single nominal T1 value, the optimized sequence using our bound-based strategy achieves improved precision and accuracy for a broad range of T1 estimates within a clinically feasible scan time. The optimization combines the downhill simplex method with a simulated annealing process. To show the effectiveness of the proposed strategy, we optimize the tissue specific imaging (TSI sequence. Preliminary Monte Carlo simulations demonstrate that the optimized TSI sequence yields improved precision and accuracy over the popular driven-equilibrium single-pulse observation of T1 (DESPOT1 approach for normal brain tissues (estimated T1 700-2000 ms at 3.0T. The relative mean estimation error (MSE for T1 estimation is less than 1.7% using the optimized TSI sequence, as opposed to less than 7.0% using DESPOT1 for normal brain tissues. The optimized TSI sequence achieves good stability by keeping the MSE under 7.0% over larger T1 values corresponding to different lesion tissues and the cerebrospinal fluid (up to 5000 ms. The T1 estimation accuracy using the new pulse sequence also shows improvement, which is more pronounced in low SNR scenarios.

  16. Sequence-specific high mobility group box factors recognize 10-12-base pair minor groove motifs

    DEFF Research Database (Denmark)

    van Beest, M; Dooijes, D; van De Wetering, M

    2000-01-01

    Sequence-specific high mobility group (HMG) box factors bind and bend DNA via interactions in the minor groove. Three-dimensional NMR analyses have provided the structural basis for this interaction. The cognate HMG domain DNA motif is generally believed to span 6-8 bases. However, alignment...

  17. Domain-specific and domain-general constraints on word and sequence learning.

    Science.gov (United States)

    Archibald, Lisa M D; Joanisse, Marc F

    2013-02-01

    The relative influences of language-related and memory-related constraints on the learning of novel words and sequences were examined by comparing individual differences in performance of children with and without specific deficits in either language or working memory. Children recalled lists of words in a Hebbian learning protocol in which occasional lists repeated, yielding improved recall over the course of the task on the repeated lists. The task involved presentation of pictures of common nouns followed immediately by equivalent presentations of the spoken names. The same participants also completed a paired-associate learning task involving word-picture and nonword-picture pairs. Hebbian learning was observed for all groups. Domain-general working memory constrained immediate recall, whereas language abilities impacted recall in the auditory modality only. In addition, working memory constrained paired-associate learning generally, whereas language abilities disproportionately impacted novel word learning. Overall, all of the learning tasks were highly correlated with domain-general working memory. The learning of nonwords was additionally related to general intelligence, phonological short-term memory, language abilities, and implicit learning. The results suggest that distinct associations between language- and memory-related mechanisms support learning of familiar and unfamiliar phonological forms and sequences.

  18. Transition metal nuclear magnetic resonance

    International Nuclear Information System (INIS)

    Pregosin, P.S.

    1991-01-01

    Transition metal NMR spectroscopy has progressed enormously in recent years. New methods, and specifically solid-state methods and new pulse sequences, have allowed access to data from nuclei with relatively low receptivities with the result that chemists have begun to consider old and new problems, previously unapproachable. Moreover, theory, computational science in particular, now permits the calculation of not just 13 C, 15 N and other light nuclei chemical shifts, but heavy main-group element and transition metals as well. These two points, combined with increasing access to high field pulsed spectrometer has produced a wealth of new data on the NMR transition metals. A new series of articles concerned with measuring, understanding and using the nuclear magnetic resonance spectra of the metals of Group 3-12 is presented. (author)

  19. Effector-independent motor sequence representations exist in extrinsic and intrinsic reference frames.

    Science.gov (United States)

    Wiestler, Tobias; Waters-Metenier, Sheena; Diedrichsen, Jörn

    2014-04-02

    Many daily activities rely on the ability to produce meaningful sequences of movements. Motor sequences can be learned in an effector-specific fashion (such that benefits of training are restricted to the trained hand) or an effector-independent manner (meaning that learning also facilitates performance with the untrained hand). Effector-independent knowledge can be represented in extrinsic/world-centered or in intrinsic/body-centered coordinates. Here, we used functional magnetic resonance imaging (fMRI) and multivoxel pattern analysis to determine the distribution of intrinsic and extrinsic finger sequence representations across the human neocortex. Participants practiced four sequences with one hand for 4 d, and then performed these sequences during fMRI with both left and right hand. Between hands, these sequences were equivalent in extrinsic or intrinsic space, or were unrelated. In dorsal premotor cortex (PMd), we found that sequence-specific activity patterns correlated higher for extrinsic than for unrelated pairs, providing evidence for an extrinsic sequence representation. In contrast, primary sensory and motor cortices showed effector-independent representations in intrinsic space, with considerable overlap of the two reference frames in caudal PMd. These results suggest that effector-independent representations exist not only in world-centered, but also in body-centered coordinates, and that PMd may be involved in transforming sequential knowledge between the two. Moreover, although effector-independent sequence representations were found bilaterally, they were stronger in the hemisphere contralateral to the trained hand. This indicates that intermanual transfer relies on motor memories that are laid down during training in both hemispheres, but preferentially draws upon sequential knowledge represented in the trained hemisphere.

  20. Screening for SNPs with Allele-Specific Methylation based on Next-Generation Sequencing Data.

    Science.gov (United States)

    Hu, Bo; Ji, Yuan; Xu, Yaomin; Ting, Angela H

    2013-05-01

    Allele-specific methylation (ASM) has long been studied but mainly documented in the context of genomic imprinting and X chromosome inactivation. Taking advantage of the next-generation sequencing technology, we conduct a high-throughput sequencing experiment with four prostate cell lines to survey the whole genome and identify single nucleotide polymorphisms (SNPs) with ASM. A Bayesian approach is proposed to model the counts of short reads for each SNP conditional on its genotypes of multiple subjects, leading to a posterior probability of ASM. We flag SNPs with high posterior probabilities of ASM by accounting for multiple comparisons based on posterior false discovery rates. Applying the Bayesian approach to the in-house prostate cell line data, we identify 269 SNPs as candidates of ASM. A simulation study is carried out to demonstrate the quantitative performance of the proposed approach.

  1. Magnetic resonance imaging of the shoulder

    International Nuclear Information System (INIS)

    Ilieva, E.

    2015-01-01

    Full text: Magnetic resonance imaging (MRI) is an excellent non-invasive imaging tool that can complement the physical examination in the evaluation of traumatic and non-traumatic injuries of the shoulder. The superb soft tissue contrast and multiplanar capabilities of MRI make it a preferred modality to provide a global assessment of the soft tissue and osseous structures of the shoulder. Learning objectives: to review briefly the anatomy of the shoulder and the specificity of sequences and planes for MRI; to demonstrate the characteristic MR findings of some of the most common shoulder disorders; to indicate how MR arthrography (MRA) of the shoulder can add extra value to the diagnostic process; to outline a systematic approach to the interpretation of the shoulder MR examination. Choosing the most suitable sequences and planes as well as the thorough knowledge of the anatomic structures assist the correct diagnosis of the pathologic disorders of the shoulder which is of great importance for the precise treatment management, surgical versus conservative, as well as for the appropriate surgical approach, open versus arthroscopic

  2. The OMERACT psoriatic arthritis magnetic resonance imaging scoring system (PsAMRIS): definitions of key pathologies, suggested MRI sequences, and preliminary scoring system for PsA Hands

    DEFF Research Database (Denmark)

    Østergaard, Mikkel; McQueen, Fiona; Wiell, Charlotte

    2009-01-01

    This article describes a preliminary OMERACT psoriatic arthritis magnetic resonance image scoring system (PsAMRIS) for evaluation of inflammatory and destructive changes in PsA hands, which was developed by the international OMERACT MRI in inflammatory arthritis group. MRI definitions of important...... pathologies in peripheral PsA and suggestions concerning appropriate MRI sequences for use in PsA hands are also provided....

  3. Selectivity in multiple quantum nuclear magnetic resonance

    International Nuclear Information System (INIS)

    Warren, W.S.

    1980-11-01

    The observation of multiple-quantum nuclear magnetic resonance transitions in isotropic or anisotropic liquids is shown to give readily interpretable information on molecular configurations, rates of motional processes, and intramolecular interactions. However, the observed intensity of high multiple-quantum transitions falls off dramatically as the number of coupled spins increases. The theory of multiple-quantum NMR is developed through the density matrix formalism, and exact intensities are derived for several cases (isotropic first-order systems and anisotropic systems with high symmetry) to shown that this intensity decrease is expected if standard multiple-quantum pulse sequences are used. New pulse sequences are developed which excite coherences and produce population inversions only between selected states, even though other transitions are simultaneously resonant. One type of selective excitation presented only allows molecules to absorb and emit photons in groups of n. Coherent averaging theory is extended to describe these selective sequences, and to design sequences which are selective to arbitrarily high order in the Magnus expansion. This theory and computer calculations both show that extremely good selectivity and large signal enhancements are possible

  4. Selectivity in multiple quantum nuclear magnetic resonance

    Energy Technology Data Exchange (ETDEWEB)

    Warren, Warren Sloan [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Materials Sciences Division

    1980-11-01

    The observation of multiple-quantum nuclear magnetic resonance transitions in isotropic or anisotropic liquids is shown to give readily interpretable information on molecular configurations, rates of motional processes, and intramolecular interactions. However, the observed intensity of high multiple-quantum transitions falls off dramatically as the number of coupled spins increases. The theory of multiple-quantum NMR is developed through the density matrix formalism, and exact intensities are derived for several cases (isotropic first-order systems and anisotropic systems with high symmetry) to shown that this intensity decrease is expected if standard multiple-quantum pulse sequences are used. New pulse sequences are developed which excite coherences and produce population inversions only between selected states, even though other transitions are simultaneously resonant. One type of selective excitation presented only allows molecules to absorb and emit photons in groups of n. Coherent averaging theory is extended to describe these selective sequences, and to design sequences which are selective to arbitrarily high order in the Magnus expansion. This theory and computer calculations both show that extremely good selectivity and large signal enhancements are possible.

  5. Flow Cytometry-Assisted Cloning of Specific Sequence Motifs from Complex 16S rRNA Gene Libraries

    DEFF Research Database (Denmark)

    Nielsen, Jeppe Lund; Schramm, Andreas; Bernhard, Anne E.

    2004-01-01

    for Systems Biology,3 Seattle, Washington, and Department of Ecological Microbiology, University of Bayreuth, Bayreuth, Germany2 A flow cytometry method was developed for rapid screening and recovery of cloned DNA containing common sequence motifs. This approach, termed fluorescence-activated cell sorting......  FLOW CYTOMETRY-ASSISTED CLONING OF SPECIFIC SEQUENCE MOTIFS FROM COMPLEX 16S RRNA GENE LIBRARIES Jeppe L. Nielsen,1 Andreas Schramm,1,2 Anne E. Bernhard,1 Gerrit J. van den Engh,3 and David A. Stahl1* Department of Civil and Environmental Engineering, University of Washington,1 and Institute......-assisted cloning, was used to recover sequences affiliated with a unique lineage within the Bacteroidetes not abundant in a clone library of environmental 16S rRNA genes.  ...

  6. Double-stranded RNA interferes in a sequence-specific manner with the infection of representative members of the two viroid families

    International Nuclear Information System (INIS)

    Carbonell, Alberto; Martinez de Alba, Angel-Emilio; Flores, Ricardo; Gago, Selma

    2008-01-01

    Infection by viroids, non-protein-coding circular RNAs, occurs with the accumulation of 21-24 nt viroid-derived small RNAs (vd-sRNAs) with characteristic properties of small interfering RNAs (siRNAs) associated to RNA silencing. The vd-sRNAs most likely derive from dicer-like (DCL) enzymes acting on viroid-specific dsRNA, the key elicitor of RNA silencing, or on the highly structured genomic RNA. Previously, viral dsRNAs delivered mechanically or agroinoculated have been shown to interfere with virus infection in a sequence-specific manner. Here, we report similar results with members of the two families of nuclear- and chloroplast-replicating viroids. Moreover, homologous vd-sRNAs co-delivered mechanically also interfered with one of the viroids examined. The interference was sequence-specific, temperature-dependent and, in some cases, also dependent on the dose of the co-inoculated dsRNA or vd-sRNAs. The sequence-specific nature of these effects suggests the involvement of the RNA induced silencing complex (RISC), which provides sequence specificity to RNA silencing machinery. Therefore, viroid titer in natural infections might be regulated by the concerted action of DCL and RISC. Viroids could have evolved their secondary structure as a compromise between resistance to DCL and RISC, which act preferentially against RNAs with compact and relaxed secondary structures, respectively. In addition, compartmentation, association with proteins or active replication might also help viroids to elude their host RNA silencing machinery

  7. Liver acquisition with acceleration volume acquisition gadolinium-enhanced magnetic resonance combined with T2 sequences in the diagnosis of local recurrence of rectal cancer.

    Science.gov (United States)

    Cao, Wuteng; Li, Fangqian; Gong, Jiaying; Liu, Dechao; Deng, Yanhong; Kang, Liang; Zhou, Zhiyang

    2016-11-22

    To investigate the efficacy of liver acquisition with acceleration volume acquisition (LAVA) gadolinium-enhanced magnetic resonance (MR) sequences and to assess its added accuracy in diagnosing local recurrence (LR) of rectal cancer with conventional T2-weighted fast spin echo (FSE) sequences. Pelvic MRI, including T2-weighted FSE sequences, gadolinium-enhanced sequences of LAVA and T1-weighted FSE with fat suppression, was performed on 225 patients with postoperative rectal cancer. Two readers evaluated the presence of LR according to "T2" (T2 sequences only), "T2 + LAVA-Gad" (LAVA and T2 imaging), and "T2 + T1-fs-Gad" (T1 fat suppression-enhanced sequence with T2 images). To evaluate diagnostic efficiency, imaging quality with LAVA and T1-fs-Gad by subjective scores and the signal intensity (SI) ratio. In the result, the SI ratio of LAVA was significantly higher than that of T1-fs-Gad (p = 0.0001). The diagnostic efficiency of "T2 + LAVA-Gad" was better than that of "T2 + T1-fs-Gad" (p = 0.0016 for Reader 1, p = 0.0001 for Reader 2) and T2 imaging only (p = 0.0001 for Reader 1; p = 0.0001 for Reader 2). Therefore, LAVA gadolinium-enhanced MR increases the accuracy of diagnosis of LR from rectal cancer and could replace conventional T1 gadolinium-enhanced sequences in the postoperative pelvic follow-up of rectal cancer.

  8. Next-generation sequencing offers new insights into DNA degradation

    DEFF Research Database (Denmark)

    Overballe-Petersen, Søren; Orlando, Ludovic Antoine Alexandre; Willerslev, Eske

    2012-01-01

    The processes underlying DNA degradation are central to various disciplines, including cancer research, forensics and archaeology. The sequencing of ancient DNA molecules on next-generation sequencing platforms provides direct measurements of cytosine deamination, depurination and fragmentation...... rates that previously were obtained only from extrapolations of results from in vitro kinetic experiments performed over short timescales. For example, recent next-generation sequencing of ancient DNA reveals purine bases as one of the main targets of postmortem hydrolytic damage, through base...... elimination and strand breakage. It also shows substantially increased rates of DNA base-loss at guanosine. In this review, we argue that the latter results from an electron resonance structure unique to guanosine rather than adenosine having an extra resonance structure over guanosine as previously suggested....

  9. Three-Dimensional Constructive Interference in Steady State Sequences and Phase-Contrast Magnetic Resonance Imaging of Arrested Hydrocephalus.

    Science.gov (United States)

    Elkafrawy, Fatma; Reda, Ihab; Elsirafy, Mohamed; Gawad, Mohamed Saied Abdel; Elnaggar, Alaa; Khalek Abdel Razek, Ahmed Abdel

    2017-02-01

    To evaluate the role of three-dimensional constructive interference in steady state (3D-CISS) sequences and phase-contrast magnetic resonance imaging (PC-MRI) in patients with arrested hydrocephalus. A prospective study of 20 patients with arrested hydrocephalus was carried out. All patients underwent PC-MRI and 3D-CISS for assessment of the aqueduct. Axial (through-plane), sagittal (in-plane) PC-MRI, and sagittal 3D-CISS were applied to assess the cerebral aqueduct and the spontaneous third ventriculostomy if present. Aqueductal patency was graded using 3D-CISS and PC-MRI. Quantitative analysis of flow through the aqueduct was performed using PC-MRI. The causes of obstruction were aqueductal obstruction in 75% (n = 15), third ventricular obstruction in 5% (n = 1), and fourth ventricular obstruction in 20% (n = 4). The cause of arrest of hydrocephalus was spontaneous third ventriculostomy in 65% (n = 13), endoscopic third ventriculostomy in 10% (n = 2), and ventriculoperitoneal shunt in 5% (n = 1), and no cause could be detected in 20% of patients (n = 4). There is a positive correlation (r = 0.80) and moderate agreement (κ = 0.509) of grading with PC-MRI and 3D-CISS sequences. The mean peak systolic velocity of cerebrospinal fluid was 1.86 ± 2.48 cm/second, the stroke volume was 6.43 ± 13.81 μL/cycle, and the mean flow was 0.21 ± 0.32 mL/minute. We concluded that 3D-CISS and PC-MRI are noninvasive sequences for diagnosis of the level and cause of arrested hydrocephalus. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery

    Directory of Open Access Journals (Sweden)

    Kirkness Ewen

    2006-10-01

    Full Text Available Abstract Background Population genetic studies of dogs have so far mainly been based on analysis of mitochondrial DNA, describing only the history of female dogs. To get a picture of the male history, as well as a second independent marker, there is a need for studies of biallelic Y-chromosome polymorphisms. However, there are no biallelic polymorphisms reported, and only 3200 bp of non-repetitive dog Y-chromosome sequence deposited in GenBank, necessitating the identification of dog Y chromosome sequence and the search for polymorphisms therein. The genome has been only partially sequenced for one male dog, disallowing mapping of the sequence into specific chromosomes. However, by comparing the male genome sequence to the complete female dog genome sequence, candidate Y-chromosome sequence may be identified by exclusion. Results The male dog genome sequence was analysed by Blast search against the human genome to identify sequences with a best match to the human Y chromosome and to the female dog genome to identify those absent in the female genome. Candidate sequences were then tested for male specificity by PCR of five male and five female dogs. 32 sequences from the male genome, with a total length of 24 kbp, were identified as male specific, based on a match to the human Y chromosome, absence in the female dog genome and male specific PCR results. 14437 bp were then sequenced for 10 male dogs originating from Europe, Southwest Asia, Siberia, East Asia, Africa and America. Nine haplotypes were found, which were defined by 14 substitutions. The genetic distance between the haplotypes indicates that they originate from at least five wolf haplotypes. There was no obvious trend in the geographic distribution of the haplotypes. Conclusion We have identified 24159 bp of dog Y-chromosome sequence to be used for population genetic studies. We sequenced 14437 bp in a worldwide collection of dogs, identifying 14 SNPs for future SNP analyses, and

  11. Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases.

    Science.gov (United States)

    Citorik, Robert J; Mimee, Mark; Lu, Timothy K

    2014-11-01

    Current antibiotics tend to be broad spectrum, leading to indiscriminate killing of commensal bacteria and accelerated evolution of drug resistance. Here, we use CRISPR-Cas technology to create antimicrobials whose spectrum of activity is chosen by design. RNA-guided nucleases (RGNs) targeting specific DNA sequences are delivered efficiently to microbial populations using bacteriophage or bacteria carrying plasmids transmissible by conjugation. The DNA targets of RGNs can be undesirable genes or polymorphisms, including antibiotic resistance and virulence determinants in carbapenem-resistant Enterobacteriaceae and enterohemorrhagic Escherichia coli. Delivery of RGNs significantly improves survival in a Galleria mellonella infection model. We also show that RGNs enable modulation of complex bacterial populations by selective knockdown of targeted strains based on genetic signatures. RGNs constitute a class of highly discriminatory, customizable antimicrobials that enact selective pressure at the DNA level to reduce the prevalence of undesired genes, minimize off-target effects and enable programmable remodeling of microbiota.

  12. ATRX mutation in two adult brothers with non-specific moderate intellectual disability identified by exome sequencing

    OpenAIRE

    Moncini, S.; Bedeschi, M.F.; Castronovo, P.; Crippa, M.; Calvello, M.; Garghentino, R.R.; Scuvera, G.; Finelli, P.; Venturin, M.

    2013-01-01

    In this report, we describe two adult brothers affected by moderate non-specific intellectual disability (ID). They showed minor facial anomalies, not clearly ascribable to any specific syndromic patterns, microcephaly, brachydactyly and broad toes. Both brothers presented seizures. Karyotype, subtelomeric and FMR1 analysis were normal in both cases. We performed array-CGH analysis that revealed no copy-number variations potentially associated with ID. Subsequent exome sequence analysis allow...

  13. Magnetic resonance imaging of the ear for patient-specific reconstructive surgery.

    Directory of Open Access Journals (Sweden)

    Luc Nimeskern

    Full Text Available INTRODUCTION: Like a fingerprint, ear shape is a unique personal feature that should be reconstructed with a high fidelity during reconstructive surgery. Ear cartilage tissue engineering (TE advantageously offers the possibility to use novel 3D manufacturing techniques to reconstruct the ear, thus allowing for a detailed auricular shape. However it also requires detailed patient-specific images of the 3D cartilage structures of the patient's intact contralateral ear (if available. Therefore the aim of this study was to develop and evaluate an imaging strategy for acquiring patient-specific ear cartilage shape, with sufficient precision and accuracy for use in a clinical setting. METHODS AND MATERIALS: Magnetic resonance imaging (MRI was performed on 14 volunteer and six cadaveric auricles and manually segmented. Reproducibility of cartilage volume (Cg.V, surface (Cg.S and thickness (Cg.Th was assessed, to determine whether raters could repeatedly define the same volume of interest. Additionally, six cadaveric auricles were harvested, scanned and segmented using the same procedure, then dissected and scanned using high resolution micro-CT. Correlation between MR and micro-CT measurements was assessed to determine accuracy. RESULTS: Good inter- and intra-rater reproducibility was observed (precision errors 0.82, but low for Cg.Th (0.95 demonstrated high accuracy. DISCUSSION AND CONCLUSION: This study demonstrated that precision and accuracy of the proposed method was high enough to detect patient-specific variation in ear cartilage geometry. The present study provides a clinical strategy to access the necessary information required for the production of 3D ear scaffolds for TE purposes, including detailed patient-specific shape. Furthermore, the protocol is applicable in daily clinical practice with existing infrastructure.

  14. The use of diffusion-weighted magnetic resonance imaging in the differentiation between benign and malignant breast lesions

    International Nuclear Information System (INIS)

    Pereira, Fernanda Philadelpho Arantes; Martins, Gabriela; Domingues, Marisa Nassar Aidar; Domingues, Romeu Cortes; Figueiredo, Eduardo; Fonseca, Lea Mirian Barbosa da

    2009-01-01

    Objective: to study the utility of diffusion-weighted magnetic resonance imaging in the differentiation between benign and malignant breast lesions. Materials and methods: forty-five women (mean age, 46.1 years) with 52 focal breast lesions underwent diffusion-weighted magnetic resonance imaging. The calculation of apparent diffusion coefficient (ADC) was based on the ADC map reflecting five b values (0, 250, 500, 750, and 1000 s/mm 2 ). The mean ADC value of each lesion was correlated with imaging findings and histopathologic results. Cutoff ADC, sensitivity and specificity of diffusion-weighted imaging in the differentiation between benign and malignant lesions were calculated. P -3 mm 2 /s) as compared with benign lesions (1.50 ± 0.34 x 10 -3 mm 2 /s) (P < 0.0001). Diffusion-weighted imaging showed high sensitivity and specificity (both, 92.3%) in the differentiation between benign and malignant lesions. Conclusion: diffusion-weighted imaging is a potential resource as an adjuvant to breast magnetic resonance imaging to differentiate benign from malignant lesions. Such sequence can be easily added to the standard breast magnetic resonance imaging protocol, without implying any significant increase in examination time. (author)

  15. Magnetic resonance imaging appearance of partial latissimus dorsi muscle tendon tear

    International Nuclear Information System (INIS)

    Le, Huy B.Q.; Lee, Steven T.; Lane, Michael D.; Munk, Peter L.; Malfair, David; Blachut, Piotr A.

    2009-01-01

    There is still a paucity of information about the clinical presentation, treatment and imaging findings of latissimus muscle tears. Only one study has specifically described the magnetic resonance imaging (MRI) features of latissimus tendon tears. We describe a case of a high-grade tear in the latissimus muscle tendon in an active water skier with no significant prior medical history. MRI demonstrated at least a 50% tear of the latissimus tendon, manifesting as increased signal intensity on T2-weighted sequences and surrounding edema, as well as a diminutive tendon at the humeral insertion. (orig.)

  16. Magnetic resonance cholangiography: comparison of two- and three-dimensional sequences for assessment of malignant biliary obstruction

    International Nuclear Information System (INIS)

    Choi, Jin-Young; Kim, Myeong-Jin; Lee, Jeong Min; Lee, Jae Young; Kim, Se Hyung; Han, Joon Koo; Choi, Byung Ihn; Kim, Ki Whang

    2008-01-01

    The purpose was to retrospectively compare two-dimensional (2D) magnetic resonance cholangiography (MRC) including breath-hold single-shot rapid acquisition with relaxation enhancement (RARE) and multislice half-Fourier RARE versus navigator-triggered 3D-RARE MRC in the evaluation of biliary malignancy. MRC findings were evaluated in 31 patients with malignant biliary obstruction, including biliary malignancy, gallbladder carcinoma, and ampullary cancer. Two observers independently reviewed the images to assess the overall image quality, artifacts, ductal conspicuity, extent of disease, diagnostic confidence of tumor extent, and origin of tumor. The results were compared with surgical and histopathologic findings. Studies obtained with 3D-MRC were of significantly higher technical quality than those obtained with 2D-MRC. However, the accuracy between two sequences for classification of tumor showed no statistical significance. There was no significant difference between the Az values of 2D- and 3D-MRC for overall tumor extent in bilateral second order branch, intrapancreatic common bile duct (CBD) involvement (Az = 0.889, 0.881 for 2D and Az = 0.903, 0.864 for 3D). Nor was there a significant difference between two sequences in the assessment of the origin of tumor. Although 3D-MRC has superior image quality over 2D-MRC, 3D-MRC showed no statistically significant difference in accuracy compared with 2D-MRC for evaluating the extent of disease in malignant biliary obstructions. (orig.)

  17. Study of {sup 14}N NQR response to SORC pulse sequence

    Energy Technology Data Exchange (ETDEWEB)

    Konnai, A., E-mail: konnai@nmri.go.jp; Odano, N. [National Maritime Research Institute, Department of Navigation and System Engineering (Japan); Asaji, T. [Nihon University, Department of Chemistry, College of Humanities and Sciences (Japan)

    2008-01-15

    The behavior of nuclear quadrupole resonance (NQR) signals between RF pulses of the strong off-resonance comb (SORC) as well as the spin-locking spin-echo (SLSE) pulse sequences was studied as for {sup 14}N NQR line {nu}{sub +} of dimethylnitramine (CH{sub 3}){sub 2}NNO{sub 2} at 77 K. The periodic variation of the signal amplitude observed by using SORC pulse sequence could be reasonably explained by the theoretical expression reported in the literature.

  18. Concepts and indications of abdominal magnetic resonance

    International Nuclear Information System (INIS)

    Murillo Viera, Wendy

    2012-01-01

    A literature review and conceptualization was performed of the main indications of magnetic resonance studies of the abdomen and the characteristic findings for each sequence, according to organ and pathology. The radiologist has had in mind main indications for magnetic resonance studies of the abdomen, with the purpose to guide the clinician in the choice of imaging modality that works best for the patient at diagnosis [es

  19. Single-cell mRNA cytometry via sequence-specific nanoparticle clustering and trapping

    Science.gov (United States)

    Labib, Mahmoud; Mohamadi, Reza M.; Poudineh, Mahla; Ahmed, Sharif U.; Ivanov, Ivaylo; Huang, Ching-Lung; Moosavi, Maral; Sargent, Edward H.; Kelley, Shana O.

    2018-05-01

    Cell-to-cell variation in gene expression creates a need for techniques that can characterize expression at the level of individual cells. This is particularly true for rare circulating tumour cells, in which subtyping and drug resistance are of intense interest. Here we describe a method for cell analysis—single-cell mRNA cytometry—that enables the isolation of rare cells from whole blood as a function of target mRNA sequences. This approach uses two classes of magnetic particles that are labelled to selectively hybridize with different regions of the target mRNA. Hybridization leads to the formation of large magnetic clusters that remain localized within the cells of interest, thereby enabling the cells to be magnetically separated. Targeting specific intracellular mRNAs enablescirculating tumour cells to be distinguished from normal haematopoietic cells. No polymerase chain reaction amplification is required to determine RNA expression levels and genotype at the single-cell level, and minimal cell manipulation is required. To demonstrate this approach we use single-cell mRNA cytometry to detect clinically important sequences in prostate cancer specimens.

  20. Nuclear-magnetic-resonance quantum calculations of the Jones polynomial

    International Nuclear Information System (INIS)

    Marx, Raimund; Spoerl, Andreas; Pomplun, Nikolas; Schulte-Herbrueggen, Thomas; Glaser, Steffen J.; Fahmy, Amr; Kauffman, Louis; Lomonaco, Samuel; Myers, John M.

    2010-01-01

    The repertoire of problems theoretically solvable by a quantum computer recently expanded to include the approximate evaluation of knot invariants, specifically the Jones polynomial. The experimental implementation of this evaluation, however, involves many known experimental challenges. Here we present experimental results for a small-scale approximate evaluation of the Jones polynomial by nuclear magnetic resonance (NMR); in addition, we show how to escape from the limitations of NMR approaches that employ pseudopure states. Specifically, we use two spin-1/2 nuclei of natural abundance chloroform and apply a sequence of unitary transforms representing the trefoil knot, the figure-eight knot, and the Borromean rings. After measuring the nuclear spin state of the molecule in each case, we are able to estimate the value of the Jones polynomial for each of the knots.

  1. Magnetic Resonance Sensors

    Directory of Open Access Journals (Sweden)

    Robert H. Morris

    2014-11-01

    Full Text Available Magnetic Resonance finds countless applications, from spectroscopy to imaging, routinely in almost all research and medical institutions across the globe. It is also becoming more frequently used for specific applications in which the whole instrument and system is designed for a dedicated application. With beginnings in borehole logging for the petro-chemical industry Magnetic Resonance sensors have been applied to fields as varied as online process monitoring for food manufacture and medical point of care diagnostics. This great diversity is seeing exciting developments in magnetic resonance sensing technology published in application specific journals where they are often not seen by the wider sensor community. It is clear that there is enormous interest in magnetic resonance sensors which represents a significant growth area. The aim of this special edition of Sensors was to address the wide distribution of relevant articles by providing a forum to disseminate cutting edge research in this field in a single open source publication.[...

  2. Preoperative magnetic resonance imaging protocol for endoscopic cranial base image-guided surgery.

    Science.gov (United States)

    Grindle, Christopher R; Curry, Joseph M; Kang, Melissa D; Evans, James J; Rosen, Marc R

    2011-01-01

    Despite the increasing utilization of image-guided surgery, no radiology protocols for obtaining magnetic resonance (MR) imaging of adequate quality are available in the current literature. At our institution, more than 300 endonasal cranial base procedures including pituitary, extended pituitary, and other anterior skullbase procedures have been performed in the past 3 years. To facilitate and optimize preoperative evaluation and assessment, there was a need to develop a magnetic resonance protocol. Retrospective Technical Assessment was performed. Through a collaborative effort between the otolaryngology, neurosurgery, and neuroradiology departments at our institution, a skull base MR image-guided (IGS) protocol was developed with several ends in mind. First, it was necessary to generate diagnostic images useful for the more frequently seen pathologies to improve work flow and limit the expense and inefficiency of case specific MR studies. Second, it was necessary to generate sequences useful for IGS, preferably using sequences that best highlight that lesion. Currently, at our institution, all MR images used for IGS are obtained using this protocol as part of preoperative planning. The protocol that has been developed allows for thin cut precontrast and postcontrast axial cuts that can be used to plan intraoperative image guidance. It also obtains a thin cut T2 axial series that can be compiled separately for intraoperative imaging, or may be fused with computed tomographic images for combined modality. The outlined protocol obtains image sequences effective for diagnostic and operative purposes for image-guided surgery using both T1 and T2 sequences. Copyright © 2011 Elsevier Inc. All rights reserved.

  3. Magnetic Resonance Imaging for Patellofemoral Chondromalacia: Is There a Role for T2 Mapping?

    OpenAIRE

    van Eck, Carola F.; Kingston, R. Scott; Crues, John V.; Kharrazi, F. Daniel

    2017-01-01

    Background: Patellofemoral pain is common, and treatment is guided by the presence and grade of chondromalacia. Purpose: To evaluate and compare the sensitivity and specificity in detecting and grading chondral abnormalities of the patella between proton density fat suppression (PDFS) and T2 mapping magnetic resonance imaging (MRI). Study Design: Cohort study; Level of evidence, 2. Methods: A total of 25 patients who underwent MRI of the knee with both a PDFS sequence and T2 mapping and subse...

  4. 4D experiments measured with APSY for automated backbone resonance assignments of large proteins

    International Nuclear Information System (INIS)

    Krähenbühl, Barbara; Boudet, Julien; Wider, Gerhard

    2013-01-01

    Detailed structural and functional characterization of proteins by solution NMR requires sequence-specific resonance assignment. We present a set of transverse relaxation optimization (TROSY) based four-dimensional automated projection spectroscopy (APSY) experiments which are designed for resonance assignments of proteins with a size up to 40 kDa, namely HNCACO, HNCOCA, HNCACB and HN(CO)CACB. These higher-dimensional experiments include several sensitivity-optimizing features such as multiple quantum parallel evolution in a ‘just-in-time’ manner, aliased off-resonance evolution, evolution-time optimized APSY acquisition, selective water-handling and TROSY. The experiments were acquired within the concept of APSY, but they can also be used within the framework of sparsely sampled experiments. The multidimensional peak lists derived with APSY provided chemical shifts with an approximately 20 times higher precision than conventional methods usually do, and allowed the assignment of 90 % of the backbone resonances of the perdeuterated primase-polymerase ORF904, which contains 331 amino acid residues and has a molecular weight of 38.4 kDa.

  5. Magnetic resonance imaging of the fetal brain.

    Science.gov (United States)

    Tee, L Mf; Kan, E Yl; Cheung, J Cy; Leung, W C

    2016-06-01

    This review covers the recent literature on fetal brain magnetic resonance imaging, with emphasis on techniques, advances, common indications, and safety. We conducted a search of MEDLINE for articles published after 2010. The search terms used were "(fetal OR foetal OR fetus OR foetus) AND (MR OR MRI OR [magnetic resonance]) AND (brain OR cerebral)". Consensus statements from major authorities were also included. As a result, 44 relevant articles were included and formed the basis of this review. One major challenge is fetal motion that is largely overcome by ultra-fast sequences. Currently, single-shot fast spin-echo T2-weighted imaging remains the mainstay for motion resistance and anatomical delineation. Recently, a snap-shot inversion recovery sequence has enabled robust T1-weighted images to be obtained, which is previously a challenge for standard gradient-echo acquisitions. Fetal diffusion-weighted imaging, diffusion tensor imaging, and magnetic resonance spectroscopy are also being developed. With multiplanar capabilities, superior contrast resolution and field of view, magnetic resonance imaging does not have the limitations of sonography, and can provide additional important information. Common indications include ventriculomegaly, callosum and posterior fossa abnormalities, and twin complications. There are safety concerns about magnetic resonance-induced heating and acoustic damage but current literature showed no conclusive evidence of deleterious fetal effects. The American College of Radiology guideline states that pregnant patients can be accepted to undergo magnetic resonance imaging at any stage of pregnancy if risk-benefit ratio to patients warrants that the study be performed. Magnetic resonance imaging of the fetal brain is a safe and powerful adjunct to sonography in prenatal diagnosis. It can provide additional information that aids clinical management, prognostication, and counselling.

  6. Fetal abdominal magnetic resonance imaging

    International Nuclear Information System (INIS)

    Brugger, Peter C.; Prayer, Daniela

    2006-01-01

    This review deals with the in vivo magnetic resonance imaging (MRI) appearance of the human fetal abdomen. Imaging findings are correlated with current knowledge of human fetal anatomy and physiology, which are crucial to understand and interpret fetal abdominal MRI scans. As fetal MRI covers a period of more than 20 weeks, which is characterized not only by organ growth, but also by changes and maturation of organ function, a different MR appearance of the fetal abdomen results. This not only applies to the fetal intestines, but also to the fetal liver, spleen, and adrenal glands. Choosing the appropriate sequences, various aspects of age-related and organ-specific function can be visualized with fetal MRI, as these are mirrored by changes in signal intensities. Knowledge of normal development is essential to delineate normal from pathological findings in the respective developmental stages

  7. Fetal abdominal magnetic resonance imaging

    Energy Technology Data Exchange (ETDEWEB)

    Brugger, Peter C. [Center of Anatomy and Cell Biology, Integrative Morphology Group, Medical University of Vienna, Waehringerstrasse 13, 1090 Vienna (Austria)]. E-mail: peter.brugger@meduniwien.ac.at; Prayer, Daniela [Department of Radiology, Medical University of Vienna, Waehringerguertel 18-20, 1090 Vienna (Austria)

    2006-02-15

    This review deals with the in vivo magnetic resonance imaging (MRI) appearance of the human fetal abdomen. Imaging findings are correlated with current knowledge of human fetal anatomy and physiology, which are crucial to understand and interpret fetal abdominal MRI scans. As fetal MRI covers a period of more than 20 weeks, which is characterized not only by organ growth, but also by changes and maturation of organ function, a different MR appearance of the fetal abdomen results. This not only applies to the fetal intestines, but also to the fetal liver, spleen, and adrenal glands. Choosing the appropriate sequences, various aspects of age-related and organ-specific function can be visualized with fetal MRI, as these are mirrored by changes in signal intensities. Knowledge of normal development is essential to delineate normal from pathological findings in the respective developmental stages.

  8. Nonlinear resonances

    CERN Document Server

    Rajasekar, Shanmuganathan

    2016-01-01

    This introductory text presents the basic aspects and most important features of various types of resonances and anti-resonances in dynamical systems. In particular, for each resonance, it covers the theoretical concepts, illustrates them with case studies, and reviews the available information on mechanisms, characterization, numerical simulations, experimental realizations, possible quantum analogues, applications and significant advances made over the years. Resonances are one of the most fundamental phenomena exhibited by nonlinear systems and refer to specific realizations of maximum response of a system due to the ability of that system to store and transfer energy received from an external forcing source. Resonances are of particular importance in physical, engineering and biological systems - they can prove to be advantageous in many applications, while leading to instability and even disasters in others. The book is self-contained, providing the details of mathematical derivations and techniques invo...

  9. Focal point determination in magnetic resonance-guided focused ultrasound using tracking coils.

    Science.gov (United States)

    Svedin, Bryant T; Beck, Michael J; Hadley, J Rock; Merrill, Robb; de Bever, Joshua T; Bolster, Bradley D; Payne, Allison; Parker, Dennis L

    2017-06-01

    To develop a method for rapid prediction of the geometric focus location in MR coordinates of a focused ultrasound (US) transducer with arbitrary position and orientation without sonicating. Three small tracker coil circuits were designed, constructed, attached to the transducer housing of a breast-specific MR-guided focused US (MRgFUS) system with 5 degrees of freedom, and connected to receiver channel inputs of an MRI scanner. A one-dimensional sequence applied in three orthogonal directions determined the position of each tracker, which was then corrected for gradient nonlinearity. In a calibration step, low-level heating located the US focus in one transducer position orientation where the tracker positions were also known. Subsequent US focus locations were determined from the isometric transformation of the trackers. The accuracy of this method was verified by comparing the tracking coil predictions to thermal center of mass calculated using MR thermometry data acquired at 16 different transducer positions for MRgFUS sonications in a homogeneous gelatin phantom. The tracker coil predicted focus was an average distance of 2.1 ± 1.1 mm from the thermal center of mass. The one-dimensional locator sequence and prediction calculations took less than 1 s to perform. This technique accurately predicts the geometric focus for a transducer with arbitrary position and orientation without sonicating. Magn Reson Med 77:2424-2430, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

  10. Magnetic resonance imaging of entheses. Part 1

    Energy Technology Data Exchange (ETDEWEB)

    Benjamin, M. [School of Biosciences, Cardiff University, Cardiff (United Kingdom); Milz, S. [AO Research Institute, Davos (Switzerland); Bydder, G.M. [Department of Radiology, University of California San Diego, San Diego (United States)], E-mail: gbydder@ucsd.edu

    2008-06-15

    Entheses are the sites of attachment of a tendon, ligament, or joint capsule to bone. Many features of entheses are adapted to disperse stress and accommodate compressive and shear forces at, or near, boundaries between tendons or ligaments and bone. Of particular interest is calcified and uncalcified fibrocartilage, which has mechanical properties that differ from those of tensile regions of tendons or ligaments, and from bone. Ultrashort echo time (UTE) pulse sequences can identify the specific tissue components of entheses and differentiate cortical bone, calcified fibrocartilage, uncalcified fibrocartilage, and fibrous connective tissue. Magic angle imaging can also differentiate tissues, such as fibrocartilage and tendon, which have different fibre orientations. Understanding the magnetic resonance (MR) appearance of entheses involves consideration of tissue properties, fibre-to-field angle, magic angle effects, pulse sequences, and geometrical factors including fibre-to-section orientation and partial volume effects. New approaches using MR imaging, allow entheses to be visualised with much greater detail than previously possible, and this may help in biomechanical studies, diagnosis of disease including overuse syndromes and spondyloarthropathies, as well as monitoring tissue repair and healing.

  11. One-year retention of general and sequence-specific skills in a probabilistic, serial reaction time task.

    Science.gov (United States)

    Romano, Jennifer C; Howard, James H; Howard, Darlene V

    2010-05-01

    Procedural skills such as riding a bicycle and playing a musical instrument play a central role in daily life. Such skills are learned gradually and are retained throughout life. The present study investigated 1-year retention of procedural skill in a version of the widely used serial reaction time task (SRTT) in young and older motor-skill experts and older controls in two experiments. The young experts were college-age piano and action video-game players, and the older experts were piano players. Previous studies have reported sequence-specific skill retention in the SRTT as long as 2 weeks but not at 1 year. Results indicated that both young and older experts and older non-experts revealed sequence-specific skill retention after 1 year with some evidence that general motor skill was retained as well. These findings are consistent with theoretical accounts of procedural skill learning such as the procedural reinstatement theory as well as with previous studies of retention of other motor skills.

  12. The"minimum information about an environmental sequence" (MIENS) specification

    Energy Technology Data Exchange (ETDEWEB)

    Yilmaz, P.; Kottmann, R.; Field, D.; Knight, R.; Cole, J.R.; Amaral-Zettler, L.; Gilbert, J.A.; Karsch-Mizrachi, I.; Johnston, A.; Cochrane, G.; Vaughan, R.; Hunter, C.; Park, J.; Morrison, N.; Rocca-Serra, P.; Sterk, P.; Arumugam, M.; Baumgartner, L.; Birren, B.W.; Blaser, M.J.; Bonazzi, V.; Bork, P.; Buttigieg, P. L.; Chain, P.; Costello, E.K.; Huot-Creasy, H.; Dawyndt, P.; DeSantis, T.; Fierer, N.; Fuhrman, J.; Gallery, R.E.; Gibbs, R.A.; Giglio, M.G.; Gil, I. San; Gonzalez, A.; Gordon, J.I.; Guralnick, R.; Hankeln, W.; Highlander, S.; Hugenholtz, P.; Jansson, J.; Kennedy, J.; Knights, D.; Koren, O.; Kuczynski, J.; Kyrpides, N.; Larsen, R.; Lauber, C.L.; Legg, T.; Ley, R.E.; Lozupone, C.A.; Ludwig, W.; Lyons, D.; Maguire, E.; Methe, B.A.; Meyer, F.; Nakieny, S.; Nelson, K.E.; Nemergut, D.; Neufeld, J.D.; Pace, N.R.; Palanisamy, G.; Peplies, J.; Peterson, J.; Petrosino, J.; Proctor, L.; Raes, J.; Ratnasingham, S.; Ravel, J.; Relman, D.A.; Assunta-Sansone, S.; Schriml, L.; Sodergren, E.; Spor, A.; Stombaugh, J.; Tiedje, J.M.; Ward, D.V.; Weinstock, G.M.; Wendel, D.; White, O.; Wikle, A.; Wortman, J.R.; Glockner, F.O.; Bushman, F.D.; Charlson, E.; Gevers, D.; Kelley, S.T.; Neubold, L.K.; Oliver, A.E.; Pruesse, E.; Quast, C.; Schloss, P.D.; Sinha, R.; Whitely, A.

    2010-10-15

    We present the Genomic Standards Consortium's (GSC) 'Minimum Information about an ENvironmental Sequence' (MIENS) standard for describing marker genes. Adoption of MIENS will enhance our ability to analyze natural genetic diversity across the Tree of Life as it is currently being documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.

  13. Genomic library screening for viruses from the human dental plaque revealed pathogen-specific lytic phage sequences.

    Science.gov (United States)

    Al-Jarbou, Ahmed Nasser

    2012-01-01

    Bacterial pathogenesis presents an astounding arsenal of virulence factors that allow them to conquer many different niches throughout the course of infection. Principally fascinating is the fact that some bacterial species are able to induce different diseases by expression of different combinations of virulence factors. Nevertheless, studies aiming at screening for the presence of bacteriophages in humans have been limited. Such screening procedures would eventually lead to identification of phage-encoded properties that impart increased bacterial fitness and/or virulence in a particular niche, and hence, would potentially be used to reverse the course of bacterial infections. As the human oral cavity represents a rich and dynamic ecosystem for several upper respiratory tract pathogens. However, little is known about virus diversity in human dental plaque which is an important reservoir. We applied the culture-independent approach to characterize virus diversity in human dental plaque making a library from a virus DNA fraction amplified using a multiple displacement method and sequenced 80 clones. The resulting sequence showed 44% significant identities to GenBank databases by TBLASTX analysis. TBLAST homology comparisons showed that 66% was viral; 18% eukarya; 10% bacterial; 6% mobile elements. These sequences were sorted into 6 contigs and 45 single sequences in which 4 contigs and a single sequence showed significant identity to a small region of a putative prophage in the Corynebacterium diphtheria genome. These findings interestingly highlight the uniqueness of over half of the sequences, whilst the dominance of a pathogen-specific prophage sequences imply their role in virulence.

  14. Theory of magnetoelectric effect in multilayer nanocomposites on a substrate: Resonant bending-mode response

    Directory of Open Access Journals (Sweden)

    Matthias C. Krantz

    2013-05-01

    Full Text Available Resonant bending-mode magnetoelectric (ME coefficients of magnetostrictive-piezoelectric multilayer cantilevers are calculated analytically using a model developed for arbitrary multilayers on a substrate. Without quality factor effects the ME coefficient maxima in the four-dimensional parameter space of layer numbers, layer sequences, piezoelectric volume fractions, and substrate thicknesses are found to be essentially constant for nonzero substrate thickness. Global maxima occur for bilayers without substrates. Vanishing magnetoelectric response regions result from voltage cancellation in piezoelectric layers or absence of bending-mode excitation. They are determined by the neutral plane position in the multilayer stack. With Q-factor effects dominated by viscous air damping ME coefficients strongly increase with cantilever thickness primarily due to increasing resonance frequencies. The results yield a layer specific prediction of ME coefficients, resonance frequencies, and Q-factors in arbitrary multilayers and thus distinction of linear-coupling and Q-factor effects from exchange interaction, interface, or nonlinear ME effects.

  15. Introduction lecture to magnetic resonance

    International Nuclear Information System (INIS)

    Conard, J.

    1980-01-01

    This lecture deals with all that is common either to electron paramagnetic resonance (E.P.R.) or to nuclear magnetic resonance (N.M.R.). It will present, in an as elementary form as possible, the main concepts used in magnetic resonance emphasizing some aspects, specific for interface science. (orig./BHO)

  16. How does MRI work? An introduction into physics and functionality of magnetic resonance imaging. 6. ed.

    International Nuclear Information System (INIS)

    Weishaupt, Dominik; Marincek, Borut

    2009-01-01

    The book provides the basic physics and describes the functionality of magnetic resonance tomography in a very illustrative way. The following topics are covered: Spins and the magnetic resonance phenomenon, image contrast, three-dimensional structure, signal-to-noise ratio, description of a magnetic resonance tomography, basic pulse sequences, fast pulse sequences, methods for fat suppression, parallel imaging, cardiovascular imaging, MR contrast media, MR image artifacts, high-field MRI, imaging beyond morphology and structure, safety and risks [de

  17. Magnetic resonance fingerprinting.

    Science.gov (United States)

    Ma, Dan; Gulani, Vikas; Seiberlich, Nicole; Liu, Kecheng; Sunshine, Jeffrey L; Duerk, Jeffrey L; Griswold, Mark A

    2013-03-14

    Magnetic resonance is an exceptionally powerful and versatile measurement technique. The basic structure of a magnetic resonance experiment has remained largely unchanged for almost 50 years, being mainly restricted to the qualitative probing of only a limited set of the properties that can in principle be accessed by this technique. Here we introduce an approach to data acquisition, post-processing and visualization--which we term 'magnetic resonance fingerprinting' (MRF)--that permits the simultaneous non-invasive quantification of multiple important properties of a material or tissue. MRF thus provides an alternative way to quantitatively detect and analyse complex changes that can represent physical alterations of a substance or early indicators of disease. MRF can also be used to identify the presence of a specific target material or tissue, which will increase the sensitivity, specificity and speed of a magnetic resonance study, and potentially lead to new diagnostic testing methodologies. When paired with an appropriate pattern-recognition algorithm, MRF inherently suppresses measurement errors and can thus improve measurement accuracy.

  18. Diagnosing ulnar neuropathy at the elbow using magnetic resonance neurography

    International Nuclear Information System (INIS)

    Keen, Nayela N.; Chin, Cynthia T.; Saloner, David; Steinbach, Lynne S.; Engstrom, John W.

    2012-01-01

    Early diagnosis of ulnar neuropathy at the elbow is important. Magnetic resonance neurography (MRN) images peripheral nerves. We evaluated the usefulness of elbow MRN in diagnosing ulnar neuropathy at the elbow. The MR neurograms of 21 patients with ulnar neuropathy were reviewed retrospectively. MRN was performed prospectively on 10 normal volunteers. The MR neurograms included axial T1 and axial T2 fat-saturated and/or axial STIR sequences. The sensitivity and specificity of MRN in detecting ulnar neuropathy were determined. The mean ulnar nerve size in the symptomatic and normal groups was 0.12 and 0.06 cm 2 (P 2 , sensitivity was 95% and specificity was 80%. Ulnar nerve size and signal intensity were greater in patients with ulnar neuropathy. MRN is a useful test in evaluating ulnar neuropathy at the elbow. (orig.)

  19. IDENTIFICATION OF AVIAN-SPECIFIC FECAL METAGENOMIC SEQUENCES USING GENOME FRAGMENT ENRICHMENTS

    Science.gov (United States)

    Sequence analysis of microbial genomes has provided biologists the opportunity to compare genetic differences between closely related microorganisms. While random sequencing has also been used to study natural microbial communities, metagenomic comparisons via sequencing analysis...

  20. BrAD-seq: Breath Adapter Directional sequencing: a streamlined, ultra-simple and fast library preparation protocol for strand specific mRNA library construction.

    Directory of Open Access Journals (Sweden)

    Brad Thomas Townsley

    2015-05-01

    Full Text Available Next Generation Sequencing (NGS is driving rapid advancement in biological understanding and RNA-sequencing (RNA-seq has become an indispensable tool for biology and medicine. There is a growing need for access to these technologies although preparation of NGS libraries remains a bottleneck to wider adoption. Here we report a novel method for the production of strand specific RNA-seq libraries utilizing inherent properties of double-stranded cDNA to capture and incorporate a sequencing adapter. Breath Adapter Directional sequencing (BrAD-seq reduces sample handling and requires far fewer enzymatic steps than most available methods to produce high quality strand-specific RNA-seq libraries. The method we present is optimized for 3-prime Digital Gene Expression (DGE libraries and can easily extend to full transcript coverage shotgun (SHO type strand-specific libraries and is modularized to accommodate a diversity of RNA and DNA input materials. BrAD-seq offers a highly streamlined and inexpensive option for RNA-seq libraries.

  1. Magnetic resonance imaging of Parkinsonism

    International Nuclear Information System (INIS)

    Mukai, Eiichiro; Makino, Naoki; Fujishiro, Kenichiro.

    1989-01-01

    We have analyzed magnetic resonance images in 33 patients; 18 patients with Parkinson's disease, 1 patient with diurnally fluctuating progressive dystonia, 1 patient with pure akinesia, 6 patients with multiple system atrophy, 1 patient with flunarizine induced parkinsonism, and 4 patients with unclassified parkinsonism. The MR images were obtained using a 1.5-T GE MR System. A spin-echo pulse sequence was used with a TE of 30 msec and 80 msec and a TR of 2000 msec. No signal abnormalities were seen in any patient with Parkinson's disease but 3 showed slightly decreased signal intensity of the putamen on T2-weighted sequences. Patients with diurnally fluctuating progressive dystonia and pure akinesia evidensed no abnormal findings. All six patients with multiple system atrophy demonstrated decreased signal intensity of the putamen, particularly along their lateral and posterior portions, and an enlarged substantia nigra. Atrophy of the pons and cerebellum was detected in all cases with multiple system atrophy. One case of flunarizine induced parkinsonism showed slightly decreased signal intensity of the putamen. Four cases of unclassified parkinsonism showed decreased signal in the putamen on T2-weighted sequences. Magnetic resonance imaging has the potential to become a useful diagnostic tool in the management of parkinsonism. (author)

  2. Magnetic resonance imaging of Parkinsonism

    Energy Technology Data Exchange (ETDEWEB)

    Mukai, Eiichiro [National Hospital of Nagoya (Japan); Makino, Naoki; Fujishiro, Kenichiro

    1989-06-01

    We have analyzed magnetic resonance images in 33 patients; 18 patients with Parkinson's disease, 1 patient with diurnally fluctuating progressive dystonia, 1 patient with pure akinesia, 6 patients with multiple system atrophy, 1 patient with flunarizine induced parkinsonism, and 4 patients with unclassified parkinsonism. The MR images were obtained using a 1.5-T GE MR System. A spin-echo pulse sequence was used with a TE of 30 msec and 80 msec and a TR of 2000 msec. No signal abnormalities were seen in any patient with Parkinson's disease but 3 showed slightly decreased signal intensity of the putamen on T2-weighted sequences. Patients with diurnally fluctuating progressive dystonia and pure akinesia evidensed no abnormal findings. All six patients with multiple system atrophy demonstrated decreased signal intensity of the putamen, particularly along their lateral and posterior portions, and an enlarged substantia nigra. Atrophy of the pons and cerebellum was detected in all cases with multiple system atrophy. One case of flunarizine induced parkinsonism showed slightly decreased signal intensity of the putamen. Four cases of unclassified parkinsonism showed decreased signal in the putamen on T2-weighted sequences. Magnetic resonance imaging has the potential to become a useful diagnostic tool in the management of parkinsonism. (author).

  3. Torque measurements reveal sequence-specific cooperative transitions in supercoiled DNA

    Science.gov (United States)

    Oberstrass, Florian C.; Fernandes, Louis E.; Bryant, Zev

    2012-01-01

    B-DNA becomes unstable under superhelical stress and is able to adopt a wide range of alternative conformations including strand-separated DNA and Z-DNA. Localized sequence-dependent structural transitions are important for the regulation of biological processes such as DNA replication and transcription. To directly probe the effect of sequence on structural transitions driven by torque, we have measured the torsional response of a panel of DNA sequences using single molecule assays that employ nanosphere rotational probes to achieve high torque resolution. The responses of Z-forming d(pGpC)n sequences match our predictions based on a theoretical treatment of cooperative transitions in helical polymers. “Bubble” templates containing 50–100 bp mismatch regions show cooperative structural transitions similar to B-DNA, although less torque is required to disrupt strand–strand interactions. Our mechanical measurements, including direct characterization of the torsional rigidity of strand-separated DNA, establish a framework for quantitative predictions of the complex torsional response of arbitrary sequences in their biological context. PMID:22474350

  4. MRI sequences and their parameters

    International Nuclear Information System (INIS)

    Teissier, J.M.

    1993-01-01

    Listing basic sequences and their present variants makes a synthetic classification of the various acquisition modes possible. The knowledge of the advantages of each of them, as well as of their disadvantages and restraints, seems to be an essential prerequisite to an optimal utilization of each magnetic resonance imaging system. (author)

  5. Magnetic resonance imaging of the wrist: Diagnostic performance statistics

    International Nuclear Information System (INIS)

    Hobby, Jonathan L.; Tom, Brian D.M.; Bearcroft, Philip W.P.; Dixon, Adrian K.

    2001-01-01

    AIM: To review the published diagnostic performance statistics for magnetic resonance imaging (MRI) of the wrist for tears of the triangular fibrocartilage complex, the intrinsic carpal ligaments, and for osteonecrosis of the carpal bones. MATERIALS AND METHODS: We used Medline and Embase to search the English language literature. Studies evaluating the diagnostic performance of MRI of the wrist in living patients with surgical confirmation of MR findings were identified. RESULTS: We identified 11 studies reporting the diagnostic performance of MRI for tears of the triangular fibrocartilage complex for a total of 410 patients, six studies for the scapho-lunate ligament (159 patients), six studies for the luno-triquetral ligament (142 patients) and four studies (56 patients) for osteonecrosis of the carpal bones. CONCLUSIONS: Magnetic resonance imaging is an accurate means of diagnosing tears of the triangular fibrocartilage and carpal osteonecrosis. Although MRI is highly specific for tears of the intrinsic carpal ligaments, its sensitivity is low. The diagnostic performance of MRI in the wrist is improved by using high-resolution T2* weighted 3D gradient echo sequences. Using current imaging techniques without intra-articular contrast medium, magnetic resonance imaging cannot reliably exclude tears of the intrinsic carpal ligaments. Hobby, J.L. (2001)

  6. Multiple-state Feshbach resonances mediated by high-order couplings

    International Nuclear Information System (INIS)

    Hemming, Christopher J.; Krems, Roman V.

    2008-01-01

    We present a study of multistate Feshbach resonances mediated by high-order couplings. Our analysis focuses on a system with one open scattering state and multiple bound states. The scattering state is coupled to one off-resonant bound state and multiple Feshbach resonances are induced by a sequence of indirect couplings between the closed channels. We derive a general recursive expression that can be used to fit the experimental data on multistate Feshbach resonances involving one continuum state and several bound states and present numerical solutions for several model systems. Our results elucidate general features of multistate Feshbach resonances induced by high-order couplings and suggest mechanisms for controlling collisions of ultracold atoms and molecules with external fields

  7. Variability in prostate and seminal vesicle delineations defined on magnetic resonance images, a multi-observer, -center and -sequence study

    DEFF Research Database (Denmark)

    Nyholm, Tufve; Jonsson, Joakim; Söderström, Karin

    2013-01-01

    and approximately equal for the prostate and seminal vesicles. Large differences in variability were observed for individual patients, and also for individual imaging sequences used at the different centers. There was however no indication of decreased variability with higher field strength. CONCLUSION: The overall......BACKGROUND: The use of magnetic resonance (MR) imaging as a part of preparation for radiotherapy is increasing. For delineation of the prostate several publications have shown decreased delineation variability using MR compared to computed tomography (CT). The purpose of the present work....... Two physicians from each center delineated the prostate and the seminal vesicles on each of the 25 image sets. The variability between the delineations was analyzed with respect to overall, intra- and inter-physician variability, and dependence between variability and origin of the MR images, i...

  8. Feasibility of real-time magnetic resonance imaging-guided endomyocardial biopsies: An in-vitro study.

    Science.gov (United States)

    Lossnitzer, Dirk; Seitz, Sebastian A; Krautz, Birgit; Schnackenburg, Bernhard; André, Florian; Korosoglou, Grigorios; Katus, Hugo A; Steen, Henning

    2015-07-26

    To investigate if magnetic resonance (MR)-guided biopsy can improve the performance and safety of such procedures. A novel MR-compatible bioptome was evaluated in a series of in-vitro experiments in a 1.5T magnetic resonance imaging (MRI) system. The bioptome was inserted into explanted porcine and bovine hearts under real-time MR-guidance employing a steady state free precession sequence. The artifact produced by the metal element at the tip and the signal voids caused by the bioptome were visually tracked for navigation and allowed its constant and precise localization. Cardiac structural elements and the target regions for the biopsy were clearly visible. Our method allowed a significantly better spatial visualization of the bioptoms tip compared to conventional X-ray guidance. The specific device design of the bioptome avoided inducible currents and therefore subsequent heating. The novel MR-compatible bioptome provided a superior cardiovascular magnetic resonance (imaging) soft-tissue visualization for MR-guided myocardial biopsies. Not at least the use of MRI guidance for endomyocardial biopsies completely avoided radiation exposure for both patients and interventionalists. MRI-guided endomyocardial biopsies provide a better than conventional X-ray guided navigation and could therefore improve the specificity and reproducibility of cardiac biopsies in future studies.

  9. Hemorrhage associated with 'bone crisis' in Gaucher's disease identified by magnetic resonance imaging

    International Nuclear Information System (INIS)

    Horev, G.; Kornreich, L.; Hadar, H.; Katz, K.

    1991-01-01

    Children suffering from Gaucher's disease were examined by magnetic resonance imaging (MRI) during a characteristic episode of 'bone crisis'. An unexpectedly high intramedullary as well as subperiosteal signal was observed on both the T1- and T2-weighted sequences in 5 patients, suggesting a subacute hemorrhage or hematoma. It is conceivable that such a painful hemorrhage is an important component of the 'bone crisis' phenomenon. Furthermore, in these cases this is a specific sign which may enable differentiation of bone crises from other types of bone pain associated with Gaucher's disease. (orig.)

  10. Assessment of magnetic resonance imaging of the breast using 0.5 T equipment

    International Nuclear Information System (INIS)

    Vilanova, J. C.; Barcelo, J.; Ferrer, J.; Castaner, F.; Miro, J.; Bassaganyas, R.; Viejo, N.; Albanell, J.; Villalon, M.

    2002-01-01

    To evaluate the efficacy of a magnetic resonance imaging technique of the breast using half-field equipment (0.5 T). We evaluated 191 magnetic resonance (MRI) studies made at our center from March 1998 to March 2001 using Signa Contour 0.5 T MRI equipment of General Electric. A dedicated bilateral breast made at fat saturation in the coronal plane before administering intravenous gadolinium, then 6 consecutive times after contrast administration. The sequence acquisition time was 70-90 seconds Image post processing included subtraction and analysis of the intensity/time curves in the region of interest (ROI) together with morphological evaluation of the lesion. Additional T2 weighted fast-spin-echo sequences (FSE T2), T1-weighted spin-echo (SE T1), FSE T2 with fat suppression, and STIR with water saturation were made for studies of breast implants. The clinical indications for MRI study of the breast were masses (n=79), microcalcifications (n=7), asymmetry (n=17), cases of indeterminate risk (n=7), postoperative control (n=51), and breast implants (n=25). The histological diagnosis was benign in 31 lesions and malignant in 73 lesions. The sensitivity specificity, and reliability of breast MRI were 93%, 81% and 89% respectively. Multicenter/multifocal neoplasms were found in 8% of patients and bilateral neoplasms in 2%. The therapeutic attitude was modified in 18% of the patients with breast cancer as a result of MRI findings. The results confirm the usefulness of MRI in the management of patients with breast cancer. Likewise, the present study demonstrated that breast MRI can be carried out with half-field equipment with the same reliability as with full-field equipment as long as specific breast cots are used rapid 3D sequences, and image processing with suitable software. (Author) 28 refs

  11. Adaptation of Organisms by Resonance of RNA Transcription with the Cellular Redox Cycle

    Science.gov (United States)

    Stolc, Viktor

    2012-01-01

    Sequence variation in organisms differs across the genome and the majority of mutations are caused by oxidation, yet its origin is not fully understood. It has also been shown that the reduction-oxidation reaction cycle is the fundamental biochemical cycle that coordinates the timing of all biochemical processes in that cell, including energy production, DNA replication, and RNA transcription. It is shown that the temporal resonance of transcriptome biosynthesis with the oscillating binary state of the reduction-oxidation reaction cycle serves as a basis for non-random sequence variation at specific genome-wide coordinates that change faster than by accumulation of chance mutations. This work demonstrates evidence for a universal, persistent and iterative feedback mechanism between the environment and heredity, whereby acquired variation between cell divisions can outweigh inherited variation.

  12. Comparison of different magnetic resonance cholangiography techniques in living liver donors including Gd-EOB-DTPA enhanced T1-weighted sequences.

    Directory of Open Access Journals (Sweden)

    Sonja Kinner

    Full Text Available Preoperative evaluation of potential living liver donors (PLLDs includes the assessment of the biliary anatomy to avoid postoperative complications. Aim of this study was to compare T2-weighted (T2w and Gd-EOB-DTPA enhanced T1-weighted (T1w magnetic resonance cholangiography (MRC techniques in the evaluation of PLLDs.30 PLLDs underwent MRC on a 1.5 T Magnetom Avanto (Siemens, Erlangen, Germany using (A 2D T2w HASTE (Half Fourier Acquisition Single Shot Turbo Spin Echo fat saturated (fs in axial plane, (B 2D T2w HASTE fs thick slices in coronal plane, (C free breathing 3D T2w TSE (turbo spin echo RESTORE (high-resolution navigator corrected plus (D maximum intensity projections (MIPs, (E T2w SPACE (sampling perfection with application optimized contrasts using different flip angle evolutions plus (F MIPs and (G T2w TSE BLADE as well as Gd-EOB-DTPA T1w images without (G and with (H inversion recovery. Contrast enhanced CT cholangiography served as reference imaging modality. Two independent reviewers evaluated the biliary tract anatomy on a 5-point scale subjectively and objectively. Data sets were compared using a Mann-Whitney-U-test. Kappa values were also calculated.Source images and maximum intensity projections of 3D T2w TSE sequences (RESTORE and SPACE proved to be best for subjective and objective evaluation directly followed by 2D HASTE sequences. Interobserver variabilities were good to excellent (k = 0.622-0.804.3D T2w sequences are essential for preoperative biliary tract evaluation in potential living liver donors. Furthermore, our results underline the value of different MRCP sequence types for the evaluation of the biliary anatomy in PLLDs including Gd-EOB-DTPA enhanced T1w MRC.

  13. Integration of hepatitis B virus DNA in chromosome-specific satellite sequences

    International Nuclear Information System (INIS)

    Shaul, Y.; Garcia, P.D.; Schonberg, S.; Rutter, W.J.

    1986-01-01

    The authors previously reported the cloning and detailed analysis of the integrated hepatitis B virus sequences in a human hepatoma cell line. They report here the integration of at least one of hepatitis B virus at human satellite DNA sequences. The majority of the cellular sequences identified by this satellite were organized as a multimeric composition of a 0.6-kilobase EcoRI fragment. This clone hybridized in situ almost exclusively to the centromeric heterochromatin of chromosomes 1 and 16 and to a lower extent to chromosome 2 and to the heterochromatic region of the Y chromosome. The immediate flanking host sequence appeared as a hierarchy of repeating units which were almost identical to a previously reported human satellite III DNA sequence

  14. The monoclonal S9.6 antibody exhibits highly variable binding affinities towards different R-loop sequences.

    Directory of Open Access Journals (Sweden)

    Fabian König

    Full Text Available The monoclonal antibody S9.6 is a widely-used tool to purify, analyse and quantify R-loop structures in cells. A previous study using the surface plasmon resonance technology and a single-chain variable fragment (scFv of S9.6 showed high affinity (0.6 nM for DNA-RNA and also a high affinity (2.7 nM for RNA-RNA hybrids. We used the microscale thermophoresis method allowing surface independent interaction studies and electromobility shift assays to evaluate additional RNA-DNA hybrid sequences and to quantify the binding affinities of the S9.6 antibody with respect to distinct sequences and their GC-content. Our results confirm high affinity binding to previously analysed sequences, but reveals that binding affinities are highly sequence specific. Our study presents R-loop sequences that independent of GC-content and in different sequence variations exhibit either no binding, binding affinities in the micromolar range and as well high affinity binding in the nanomolar range. Our study questions the usefulness of the S9.6 antibody in the quantitative analysis of R-loop sequences in vivo.

  15. Thermodynamic Molecular Switch in Sequence-Specific Hydrophobic Interaction: Two Computational Models Compared

    Directory of Open Access Journals (Sweden)

    Paul Chun

    2003-01-01

    Full Text Available We have shown in our published work the existence of a thermodynamic switch in biological systems wherein a change of sign in ΔCp°(Treaction leads to a true negative minimum in the Gibbs free energy change of reaction, and hence, a maximum in the related Keq. We have examined 35 pair-wise, sequence-specific hydrophobic interactions over the temperature range of 273–333 K, based on data reported by Nemethy and Scheraga in 1962. A closer look at a single example, the pair-wise hydrophobic interaction of leucine-isoleucine, will demonstrate the significant differences when the data are analyzed using the Nemethy-Scheraga model or treated by the Planck-Benzinger methodology which we have developed. The change in inherent chemical bond energy at 0 K, ΔH°(T0 is 7.53 kcal mol-1 compared with 2.4 kcal mol-1, while ‹ts› is 365 K as compared with 355 K, for the Nemethy-Scheraga and Planck-Benzinger model, respectively. At ‹tm›, the thermal agitation energy is about five times greater than ΔH°(T0 in the Planck-Benzinger model, that is 465 K compared to 497 K in the Nemethy-Scheraga model. The results imply that the negative Gibbs free energy minimum at a well-defined ‹ts›, where TΔS° = 0 at about 355 K, has its origin in the sequence-specific hydrophobic interactions, which are highly dependent on details of molecular structure. The Nemethy-Scheraga model shows no evidence of the thermodynamic molecular switch that we have found to be a universal feature of biological interactions. The Planck-Benzinger method is the best known for evaluating the innate temperature-invariant enthalpy, ΔH°(T0, and provides for better understanding of the heat of reaction for biological molecules.

  16. Role of diffusion-weighted magnetic resonance imaging in the diagnosis of extrahepatic cholangiocarcinoma

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    AIM: To determine the clinical value of diffusion-weight- ed imaging (DWI) for the diagnosis of extrahepatic cholangiocarcinoma (EHCC) by comparing the diagnostic sensitivity of DWI and magnetic resonance cholan-giopancreatography (MRCP). METHODS: Magnetic resonance imaging examination was performed in 56 patients with suspected EHCC. T1- weighted imaging, T2-weighted imaging, MRCP and DWI sequence, DWI using single-shot spin-echo echoplanar imaging sequence with different b values (100, 300, 500, 800 and 1...

  17. MR pulse sequences for selective relaxation time measurements: a phantom study

    DEFF Research Database (Denmark)

    Thomsen, C; Jensen, K E; Jensen, M

    1990-01-01

    a Siemens Magnetom wholebody magnetic resonance scanner operating at 1.5 Tesla was used. For comparison six imaging pulse sequences for relaxation time measurements were tested on the same phantom. The spectroscopic pulse sequences all had an accuracy better than 10% of the reference values....

  18. Machine-Specific Magnetic Resonance Imaging Quality Control Procedures for Stereotactic Radiosurgery Treatment Planning.

    Science.gov (United States)

    Fatemi, Ali; Taghizadeh, Somayeh; Yang, Claus Chunli; R Kanakamedala, Madhava; Morris, Bart; Vijayakumar, Srinivasan

    2017-12-18

    Purpose Magnetic resonance (MR) images are necessary for accurate contouring of intracranial targets, determination of gross target volume and evaluation of organs at risk during stereotactic radiosurgery (SRS) treatment planning procedures. Many centers use magnetic resonance imaging (MRI) simulators or regular diagnostic MRI machines for SRS treatment planning; while both types of machine require two stages of quality control (QC), both machine- and patient-specific, before use for SRS, no accepted guidelines for such QC currently exist. This article describes appropriate machine-specific QC procedures for SRS applications. Methods and materials We describe the adaptation of American College of Radiology (ACR)-recommended QC tests using an ACR MRI phantom for SRS treatment planning. In addition, commercial Quasar MRID 3D and Quasar GRID 3D phantoms were used to evaluate the effects of static magnetic field (B 0 ) inhomogeneity, gradient nonlinearity, and a Leksell G frame (SRS frame) and its accessories on geometrical distortion in MR images. Results QC procedures found in-plane distortions (Maximum = 3.5 mm, Mean = 0.91 mm, Standard deviation = 0.67 mm, >2.5 mm (%) = 2) in X-direction (Maximum = 2.51 mm, Mean = 0.52 mm, Standard deviation = 0.39 mm, > 2.5 mm (%) = 0) and in Y-direction (Maximum = 13. 1 mm , Mean = 2.38 mm, Standard deviation = 2.45 mm, > 2.5 mm (%) = 34) in Z-direction and < 1 mm distortion at a head-sized region of interest. MR images acquired using a Leksell G frame and localization devices showed a mean absolute deviation of 2.3 mm from isocenter. The results of modified ACR tests were all within recommended limits, and baseline measurements have been defined for regular weekly QC tests. Conclusions With appropriate QC procedures in place, it is possible to routinely obtain clinically useful MR images suitable for SRS treatment planning purposes. MRI examination for SRS planning can benefit from the improved localization and planning

  19. Endometrial carcinoma: merit of magnetic resonance in pre-surgical staging

    International Nuclear Information System (INIS)

    Fernandez, E.; Barrera, M. C.; Gervas, C.; Salvador, E.; Rivero, B.; Sentis, M.

    2003-01-01

    To evaluate MR capacity in assessing deep myometrial and cervical infiltrations in cases of endometrial carcinoma. A series of 30 consecutively diagnosed endometrial cancer patients was pre-surgically evaluated by means of magnetic resonance (MR). TSE-T2 sequences with fat saturation and dynamic FFe sequence were used after gadolinium administration. A correlation with post-surgical histological stating was made. There were then determined sensitivity (S), specificity (SP), positive predictive value (PPV) and negative predictive value (NPV) for the deep myometrial infiltration and cervical invasion. Cases of overestimation and underestimation were analyzed. Values obtained for myometrium and cervix were, respectively, S of 67% and 63%, SP of 89% and 91%, PPV of 80% and 71% and NPV of 80% and 87%. Two cases each were over valued for myometrial infiltration and cervix: four cases and 3 cases, respectively, were undervalues. MR stating in cases of endometrial carcinoma is a highly reliable diagnostic technique, but it does present certain limitations. (Author) 19 refs

  20. 1H and 15N resonance assignments of oxidized flavodoxin from Anacystis nidulans with 3D NMR

    International Nuclear Information System (INIS)

    Clubb, R.T.; Thanabal, V.; Wagner, G.; Osborne, C.

    1991-01-01

    Proton and nitrogen-15 sequence-specific nuclear magnetic resonance assignments have been determined for recombinant oxidized flavodoxin from Anacystis nidulans. Assignments were obtained by using 15 N- 1 H heteronuclear three-dimensional (3D) NMR spectroscopy on a uniformly nitrogen-15 enriched sample of the protein, pH 6.6, at 30C. For 165 residues, the backbone and a large fraction of the side-chain proton resonances have been assigned. Medium- and long-range NOE's have been used to characterize the secondary structure. In solution, flavodoxin consists of a five-stranded parallel β sheet involving residues 3-9, 31-37, 49-56, 81-89, 114-117, and 141-144. Medium-range NOE's indicate that presence of several helices. Several 15 N and 1 H resonances of the flavin mononucleotide (FMN) prosthetic group have been assigned. The FMN-binding site has been investigated by using polypeptide-FMN NOE's

  1. DNA minor groove electrostatic potential: influence of sequence-specific transitions of the torsion angle gamma and deoxyribose conformations.

    Science.gov (United States)

    Zhitnikova, M Y; Shestopalova, A V

    2017-11-01

    The structural adjustments of the sugar-phosphate DNA backbone (switching of the γ angle (O5'-C5'-C4'-C3') from canonical to alternative conformations and/or C2'-endo → C3'-endo transition of deoxyribose) lead to the sequence-specific changes in accessible surface area of both polar and non-polar atoms of the grooves and the polar/hydrophobic profile of the latter ones. The distribution of the minor groove electrostatic potential is likely to be changing as a result of such conformational rearrangements in sugar-phosphate DNA backbone. Our analysis of the crystal structures of the short free DNA fragments and calculation of their electrostatic potentials allowed us to determine: (1) the number of classical and alternative γ angle conformations in the free B-DNA; (2) changes in the minor groove electrostatic potential, depending on the conformation of the sugar-phosphate DNA backbone; (3) the effect of the DNA sequence on the minor groove electrostatic potential. We have demonstrated that the structural adjustments of the DNA double helix (the conformations of the sugar-phosphate backbone and the minor groove dimensions) induce changes in the distribution of the minor groove electrostatic potential and are sequence-specific. Therefore, these features of the minor groove sizes and distribution of minor groove electrostatic potential can be used as a signal for recognition of the target DNA sequence by protein in the implementation of the indirect readout mechanism.

  2. Advances and applications of dynamic-angle spinning nuclear magnetic resonance

    International Nuclear Information System (INIS)

    Baltisberger, J.H.

    1993-06-01

    This dissertation describes nuclear magnetic resonance experiments and theory which have been developed to study quadrupolar nuclei (those nuclei with spin greater than one-half) in the solid state. Primarily, the technique of dynamic-angle spinning (DAS) is extensively reviewed and expanded upon in this thesis. Specifically, the improvement in both the resolution (two-dimensional pure-absorptive phase methods and DAS angle choice) and sensitivity (pulse-sequence development), along with effective spinning speed enhancement (again through choice of DAS conditions or alternative multiple pulse schemes) of dynamic-angle spinning experiment was realized with both theory and experimental examples. The application of DAS to new types of nuclei (specifically the 87 Rb and 85 Rb nuclear spins) and materials (specifically amorphous solids) has also greatly expanded the possibilities of the use of DAS to study a larger range of materials. This dissertation is meant to demonstrate both recent advances and applications of the DAS technique, and by no means represents a comprehensive study of any particular chemical problem

  3. Radiofrequency power deposition during magnetic resonance diagnostic examinations

    International Nuclear Information System (INIS)

    Grandolfo, M.; Vecchia, P.

    1988-01-01

    Magnetic Resonance Imaging and Spectroscopy (MRI, MRS) require that subjects be exposed to radiofrequency field, and the corresponding energy absorption leads to tissue heating. The main question, thus, to be considered in connection to safety and health aspects is related to the specific absorption rate (SAR) in the imaged subject and the exposure durations which might put a practical limit on the pulse sequence which can be used. In this paper some models and experimental results for radiofrequency power deposition in MRI and MRS machines are reviewed. Models show that energy dissipation is a function of the frequency, RF incident power density, exposure duration, coupling between the RF coil and the subject, and several properties of the exposed tissue, including conductivity, dielectric constant, specific gravity, size, and orientation relative to the field polarization. The ability of the body's normal thermoregulatory responses to cope with high levels of RF energy deposition must be also taken into account

  4. The role of MR imaging with Half Fourier Acquired Single Shot Turbo Spin Echo sequence in the diagnosis of lung lesions in comparison with multislice CT

    International Nuclear Information System (INIS)

    Hekimoglu, B.; Gurgen, F.; Tatar, I.G.; Aydin, H.; Kizilgoz, V.; Keyik, B.

    2013-01-01

    Objective: To compare the diagnostic values of magnetic resonance imaging using Half Fourier Acquired Single Shot Turbo Spin Echo sequence and multidetector computed tomography in patients with pathologically examined pulmonary lesions. Methods: The retrospective, descriptive study was conducted at Radiology Department, Diskapi Research Hospital, Ankara, Turkey, and comprised records of patients with pathologically examined pulmonary lesions between May 2009 and March 2012. Patients were divided into three groups and examined by both multi dedector computed tomography and magnetic resonance imaging. During the imaging, patients were not administered any intravenous contrast medium. Electrocardiogram gating and breath holding were not performed in echo sequence. Pulmonary lesions were evaluated on the basis of their dimensions, numbers, differentiation from atelectasis and consolidation, invasion to the thoracic wall-mediastinal structures and presence of lymphadenopathies. Results: Sensitivity of all patients was 50% (p=0.214) and specificity of CT and MRI were 82.5% (p=0.134) for the detectability of submilimetric nodules . For differentiation of the mass from atelectasis and consolidation, the sensitivity of computed tomography was statistically more significant compared to magnetic resonance imaging (86.6%; p=0.035). For the invasion of the mass to the mediastinal structures and the thoracic wall, the sensitivity of magnetic resonance imaging was statistically more significant compared to tomography (86.6%; p=0.035). Conclusion: HASTE sequence can be used to determine the invasion of the pulmonary mass to the mediastinal structures and the thoracic wall since it is more sensitive than computed tomography. It can also be used to detect submilimetric nodules. It has equal sensitivity and specificity compared to computed tomography. But computed tomography is superior for the differentiation of the mass from atelectasis and consolidation. (author)

  5. Direct magnetic resonance arthrography of the canine elbow

    Directory of Open Access Journals (Sweden)

    Yauheni Zhalniarovich

    2017-01-01

    Full Text Available This study compares the effects of four dilutions of the gadolinium-containing contrast media (1:100; 1:400; 1:800; 1:1,200 administered to the elbow on the quality of magnetic resonance images. All the examined dilutions had a positive effect on image quality, and 1:800 was regarded as the optimal dilution of gadolinium for viewing the elbow because it imparted good contrast to the joint cavity without obliterating the contours of articular surfaces. Transverse, sagittal, and dorsal low-field magnetic resonance images were obtained in 24 canine cadaver front limbs. The musculus biceps brachii, m. triceps brachii, m. extensor carpi radialis, m. flexor carpi ulnaris, the articular surfaces, the medial coronoid process and the anconeal process of the ulna were well visualized by High Resolution Gradient Echo, XBONE T2 and Spin Echo T1 sequences in the sagittal plane. The biceps brachii, pronator teres, flexor carpi radialis, extensor digitorum communis, extensor carpi radialis, deltoid muscle and the articular surface of the medial condyle of the humerus were very well visualized by 3D SST1 and XBONE T2 sequences in the transverse plane. The triceps brachii muscle, extensor digitorum lateralis muscle, superficial digital flexor, deep digital flexor and the medial condyle of the humerus were very well visualized by the Spin Echo T1 sequence in the dorsal plane. This article describes for the first time the use of the gadolinium contrast agent administered to the canine elbow joint during magnetic resonance modality. Magnetic resonance arthrography can be a helpful visualization technique in treating canine soft tissue elbow injury.

  6. Thermodynamics of sequence-specific binding of PNA to DNA

    DEFF Research Database (Denmark)

    Ratilainen, T; Holmén, A; Tuite, E

    2000-01-01

    For further characterization of the hybridization properties of peptide nucleic acids (PNAs), the thermodynamics of hybridization of mixed sequence PNA-DNA duplexes have been studied. We have characterized the binding of PNA to DNA in terms of binding affinity (perfectly matched duplexes) and seq......For further characterization of the hybridization properties of peptide nucleic acids (PNAs), the thermodynamics of hybridization of mixed sequence PNA-DNA duplexes have been studied. We have characterized the binding of PNA to DNA in terms of binding affinity (perfectly matched duplexes...

  7. Los resonance lines in promethiumlike heavy ions

    International Nuclear Information System (INIS)

    Nakamura, Nobuyuki; Kobayashi, Yusuke; Kato, Daiji; Sakaue, Hiroyuki A.; Murakami, Izumi

    2016-01-01

    Identifying the ns - np resonance lines in alkali-metal-like ions is an important issue in fusion plasma science in the view of spectroscopic diagnostics and radiation power loss. Whereas for n=2, 3 and 4 these resonances are prominent and well studied, so far no one could clearly identify the resonance lines for n=5 in the promethiumlike sequence. We have now experimentally clarified the reason for the 'lost resonance lines. In the present study, highly-charged bismuth ions have been studied using a compact electron beam ion trap (EBIT). Extreme ultraviolet emission from the bismuth ions produced and trapped in the EBIT is observed with a grazing-incidence flat-field spectrometer. The energy dependent spectra are compared with a collisional-radiative model calculation, and we show that the 5s - 5p resonance lines are very weak in plasma with a wide range of electron density due to the presence of a long-lived metastable state. (author)

  8. Stating of cervical carcinoma using magnetic resonance imaging

    International Nuclear Information System (INIS)

    Oleaga, L.; Vela, M. C.; Grande, J.; Cura del, J. L.; Grande, D.

    1999-01-01

    The infiltration of the parametrium represents one of the most important factors that determine the prediction and treatment of cervical carcinoma. Our objective is to evaluate the utility of magnetic resonance imaging (MRI) in the staging of cervical carcinomas, to establish the reliability of this technique and to carry out a comparative study of the sequences used to demonstrate the parametrial invasion. We have carried out a retrospective study on 44 patients diagnosed with cervix neoplasia, using clinical exploration and performing a biopsy. the MRI studies have been carried out using a 1 Tesla magnet and the sequences used have been SE T1, Se proton density (PD) and T2 and dynamic GRE after administering gadolinium intravenously in the axial and sagital projections. The stages determined by MRI have been compared to the anatomo-pathological stages of the surgical specimens in cases where surgery was carried out and with the clinical stage in cases where no radical surgery was carried out. A diagnosis value of MRI has been determined to demonstrate the parametrial invasion, comparing the SE T2 sequence with the dynamic GE sequence with gadolinium. We calculate the volume of the tumour in the MRI studies to evaluate the difference of the volume between patients with tumoral stages that are clinically surgical and not surgical. MRI determines the invasion of the parametrium with a sensitivity of 88.8%, a specificity of 80% a positive value of 76.1%, a negative predictive value of 90.9% and a reliability of 83.7%. For the SE T2 sequences the sensitivity was 86.6%, the specifity 80%, the posistive predictive value 81.25%, the negative predictive value 85.7% and the reliability 83.3%. For the dynamic GE sequence with intravenous gadolinium the sensitivity was 86.6%, the specificity 86.6%, the positive predictive value 86.6%, the negative predictive value 86.6% and the reliability 86.6%. The use of the dynamic GE sequence after the intravenous administration of

  9. Preparation of genosensor for detection of specific DNA sequence of the hepatitis B virus

    Science.gov (United States)

    Honorato Castro, Ana C.; França, Erick G.; de Paula, Lucas F.; Soares, Marcia M. C. N.; Goulart, Luiz R.; Madurro, João M.; Brito-Madurro, Ana G.

    2014-09-01

    An electrochemical genosensor was constructed for detection of specific DNA sequence of the hepatitis B virus, based on graphite electrodes modified with poly(4-aminophenol) and incorporating a specific oligonucleotide probe. The modified electrode containing the probe was evaluated by differential pulse voltammetry, before and after incubation with the complementary oligonucleotide target. Detection was performed by monitoring oxidizable DNA bases (direct detection) or using ethidium bromide as indicator of the hybridization process (indirect detection). The device showed a detection limit for the oligonucleotide target of 2.61 nmol L-1. Indirect detection using ethidium bromide was promising in discriminating mismatches, which is a very desirable attribute for detection of disease-related point mutations. In addition, it was possible to observe differences between hybridized and non-hybridized surfaces by atomic force microscopy.

  10. Understanding Magnetic Resonance Imaging of Knee Cartilage Repair: A Focus on Clinical Relevance.

    Science.gov (United States)

    Hayashi, Daichi; Li, Xinning; Murakami, Akira M; Roemer, Frank W; Trattnig, Siegfried; Guermazi, Ali

    2017-06-01

    The aims of this review article are (a) to describe the principles of morphologic and compositional magnetic resonance imaging (MRI) techniques relevant for the imaging of knee cartilage repair surgery and their application to longitudinal studies and (b) to illustrate the clinical relevance of pre- and postsurgical MRI with correlation to intraoperative images. First, MRI sequences that can be applied for imaging of cartilage repair tissue in the knee are described, focusing on comparison of 2D and 3D fast spin echo and gradient recalled echo sequences. Imaging features of cartilage repair tissue are then discussed, including conventional (morphologic) MRI and compositional MRI techniques. More specifically, imaging techniques for specific cartilage repair surgery techniques as described above, as well as MRI-based semiquantitative scoring systems for the knee cartilage repair tissue-MR Observation of Cartilage Repair Tissue and Cartilage Repair OA Knee Score-are explained. Then, currently available surgical techniques are reviewed, including marrow stimulation, osteochondral autograft, osteochondral allograft, particulate cartilage allograft, autologous chondrocyte implantation, and others. Finally, ongoing research efforts and future direction of cartilage repair tissue imaging are discussed.

  11. Mouse tetranectin: cDNA sequence, tissue-specific expression, and chromosomal mapping

    DEFF Research Database (Denmark)

    Ibaraki, K; Kozak, C A; Wewer, U M

    1995-01-01

    regulation, mouse tetranectin cDNA was cloned from a 16-day-old mouse embryo library. Sequence analysis revealed a 992-bp cDNA with an open reading frame of 606 bp, which is identical in length to the human tetranectin cDNA. The deduced amino acid sequence showed high homology to the human cDNA with 76......(s) of tetranectin. The sequence analysis revealed a difference in both sequence and size of the noncoding regions between mouse and human cDNAs. Northern analysis of the various tissues from mouse, rat, and cow showed the major transcript(s) to be approximately 1 kb, which is similar in size to that observed...

  12. Two-dimensional NMR studies of squash family inhibitors. Sequence-specific proton assignments and secondary structure of reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor III.

    Science.gov (United States)

    Krishnamoorthi, R; Gong, Y X; Lin, C L; VanderVelde, D

    1992-01-28

    The solution structure of reactive-site hydrolyzed Cucurbita maxima trypsin inhibitor III (CMTI-III*) was investigated by two-dimensional proton nuclear magnetic resonance (2D NMR) spectroscopy. CMTI-III*, prepared by reacting CMTI-III with trypsin which cleaved the Arg5-Ile6 peptide bond, had the two fragments held together by a disulfide linkage. Sequence-specific 1H NMR resonance assignments were made for all the 29 amino acid residues of the protein. The secondary structure of CMTI-III*, as deduced from NOESY cross peaks and identification of slowly exchanging hydrogens, contains two turns (residues 8-12 and 24-27), a 3(10)-helix (residues 13-16), and a triple-stranded beta-sheet (residues 8-10, 29-27, and 21-25). This secondary structure is similar to that of CMTI-I [Holak, T. A., Gondol, D., Otlewski, J., & Wilusz, T. (1989) J. Mol. Biol. 210, 635-648], which has a Glu instead of a Lys at position 9. Sequential proton assignments were also made for the virgin inhibitor, CMTI-III, at pH 4.71, 30 degrees C. Comparison of backbone hydrogen chemical shifts of CMTI-III and CMTI-III* revealed significant changes for residues located far away from the reactive-site region as well as for those located near it, indicating tertiary structural changes that are transmitted through most of the 29 residues of the inhibitor protein. Many of these residues are functionally important in that they make contact with atoms of the enzyme in the trypsin-inhibitor complex, as revealed by X-ray crystallography [Bode, W., Greyling, H. J., Huber, R., Otlewski, J., & Wilusz, T. (1989) FEBS Lett. 242, 285-292].(ABSTRACT TRUNCATED AT 250 WORDS)

  13. A Compressed Sensing Framework for Magnetic Resonance Fingerprinting

    OpenAIRE

    Davies, Mike; Puy, Gilles; Vandergheynst, Pierre; Wiaux, Yves

    2013-01-01

    Inspired by the recently proposed Magnetic Resonance Fingerprinting (MRF) technique, we develop a principled compressed sensing framework for quantitative MRI. The three key components are: a random pulse excitation sequence following the MRF technique; a random EPI subsampling strategy and an iterative projection algorithm that imposes consistency with the Bloch equations. We show that theoretically, as long as the excitation sequence possesses an appropriate form of persistent excitation, w...

  14. Localized surface plasmon resonance (LSPR) study of DNA hybridization at single nanoparticle transducers

    International Nuclear Information System (INIS)

    Schneider, T.; Jahr, N.; Jatschka, J.; Csaki, A.; Stranik, O.; Fritzsche, W.

    2013-01-01

    The effect of DNA–DNA interaction on the localized surface plasmon resonance of single 80 nm gold nanoparticles is studied. Therefore, both the attachment of the capture DNA strands at the particle surface and the sequence-specific DNA binding (hybridization) of analyte DNA to the immobilized capture DNA is subject of investigations. The influence of substrate attachment chemistry, the packing density of DNA as controlled by an assisting layer of smaller molecules, and the distance as increased by a linker on the LSPR efficiency is investigated. The resulting changes in signal can be related to a higher hybridization efficiency of the analyte DNA to the immobilized capture DNA. The subsequent attachment of additional DNA strands to this system is studied, which allows for a multiple step detection of binding and an elucidation of the resulting resonance shifts. The detection limit was determined for the utilized DNA system by incubation with various concentration of analyte DNA. Although the method allows for a marker-free detection, we show that additional markers such as 20 nm gold particle labels increase the signal and thereby the sensitivity significantly. The study of resonance shift for various DNA lengths revealed that the resonance shift per base is stronger for shorter DNA molecules (20 bases) as compared to longer ones (46 bases).

  15. The use of diffusion-weighted magnetic resonance imaging in the differentiation between benign and malignant breast lesions

    Energy Technology Data Exchange (ETDEWEB)

    Pereira, Fernanda Philadelpho Arantes; Martins, Gabriela; Domingues, Marisa Nassar Aidar; Domingues, Romeu Cortes [Clinica de Diagnostico por Imagem (CDPI), Rio de Janeiro, RJ (Brazil)], e-mail: fephila@gmail.com; Figueiredo, Eduardo [GE Healthcare, Sao Paulo, SP (Brazil); Fonseca, Lea Mirian Barbosa da [Universidade Federal do Rio de Janeiro (UFRJ), RJ (Brazil). Faculdade de Medicina

    2009-09-15

    Objective: to study the utility of diffusion-weighted magnetic resonance imaging in the differentiation between benign and malignant breast lesions. Materials and methods: forty-five women (mean age, 46.1 years) with 52 focal breast lesions underwent diffusion-weighted magnetic resonance imaging. The calculation of apparent diffusion coefficient (ADC) was based on the ADC map reflecting five b values (0, 250, 500, 750, and 1000 s/mm{sup 2}). The mean ADC value of each lesion was correlated with imaging findings and histopathologic results. Cutoff ADC, sensitivity and specificity of diffusion-weighted imaging in the differentiation between benign and malignant lesions were calculated. P < 0.05 was considered as statistically significant. Results: the mean ADC was significantly lower for malignant lesions (0.92 {+-} 0.26 x 10{sup -3} mm{sup 2}/s) as compared with benign lesions (1.50 {+-} 0.34 x 10{sup -3} mm{sup 2}/s) (P < 0.0001). Diffusion-weighted imaging showed high sensitivity and specificity (both, 92.3%) in the differentiation between benign and malignant lesions. Conclusion: diffusion-weighted imaging is a potential resource as an adjuvant to breast magnetic resonance imaging to differentiate benign from malignant lesions. Such sequence can be easily added to the standard breast magnetic resonance imaging protocol, without implying any significant increase in examination time. (author)

  16. Optic Tract Edema: A Highly Specific Magnetic Resonance Imaging Finding for the Diagnosis of Craniopharyngiomas

    International Nuclear Information System (INIS)

    Hirunpat, S.; Tanomkiat, W.; Sriprung, H.; Chetpaophan, J.

    2005-01-01

    Purpose: To clarify the accuracy, sensitivity, and specificity of optic tract edema in the diagnosis of craniopharyngiomas. Material and Methods: Preoperative magnetic resonance images (MRIs) of 49 patients (between May 1996 and March 2003) who had a diagnosis of parasellar masses were blindly reviewed by two radiologists. The spread of edema surrounding the tumor on the coronal TSE T2-weighted images was analyzed. Sensitivity and specificity were calculated based on the numbers in this series and also pooled numbers from previous known reported series. Results: Edema along the optic tracts was detected in 7 of 1 craniopharyngiomas, giving a sensitivity of 63.6% (95% CI≅30.8-89.1) for our series and 66.7% (95% CI≅47.2-82.7) for the pooled numbers. The specificity was 00% (95% CI≅90.7-100.0) for our series and 93.9% (95% CI≅87.1-97.7) for the pooled numbers. None of the 28 pituitary macroadenomas, 4 meningiomas, 2 hypothalamic astrocytomas, 2 germinomas, mixed-germ cell tumor and arachnoid cyst in our study showed edema of the optic pathways. Conclusion: Optic tract edema, commonly seen in craniopharyngiomas, is a useful MR finding for distinguishing craniopharyngiomas from other parasellar tumors with considerable sensitivity and high specificity

  17. Optic Tract Edema: A Highly Specific Magnetic Resonance Imaging Finding for the Diagnosis of Craniopharyngiomas

    Energy Technology Data Exchange (ETDEWEB)

    Hirunpat, S.; Tanomkiat, W.; Sriprung, H.; Chetpaophan, J. [Prince of Songkla Univ., Hat Yai (Thailand). Dept. of Radiology and Epidemiology Unit

    2005-07-01

    Purpose: To clarify the accuracy, sensitivity, and specificity of optic tract edema in the diagnosis of craniopharyngiomas. Material and Methods: Preoperative magnetic resonance images (MRIs) of 49 patients (between May 1996 and March 2003) who had a diagnosis of parasellar masses were blindly reviewed by two radiologists. The spread of edema surrounding the tumor on the coronal TSE T2-weighted images was analyzed. Sensitivity and specificity were calculated based on the numbers in this series and also pooled numbers from previous known reported series. Results: Edema along the optic tracts was detected in 7 of 1 craniopharyngiomas, giving a sensitivity of 63.6% (95% CI{approx_equal}30.8-89.1) for our series and 66.7% (95% CI{approx_equal}47.2-82.7) for the pooled numbers. The specificity was 00% (95% CI{approx_equal}90.7-100.0) for our series and 93.9% (95% CI{approx_equal}87.1-97.7) for the pooled numbers. None of the 28 pituitary macroadenomas, 4 meningiomas, 2 hypothalamic astrocytomas, 2 germinomas, mixed-germ cell tumor and arachnoid cyst in our study showed edema of the optic pathways. Conclusion: Optic tract edema, commonly seen in craniopharyngiomas, is a useful MR finding for distinguishing craniopharyngiomas from other parasellar tumors with considerable sensitivity and high specificity.

  18. Preparation of genosensor for detection of specific DNA sequence of the hepatitis B virus

    International Nuclear Information System (INIS)

    Honorato Castro, Ana C.; França, Erick G.; Paula, Lucas F. de; Soares, Marcia M.C.N.; Goulart, Luiz R.; Madurro, João M.; Brito-Madurro, Ana G.

    2014-01-01

    Graphical abstract: - Highlights: • Specific oligonucleotide detection for hepatitis B based on poly-4-aminophenol matrix. • Electrochemical detection of the gene specific using ethidium bromide as indicator. • The detection limit was 2.61 nmol L −1 , with a correlation coefficient of 0.998 (n = 3). • The system discriminates three-base mismatches and non-complementary target. - Abstract: An electrochemical genosensor was constructed for detection of specific DNA sequence of the hepatitis B virus, based on graphite electrodes modified with poly(4-aminophenol) and incorporating a specific oligonucleotide probe. The modified electrode containing the probe was evaluated by differential pulse voltammetry, before and after incubation with the complementary oligonucleotide target. Detection was performed by monitoring oxidizable DNA bases (direct detection) or using ethidium bromide as indicator of the hybridization process (indirect detection). The device showed a detection limit for the oligonucleotide target of 2.61 nmol L −1 . Indirect detection using ethidium bromide was promising in discriminating mismatches, which is a very desirable attribute for detection of disease-related point mutations. In addition, it was possible to observe differences between hybridized and non-hybridized surfaces by atomic force microscopy

  19. Preparation of genosensor for detection of specific DNA sequence of the hepatitis B virus

    Energy Technology Data Exchange (ETDEWEB)

    Honorato Castro, Ana C.; França, Erick G. [Institute of Genetics and Biochemistry, Federal University of Uberlândia, Uberlândia (Brazil); Paula, Lucas F. de [Institute of Chemistry, Federal University of Uberlândia, Uberlândia (Brazil); Soares, Marcia M.C.N. [Adolfo Lutz Institute, Regional Laboratory in São José do Rio Preto (Brazil); Goulart, Luiz R. [Institute of Genetics and Biochemistry, Federal University of Uberlândia, Uberlândia (Brazil); Madurro, João M. [Institute of Chemistry, Federal University of Uberlândia, Uberlândia (Brazil); Brito-Madurro, Ana G., E-mail: agbrito@iqufu.ufu.br [Institute of Genetics and Biochemistry, Federal University of Uberlândia, Uberlândia (Brazil)

    2014-09-30

    Graphical abstract: - Highlights: • Specific oligonucleotide detection for hepatitis B based on poly-4-aminophenol matrix. • Electrochemical detection of the gene specific using ethidium bromide as indicator. • The detection limit was 2.61 nmol L{sup −1}, with a correlation coefficient of 0.998 (n = 3). • The system discriminates three-base mismatches and non-complementary target. - Abstract: An electrochemical genosensor was constructed for detection of specific DNA sequence of the hepatitis B virus, based on graphite electrodes modified with poly(4-aminophenol) and incorporating a specific oligonucleotide probe. The modified electrode containing the probe was evaluated by differential pulse voltammetry, before and after incubation with the complementary oligonucleotide target. Detection was performed by monitoring oxidizable DNA bases (direct detection) or using ethidium bromide as indicator of the hybridization process (indirect detection). The device showed a detection limit for the oligonucleotide target of 2.61 nmol L{sup −1}. Indirect detection using ethidium bromide was promising in discriminating mismatches, which is a very desirable attribute for detection of disease-related point mutations. In addition, it was possible to observe differences between hybridized and non-hybridized surfaces by atomic force microscopy.

  20. Sequence-specific capture of protein-DNA complexes for mass spectrometric protein identification.

    Directory of Open Access Journals (Sweden)

    Cheng-Hsien Wu

    Full Text Available The regulation of gene transcription is fundamental to the existence of complex multicellular organisms such as humans. Although it is widely recognized that much of gene regulation is controlled by gene-specific protein-DNA interactions, there presently exists little in the way of tools to identify proteins that interact with the genome at locations of interest. We have developed a novel strategy to address this problem, which we refer to as GENECAPP, for Global ExoNuclease-based Enrichment of Chromatin-Associated Proteins for Proteomics. In this approach, formaldehyde cross-linking is employed to covalently link DNA to its associated proteins; subsequent fragmentation of the DNA, followed by exonuclease digestion, produces a single-stranded region of the DNA that enables sequence-specific hybridization capture of the protein-DNA complex on a solid support. Mass spectrometric (MS analysis of the captured proteins is then used for their identification and/or quantification. We show here the development and optimization of GENECAPP for an in vitro model system, comprised of the murine insulin-like growth factor-binding protein 1 (IGFBP1 promoter region and FoxO1, a member of the forkhead rhabdomyosarcoma (FoxO subfamily of transcription factors, which binds specifically to the IGFBP1 promoter. This novel strategy provides a powerful tool for studies of protein-DNA and protein-protein interactions.

  1. Evaluation of biexponential relaxation behaviour in the human brain by magnetic resonance imaging

    DEFF Research Database (Denmark)

    Kjaer, L; Thomsen, C; Henriksen, O

    1989-01-01

    Quantitative estimation of individual biologic components in relaxation curves obtained in vivo may increase the specificity of tissue characterization by magnetic resonance imaging. In this study, the potential of biexponential curve analysis was evaluated in T1 and T2 measurements on the human...... brain at 1.5 tesla. Optimal experimental conditions were carefully observed, including the use of long TR values and a very small voxel size. T1 determination was based on a 12-points partial saturation inversion recovery pulse sequence. T2 determination involved a multiple spin echo sequence with 32...... echoes. No genuine biexponentiality was demonstrated in the T1 and T2 relaxation processes of white matter, cortical grey matter, or cerebrospinal fluid. Thus, a monoexponential model seems adequate for description of the relaxation behaviour in these cases. Furthermore, the results suggest...

  2. Mediators of exposure therapy for youth obsessive-compulsive disorder: specificity and temporal sequence of client and treatment factors.

    Science.gov (United States)

    Chu, Brian C; Colognori, Daniela B; Yang, Guang; Xie, Min-ge; Lindsey Bergman, R; Piacentini, John

    2015-05-01

    Behavioral engagement and cognitive coping have been hypothesized to mediate effectiveness of exposure-based therapies. Identifying which specific child factors mediate successful therapy and which therapist factors facilitate change can help make our evidence-based treatments more efficient and robust. The current study examines the specificity and temporal sequence of relations among hypothesized client and therapist mediators in exposure therapy for pediatric Obsessive Compulsive Disorder (OCD). Youth coping (cognitive, behavioral), youth safety behaviors (avoidance, escape, compulsive behaviors), therapist interventions (cognitive, exposure extensiveness), and youth anxiety were rated via observational ratings of therapy sessions of OCD youth (N=43; ages=8 - 17; 62.8% male) who had received Exposure and Response Prevention (ERP). Regression analysis using Generalized Estimation Equations and cross-lagged panel analysis (CLPA) were conducted to model anxiety change within and across sessions, to determine formal mediators of anxiety change, and to establish sequence of effects. Anxiety ratings decreased linearly across exposures within sessions. Youth coping and therapist interventions significantly mediated anxiety change across exposures, and youth-interfering behavior mediated anxiety change at the trend level. In CLPA, youth-interfering behaviors predicted, and were predicted by, changes in anxiety. Youth coping was predicted by prior anxiety change. The study provides a preliminary examination of specificity and temporal sequence among child and therapist behaviors in predicting youth anxiety. Results suggest that therapists should educate clients in the natural rebound effects of anxiety between sessions and should be aware of the negatively reinforcing properties of avoidance during exposure. Copyright © 2015. Published by Elsevier Ltd.

  3. Multi-species sequence comparison reveals dynamic evolution of the elastin gene that has involved purifying selection and lineage-specific insertions/deletions

    Directory of Open Access Journals (Sweden)

    Green Eric D

    2004-05-01

    Full Text Available Abstract Background The elastin gene (ELN is implicated as a factor in both supravalvular aortic stenosis (SVAS and Williams Beuren Syndrome (WBS, two diseases involving pronounced complications in mental or physical development. Although the complete spectrum of functional roles of the processed gene product remains to be established, these roles are inferred to be analogous in human and mouse. This view is supported by genomic sequence comparison, in which there are no large-scale differences in the ~1.8 Mb sequence block encompassing the common region deleted in WBS, with the exception of an overall reversed physical orientation between human and mouse. Results Conserved synteny around ELN does not translate to a high level of conservation in the gene itself. In fact, ELN orthologs in mammals show more sequence divergence than expected for a gene with a critical role in development. The pattern of divergence is non-conventional due to an unusually high ratio of gaps to substitutions. Specifically, multi-sequence alignments of eight mammalian sequences reveal numerous non-aligning regions caused by species-specific insertions and deletions, in spite of the fact that the vast majority of aligning sites appear to be conserved and undergoing purifying selection. Conclusions The pattern of lineage-specific, in-frame insertions/deletions in the coding exons of ELN orthologous genes is unusual and has led to unique features of the gene in each lineage. These differences may indicate that the gene has a slightly different functional mechanism in mammalian lineages, or that the corresponding regions are functionally inert. Identified regions that undergo purifying selection reflect a functional importance associated with evolutionary pressure to retain those features.

  4. Representational difference analysis of Neisseria meningitidis identifies sequences that are specific for the hyper-virulent lineage III clone

    NARCIS (Netherlands)

    Bart, A.; Dankert, J.; van der Ende, A.

    2000-01-01

    Neisseria meningitidis may cause meningitis and septicemia. Since the early 1980s, an increased incidence of meningococcal disease has been caused by the lineage III clone in many countries in Europe and in New Zealand. We hypothesized that lineage III meningococci have specific DNA sequences,

  5. Magnetic resonance imaging of the male pelvis

    International Nuclear Information System (INIS)

    Lamarque, J.L.; Rouanet, J.P.; Pujol, J.

    1986-01-01

    The authors present their preliminary results in the investigation of the male pelvis by means of a 0.35 Tesla superconductor apparatus. They present the different sequences used. The signal of the various pelvic organs in man is analysed together with the different anatomical possibilities. Magnetic resonance imaging appears to present very important advantages. The authors consider that the major limitations involve the prostate: new sequences of investigation, in particular a long TR, should be used for the purposes of tissue differentiation [fr

  6. Design of Tail-Clamp Peptide Nucleic Acid Tethered with Azobenzene Linker for Sequence-Specific Detection of Homopurine DNA

    Directory of Open Access Journals (Sweden)

    Shinjiro Sawada

    2017-10-01

    Full Text Available DNA carries genetic information in its sequence of bases. Synthetic oligonucleotides that can sequence-specifically recognize a target gene sequence are a useful tool for regulating gene expression or detecting target genes. Among the many synthetic oligonucleotides, tail-clamp peptide nucleic acid (TC-PNA offers advantages since it has two homopyrimidine PNA strands connected via a flexible ethylene glycol-type linker that can recognize complementary homopurine sequences via Watson-Crick and Hoogsteen base pairings and form thermally-stable PNA/PNA/DNA triplex structures. Here, we synthesized a series of TC-PNAs that can possess different lengths of azobenzene-containing linkers and studied their binding behaviours to homopurine single-stranded DNA. Introduction of azobenzene at the N-terminus amine of PNA increased the thermal stability of PNA-DNA duplexes. Further extension of the homopyrimidine PNA strand at the N-terminus of PNA-AZO further increased the binding stability of the PNA/DNA/PNA triplex to the target homopurine sequence; however, it induced TC-PNA/DNA/TC-PNA complex formation. Among these TC-PNAs, 9W5H-C4-AZO consisting of nine Watson-Crick bases and five Hoogsteen bases tethered with a beta-alanine conjugated azobenzene linker gave a stable 1:1 TC-PNA/ssDNA complex and exhibited good mismatch recognition. Our design for TC-PNA-AZO can be utilized for detecting homopurine sequences in various genes.

  7. Magnetic resonance imaging of the femoral trochlea: evaluation of anatomical landmarks and grading articular cartilage in cadaveric knees

    Energy Technology Data Exchange (ETDEWEB)

    Muhle, Claus [Marienhospital Vechta, Department of Radiology, Vechta (Germany); Veterans Affairs Medical Center, Department of Radiology, San Diego, CA (United States); Mo Ahn, Joong [University of Iowa, Department of Radiology, Iowa, IA (United States); Trudell, Debra; Resnick, Donald [Veterans Affairs Medical Center, Department of Radiology, San Diego, CA (United States)

    2008-06-15

    The purpose of the study was to define magnetic resonance imaging (MRI) findings before and after contrast medium opacification of the knee joint in cadaveric specimens to demonstrate anatomical landmarks of the trochlear surface in relation to the neighboring structures, and to evaluate different MRI sequences in the detection of cartilage defects of the trochlear and patellar surface of the knee. The morphology and relationship of the proximal trochlear surface to the prefemoral fat of the distal femur were investigated by use of different MR sequences before and after intra-articular gadolinium administration into the knee joint in ten cadaveric knees. Anatomic sections were subsequently obtained. In addition, evaluation of the articular surface of the trochlea was performed by two independent observers. The cartilage surfaces were graded using a 2-point system, and results were compared with macroscopic findings. Of 40 cartilage surfaces evaluated, histopathologic findings showed 9 normal surfaces, 20 containing partial-thickness defects, and 11 containing full-thickness defects. Compared with macroscopic data, sensitivity of MR sequences for the two reviewers was between 17 and 90%; specificity, 75 and 100%; positive predictive value, 75 and 100%; negative predictive value, 20 and 100%, depending on patellar or trochlea lesions. Interobserver variability for the presence of disease, which was measured using the kappa statistic, was dependent on the MR sequence used between 0.243 and 0.851. Magnetic resonance imaging sequences can be used to evaluate the cartilage of the trochlear surface with less accuracy when compared with the results of grading the articular cartilage of the patella. (orig.)

  8. Acute vertebral fracture: differentiation of malignant and benign causes by diffusion weighted magnetic resonance imaging

    International Nuclear Information System (INIS)

    Mubarak, F.; Akhtar, W.

    2011-01-01

    Objective: To evaluate the sensitivity, specificity and accuracy of diffusion weighted (DWI) magnetic resonance imaging (MRI) in the diagnosis and differentiation between benign (osteoporotic/infectious) and malignant vertebral compression fractures in comparison with histology findings and clinical follow up. Methods: The study was conducted at the Radiology Department, Aga Khan University Hospital (AKUH) Karachi. It was a one year cross-sectional study from 01/01/2009 to 01/01/2010. Forty patients with sixty three vertebral compression fractures were included. Diffusion-weighted sequences and apparent diffusion coefficient (ADC) images on a 1.5 T MR scanner were obtained in all patients to identify the vertebral compression fracture along with benign and malignant causes. Imaging findings were compared with histopathologic results and clinical follow-up. Results: Diffusion-weighted MR imaging found to have, 92% sensitivity, 90% specificity and accuracy of 85% in differentiation of benign and malignant vertebral compression fracture while PPV and NPV were 78 % and 90% respectively. Conclusion: Diffusion weighted magnetic resonance imaging offers a safe, accurate and non invasive modality to differentiate between the benign and malignant vertebral compression fracture. (author)

  9. Mutations of the kissing-loop dimerization sequence influence the site specificity of murine leukemia virus recombination in vivo

    DEFF Research Database (Denmark)

    Mikkelsen, J G; Lund, Anders Henrik; Duch, M

    2000-01-01

    synthesis in newly infected cells. We have previously shown that template shifts within the 5' leader of murine leukemia viruses occur preferentially within the kissing stem-loop motif, a cis element crucial for in vitro RNA dimer formation. By use of a forced recombination approach based on single......-cycle transfer of Akv murine leukemia virus-based vectors harboring defective primer binding site sequences, we now report that modifications of the kissing-loop structure, ranging from a deletion of the entire sequence to introduction of a single point mutation in the loop motif, significantly disturb site...... specificity of recombination within the highly structured 5' leader region. In addition, we find that an intact kissing-loop sequence favors optimal RNA encapsidation and vector transduction. Our data are consistent with the kissing-loop dimerization model and suggest that a direct intermolecular RNA...

  10. Variations in CCL3L gene cluster sequence and non-specific gene copy numbers

    Directory of Open Access Journals (Sweden)

    Edberg Jeffrey C

    2010-03-01

    Full Text Available Abstract Background Copy number variations (CNVs of the gene CC chemokine ligand 3-like1 (CCL3L1 have been implicated in HIV-1 susceptibility, but the association has been inconsistent. CCL3L1 shares homology with a cluster of genes localized to chromosome 17q12, namely CCL3, CCL3L2, and, CCL3L3. These genes are involved in host defense and inflammatory processes. Several CNV assays have been developed for the CCL3L1 gene. Findings Through pairwise and multiple alignments of these genes, we have shown that the homology between these genes ranges from 50% to 99% in complete gene sequences and from 70-100% in the exonic regions, with CCL3L1 and CCL3L3 being identical. By use of MEGA 4 and BioEdit, we aligned sense primers, anti-sense primers, and probes used in several previously described assays against pre-multiple alignments of all four chemokine genes. Each set of probes and primers aligned and matched with overlapping sequences in at least two of the four genes, indicating that previously utilized RT-PCR based CNV assays are not specific for only CCL3L1. The four available assays measured median copies of 2 and 3-4 in European and African American, respectively. The concordance between the assays ranged from 0.44-0.83 suggesting individual discordant calls and inconsistencies with the assays from the expected gene coverage from the known sequence. Conclusions This indicates that some of the inconsistencies in the association studies could be due to assays that provide heterogenous results. Sequence information to determine CNV of the three genes separately would allow to test whether their association with the pathogenesis of a human disease or phenotype is affected by an individual gene or by a combination of these genes.

  11. Phase-Specific Vocalizations of Male Mice at the Initial Encounter during the Courtship Sequence.

    Directory of Open Access Journals (Sweden)

    Yui K Matsumoto

    Full Text Available Mice produce ultrasonic vocalizations featuring a variety of syllables. Vocalizations are observed during social interactions. In particular, males produce numerous syllables during courtship. Previous studies have shown that vocalizations change according to sexual behavior, suggesting that males vary their vocalizations depending on the phase of the courtship sequence. To examine this process, we recorded large sets of mouse vocalizations during male-female interactions and acoustically categorized these sounds into 12 vocal types. We found that males emitted predominantly short syllables during the first minute of interaction, more long syllables in the later phases, and mainly harmonic sounds during mounting. These context- and time-dependent changes in vocalization indicate that vocal communication during courtship in mice consists of at least three stages and imply that each vocalization type has a specific role in a phase of the courtship sequence. Our findings suggest that recording for a sufficiently long time and taking the phase of courtship into consideration could provide more insights into the role of vocalization in mouse courtship behavior in future study.

  12. Cardiovascular magnetic resonance physics for clinicians: part I.

    Science.gov (United States)

    Ridgway, John P

    2010-11-30

    There are many excellent specialised texts and articles that describe the physical principles of cardiovascular magnetic resonance (CMR) techniques. There are also many texts written with the clinician in mind that provide an understandable, more general introduction to the basic physical principles of magnetic resonance (MR) techniques and applications. There are however very few texts or articles that attempt to provide a basic MR physics introduction that is tailored for clinicians using CMR in their daily practice. This is the first of two reviews that are intended to cover the essential aspects of CMR physics in a way that is understandable and relevant to this group. It begins by explaining the basic physical principles of MR, including a description of the main components of an MR imaging system and the three types of magnetic field that they generate. The origin and method of production of the MR signal in biological systems are explained, focusing in particular on the two tissue magnetisation relaxation properties (T1 and T2) that give rise to signal differences from tissues, showing how they can be exploited to generate image contrast for tissue characterisation. The method most commonly used to localise and encode MR signal echoes to form a cross sectional image is described, introducing the concept of k-space and showing how the MR signal data stored within it relates to properties within the reconstructed image. Before describing the CMR acquisition methods in detail, the basic spin echo and gradient pulse sequences are introduced, identifying the key parameters that influence image contrast, including appearances in the presence of flowing blood, resolution and image acquisition time. The main derivatives of these two pulse sequences used for cardiac imaging are then described in more detail. Two of the key requirements for CMR are the need for data acquisition first to be to be synchronised with the subject's ECG and to be fast enough for the subject

  13. Parametric resonance in neutrino oscillations in matter

    Indian Academy of Sciences (India)

    Neutrino oscillations in matter can exhibit a specific resonance enhancement - parametric resonance, which is different from the MSW resonance. Oscillations of atmospheric and solar neutrinos inside the earth can undergo parametric enhancement when neutrino trajectories cross the core of the earth. In this paper we ...

  14. Geometrical optics model of Mie resonances

    Science.gov (United States)

    Roll; Schweiger

    2000-07-01

    The geometrical optics model of Mie resonances is presented. The ray path geometry is given and the resonance condition is discussed with special emphasis on the phase shift that the rays undergo at the surface of the dielectric sphere. On the basis of this model, approximate expressions for the positions of first-order resonances are given. Formulas for the cavity mode spacing are rederived in a simple manner. It is shown that the resonance linewidth can be calculated regarding the cavity losses. Formulas for the mode density of Mie resonances are given that account for the different width of resonances and thus may be adapted to specific experimental situations.

  15. Clinical evaluation of further-developed MRCP sequences in comparison with standard MRCP sequences

    International Nuclear Information System (INIS)

    Hundt, W.; Scheidler, J.; Reiser, M.; Petsch, R.

    2002-01-01

    The purpose of this study was the comparison of technically improved single-shot magnetic resonance cholangiopancreatography (MRCP) sequences with standard single-shot rapid acquisition with relaxation enhancement (RARE) and half-Fourier acquired single-shot turbo spin-echo (HASTE) sequences in evaluating the normal and abnormal biliary duct system. The bile duct system of 45 patients was prospectively investigated on a 1.5-T MRI system. The investigation was performed with RARE and HASTE MR cholangiography sequences with standard and high spatial resolutions, and with a delayed-echo half-Fourier RARE (HASTE) sequence. Findings of the improved MRCP sequences were compared with the standard MRCP sequences. The level of confidence in assessing the diagnosis was divided into five groups. The Wilcoxon signed-rank test at a level of p<0.05 was applied. In 15 patients no pathology was found. The MRCP showed stenoses of the bile duct system in 10 patients and choledocholithiasis and cholecystolithiasis in 16 patients. In 12 patients a dilatation of the bile duct system was found. Comparison of the low- and high spatial resolution sequences and the short and long TE times of the half-Fourier RARE (HASTE) sequence revealed no statistically significant differences regarding accuracy of the examination. The diagnostic confidence level in assessing normal or pathological findings for the high-resolution RARE and half-Fourier RARE (HASTE) was significantly better than for the standard sequences. For the delayed-echo half-Fourier RARE (HASTE) sequence no statistically significant difference was seen. The high-resolution RARE and half-Fourier RARE (HASTE) sequences had a higher confidence level, but there was no significant difference in diagnosis in terms of detection and assessment of pathological changes in the biliary duct system compared with standard sequences. (orig.)

  16. Somatic sex-specific transcriptome differences in Drosophila revealed by whole transcriptome sequencing

    Directory of Open Access Journals (Sweden)

    Arbeitman Michelle N

    2011-07-01

    Full Text Available Abstract Background Understanding animal development and physiology at a molecular-biological level has been advanced by the ability to determine at high resolution the repertoire of mRNA molecules by whole transcriptome resequencing. This includes the ability to detect and quantify rare abundance transcripts and isoform-specific mRNA variants produced from a gene. The sex hierarchy consists of a pre-mRNA splicing cascade that directs the production of sex-specific transcription factors that specify nearly all sexual dimorphism. We have used deep RNA sequencing to gain insight into how the Drosophila sex hierarchy generates somatic sex differences, by examining gene and transcript isoform expression differences between the sexes in adult head tissues. Results Here we find 1,381 genes that differ in overall expression levels and 1,370 isoform-specific transcripts that differ between males and females. Additionally, we find 512 genes not regulated downstream of transformer that are significantly more highly expressed in males than females. These 512 genes are enriched on the × chromosome and reside adjacent to dosage compensation complex entry sites, which taken together suggests that their residence on the × chromosome might be sufficient to confer male-biased expression. There are no transcription unit structural features, from a set of features, that are robustly significantly different in the genes with significant sex differences in the ratio of isoform-specific transcripts, as compared to random isoform-specific transcripts, suggesting that there is no single molecular mechanism that generates isoform-specific transcript differences between the sexes, even though the sex hierarchy is known to include three pre-mRNA splicing factors. Conclusions We identify thousands of genes that show sex-specific differences in overall gene expression levels, and identify hundreds of additional genes that have differences in the abundance of isoform-specific

  17. Histopathologic correlation of magnetic resonance imaging signal patterns in a spinal cord injury model.

    Science.gov (United States)

    Weirich, S D; Cotler, H B; Narayana, P A; Hazle, J D; Jackson, E F; Coupe, K J; McDonald, C L; Langford, L A; Harris, J H

    1990-07-01

    Magnetic resonance imaging (MRI) provides a noninvasive method of monitoring the pathologic response to spinal cord injury. Specific MR signal intensity patterns appear to correlate with degrees of improvement in the neurologic status in spinal cord injury patients. Histologic correlation of two types of MR signal intensity patterns are confirmed in the current study using a rat animal model. Adult male Sprague-Dawley rats underwent spinal cord trauma at the midthoracic level using a weight-dropping technique. After laminectomy, 5- and 10-gm brass weights were dropped from designated heights onto a 0.1-gm impounder placed on the exposed dura. Animals allowed to regain consciousness demonstrated variable recovery of hind limb paraplegia. Magnetic resonance images were obtained from 2 hours to 1 week after injury using a 2-tesla MRI/spectrometer. Sacrifice under anesthesia was performed by perfusive fixation; spinal columns were excised en bloc, embedded, sectioned, and observed with the compound light microscope. Magnetic resonance axial images obtained during the time sequence after injury demonstrate a distinct correlation between MR signal intensity patterns and the histologic appearance of the spinal cord. Magnetic resonance imaging delineates the pathologic processes resulting from acute spinal cord injury and can be used to differentiate the type of injury and prognosis.

  18. Non-contrast enhanced magnetic resonance angiography techniques in candidates for kidney transplantation: A comparative study

    International Nuclear Information System (INIS)

    Blankholm, Anne Dorte; Ginnerup-Pedersen, Bodil; Stausbøl-Grøn, Brian; Haislund, Margit; Laustsen, Sussie; Ringgaard, Steffen

    2013-01-01

    Aim: Detailed knowledge of vessel status in potential candidates for kidney transplantation is essential for the surgeon. Contrast enhanced magnetic resonance angiography has previously been used intensively for assessing this, but the discovery that use of gadolinium based contrast agents in magnetic resonance imaging can cause Nephrogenic Systemic Fibrosis in patients suffering from severe kidney disease has lead to renewed interest in non-contrast enhanced magnetic resonance angiography. The aim of this study was to find a non-contrast enhanced magnetic resonance angiography method for preoperative evaluation of the pelvic vessels prior to kidney transplantation, providing a sufficient image quality. Method: In a prospective study we consecutively included 54 patients undergoing examinations prior to kidney transplantation. The patients were examined with the following magnetic resonance angiography sequences: A 2D Time of flight (n = 54), 3D Time of flight (n = 52) patients, 3D Phase Contrast (n = 54), 3D Balanced Steady State Free Precession (n = 52) and a 2D TRiggered Angiography Non-Contrast Enhanced (TRANCE) (a Spin Echo sequence with subtraction) (n = 48). The sequences were evaluated with respect to contrast, diagnostic performance and artefact burden. Results: Evaluating contrast, 3D Phase Contrast was significantly better than 2D Time of flight (p 0.2). The 2D Time of flight was significantly better than the other sequences (p < 0.001) in all cases. The artefact score was lowest for the Phase Contrast images and significantly superior to the 2D Time of flight (p < 0.005). The 2D Time of flight was significantly better than the three other sequences (p < 0.001) in all cases. Conclusion: Non-contrast enhanced magnetic resonance angiography offers a safe preoperative examination for assessment of vessel status before kidney transplantation. A combination of 2D Time of flight and 3D Phase Contrast acquisitions is recommended and can be performed within a

  19. Sequence-Specific Model for Peptide Retention Time Prediction in Strong Cation Exchange Chromatography.

    Science.gov (United States)

    Gussakovsky, Daniel; Neustaeter, Haley; Spicer, Victor; Krokhin, Oleg V

    2017-11-07

    The development of a peptide retention prediction model for strong cation exchange (SCX) separation on a Polysulfoethyl A column is reported. Off-line 2D LC-MS/MS analysis (SCX-RPLC) of S. cerevisiae whole cell lysate was used to generate a retention dataset of ∼30 000 peptides, sufficient for identifying the major sequence-specific features of peptide retention mechanisms in SCX. In contrast to RPLC/hydrophilic interaction liquid chromatography (HILIC) separation modes, where retention is driven by hydrophobic/hydrophilic contributions of all individual residues, SCX interactions depend mainly on peptide charge (number of basic residues at acidic pH) and size. An additive model (incorporating the contributions of all 20 residues into the peptide retention) combined with a peptide length correction produces a 0.976 R 2 value prediction accuracy, significantly higher than the additive models for either HILIC or RPLC. Position-dependent effects on peptide retention for different residues were driven by the spatial orientation of tryptic peptides upon interaction with the negatively charged surface functional groups. The positively charged N-termini serve as a primary point of interaction. For example, basic residues (Arg, His, Lys) increase peptide retention when located closer to the N-terminus. We also found that hydrophobic interactions, which could lead to a mixed-mode separation mechanism, are largely suppressed at 20-30% of acetonitrile in the eluent. The accuracy of the final Sequence-Specific Retention Calculator (SSRCalc) SCX model (∼0.99 R 2 value) exceeds all previously reported predictors for peptide LC separations. This also provides a solid platform for method development in 2D LC-MS protocols in proteomics and peptide retention prediction filtering of false positive identifications.

  20. Intradiurnal fluctuations of off-resonance saturation effects in healthy human achilles tendons assessed with a 3D ultrashort echo time MRI sequence at 3 tesla

    Energy Technology Data Exchange (ETDEWEB)

    Grosse, U.; Syha, R.; Kessler, D.E.; Bongers, M.; Seith, F.; Nikolaou, K.; Springer, F. [University Hospital Tuebingen (Germany). Dept. of Diagnostic and Interventional Radiology; Partovi, S.; Robbin, M. [Case Western Reserve Univ., Cleveland, OH (United States). Dept. of Radiology; Schick, F. [University Hospital Tuebingen (Germany). Section on Experimental Radiology

    2015-11-15

    The purpose of this study was to evaluate whether gravitational interstitial fluid accumulation in healthy subjects has an impact on off-resonance saturation ratios (OSR) or the volume of the Achilles tendon after a prolonged time of reduced levels of physical activity. 7 healthy volunteers were repeatedly investigated on 3 consecutive days on a 3 T whole body MR scanner using an ultrashort echo time (UTE) imaging sequence with a Gaussian off-resonance saturation pulse at a frequency offset of 2000 Hz to calculate OSR values. For accurate volumetric quantification of the Achilles tendon, a newly developed contour detection snake algorithm was applied on high-resolution isotropic T2-weighted SPACE sequence datasets. Single-measure intraclass correlation coefficients (ICC) were calculated to estimate test-retest reliability. For OSR and tendon volume measurements on three consecutive days, excellent reproducibility could be achieved with ICC values above 0.96 and 0.97, respectively. Comparing the results of all three days, a statistically significant mean individual percentage decrease (-4.1 ± 1.5 %; p=0.001) of calculated tendon OSR values was found for the evening measurements. No statistically significant difference between tendon volumes in the morning and the evening could be detected (p=0.589). The results of this in-vivo study demonstrate a significant influence of gravitational interstitial fluid accumulation after reduced physical activity on OSR values in the Achilles tendon, but not on tendon volume. Taken together with the demonstrated excellent reproducibility, these findings are important for future studies investigating temporal changes of the Achilles tendon microstructure.

  1. Intradiurnal fluctuations of off-resonance saturation effects in healthy human achilles tendons assessed with a 3D ultrashort echo time MRI sequence at 3 tesla

    International Nuclear Information System (INIS)

    Grosse, U.; Syha, R.; Kessler, D.E.; Bongers, M.; Seith, F.; Nikolaou, K.; Springer, F.; Partovi, S.; Robbin, M.; Schick, F.

    2015-01-01

    The purpose of this study was to evaluate whether gravitational interstitial fluid accumulation in healthy subjects has an impact on off-resonance saturation ratios (OSR) or the volume of the Achilles tendon after a prolonged time of reduced levels of physical activity. 7 healthy volunteers were repeatedly investigated on 3 consecutive days on a 3 T whole body MR scanner using an ultrashort echo time (UTE) imaging sequence with a Gaussian off-resonance saturation pulse at a frequency offset of 2000 Hz to calculate OSR values. For accurate volumetric quantification of the Achilles tendon, a newly developed contour detection snake algorithm was applied on high-resolution isotropic T2-weighted SPACE sequence datasets. Single-measure intraclass correlation coefficients (ICC) were calculated to estimate test-retest reliability. For OSR and tendon volume measurements on three consecutive days, excellent reproducibility could be achieved with ICC values above 0.96 and 0.97, respectively. Comparing the results of all three days, a statistically significant mean individual percentage decrease (-4.1 ± 1.5 %; p=0.001) of calculated tendon OSR values was found for the evening measurements. No statistically significant difference between tendon volumes in the morning and the evening could be detected (p=0.589). The results of this in-vivo study demonstrate a significant influence of gravitational interstitial fluid accumulation after reduced physical activity on OSR values in the Achilles tendon, but not on tendon volume. Taken together with the demonstrated excellent reproducibility, these findings are important for future studies investigating temporal changes of the Achilles tendon microstructure.

  2. Fat-Suppressed T2* Sequences for Routine 3.0-Tesla Lumbar Spine Magnetic Resonance Imaging: A Preliminary Report

    International Nuclear Information System (INIS)

    McKinney, A. M.; Gadani, S.; Palmer, C. S.; Vidarsson, L.

    2008-01-01

    Background: Clear depiction of the ligamentum flavum on routine lumbar magnetic resonance imaging (MRI) is essential in accurately describing the extent of degenerative disease. In routine, noncontrast evaluations, focal fatty deposition or hemangiomas can be difficult to distinguish from malignant foci on fast spin-echo (FSE) T2-weighted images. Purpose: To describe the use of T2* fast field echo (T2FFE) in combination with spectral presaturation inversion recovery (SPIR) fat suppression for noncontrast, routine lumbar spine outpatient MR imaging at 3.0 Tesla (3T). Material and Methods: An axial gradient echo (GE) T2FFE sequence was combined with SPIR fat suppression (T2FFE-SPIR), via a 3T Philips Intera (Philips Medical Systems, Best, The Netherlands) scanner, and added to the routine, noncontrast lumbar MRI examinations, which included sagittal FSE T1-weighted (T1WI), T2-weighted (T2WI), short-tau inversion recovery (STIR), and axial FSE T2WI. The sequence was performed in over 500 patients over a 1-year period, without intravenous contrast, and with slice thickness and planes of section identical to the axial FSE T1WI and T2WI images. The sequence typically lasted about 4.5-6 min. Results: The use of T2FFE-SPIR enabled visualization of the ligamentum flavum in degenerative disease, and the exclusion of focal fatty lesions on FSE T2WI. Other benefits included: the identification of malignant foci, the uncommon detection of hemorrhage, and the elimination of spurious flow voids. Several brief examples are provided to demonstrate the utility of this technique. Conclusion: The addition of T2FFE-SPIR to routine, noncontrast protocols in outpatients could provide further confidence in the visualization of the ligamentum flavum in degenerative disease, and can exclude malignancy in T2-bright areas of focal fatty marrow. Larger studies would be helpful to evaluate the accuracy of this technique versus FSE techniques in depicting degenerative, malignant, or inflammatory

  3. Fat-Suppressed T2 Sequences for Routine 3.0-Tesla Lumbar Spine Magnetic Resonance Imaging: A Preliminary Report

    Energy Technology Data Exchange (ETDEWEB)

    McKinney, A. M.; Gadani, S.; Palmer, C. S.; Vidarsson, L. (Dept. of Radiology, Hennepin County and Univ. of Minnesota Medical Centers, Minneapolis, MN (United States))

    2008-09-15

    Background: Clear depiction of the ligamentum flavum on routine lumbar magnetic resonance imaging (MRI) is essential in accurately describing the extent of degenerative disease. In routine, noncontrast evaluations, focal fatty deposition or hemangiomas can be difficult to distinguish from malignant foci on fast spin-echo (FSE) T2-weighted images. Purpose: To describe the use of T2 fast field echo (T2FFE) in combination with spectral presaturation inversion recovery (SPIR) fat suppression for noncontrast, routine lumbar spine outpatient MR imaging at 3.0 Tesla (3T). Material and Methods: An axial gradient echo (GE) T2FFE sequence was combined with SPIR fat suppression (T2FFE-SPIR), via a 3T Philips Intera (Philips Medical Systems, Best, The Netherlands) scanner, and added to the routine, noncontrast lumbar MRI examinations, which included sagittal FSE T1-weighted (T1WI), T2-weighted (T2WI), short-tau inversion recovery (STIR), and axial FSE T2WI. The sequence was performed in over 500 patients over a 1-year period, without intravenous contrast, and with slice thickness and planes of section identical to the axial FSE T1WI and T2WI images. The sequence typically lasted about 4.5-6 min. Results: The use of T2FFE-SPIR enabled visualization of the ligamentum flavum in degenerative disease, and the exclusion of focal fatty lesions on FSE T2WI. Other benefits included: the identification of malignant foci, the uncommon detection of hemorrhage, and the elimination of spurious flow voids. Several brief examples are provided to demonstrate the utility of this technique. Conclusion: The addition of T2FFE-SPIR to routine, noncontrast protocols in outpatients could provide further confidence in the visualization of the ligamentum flavum in degenerative disease, and can exclude malignancy in T2-bright areas of focal fatty marrow. Larger studies would be helpful to evaluate the accuracy of this technique versus FSE techniques in depicting degenerative, malignant, or inflammatory

  4. Enactment versus observation: item-specific and relational processing in goal-directed action sequences (and lists of single actions.

    Directory of Open Access Journals (Sweden)

    Janette Schult

    Full Text Available What are the memory-related consequences of learning actions (such as "apply the patch" by enactment during study, as compared to action observation? Theories converge in postulating that enactment encoding increases item-specific processing, but not the processing of relational information. Typically, in the laboratory enactment encoding is studied for lists of unrelated single actions in which one action execution has no overarching purpose or relation with other actions. In contrast, real-life actions are usually carried out with the intention to achieve such a purpose. When actions are embedded in action sequences, relational information provides efficient retrieval cues. We contrasted memory for single actions with memory for action sequences in three experiments. We found more reliance on relational processing for action-sequences than single actions. To what degree can this relational information be used after enactment versus after the observation of an actor? We found indicators of superior relational processing after observation than enactment in ordered pair recall (Experiment 1A and in emerging subjective organization of repeated recall protocols (recall runs 2-3, Experiment 2. An indicator of superior item-specific processing after enactment compared to observation was recognition (Experiment 1B, Experiment 2. Similar net recall suggests that observation can be as good a learning strategy as enactment. We discuss possible reasons why these findings only partly converge with previous research and theorizing.

  5. RNA-Mediated Gene Duplication and Retroposons: Retrogenes, LINEs, SINEs, and Sequence Specificity

    Science.gov (United States)

    2013-01-01

    A substantial number of “retrogenes” that are derived from the mRNA of various intron-containing genes have been reported. A class of mammalian retroposons, long interspersed element-1 (LINE1, L1), has been shown to be involved in the reverse transcription of retrogenes (or processed pseudogenes) and non-autonomous short interspersed elements (SINEs). The 3′-end sequences of various SINEs originated from a corresponding LINE. As the 3′-untranslated regions of several LINEs are essential for retroposition, these LINEs presumably require “stringent” recognition of the 3′-end sequence of the RNA template. However, the 3′-ends of mammalian L1s do not exhibit any similarity to SINEs, except for the presence of 3′-poly(A) repeats. Since the 3′-poly(A) repeats of L1 and Alu SINE are critical for their retroposition, L1 probably recognizes the poly(A) repeats, thereby mobilizing not only Alu SINE but also cytosolic mRNA. Many flowering plants only harbor L1-clade LINEs and a significant number of SINEs with poly(A) repeats, but no homology to the LINEs. Moreover, processed pseudogenes have also been found in flowering plants. I propose that the ancestral L1-clade LINE in the common ancestor of green plants may have recognized a specific RNA template, with stringent recognition then becoming relaxed during the course of plant evolution. PMID:23984183

  6. Polyvinyl-alcohol-based magnetic beads for rapid and efficient separation of specific or unspecific nucleic acid sequences

    International Nuclear Information System (INIS)

    Oster, J.; Parker, Jeffrey; Brassard, Lothar

    2001-01-01

    The versatile application of polyvinyl-alcohol-based magnetic M-PVA beads is demonstrated in the separation of genomic DNA, sequence specific nucleic acid purification, and binding of bacteria for subsequent DNA extraction and detection. It is shown that nucleic acids can be obtained in high yield and purity using M-PVA beads, making sample preparation efficient, fast and highly adaptable for automation processes

  7. Age determination of vessel wall hematoma in spontaneous cervical artery dissection: A multi-sequence 3T Cardiovascular Magnetic resonance study

    Directory of Open Access Journals (Sweden)

    Habs Maximilian

    2011-11-01

    Full Text Available Abstract Background Previously proposed classifications for carotid plaque and cerebral parenchymal hemorrhages are used to estimate the age of hematoma according to its signal intensities on T1w and T2w MR images. Using these classifications, we systematically investigated the value of cardiovascular magnetic resonance (CMR in determining the age of vessel wall hematoma (VWH in patients with spontaneous cervical artery dissection (sCAD. Methods 35 consecutive patients (mean age 43.6 ± 9.8 years with sCAD received a cervical multi-sequence 3T CMR with fat-saturated black-blood T1w-, T2w- and TOF images. Age of sCAD was defined as time between onset of symptoms (stroke, TIA or Horner's syndrome and the CMR scan. VWH were categorized into hyperacute, acute, early subacute, late subacute and chronic based on their signal intensities on T1w- and T2w images. Results The mean age of sCAD was 2.0, 5.8, 15.7 and 58.7 days in patients with acute, early subacute, late subacute and chronic VWH as classified by CMR (p Conclusions Signal intensities of VWH in sCAD vary over time and multi-sequence CMR can help to determine the age of an arterial dissection. Furthermore, findings of this study suggest that the time course of carotid hematomas differs from that of cerebral hematomas.

  8. Neutronics benchmarks of mixed-oxide fuels using the SCALE/CENTRM sequence

    International Nuclear Information System (INIS)

    Hollenbach, D.F.; Fox, P.B.

    2000-01-01

    The purpose of this study is to determine and document the reactor physics parameters (multiplication factors, spatially dependent flux ratios, and spacially dependent reaction rates ) for several distinct sets of problems using two distinct resonance cross-section processing techniques. In SCALE, by default, resonances are processed using NITAWL, which utilizes the Nordheim Integral Treatment. The results produced using this sequence are considered to be the base results. A second set of results are produced by replacing NITAWL with CENTRM/PMC. CENTRM produces point-wise fluxes for a given geometry configuration and set of isotopes. Using these fluxes, PMC produces problem-dependent self-shielding cross sections. Both sequences use ENDF/B-V cross-section data

  9. Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

    DEFF Research Database (Denmark)

    Yilmaz, Pelin; Kottmann, Renzo; Field, Dawn

    2011-01-01

    Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences--the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The 'environment...

  10. Sequence-Specific Targeting of Bacterial Resistance Genes Increases Antibiotic Efficacy

    Science.gov (United States)

    Wong, Michael; Daly, Seth M.; Greenberg, David E.; Toprak, Erdal

    2016-01-01

    The lack of effective and well-tolerated therapies against antibiotic-resistant bacteria is a global public health problem leading to prolonged treatment and increased mortality. To improve the efficacy of existing antibiotic compounds, we introduce a new method for strategically inducing antibiotic hypersensitivity in pathogenic bacteria. Following the systematic verification that the AcrAB-TolC efflux system is one of the major determinants of the intrinsic antibiotic resistance levels in Escherichia coli, we have developed a short antisense oligomer designed to inhibit the expression of acrA and increase antibiotic susceptibility in E. coli. By employing this strategy, we can inhibit E. coli growth using 2- to 40-fold lower antibiotic doses, depending on the antibiotic compound utilized. The sensitizing effect of the antisense oligomer is highly specific to the targeted gene’s sequence, which is conserved in several bacterial genera, and the oligomer does not have any detectable toxicity against human cells. Finally, we demonstrate that antisense oligomers improve the efficacy of antibiotic combinations, allowing the combined use of even antagonistic antibiotic pairs that are typically not favored due to their reduced activities. PMID:27631336

  11. Mouse Nkrp1-Clr gene cluster sequence and expression analyses reveal conservation of tissue-specific MHC-independent immunosurveillance.

    Directory of Open Access Journals (Sweden)

    Qiang Zhang

    Full Text Available The Nkrp1 (Klrb1-Clr (Clec2 genes encode a receptor-ligand system utilized by NK cells as an MHC-independent immunosurveillance strategy for innate immune responses. The related Ly49 family of MHC-I receptors displays extreme allelic polymorphism and haplotype plasticity. In contrast, previous BAC-mapping and aCGH studies in the mouse suggest the neighboring and related Nkrp1-Clr cluster is evolutionarily stable. To definitively compare the relative evolutionary rate of Nkrp1-Clr vs. Ly49 gene clusters, the Nkrp1-Clr gene clusters from two Ly49 haplotype-disparate inbred mouse strains, BALB/c and 129S6, were sequenced. Both Nkrp1-Clr gene cluster sequences are highly similar to the C57BL/6 reference sequence, displaying the same gene numbers and order, complete pseudogenes, and gene fragments. The Nkrp1-Clr clusters contain a strikingly dissimilar proportion of repetitive elements compared to the Ly49 clusters, suggesting that certain elements may be partly responsible for the highly disparate Ly49 vs. Nkrp1 evolutionary rate. Focused allelic polymorphisms were found within the Nkrp1b/d (Klrb1b, Nkrp1c (Klrb1c, and Clr-c (Clec2f genes, suggestive of possible immune selection. Cell-type specific transcription of Nkrp1-Clr genes in a large panel of tissues/organs was determined. Clr-b (Clec2d and Clr-g (Clec2i showed wide expression, while other Clr genes showed more tissue-specific expression patterns. In situ hybridization revealed specific expression of various members of the Clr family in leukocytes/hematopoietic cells of immune organs, various tissue-restricted epithelial cells (including intestinal, kidney tubular, lung, and corneal progenitor epithelial cells, as well as myocytes. In summary, the Nkrp1-Clr gene cluster appears to evolve more slowly relative to the related Ly49 cluster, and likely regulates innate immunosurveillance in a tissue-specific manner.

  12. Parametric methods for characterizing myocardial tissue by magnetic resonance imaging (part 2): T2 mapping.

    Science.gov (United States)

    Perea Palazón, R J; Solé Arqués, M; Prat González, S; de Caralt Robira, T M; Cibeira López, M T; Ortiz Pérez, J T

    2015-01-01

    Cardiac magnetic resonance imaging is considered the reference technique for characterizing myocardial tissue; for example, T2-weighted sequences make it possible to evaluate areas of edema or myocardial inflammation. However, traditional sequences have many limitations and provide only qualitative information. Moreover, traditional sequences depend on the reference to remote myocardium or skeletal muscle, which limits their ability to detect and quantify diffuse myocardial damage. Recently developed magnetic resonance myocardial mapping techniques enable quantitative assessment of parameters indicative of edema. These techniques have proven better than traditional sequences both in acute cardiomyopathy and in acute ischemic heart disease. This article synthesizes current developments in T2 mapping as well as their clinical applications and limitations. Copyright © 2014 SERAM. Published by Elsevier España, S.L.U. All rights reserved.

  13. Cerebral staging of lung cancer: is one single contrast-enhanced T1-weighted three-dimensional gradient-echo sequence sufficient?

    Energy Technology Data Exchange (ETDEWEB)

    Ohana, Mickael; Jeung, Mi-Young; Roy, Catherine [Nouvel Hopital Civil-Hopitaux Universitaires de Strasbourg, Service de Radiologie B/Radiology Department, Strasbourg (France); Bazille, Gauthier [Clinique Saint Anne-Groupe Radiologique MIM, Strasbourg (France)

    2014-08-15

    Gadolinium-enhanced magnetic resonance imaging (MRI) is the gold standard for cerebral staging in thoracic oncology. We hypothesize that a minimalist examination, consisting of a single contrast-enhanced T1-weighted three-dimensional gradient-echo sequence (CE 3D-GRE), would be sufficient for the cerebral staging of nonsymptomatic lung cancer patients. Seventy nonsymptomatic patients (50 % men; 62 years ± 10.2) referred for cerebral staging of a lung cancer were retrospectively included. All underwent a standard 3 T MRI examination with T1, FLAIR, T2* GRE, diffusion, and CE 3D-GRE sequences, for a total examination time of 20 min. The sole CE 3D-GRE (acquisition time: 6 min) was extracted and blindly interpreted by two radiologists in search of brain metastases. Hemorrhagic features of potential lesions and relevant incidental findings were also noted. Discrepant cases were reviewed by a third reader. The full MRI examination and follow-up studies were used as a reference to calculate sensitivity and specificity of the sole CE 3D-GRE. Thirty-eight point six percent (27 out of 70) of the patients had brain metastases. Performances and reader's agreement with the sole CE 3D-GRE sequence were excellent for the diagnosis of brain metastases (sensitivity = 96.3 %, specificity = 100 %, κ = 0.91) and incidental findings (sensitivity = 85.7 %, specificity = 100 %, κ = 0.62) but insufficient for the identification of hemorrhages within the metastases (sensitivity = 33.3 %, specificity = 85.7 %, κ = 0.47). In the specific case of lung cancer, cerebral staging in nonsymptomatic patients can be efficiently achieved with a minimalistic protocol consisting of a single CE 3D-GRE sequence, completed if positive with a T2* sequence for hemorrhagic assessment, thus halving appointment delays. (orig.)

  14. Event-specific qualitative and quantitative PCR detection of the GMO carnation (Dianthus caryophyllus) variety Moonlite based upon the 5'-transgene integration sequence.

    Science.gov (United States)

    Li, P; Jia, J W; Jiang, L X; Zhu, H; Bai, L; Wang, J B; Tang, X M; Pan, A H

    2012-04-27

    To ensure the implementation of genetically modified organism (GMO)-labeling regulations, an event-specific detection method was developed based on the junction sequence of an exogenous integrant in the transgenic carnation variety Moonlite. The 5'-transgene integration sequence was isolated by thermal asymmetric interlaced PCR. Based upon the 5'-transgene integration sequence, the event-specific primers and TaqMan probe were designed to amplify the fragments, which spanned the exogenous DNA and carnation genomic DNA. Qualitative and quantitative PCR assays were developed employing the designed primers and probe. The detection limit of the qualitative PCR assay was 0.05% for Moonlite in 100 ng total carnation genomic DNA, corresponding to about 79 copies of the carnation haploid genome; the limit of detection and quantification of the quantitative PCR assay were estimated to be 38 and 190 copies of haploid carnation genomic DNA, respectively. Carnation samples with different contents of genetically modified components were quantified and the bias between the observed and true values of three samples were lower than the acceptance criterion (GMO detection method. These results indicated that these event-specific methods would be useful for the identification and quantification of the GMO carnation Moonlite.

  15. Advances and applications of dynamic-angle spinning nuclear magnetic resonance

    Energy Technology Data Exchange (ETDEWEB)

    Baltisberger, Jay Harvey [Univ. of California, Berkeley, CA (United States)

    1993-06-01

    This dissertation describes nuclear magnetic resonance experiments and theory which have been developed to study quadrupolar nuclei (those nuclei with spin greater than one-half) in the solid state. Primarily, the technique of dynamic-angle spinning (DAS) is extensively reviewed and expanded upon in this thesis. Specifically, the improvement in both the resolution (two-dimensional pure-absorptive phase methods and DAS angle choice) and sensitivity (pulse-sequence development), along with effective spinning speed enhancement (again through choice of DAS conditions or alternative multiple pulse schemes) of dynamic-angle spinning experiment was realized with both theory and experimental examples. The application of DAS to new types of nuclei (specifically the {sup 87}Rb and {sup 85}Rb nuclear spins) and materials (specifically amorphous solids) has also greatly expanded the possibilities of the use of DAS to study a larger range of materials. This dissertation is meant to demonstrate both recent advances and applications of the DAS technique, and by no means represents a comprehensive study of any particular chemical problem.

  16. Sequence-Based Discovery Demonstrates That Fixed Light Chain Human Transgenic Rats Produce a Diverse Repertoire of Antigen-Specific Antibodies

    Directory of Open Access Journals (Sweden)

    Katherine E. Harris

    2018-04-01

    Full Text Available We created a novel transgenic rat that expresses human antibodies comprising a diverse repertoire of heavy chains with a single common rearranged kappa light chain (IgKV3-15-JK1. This fixed light chain animal, called OmniFlic, presents a unique system for human therapeutic antibody discovery and a model to study heavy chain repertoire diversity in the context of a constant light chain. The purpose of this study was to analyze heavy chain variable gene usage, clonotype diversity, and to describe the sequence characteristics of antigen-specific monoclonal antibodies (mAbs isolated from immunized OmniFlic animals. Using next-generation sequencing antibody repertoire analysis, we measured heavy chain variable gene usage and the diversity of clonotypes present in the lymph node germinal centers of 75 OmniFlic rats immunized with 9 different protein antigens. Furthermore, we expressed 2,560 unique heavy chain sequences sampled from a diverse set of clonotypes as fixed light chain antibody proteins and measured their binding to antigen by ELISA. Finally, we measured patterns and overall levels of somatic hypermutation in the full B-cell repertoire and in the 2,560 mAbs tested for binding. The results demonstrate that OmniFlic animals produce an abundance of antigen-specific antibodies with heavy chain clonotype diversity that is similar to what has been described with unrestricted light chain use in mammals. In addition, we show that sequence-based discovery is a highly effective and efficient way to identify a large number of diverse monoclonal antibodies to a protein target of interest.

  17. Diagnostic accuracy of unenhanced, contrast-enhanced perfusion and angiographic MRI sequences for pulmonary embolism diagnosis: results of independent sequence readings

    Energy Technology Data Exchange (ETDEWEB)

    Revel, Marie Pierre [Hopital Europeen Georges Pompidou, APHP, Departments of Radiology, Paris (France); Universite Paris Descartes Sorbonne Paris Cite, Paris (France); Hotel-Dieu, Service de Radiologie, Paris (France); Sanchez, Olivier; Meyer, Guy [Hopital Europeen Georges Pompidou, APHP, Respiratory and intensive care and, Paris (France); Universite Paris Descartes Sorbonne Paris Cite, Paris (France); INSERM Unite 765, Paris (France); Lefort, Catherine; Couchon, Sophie; Hernigou, Anne; Frija, Guy [Hopital Europeen Georges Pompidou, APHP, Departments of Radiology, Paris (France); Niarra, Ralph [Hopital Europeen Georges Pompidou, APHP, Clinical Epidemiology, Paris (France); Universite Paris Descartes Sorbonne Paris Cite, Paris (France); Chatellier, Gilles [Hopital Europeen Georges Pompidou, APHP, Clinical Epidemiology, Paris (France); Universite Paris Descartes Sorbonne Paris Cite, Paris (France); INSERM CIC-EC E4, Paris (France)

    2013-09-15

    To independently evaluate unenhanced, contrast-enhanced perfusion and angiographic MR sequences for pulmonary embolism (PE) diagnosis. Prospective investigation, including 274 patients who underwent perfusion, unenhanced 2D steady-state-free-precession (SSFP) and contrast-enhanced 3D angiographic MR sequences on a 1.5-T unit, in addition to CTA (CT angiography). Two independent readers evaluated each sequence independently in random order. Sensitivity, specificity, predictive values and inter-reader agreement were calculated for each sequence, excluding sequences judged inconclusive. Sensitivity was also calculated according to PE location. Contrast-enhanced angiographic sequences showed the highest sensitivity (82.9 and 89.7 %, reader 1 and reader 2, respectively), specificity (98.5 and 100 %) and agreement (kappa value 0.77). Unenhanced angiographic sequences, although less sensitive overall (68.7 and 76.4 %), were sensitive for the detection of proximal PE (92.7 and 100 %) and showed high specificity (96.1 and 99.1 %) and good agreement (kappa value 0.62). Perfusion sequences showed lower sensitivity (75.0 and 79.3 %), specificity (84.8 and 89.7 %) and agreement (kappa value 0.51), and a negative predictive value of 84.8 % at best. Compared with contrast-enhanced angiographic sequences, unenhanced sequences demonstrate lower sensitivity, except for proximal PE, but high specificity and agreement. The negative predictive value of perfusion sequences was insufficient to safely rule out PE. (orig.)

  18. Sequencing Cyclic Peptides by Multistage Mass Spectrometry

    Science.gov (United States)

    Mohimani, Hosein; Yang, Yu-Liang; Liu, Wei-Ting; Hsieh, Pei-Wen; Dorrestein, Pieter C.; Pevzner, Pavel A.

    2012-01-01

    Some of the most effective antibiotics (e.g., Vancomycin and Daptomycin) are cyclic peptides produced by non-ribosomal biosynthetic pathways. While hundreds of biomedically important cyclic peptides have been sequenced, the computational techniques for sequencing cyclic peptides are still in their infancy. Previous methods for sequencing peptide antibiotics and other cyclic peptides are based on Nuclear Magnetic Resonance spectroscopy, and require large amount (miligrams) of purified materials that, for most compounds, are not possible to obtain. Recently, development of mass spectrometry based methods has provided some hope for accurate sequencing of cyclic peptides using picograms of materials. In this paper we develop a method for sequencing of cyclic peptides by multistage mass spectrometry, and show its advantages over single stage mass spectrometry. The method is tested on known and new cyclic peptides from Bacillus brevis, Dianthus superbus and Streptomyces griseus, as well as a new family of cyclic peptides produced by marine bacteria. PMID:21751357

  19. Development of a Species-specific PCR Assay for Three Xanthomonas Species, Causing Bulb and Flower Diseases, Based on Their Genome Sequences

    Directory of Open Access Journals (Sweden)

    Chang-Gi Back

    2015-09-01

    Full Text Available In this study, we developed a species-specific PCR assay for rapid and accurate detection of three Xanthomonas species, X. axonopodis pv. poinsettiicola (XAP, X. hyacinthi (XH and X. campestris pv. zantedeschiae (XCZ, based on their draft genome sequences. XAP, XH and XCZ genomes consist of single chromosomes that contain 5,221, 4,395 and 7,986 protein coding genes, respectively. Species-specific primers were designed from variable regions of the draft genome sequence data and assessed by a PCR-based detection method. These primers were also tested for specificity against 17 allied Xanthomonas species as well as against the host DNA and the microbial community of the host surface. Three primer sets were found to be very specific and no amplification product was obtained with the host DNA and the microbial community of the host surface. In addition, a detection limit of 1 pg/μl per PCR reaction was detected when these primer sets were used to amplify corresponding bacterial DNAs. Therefore, these primer sets and the developed species-specific PCR assay represent a valuable, sensitive, and rapid diagnostic tool that can be used to detect three specific pathogens at early stages of infection and may help control diseases.

  20. Bellerophon: a program to detect chimeric sequences in multiple sequence alignments.

    Science.gov (United States)

    Huber, Thomas; Faulkner, Geoffrey; Hugenholtz, Philip

    2004-09-22

    Bellerophon is a program for detecting chimeric sequences in multiple sequence datasets by an adaption of partial treeing analysis. Bellerophon was specifically developed to detect 16S rRNA gene chimeras in PCR-clone libraries of environmental samples but can be applied to other nucleotide sequence alignments. Bellerophon is available as an interactive web server at http://foo.maths.uq.edu.au/~huber/bellerophon.pl

  1. Magnetic resonance imaging of the cirrhotic liver: Anupdate

    Institute of Scientific and Technical Information of China (English)

    Agnes Watanabe; Miguel Ramalho; Mamdoh AlObaidy; Hye Jin Kim; Fernanda G Velloni; Richard C Semelka

    2015-01-01

    Noninvasive imaging has become the standard forhepatocellular carcinoma (HCC) diagnosis in cirrhoticlivers. In this review paper, we go over the basics ofMR imaging in cirrhotic livers and describe the imagingappearance of a spectrum of hepatic nodules markingthe progression from regenerative nodules to low- andhigh-grade dysplastic nodules, and ultimately to HCCs.We detail and illustrate the typical imaging appearancesof different types of HCC including focal, multifocal,massive, diffuse/infiltrative, and intra-hepaticmetastases; with emphasis on the diagnostic value ofMR in imaging these lesions. We also shed some lighton liver imaging reporting and data system, and therole of different magnetic resonance imaging (MRI)contrast agents and future MRI techniques includingthe use of advanced MR pulse sequences and utilizationof hepatocyte-specific MRI contrast agents, and howthey might contribute to improving the diagnosticperformance of MRI in early stage HCC diagnosis.

  2. A sex-specific metabolite identified in a marine invertebrate utilizing phosphorus-31 nuclear magnetic resonance.

    Directory of Open Access Journals (Sweden)

    Robert A Kleps

    Full Text Available Hormone level differences are generally accepted as the primary cause for sexual dimorphism in animal and human development. Levels of low molecular weight metabolites also differ between men and women in circulating amino acids, lipids and carbohydrates and within brain tissue. While investigating the metabolism of blue crab tissues using Phosphorus-31 Nuclear Magnetic Resonance, we discovered that only the male blue crab (Callinectes sapidus contained a phosphorus compound with a chemical shift well separated from the expected phosphate compounds. Spectra obtained from male gills were readily differentiated from female gill spectra. Analysis from six years of data from male and female crabs documented that the sex-specificity of this metabolite was normal for this species. Microscopic analysis of male and female gills found no differences in their gill anatomy or the presence of parasites or bacteria that might produce this phosphorus compound. Analysis of a rare gynandromorph blue crab (laterally, half male and half female proved that this sex-specificity was an intrinsic biochemical process and was not caused by any variations in the diet or habitat of male versus female crabs. The existence of a sex-specific metabolite is a previously unrecognized, but potentially significant biochemical phenomenon. An entire enzyme system has been synthesized and activated only in one sex. Unless blue crabs are a unique species, sex-specific metabolites are likely to be present in other animals. Would the presence or absence of a sex-specific metabolite affect an animal's development, anatomy and biochemistry?

  3. Structure and Sequence Analyses of Clustered Protocadherins Reveal Antiparallel Interactions that Mediate Homophilic Specificity.

    Science.gov (United States)

    Nicoludis, John M; Lau, Sze-Yi; Schärfe, Charlotta P I; Marks, Debora S; Weihofen, Wilhelm A; Gaudet, Rachelle

    2015-11-03

    Clustered protocadherin (Pcdh) proteins mediate dendritic self-avoidance in neurons via specific homophilic interactions in their extracellular cadherin (EC) domains. We determined crystal structures of EC1-EC3, containing the homophilic specificity-determining region, of two mouse clustered Pcdh isoforms (PcdhγA1 and PcdhγC3) to investigate the nature of the homophilic interaction. Within the crystal lattices, we observe antiparallel interfaces consistent with a role in trans cell-cell contact. Antiparallel dimerization is supported by evolutionary correlations. Two interfaces, located primarily on EC2-EC3, involve distinctive clustered Pcdh structure and sequence motifs, lack predicted glycosylation sites, and contain residues highly conserved in orthologs but not paralogs, pointing toward their biological significance as homophilic interaction interfaces. These two interfaces are similar yet distinct, reflecting a possible difference in interaction architecture between clustered Pcdh subfamilies. These structures initiate a molecular understanding of clustered Pcdh assemblies that are required to produce functional neuronal networks. Copyright © 2015 Elsevier Ltd. All rights reserved.

  4. In silico site-directed mutagenesis informs species-specific predictions of chemical susceptibility derived from the Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool

    Science.gov (United States)

    The Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool was developed to address needs for rapid, cost effective methods of species extrapolation of chemical susceptibility. Specifically, the SeqAPASS tool compares the primary sequence (Level 1), functiona...

  5. Diagnosing ulnar neuropathy at the elbow using magnetic resonance neurography

    Energy Technology Data Exchange (ETDEWEB)

    Keen, Nayela N.; Chin, Cynthia T.; Saloner, David; Steinbach, Lynne S. [University of California San Francisco, Dept of Radiology and Biomedical Imaging, San Francisco, CA (United States); Engstrom, John W. [University of California San Francisco, Department of Neurology, San Francisco, CA (United States)

    2012-04-15

    Early diagnosis of ulnar neuropathy at the elbow is important. Magnetic resonance neurography (MRN) images peripheral nerves. We evaluated the usefulness of elbow MRN in diagnosing ulnar neuropathy at the elbow. The MR neurograms of 21 patients with ulnar neuropathy were reviewed retrospectively. MRN was performed prospectively on 10 normal volunteers. The MR neurograms included axial T1 and axial T2 fat-saturated and/or axial STIR sequences. The sensitivity and specificity of MRN in detecting ulnar neuropathy were determined. The mean ulnar nerve size in the symptomatic and normal groups was 0.12 and 0.06 cm{sup 2} (P < 0.001). The mean relative signal intensity in the symptomatic and normal groups was 2.7 and 1.4 (P < 0.01). When using a size of 0.08 cm{sup 2}, sensitivity was 95% and specificity was 80%. Ulnar nerve size and signal intensity were greater in patients with ulnar neuropathy. MRN is a useful test in evaluating ulnar neuropathy at the elbow. (orig.)

  6. Endoplasmic reticulum targeting sequence enhances HBV-specific cytotoxic T lymphocytes induced by a CTL epitope-based DNA vaccine

    International Nuclear Information System (INIS)

    Xu Wei; Chu Yiwei; Zhang Ruihua; Xu Huanbin; Wang Ying; Xiong Sidong

    2005-01-01

    CD8 + T cells play a critical role in protective immunity against Hepatitis B Virus (HBV). Epitope-based DNA vaccines expressing HBV-dominant CTL epitopes can be used as candidate vaccines capable of inducing cytotoxic T Lymphocytes (CTL) responses. A plasmid DNA encoding a CTL epitope of HBV core antigen, HBc 18-27 , was constructed. Intramuscular immunization of C57BL/6 mice with this DNA vaccine resulted in successful induction of HBV-specific CTL responses. In order to promote transportation of the peptide into endoplasmic reticulum (ER) to bind to MHC class I molecules for optimal class I antigen presentation, an ER targeting sequence (ERTS) was fused with the C 18-27 encoding gene. ERTS fusion significantly enhanced specific CD8 + T cell responses in terms of CTL cytolysis as well as IFN-γ secretion. This enhancement was correlated with promoted epitope presentation on target cell surface. We report here an enhanced immunogenicity of an epitope-based DNA vaccine using an ER targeting signal sequence, which has significant implications for future design of therapeutic HBV vaccine

  7. Magnetic resonance imaging in pediatric appendicitis: a systematic review

    International Nuclear Information System (INIS)

    Moore, Michael M.; Methratta, Sosamma T.; Kulaylat, Afif N.; Engbrecht, Brett W.; Hollenbeak, Christopher S.; Dillman, Jonathan R.

    2016-01-01

    Magnetic resonance imaging for the evaluation of appendicitis in children has rapidly increased recently. This change has been primarily driven by the desire to avoid CT radiation dose. This meta-analysis reviews the diagnostic performance of MRI for pediatric appendicitis and discusses current knowledge of cost-effectiveness. We used a conservative Haldane correction statistical method and found pooled diagnostic parameters including a sensitivity of 96.5% (95% confidence interval [CI]: 94.3-97.8%), specificity of 96.1% (95% CI: 93.5-97.7%), positive predictive value of 92.0% (95% CI: 89.3-94.0%) and negative predictive value of 98.3% (95% CI: 97.3-99.0%), based on 11 studies. Assessment of patient outcomes associated with MRI use at two institutions indicates that time to antibiotics was 4.7 h and 8.2 h, time to appendectomy was 9.1 h and 13.9 h, and negative appendectomy rate was 3.1% and 1.4%, respectively. Alternative diagnoses were present in ∝20% of cases, most commonly adnexal cysts and enteritis/colitis. Regarding technique, half-acquisition single-shot fast spin-echo (SSFSE) pulse sequences are crucial. While gadolinium-enhanced T1-weighted pulse sequences might be helpful, any benefit beyond non-contrast MRI has not been confirmed. Balanced steady-state free precession (SSFP) sequences are generally noncontributory. Protocols do not need to exceed five sequences; four-sequence protocols are commonly utilized. Sedation generally is not indicated; patients younger than 5 years might be attempted based on the child's ability to cooperate. A comprehensive pediatric cost-effectiveness analysis that includes both direct and indirect costs is needed. (orig.)

  8. Magnetic Resonance Imaging for Patellofemoral Chondromalacia: Is There a Role for T2 Mapping?

    Science.gov (United States)

    van Eck, Carola F; Kingston, R Scott; Crues, John V; Kharrazi, F Daniel

    2017-11-01

    Patellofemoral pain is common, and treatment is guided by the presence and grade of chondromalacia. To evaluate and compare the sensitivity and specificity in detecting and grading chondral abnormalities of the patella between proton density fat suppression (PDFS) and T2 mapping magnetic resonance imaging (MRI). Cohort study; Level of evidence, 2. A total of 25 patients who underwent MRI of the knee with both a PDFS sequence and T2 mapping and subsequently underwent arthroscopic knee surgery were included. The cartilage surface of the patella was graded on both MRI sequences by 2 independent, blinded radiologists. Cartilage was then graded during arthroscopic surgery by a sports medicine fellowship-trained orthopaedic surgeon. Reliability, sensitivity, specificity, and accuracy were determined for both MRI methods. The findings during arthroscopic surgery were considered the gold standard. Intraobserver and interobserver agreement for both PDFS (98.5% and 89.4%, respectively) and T2 mapping (99.4% and 91.3%, respectively) MRI were excellent. For T2 mapping, the sensitivity (61%) and specificity (64%) were comparable, whereas for PDFS there was a lower sensitivity (37%) but higher specificity (81%) in identifying cartilage abnormalities. This resulted in a similar accuracy for PDFS (59%) and T2 mapping (62%). Both PDFS and T2 mapping MRI were reliable but only moderately accurate in predicting patellar chondromalacia found during knee arthroscopic surgery.

  9. Towards predicting the encoding capability of MR fingerprinting sequences.

    Science.gov (United States)

    Sommer, K; Amthor, T; Doneva, M; Koken, P; Meineke, J; Börnert, P

    2017-09-01

    Sequence optimization and appropriate sequence selection is still an unmet need in magnetic resonance fingerprinting (MRF). The main challenge in MRF sequence design is the lack of an appropriate measure of the sequence's encoding capability. To find such a measure, three different candidates for judging the encoding capability have been investigated: local and global dot-product-based measures judging dictionary entry similarity as well as a Monte Carlo method that evaluates the noise propagation properties of an MRF sequence. Consistency of these measures for different sequence lengths as well as the capability to predict actual sequence performance in both phantom and in vivo measurements was analyzed. While the dot-product-based measures yielded inconsistent results for different sequence lengths, the Monte Carlo method was in a good agreement with phantom experiments. In particular, the Monte Carlo method could accurately predict the performance of different flip angle patterns in actual measurements. The proposed Monte Carlo method provides an appropriate measure of MRF sequence encoding capability and may be used for sequence optimization. Copyright © 2017 Elsevier Inc. All rights reserved.

  10. Haemodynamic imaging of thoracic stent-grafts by computational fluid dynamics (CFD): presentation of a patient-specific method combining magnetic resonance imaging and numerical simulations.

    Science.gov (United States)

    Midulla, Marco; Moreno, Ramiro; Baali, Adil; Chau, Ming; Negre-Salvayre, Anne; Nicoud, Franck; Pruvo, Jean-Pierre; Haulon, Stephan; Rousseau, Hervé

    2012-10-01

    In the last decade, there was been increasing interest in finding imaging techniques able to provide a functional vascular imaging of the thoracic aorta. The purpose of this paper is to present an imaging method combining magnetic resonance imaging (MRI) and computational fluid dynamics (CFD) to obtain a patient-specific haemodynamic analysis of patients treated by thoracic endovascular aortic repair (TEVAR). MRI was used to obtain boundary conditions. MR angiography (MRA) was followed by cardiac-gated cine sequences which covered the whole thoracic aorta. Phase contrast imaging provided the inlet and outlet profiles. A CFD mesh generator was used to model the arterial morphology, and wall movements were imposed according to the cine imaging. CFD runs were processed using the finite volume (FV) method assuming blood as a homogeneous Newtonian fluid. Twenty patients (14 men; mean age 62.2 years) with different aortic lesions were evaluated. Four-dimensional mapping of velocity and wall shear stress were obtained, depicting different patterns of flow (laminar, turbulent, stenosis-like) and local alterations of parietal stress in-stent and along the native aorta. A computational method using a combined approach with MRI appears feasible and seems promising to provide detailed functional analysis of thoracic aorta after stent-graft implantation. • Functional vascular imaging of the thoracic aorta offers new diagnostic opportunities • CFD can model vascular haemodynamics for clinical aortic problems • Combining CFD with MRI offers patient specific method of aortic analysis • Haemodynamic analysis of stent-grafts could improve clinical management and follow-up.

  11. Leishmania-specific surface antigens show sub-genus sequence variation and immune recognition.

    Directory of Open Access Journals (Sweden)

    Daniel P Depledge

    2010-09-01

    Full Text Available A family of hydrophilic acylated surface (HASP proteins, containing extensive and variant amino acid repeats, is expressed at the plasma membrane in infective extracellular (metacyclic and intracellular (amastigote stages of Old World Leishmania species. While HASPs are antigenic in the host and can induce protective immune responses, the biological functions of these Leishmania-specific proteins remain unresolved. Previous genome analysis has suggested that parasites of the sub-genus Leishmania (Viannia have lost HASP genes from their genomes.We have used molecular and cellular methods to analyse HASP expression in New World Leishmania mexicana complex species and show that, unlike in L. major, these proteins are expressed predominantly following differentiation into amastigotes within macrophages. Further genome analysis has revealed that the L. (Viannia species, L. (V. braziliensis, does express HASP-like proteins of low amino acid similarity but with similar biochemical characteristics, from genes present on a region of chromosome 23 that is syntenic with the HASP/SHERP locus in Old World Leishmania species and the L. (L. mexicana complex. A related gene is also present in Leptomonas seymouri and this may represent the ancestral copy of these Leishmania-genus specific sequences. The L. braziliensis HASP-like proteins (named the orthologous (o HASPs are predominantly expressed on the plasma membrane in amastigotes and are recognised by immune sera taken from 4 out of 6 leishmaniasis patients tested in an endemic region of Brazil. Analysis of the repetitive domains of the oHASPs has shown considerable genetic variation in parasite isolates taken from the same patients, suggesting that antigenic change may play a role in immune recognition of this protein family.These findings confirm that antigenic hydrophilic acylated proteins are expressed from genes in the same chromosomal region in species across the genus Leishmania. These proteins are

  12. Differentiation of Actinobacillus pleuropneumoniae strains by sequence analysis of 16S rDNA and ribosomal intergenic regions, and development of a species specific oligonucleotide for in situ detection

    DEFF Research Database (Denmark)

    Fussing, Vivian; Paster, Bruce J.; Dewhirst, Floyd E.

    1998-01-01

    . The larger RIS's were different between the 3 species tested. The sequence of the 16S ribosomal gene was determined for 8 serotypes of A. pleuropneumoniae. These sequences showed only minor base differences, indicating a close genetic relatedness of these serotypes within the species. An oligonucleotide DNA...... probe designed from the 16S rRNA gene sequence of A. pleuropneumoniae was specific for all strains of the target species and did not cross react with A. lignieresii, the closest known relative of A. pleuropneumoniae. This species-specific DNA probe labeled with fluorescein was used for in situ......The aims of this study were to characterize and determine intraspecies and interspecies relatedness of Actinobacillus pleuropneumoniae to Actinobacillus lignieresii and Actinobacillus suis by sequence analysis of the ribosomal operon and to find a species-specific area for in situ detection of A...

  13. Improved annotation of 3' untranslated regions and complex loci by combination of strand-specific direct RNA sequencing, RNA-Seq and ESTs.

    Directory of Open Access Journals (Sweden)

    Nicholas J Schurch

    Full Text Available The reference annotations made for a genome sequence provide the framework for all subsequent analyses of the genome. Correct and complete annotation in addition to the underlying genomic sequence is particularly important when interpreting the results of RNA-seq experiments where short sequence reads are mapped against the genome and assigned to genes according to the annotation. Inconsistencies in annotations between the reference and the experimental system can lead to incorrect interpretation of the effect on RNA expression of an experimental treatment or mutation in the system under study. Until recently, the genome-wide annotation of 3' untranslated regions received less attention than coding regions and the delineation of intron/exon boundaries. In this paper, data produced for samples in Human, Chicken and A. thaliana by the novel single-molecule, strand-specific, Direct RNA Sequencing technology from Helicos Biosciences which locates 3' polyadenylation sites to within +/- 2 nt, were combined with archival EST and RNA-Seq data. Nine examples are illustrated where this combination of data allowed: (1 gene and 3' UTR re-annotation (including extension of one 3' UTR by 5.9 kb; (2 disentangling of gene expression in complex regions; (3 clearer interpretation of small RNA expression and (4 identification of novel genes. While the specific examples displayed here may become obsolete as genome sequences and their annotations are refined, the principles laid out in this paper will be of general use both to those annotating genomes and those seeking to interpret existing publically available annotations in the context of their own experimental data.

  14. Impact of cadmium, cobalt and nickel on sequence-specific DNA binding of p63 and p73 in vitro and in cells

    International Nuclear Information System (INIS)

    Adámik, Matej; Bažantová, Pavla; Navrátilová, Lucie; Polášková, Alena; Pečinka, Petr; Holaňová, Lucie; Tichý, Vlastimil; Brázdová, Marie

    2015-01-01

    Highlights: • DNA binding of p53 family core domains is inhibited by cadmium, cobalt and nickel. • Binding to DNA protects p53 family core domains from metal induced inhibition. • Cadmium, cobalt and nickel induced inhibition was reverted by EDTA in vitro. - Abstract: Site-specific DNA recognition and binding activity belong to common attributes of all three members of tumor suppressor p53 family proteins: p53, p63 and p73. It was previously shown that heavy metals can affect p53 conformation, sequence-specific binding and suppress p53 response to DNA damage. Here we report for the first time that cadmium, nickel and cobalt, which have already been shown to disturb various DNA repair mechanisms, can also influence p63 and p73 sequence-specific DNA binding activity and transactivation of p53 family target genes. Based on results of electrophoretic mobility shift assay and luciferase reporter assay, we conclude that cadmium inhibits sequence-specific binding of all three core domains to p53 consensus sequences and abolishes transactivation of several promoters (e.g. BAX and MDM2) by 50 μM concentrations. In the presence of specific DNA, all p53 family core domains were partially protected against loss of DNA binding activity due to cadmium treatment. Effective cadmium concentration to abolish DNA–protein interactions was about two times higher for p63 and p73 proteins than for p53. Furthermore, we detected partial reversibility of cadmium inhibition for all p53 family members by EDTA. DTT was able to reverse cadmium inhibition only for p53 and p73. Nickel and cobalt abolished DNA–p53 interaction at sub-millimolar concentrations while inhibition of p63 and p73 DNA binding was observed at millimolar concentrations. In summary, cadmium strongly inhibits p53, p63 and p73 DNA binding in vitro and in cells in comparison to nickel and cobalt. The role of cadmium inhibition of p53 tumor suppressor family in carcinogenesis is discussed

  15. Impact of cadmium, cobalt and nickel on sequence-specific DNA binding of p63 and p73 in vitro and in cells

    Energy Technology Data Exchange (ETDEWEB)

    Adámik, Matej [Institute of Biophysics, Academy of Science of the Czech Republic, v.v.i., Královopolská 135, 612 65 Brno (Czech Republic); Bažantová, Pavla [Institute of Biophysics, Academy of Science of the Czech Republic, v.v.i., Královopolská 135, 612 65 Brno (Czech Republic); Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 701 03 Ostrava (Czech Republic); Navrátilová, Lucie; Polášková, Alena [Institute of Biophysics, Academy of Science of the Czech Republic, v.v.i., Královopolská 135, 612 65 Brno (Czech Republic); Pečinka, Petr [Institute of Biophysics, Academy of Science of the Czech Republic, v.v.i., Královopolská 135, 612 65 Brno (Czech Republic); Department of Biology and Ecology, Faculty of Science, University of Ostrava, Chittussiho 10, 701 03 Ostrava (Czech Republic); Holaňová, Lucie [Department of Chemical Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Palackého 1/3, 61242 Brno (Czech Republic); Tichý, Vlastimil [Institute of Biophysics, Academy of Science of the Czech Republic, v.v.i., Královopolská 135, 612 65 Brno (Czech Republic); Brázdová, Marie, E-mail: maruska@ibp.cz [Institute of Biophysics, Academy of Science of the Czech Republic, v.v.i., Královopolská 135, 612 65 Brno (Czech Republic); Department of Chemical Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Palackého 1/3, 61242 Brno (Czech Republic)

    2015-01-02

    Highlights: • DNA binding of p53 family core domains is inhibited by cadmium, cobalt and nickel. • Binding to DNA protects p53 family core domains from metal induced inhibition. • Cadmium, cobalt and nickel induced inhibition was reverted by EDTA in vitro. - Abstract: Site-specific DNA recognition and binding activity belong to common attributes of all three members of tumor suppressor p53 family proteins: p53, p63 and p73. It was previously shown that heavy metals can affect p53 conformation, sequence-specific binding and suppress p53 response to DNA damage. Here we report for the first time that cadmium, nickel and cobalt, which have already been shown to disturb various DNA repair mechanisms, can also influence p63 and p73 sequence-specific DNA binding activity and transactivation of p53 family target genes. Based on results of electrophoretic mobility shift assay and luciferase reporter assay, we conclude that cadmium inhibits sequence-specific binding of all three core domains to p53 consensus sequences and abolishes transactivation of several promoters (e.g. BAX and MDM2) by 50 μM concentrations. In the presence of specific DNA, all p53 family core domains were partially protected against loss of DNA binding activity due to cadmium treatment. Effective cadmium concentration to abolish DNA–protein interactions was about two times higher for p63 and p73 proteins than for p53. Furthermore, we detected partial reversibility of cadmium inhibition for all p53 family members by EDTA. DTT was able to reverse cadmium inhibition only for p53 and p73. Nickel and cobalt abolished DNA–p53 interaction at sub-millimolar concentrations while inhibition of p63 and p73 DNA binding was observed at millimolar concentrations. In summary, cadmium strongly inhibits p53, p63 and p73 DNA binding in vitro and in cells in comparison to nickel and cobalt. The role of cadmium inhibition of p53 tumor suppressor family in carcinogenesis is discussed.

  16. Evaluation of urogenital fistulas by magnetic resonance urography

    International Nuclear Information System (INIS)

    Mamere, Augusto Elias; Coelho, Rafael Darahem Souza; Cecin, Alexandre Oliveira; Feltrin, Leonir Terezinha; Lucchesi, Fabiano Rubiao; Seabra, Daniel

    2008-01-01

    Objective: Vesicovaginal and ureterovaginal fistulas are unusual complications secondary to pelvic surgery or pelvic diseases. The therapeutic success in these cases depends on an appropriate preoperative evaluation for diagnosis and visualization of the fistulous tract. The present study is aimed at demonstrating the potential of magnetic resonance urography for the diagnosis of vesicovaginal and ureterovaginal fistulas as well as for defining the fistulous tracts. Materials And Methods: Seven female patients clinically diagnosed with vesicovaginal or ureterovaginal fistulas had their medical records, radiological and magnetic resonance images retrospectively reviewed. Magnetic resonance urography included 3D-HASTE sequences with fat saturation. Results: Six patients presented vesicovaginal fistulas and, in one patient, a right-sided ureterovaginal fistula was diagnosed. Magnetic resonance urography allowed the demonstration of the fistulous tract in six (85.7%) of the seven patients evaluated in the present study, without the need of bladder catheterization or contrast injection. Conclusion: This study demonstrates both the potential and applicability of magnetic resonance urography in the evaluation of these types of fistulas. (author)

  17. Formal Specification and Description Language and Message Sequence Chart to Model and Validate Session Initiation Protocol Services

    OpenAIRE

    Sa'ed Abed; Mohammad H. Al Shayeji; Ovais Ahmed; Sahel Alouneh

    2016-01-01

    Session Initiation Protocol (SIP) is a signaling layer protocol for building, adjusting and ending sessions among participants including Internet conferences, telephone calls and multimedia distribution. SIP facilitates user movement by proxying and forwarding requests to the present location of the user. In this paper, we provide a formal Specification and Description Language (SDL) and Message Sequence Chart (MSC) to model and define the Internet Engineering Task Force (IETF) SIP protocol a...

  18. Use of next generation sequencing data to develop a qPCR method for specific detection of EU-unauthorized genetically modified Bacillus subtilis overproducing riboflavin.

    Science.gov (United States)

    Barbau-Piednoir, Elodie; De Keersmaecker, Sigrid C J; Delvoye, Maud; Gau, Céline; Philipp, Patrick; Roosens, Nancy H

    2015-11-11

    Recently, the presence of an unauthorized genetically modified (GM) Bacillus subtilis bacterium overproducing vitamin B2 in a feed additive was notified by the Rapid Alert System for Food and Feed (RASFF). This has demonstrated that a contamination by a GM micro-organism (GMM) may occur in feed additives and has confronted for the first time,the enforcement laboratories with this type of RASFF. As no sequence information of this GMM nor any specific detection or identification method was available, Next GenerationSequencing (NGS) was used to generate sequence information. However, NGS data analysis often requires appropriate tools, involving bioinformatics expertise which is not alwayspresent in the average enforcement laboratory. This hampers the use of this technology to rapidly obtain critical sequence information in order to be able to develop a specific qPCRdetection method. Data generated by NGS were exploited using a simple BLAST approach. A TaqMan® qPCR method was developed and tested on isolated bacterial strains and on the feed additive directly. In this study, a very simple strategy based on the common BLAST tools that can be used by any enforcement lab without profound bioinformatics expertise, was successfully used toanalyse the B. subtilis data generated by NGS. The results were used to design and assess a new TaqMan® qPCR method, specifically detecting this GM vitamin B2 overproducing bacterium. The method complies with EU critical performance parameters for specificity, sensitivity, PCR efficiency and repeatability. The VitB2-UGM method also could detect the B. subtilis strain in genomic DNA extracted from the feed additive, without prior culturing step. The proposed method, provides a crucial tool for specifically and rapidly identifying this unauthorized GM bacterium in food and feed additives by enforcement laboratories. Moreover, this work can be seen as a case study to substantiate how the use of NGS data can offer an added value to easily

  19. Pulseq-Graphical Programming Interface: Open source visual environment for prototyping pulse sequences and integrated magnetic resonance imaging algorithm development.

    Science.gov (United States)

    Ravi, Keerthi Sravan; Potdar, Sneha; Poojar, Pavan; Reddy, Ashok Kumar; Kroboth, Stefan; Nielsen, Jon-Fredrik; Zaitsev, Maxim; Venkatesan, Ramesh; Geethanath, Sairam

    2018-03-11

    To provide a single open-source platform for comprehensive MR algorithm development inclusive of simulations, pulse sequence design and deployment, reconstruction, and image analysis. We integrated the "Pulseq" platform for vendor-independent pulse programming with Graphical Programming Interface (GPI), a scientific development environment based on Python. Our integrated platform, Pulseq-GPI, permits sequences to be defined visually and exported to the Pulseq file format for execution on an MR scanner. For comparison, Pulseq files using either MATLAB only ("MATLAB-Pulseq") or Python only ("Python-Pulseq") were generated. We demonstrated three fundamental sequences on a 1.5 T scanner. Execution times of the three variants of implementation were compared on two operating systems. In vitro phantom images indicate equivalence with the vendor supplied implementations and MATLAB-Pulseq. The examples demonstrated in this work illustrate the unifying capability of Pulseq-GPI. The execution times of all the three implementations were fast (a few seconds). The software is capable of user-interface based development and/or command line programming. The tool demonstrated here, Pulseq-GPI, integrates the open-source simulation, reconstruction and analysis capabilities of GPI Lab with the pulse sequence design and deployment features of Pulseq. Current and future work includes providing an ISMRMRD interface and incorporating Specific Absorption Ratio and Peripheral Nerve Stimulation computations. Copyright © 2018 Elsevier Inc. All rights reserved.

  20. Secretin-enhanced magnetic resonance cholangiopancreaticography: value for the diagnosis of chronic pancreatitis

    International Nuclear Information System (INIS)

    Heverhagen, J.T.; Burbelko, M.; Schenck zu Schweinsberg, T.; Funke, C.; Wecker, C.; Walthers, E.M.; Rominger, M.

    2007-01-01

    Endoscopic retrograde cholangiopancreaticography (ERCP) is the morphologic gold standard for the diagnosis of chronic pancreatitis. Magnetic Resonance Imaging (MRI) enables the visualization of not only the pancreatic duct but also the surrounding parenchyma using T2- and T1-weighted sequences before and after the application of a contrast agent. Moreover, it allows the depiction of ductal segments distal to a stenosis or occlusion. However, conventional Magnetic Resonance Cholangiopancreaticography (MRCP) was not able to achieve accuracy similar to that of ERCP. Despite many technological innovations, such as fast breath-hold acquisitions or respiratory-gated 3D sequences, this drawback could not be overcome. In recent years, secretin-enhanced MRCP has been used for the diagnosis of chronic pancreatitis. A recent study showed that secretin not only improves the visibility of the pancreatic duct and its side branches but it also enhances the diagnostic accuracy of MRCP. The sensitivity, specificity, and positive and negative predictive values were improved by the application of secretin. Moreover, the agreement between independent observers increased after the use of secretin. In addition, quantitative post-processing tools have been developed that enable the measurement of the exocrine pancreatic output non-invasively using secretin-enhanced MRCP. These tools facilitate applications, such as functional follow-up after pancreaticogastrostomy and pancreaticogastric anastomoses, evaluation of the functional status of the graft after pancreas transplantation and follow-up of pancreatic drainage procedures and duct disruption. (orig.)

  1. ABC of the cardiac magnetic resonance. Part 1: anatomy and function

    International Nuclear Information System (INIS)

    Loureiro, Ricardo; Rached, Heron; Castro, Claudio C.; Cerri, Giovanni G.; Favaro, Daniele; Baptista, Luciana; Andrade, Joalbo; Rochitte, Carlos E.; Parga Filho, Jose; Avila, Luiz F.; Piva, Rosa M.V.

    2003-01-01

    The objective of this work is to demonstrate the fundamental concepts, the basic sequences and the clinical and potential applications of cardiac magnetic resonance as a diagnostic technique in updated radiology and cardiology practices. In this first part, we present the basic planning of the cardiac image acquisition, the nomenclature and standardized myocardial segmentation, image synchronization principles for electrocardiogram and the heart functional and anatomical evaluation by cardiac magnetic resonance. (author)

  2. Value of non-contrast sequences in magnetic resonance angiography of hepatic arterial vasculature

    Energy Technology Data Exchange (ETDEWEB)

    Kalra, Vivek B., E-mail: vivek.kalra@yale.edu [Department of Diagnostic Radiology, Yale School of Medicine, Box 208042, Tompkins East 2, 333 Cedar Street, New Haven, CT 06520-8042, United States of America (United States); Gilbert, John W., E-mail: jwgilbert@partners.org [Department of Radiology, Brigham and Women' s Hospital, Harvard Medical School, Francis Street, Boston, MA 02115, United States of America (United States); Krishnamoorthy, Saravanan, E-mail: sk3552@columbia.edu [Department of Radiology, Columbia University Medical Center, Milstein 3rd Fl, New York NY 10032 United States (United States); Cornfeld, Daniel, E-mail: daniel.cornfeld@yale.edu [Department of Diagnostic Radiology, Yale School of Medicine, Box 208042, Tompkins East 2, 333 Cedar St, New Haven, CT 06520-8042, United States of America (United States)

    2014-06-15

    Objective: To evaluate value of adding non-contrast MR angiographic sequence (In-Flow Inversion Recovery [IFIR]) to standard fat-suppressed T1-weighted postcontrast sequence (3D spoiled gradient echo [3D-GRE]) for evaluating hepatic arterial anatomy. Methods: Retrospective evaluation of 30 consecutive patients undergoing multiphase liver MRI. Individual vessels for IFIR/3D-GRE sequences were evaluated by two blinded readers using a four-point scale. Statistical analysis was performed using the Wilcoxon signed-rank test for vessel conspicuity between IFIR/3D-GRE sequences. Results: IFIR alone diagnostically imaged 8.1% of vessels, 3D-GRE alone 25.8%, 55.8% by both 3D-GRE/IFIR, and 10.3% of vessels by neither. Two patients with variant vascular anatomy were visualized with both sequences. Addition of IFIR to 3D-GRE resulted in statistically significant increase in arterial visualization (p < 0.001), 10% relative increase in identified vessels, and 3–5 mi increase in acquisition time for total scan time of 30–35 min. Conclusions: IFIR may be a useful adjunct to 3D-GRE in hepatic angiography without adding considerably to scan time. 10% more hepatic arteries were seen when combining information from IFIR/3D-GRE vs. 3D-GRE alone.

  3. Value of magnetic resonance imaging in prenatal diagnosis of placental accretism

    International Nuclear Information System (INIS)

    Francisco, Viviane Vieira; Goldman, Suzan Menasce; Faria, Juliano; Szejnfeld, Jacob

    2006-01-01

    Purpose: to establish the main signs of placental accretism in magnetic resonance imaging (MRI) in patients with clinical suspicion and to estimate the benefit of this method. Methods: prospective transversal study with 15 patients suspected of placental accretism, referred between March 2003 and February 2006. Gestational age varied from 20 to 31 weeks. All patients underwent MRI to study the placenta and had previously done an ultrasonography. Material was sent to histological study. MRI was done on Magnetom Impact and Sonata Maestro Class Siemens R , with acquired sequences HASTE, TURBO SPIN in axial, sagittal, coronal planes and echo gradient (GE R ), pre- and post-dynamic contrast in the best plan for acquisition. Images were analyzed by a team of two radiologists. Results: mean gestational age was 24.3 weeks. We studied seven placenta previa (47%), six anterior placentas (40%) and two posterior placentas (13%). Ultrasonography was positive in 80% of the placentas and MRI in 53%. However, echography had a low concordance with anatomic pathological studies by Kappa test (11%), revealing 75% of sensitivity, 14% of specificity, 50% as positive predictive value (PPV) and 33% as negative predictive value (NPV). MRI had an excellent concordance with anatomic pathological studies (0.86), showing 100% of sensitivity, 86% of specificity, 89% as PPV and 100% as NPV. Conclusions: MRI is useful for placental accretism diagnosis. The principal findings are transmural hyper-signal, the loss of continuity in myometrial wall in fast sequences and the identification of vessels invading myometrial layer in dynamic sequences. (author)

  4. Magnetic resonance angiography of fetal vasculature at 3.0 T

    OpenAIRE

    Neelavalli, Jaladhar; Krishnamurthy, Uday; Jella, Pavan K.; Mody, Swati S.; Yadav, Brijesh K.; Hendershot, Kelly; Hernandez-Andrade, Edgar; Yeo, Lami; Cabrera, Maria D.; Haacke, Ewart M.; Hassan, Sonia S.; Romero, Roberto

    2016-01-01

    Magnetic resonance angiography has not been used much previously for visualizing fetal vessels in utero for reasons that include a contraindication for the use of exogenous contrast agents, maternal respiratory motion and fetal motion. In this work, we report the feasibility of using an appropriately modified clinical time-of-flight magnetic resonance imaging sequence for non-contrast angiography of human fetal and placental vessels at 3.0 T. Using this 2D angiography technique, it is possibl...

  5. ABC of the cardiac magnetic resonance. Part 1: perfusion, viability and coronary anatomy

    International Nuclear Information System (INIS)

    Loureiro, Ricardo; Rached, Heron; Castro, Claudio C.; Cerri, Giovanni G.; Favaro, Daniele; Baptista, Luciana; Andrade, Joalbo; Rochitte, Carlos E.; Parga Filho, Jose; Avila, Luiz F.; Piva, Rosa M.V.

    2003-01-01

    The objective of this work is to demonstrate the fundamental concepts, the basic sequences and the clinical and potential applications of cardiac magnetic resonance as a diagnostic technique in updated radiology and cardiology practices. In this second part, we present basic aspects of the cardiac magnetic resonance application in the coronary anatomy and myocardial perfusion and viability. (author)

  6. Targeted sequencing of clade-specific markers from skin microbiomes for forensic human identification.

    Science.gov (United States)

    Schmedes, Sarah E; Woerner, August E; Novroski, Nicole M M; Wendt, Frank R; King, Jonathan L; Stephens, Kathryn M; Budowle, Bruce

    2018-01-01

    The human skin microbiome is comprised of diverse communities of bacterial, eukaryotic, and viral taxa and contributes millions of additional genes to the repertoire of human genes, affecting human metabolism and immune response. Numerous genetic and environmental factors influence the microbiome composition and as such contribute to individual-specific microbial signatures which may be exploited for forensic applications. Previous studies have demonstrated the potential to associate skin microbial profiles collected from touched items to their individual owner, mainly using unsupervised methods from samples collected over short time intervals. Those studies utilize either targeted 16S rRNA or shotgun metagenomic sequencing to characterize skin microbiomes; however, these approaches have limited species and strain resolution and susceptibility to stochastic effects, respectively. Clade-specific markers from the skin microbiome, using supervised learning, can predict individual identity using skin microbiomes from their respective donors with high accuracy. In this study the hidSkinPlex is presented, a novel targeted sequencing method using skin microbiome markers developed for human identification. The hidSkinPlex (comprised of 286 bacterial (and phage) family-, genus-, species-, and subspecies-level markers), initially was evaluated on three bacterial control samples represented in the panel (i.e., Propionibacterium acnes, Propionibacterium granulosum, and Rothia dentocariosa) to assess the performance of the multiplex. The hidSkinPlex was further evaluated for prediction purposes. The hidSkinPlex markers were used to attribute skin microbiomes collected from eight individuals from three body sites (i.e., foot (Fb), hand (Hp) and manubrium (Mb)) to their host donor. Supervised learning, specifically regularized multinomial logistic regression and 1-nearest-neighbor classification were used to classify skin microbiomes to their hosts with up to 92% (Fb), 96% (Mb

  7. Locomotor sequence learning in visually guided walking

    DEFF Research Database (Denmark)

    Choi, Julia T; Jensen, Peter; Nielsen, Jens Bo

    2016-01-01

    walking. In addition, we determined how age (i.e., healthy young adults vs. children) and biomechanical factors (i.e., walking speed) affected the rate and magnitude of locomotor sequence learning. The results showed that healthy young adults (age 24 ± 5 years, N = 20) could learn a specific sequence...... of step lengths over 300 training steps. Younger children (age 6-10 years, N = 8) have lower baseline performance, but their magnitude and rate of sequence learning was the same compared to older children (11-16 years, N = 10) and healthy adults. In addition, learning capacity may be more limited...... to modify step length from one trial to the next. Our sequence learning paradigm is derived from the serial reaction-time (SRT) task that has been used in upper limb studies. Both random and ordered sequences of step lengths were used to measure sequence-specific and sequence non-specific learning during...

  8. Sequence specificity of alkali-labile DNA damage photosensitized by suprofen.

    Science.gov (United States)

    Starrs, S M; Davies, R J

    2000-09-01

    On irradiation at UVB wavelengths, in aerated neutral aqueous solution, the anti-inflammatory drug suprofen (SP) photosensitizes the production of alkali-labile cleavage sites in DNA much more efficiently than direct strand breaks. It is active at submillimolar concentrations despite having no significant binding affinity for DNA. Gel sequencing studies utilizing 32P-end-labeled oligonucleotides have revealed that piperidine-sensitive lesions are formed predominantly at the positions of guanine (G) bases, with the extent of modification being UV dose- and SP concentration-dependent. Quite distinct patterns of G-specific damage are observed in single-stranded and duplex DNA molecules. The uniform attack at all G residues in single-stranded DNA, which is enhanced in D2O, is compatible with a Type-II mechanism. SP is a known generator of singlet oxygen whose participation in the reaction is supported by the effects of quenchers and scavengers. In duplex DNA, piperidine-induced cleavage occurs with high selectivity at the 5'-G of GG and (less prominently) GA doublets. This behavior is characteristic of a Type-I process involving electron transfer from DNA to photoexcited SP molecules. The ability of SP to sensitize the formation of Type-I and Type-II photo-oxidation products from 2'-deoxyguanosine attests to the feasibility of competing mechanisms in DNA.

  9. The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes.

    Science.gov (United States)

    Shmakov, Sergey A; Sitnik, Vassilii; Makarova, Kira S; Wolf, Yuri I; Severinov, Konstantin V; Koonin, Eugene V

    2017-09-19

    Clustered regularly interspaced short palindromic repeats and CRISPR-associated protein (CRISPR-Cas) systems store the memory of past encounters with foreign DNA in unique spacers that are inserted between direct repeats in CRISPR arrays. For only a small fraction of the spacers, homologous sequences, called protospacers, are detectable in viral, plasmid, and microbial genomes. The rest of the spacers remain the CRISPR "dark matter." We performed a comprehensive analysis of the spacers from all CRISPR- cas loci identified in bacterial and archaeal genomes, and we found that, depending on the CRISPR-Cas subtype and the prokaryotic phylum, protospacers were detectable for 1% to about 19% of the spacers (~7% global average). Among the detected protospacers, the majority, typically 80 to 90%, originated from viral genomes, including proviruses, and among the rest, the most common source was genes that are integrated into microbial chromosomes but are involved in plasmid conjugation or replication. Thus, almost all spacers with identifiable protospacers target mobile genetic elements (MGE). The GC content, as well as dinucleotide and tetranucleotide compositions, of microbial genomes, their spacer complements, and the cognate viral genomes showed a nearly perfect correlation and were almost identical. Given the near absence of self-targeting spacers, these findings are most compatible with the possibility that the spacers, including the dark matter, are derived almost completely from the species-specific microbial mobilomes. IMPORTANCE The principal function of CRISPR-Cas systems is thought to be protection of bacteria and archaea against viruses and other parasitic genetic elements. The CRISPR defense function is mediated by sequences from parasitic elements, known as spacers, that are inserted into CRISPR arrays and then transcribed and employed as guides to identify and inactivate the cognate parasitic genomes. However, only a small fraction of the CRISPR spacers

  10. Brain pathology after mild traumatic brain injury: an exploratory study by repeated magnetic resonance examination.

    Science.gov (United States)

    Lannsjö, Marianne; Raininko, Raili; Bustamante, Mariana; von Seth, Charlotta; Borg, Jörgen

    2013-09-01

    To explore brain pathology after mild traumatic brain injury by repeated magnetic resonance examination. A prospective follow-up study. Nineteen patients with mild traumatic brain injury presenting with Glasgow Coma Scale (GCS) 14-15. The patients were examined on day 2 or 3 and 3-7 months after the injury. The magnetic resonance protocol comprised conventional T1- and T2-weighted sequences including fluid attenuated inversion recovery (FLAIR), two susceptibility-weighted sequences to reveal haemorrhages, and diffusion-weighted sequences. Computer-aided volume comparison was performed. Clinical outcome was assessed by the Rivermead Post-Concussion Symptoms Questionnaire (RPQ), Hospital Anxiety and Depression Scale (HADS) and Glasgow Outcome Scale Extended (GOSE). At follow-up, 7 patients (37%) reported ≥  3 symptoms in RPQ, 5 reported some anxiety and 1 reported mild depression. Fifteen patients reported upper level of good recovery and 4 patients lower level of good recovery (GOSE 8 and 7, respectively). Magnetic resonance pathology was found in 1 patient at the first examination, but 4 patients (21%) showed volume loss at the second examination, at which 3 of them reported GOSE scores of 8. Loss of brain volume, demonstrated by computer-aided magnetic resonance imaging volumetry, may be a feasible marker of brain pathology after mild traumatic brain injury.

  11. Resonance ionization scheme development for europium

    Energy Technology Data Exchange (ETDEWEB)

    Chrysalidis, K., E-mail: katerina.chrysalidis@cern.ch; Goodacre, T. Day; Fedosseev, V. N.; Marsh, B. A. [CERN (Switzerland); Naubereit, P. [Johannes Gutenberg-Universität, Institiut für Physik (Germany); Rothe, S.; Seiffert, C. [CERN (Switzerland); Kron, T.; Wendt, K. [Johannes Gutenberg-Universität, Institiut für Physik (Germany)

    2017-11-15

    Odd-parity autoionizing states of europium have been investigated by resonance ionization spectroscopy via two-step, two-resonance excitations. The aim of this work was to establish ionization schemes specifically suited for europium ion beam production using the ISOLDE Resonance Ionization Laser Ion Source (RILIS). 13 new RILIS-compatible ionization schemes are proposed. The scheme development was the first application of the Photo Ionization Spectroscopy Apparatus (PISA) which has recently been integrated into the RILIS setup.

  12. Initial Clinical Experience in Multiple Myeloma Staging by Means of Whole-Body Resonance Techniques

    International Nuclear Information System (INIS)

    Gallego, J. I.; Concepcion, L.; Alonso, S.; Sanchez, B.; Manzi, F.

    2003-01-01

    To develop a magnetic resonance (MR) exploratory technique equivalent to serial bone X-ray, and to compare their precision in the staging of multiple myeloma (MM) patients. Multiple acquisition T1-weights TSE and STIR sequences in the coronal plane were performed. Ten healthy volunteers and 11 multiple myeloma diagnosed patients were included. The visualization of bony structures was particularly noted,with special attention given to those which would normally be included in a serial bone X-ray. In the case of the patients, a comparison was made between diagnostic capacities of the MR sequences. MR highlighters significantly more (p<0.05) bony elements than did the serial bone X-ray. This was greatly due to a sequential displacement of the scanner bed, allowing for field-of-views which were minimally from head to third proximal of the leg. Magnetic resonance detected a significantly higher number (p<0.05) of lesions. It was, in turn, capable of revealing greater lesion extensions, even to the point of implying staging classification changes in 18% of the patients. The utilization of whole-body MR techniques in multiple myeloma patients is feasible and clinically beneficial. MR is both more sensitive and more specific than serial bone X-ray for evaluation of bony lesions in MM. It is currently serving as a valid alternative in a growing numbers of patients. (Author) 10 refs

  13. SATB1 regulates SPARC expression in K562 cell line through binding to a specific sequence in the third intron

    International Nuclear Information System (INIS)

    Li, K.; Cai, R.; Dai, B.B.; Zhang, X.Q.; Wang, H.J.; Ge, S.F.; Xu, W.R.; Lu, J.

    2007-01-01

    Special AT-rich binding protein 1 (SATB1), a cell type-specific nuclear matrix attachment region (MAR) DNA-binding protein, tethers to a specific DNA sequence and regulates gene expression through chromatin remodeling and HDAC (histone deacetylase complex) recruitment. In this study, a SATB1 eukaryotic expression plasmid was transfected into the human erythroleukemia K562 cell line and individual clones that stably over-expressed the SATB1 protein were isolated. Microarray analysis revealed that hundreds of genes were either up- or down-regulated in the SATB1 over-expressing K562 cell lines. One of these was the extra-cellular matrix glycoprotein, SPARC (human secreted protein acidic and rich in cysteine). siRNA knock-down of SATB1 also reduced SPARC expression, which was consistent with elevated SPARC levels in the SATB1 over-expressing cell line. Bioinformatics software Mat-inspector showed that a 17 bp DNA sequence in the third intron of SPARC possessed a high potential for SATB1 binding; a finding confirmed by Chromatin immunoprecipitation (ChIP) with anti-SATB1 antibody. Our results show for the first time that forced-expression of SATB1 in K562 cells triggers SPARC up-regulation by binding to a 17 bp DNA sequence in the third intron

  14. Ultra-small v-shaped gold split ring resonators for biosensing using fundamental magnetic resonance in the visible spectrum

    Science.gov (United States)

    Mauluidy Soehartono, Alana; Mueller, Aaron David; Tobing, Landobasa Yosef Mario; Chan, Kok Ken; Zhang, Dao Hua; Yong, Ken-Tye

    2017-10-01

    Strong light localization within metal nanostructures occurs by collective oscillations of plasmons in the form of electric and magnetic resonances. This so-called localized surface plasmon resonance (LSPR) has gained much interest in the development of low-cost sensing platforms in the visible spectrum. However, demonstrations of LSPR-based sensing are mostly limited to electric resonances due to the technological limitations for achieving magnetic resonances in the visible spectrum. In this work, we report the first demonstration of LSPR sensing based on fundamental magnetic resonance in the visible spectrum using ultrasmall gold v-shaped split ring resonators. Specifically, we show the ability for detecting adsorption of bovine serum albumin and cytochrome c biomolecules at monolayer levels, and the selective binding of protein A/G to immunoglobulin G.

  15. Protocols for 16S rDNA Array Analyses of Microbial Communities by Sequence-Specific Labeling of DNA Probes

    Directory of Open Access Journals (Sweden)

    Knut Rudi

    2003-01-01

    Full Text Available Analyses of complex microbial communities are becoming increasingly important. Bottlenecks in these analyses, however, are the tools to actually describe the biodiversity. Novel protocols for DNA array-based analyses of microbial communities are presented. In these protocols, the specificity obtained by sequence-specific labeling of DNA probes is combined with the possibility of detecting several different probes simultaneously by DNA array hybridization. The gene encoding 16S ribosomal RNA was chosen as the target in these analyses. This gene contains both universally conserved regions and regions with relatively high variability. The universally conserved regions are used for PCR amplification primers, while the variable regions are used for the specific probes. Protocols are presented for DNA purification, probe construction, probe labeling, and DNA array hybridizations.

  16. Noncontrast Magnetic Resonance Lymphography.

    Science.gov (United States)

    Arrivé, Lionel; Derhy, Sarah; El Mouhadi, Sanaâ; Monnier-Cholley, Laurence; Menu, Yves; Becker, Corinne

    2016-01-01

    Different imaging techniques have been used for the investigation of the lymphatic channels and lymph glands. Noncontrast magnetic resonance (MR) lymphography has significant advantages in comparison with other imaging modalities. Noncontrast MR lymphography uses very heavily T2-weighted fast spin echo sequences which obtain a nearly complete signal loss in tissue background and specific display of lymphatic vessels with a long T2 relaxation time. The raw data can be processed with different algorithms such as maximum intensity projection algorithm to obtain an anatomic representation. Standard T2-weighted MR images easily demonstrate the location of edema. It appears as subcutaneous infiltration of soft tissue with a classical honeycomb pattern. True collection around the muscular area may be demonstrated in case of severe lymphedema. Lymph nodes may be normal in size, number, and signal intensity; in other cases, lymph nodes may be smaller in size or number of lymph nodes may be restricted. MR lymphography allows a classification of lymphedema in aplasia (no collecting vessels demonstrated); hypoplasia (a small number of lymphatic vessels), and numerical hyperplasia or hyperplasia (with an increased number of lymphatic vessels of greater and abnormal diameter). Noncontrast MR lymphography is a unique noninvasive imaging modality for the diagnosis of lymphedema. It can be used for positive diagnosis, differential diagnosis, and specific evaluation of lymphedema severity. It may also be used for follow-up evaluation after treatment. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

  17. Concordance of the ForenSeq™ system and characterisation of sequence-specific autosomal STR alleles across two major population groups.

    Science.gov (United States)

    Devesse, Laurence; Ballard, David; Davenport, Lucinda; Riethorst, Immy; Mason-Buck, Gabriella; Syndercombe Court, Denise

    2018-05-01

    By using sequencing technology to genotype loci of forensic interest it is possible to simultaneously target autosomal, X and Y STRs as well as identity, ancestry and phenotypic informative SNPs, resulting in a breadth of data obtained from a single run that is considerable when compared to that generated with standard technologies. It is important however that this information aligns with the genotype data currently obtained using commercially available kits for CE-based investigations such that results are compatible with existing databases and hence can be of use to the forensic community. In this work, 400 samples were typed using commercially available STR kits and CE, as well as using the Ilumina ForenSeq™ DNA Signature Prep Kit and MiSeq ® FGx to assess concordance of autosomal STRs and population variability. Results show a concordance rate between the two technologies exceeding 99.98% while numerous novel sequence based alleles are described. In order to make use of the sequence variation observed, sequence specific allele frequencies were generated for White British and British Chinese populations. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. Determination of allergen specificity by heavy chains in grass pollen allergen-specific IgE antibodies.

    Science.gov (United States)

    Gadermaier, Elisabeth; Flicker, Sabine; Lupinek, Christian; Steinberger, Peter; Valenta, Rudolf

    2013-04-01

    Affinity and clonality of allergen-specific IgE antibodies are important determinants for the magnitude of IgE-mediated allergic inflammation. We sought to analyze the contribution of heavy and light chains of human allergen-specific IgE antibodies for allergen specificity and to test whether promiscuous pairing of heavy and light chains with different allergen specificity allows binding and might affect affinity. Ten IgE Fabs specific for 3 non-cross-reactive major timothy grass pollen allergens (Phl p 1, Phl p 2, and Phl p 5) obtained by means of combinatorial cloning from patients with grass pollen allergy were used to construct stable recombinant single chain variable fragments (ScFvs) representing the original Fabs and shuffled ScFvs in which heavy chains were recombined with light chains from IgE Fabs with specificity for other allergens by using the pCANTAB 5 E expression system. Possible ancestor genes for the heavy chain and light chain variable region-encoding genes were determined by using sequence comparison with the ImMunoGeneTics database, and their chromosomal locations were determined. Recombinant ScFvs were tested for allergen specificity and epitope recognition by means of direct and sandwich ELISA, and affinity by using surface plasmon resonance experiments. The shuffling experiments demonstrate that promiscuous pairing of heavy and light chains is possible and maintains allergen specificity, which is mainly determined by the heavy chains. ScFvs consisting of different heavy and light chains exhibited different affinities and even epitope specificity for the corresponding allergen. Our results indicate that allergen specificity of allergen-specific IgE is mainly determined by the heavy chains. Different heavy and light chain pairings in allergen-specific IgE antibodies affect affinity and epitope specificity and thus might influence clinical reactivity to allergens. Copyright © 2012 American Academy of Allergy, Asthma & Immunology. Published by

  19. Development of Prevotella intermedia-specific PCR primers based on the nucleotide sequences of a DNA probe Pig27.

    Science.gov (United States)

    Kim, Min Jung; Hwang, Kyung Hwan; Lee, Young-Seok; Park, Jae-Yoon; Kook, Joong-Ki

    2011-03-01

    The aim of this study was to develop Prevotella intermedia-specific PCR primers based on the P. intermedia-specific DNA probe. The P. intermedia-specific DNA probe was screened by inverted dot blot hybridization and confirmed by Southern blot hybridization. The nucleotide sequences of the species-specific DNA probes were determined using a chain termination method. Southern blot analysis showed that the DNA probe, Pig27, detected only the genomic DNA of P. intermedia strains. PCR showed that the PCR primers, Pin-F1/Pin-R1, had species-specificity for P. intermedia. The detection limits of the PCR primer sets were 0.4pg of the purified genomic DNA of P. intermedia ATCC 49046. These results suggest that the PCR primers, Pin-F1/Pin-R1, could be useful in the detection of P. intermedia as well as in the development of a PCR kit in epidemiological studies related to periodontal diseases. Crown Copyright © 2010. Published by Elsevier B.V. All rights reserved.

  20. Sequence specific DNA binding by P53 is enhanced by ionizing radiation and is mediated via DNA-PK activity

    International Nuclear Information System (INIS)

    Kachnic, L.A.; Wunsch, H.; Mekeel, K.L.; De Frank, J.S.; Powell, S.N.

    1996-01-01

    Purpose: P53 is known to be involved in the cellular response to DNA damage. It mediates many of its effects by acting as a transcription factor via sequence-specific DNA binding. The half-life of p53 is prolonged following DNA damage, and this results in elevated levels of p53 for a period of 2-8 hours. The increase in p53 is often relatively small, but this produces significant stimulation of a downstream gene such as p21(WAF1/cip1). We investigated post-translational modification of p53 following ionizing radiation damage. Materials and Methods: The response of normal Balb-C mouse fibroblasts (FC) to ionizing radiation (IR, 8 Gy) was measured at 0,3,6,9 and 24 hours, by the levels of p53, p21, flow cytometry and the electrophoretic mobility shift assay (EMSA). EMSA utilized a 26 bp consensus sequence end-labeled oligonucleotide to measure sequence-specific p53 binding. P53 specificity was confirmed by an enhanced mobility shift (retardation) when using p53 antibody. Comparison was made with scid fibroblasts (FS) and FC cells transfected with a plasmid (CX3) containing mutant p53 (alanine-143) or infected with a retrovirus containing the E6 protein of human papilloma virus type 16. Results: The response of p53 to DNA damage shows a 3-fold increase at 3-6 hours, and was not significantly different between FC and FS. FC-CX3 showed detectable basal levels of p53, and a 2-fold further induction of p53 after IR. FC-E6 showed no detectable levels of p53 before or after IR. No induction of p21 or G1/S arrest was seen in FC-CX3 or FC-E6, as has been observed previously. The induction of p21 in FS cells was attenuated and delayed: a 2-3-fold increase seen maximally at 9 hours, compared with a 5-fold increase seen maximally at 3-6 hours in FC cells. The accumulation of cells at the G1/S junction after IR showed the same kinetics as p21 induction: the peak of cells in G1 occurs at 3-6 hours in FC, but not until 9-24 hours in FS. The response is reminiscent of that seen in

  1. Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets.

    Science.gov (United States)

    Samadian, Soroush; Bruce, Jeff P; Pugh, Trevor J

    2018-03-01

    Somatic copy number variations (CNVs) play a crucial role in development of many human cancers. The broad availability of next-generation sequencing data has enabled the development of algorithms to computationally infer CNV profiles from a variety of data types including exome and targeted sequence data; currently the most prevalent types of cancer genomics data. However, systemic evaluation and comparison of these tools remains challenging due to a lack of ground truth reference sets. To address this need, we have developed Bamgineer, a tool written in Python to introduce user-defined haplotype-phased allele-specific copy number events into an existing Binary Alignment Mapping (BAM) file, with a focus on targeted and exome sequencing experiments. As input, this tool requires a read alignment file (BAM format), lists of non-overlapping genome coordinates for introduction of gains and losses (bed file), and an optional file defining known haplotypes (vcf format). To improve runtime performance, Bamgineer introduces the desired CNVs in parallel using queuing and parallel processing on a local machine or on a high-performance computing cluster. As proof-of-principle, we applied Bamgineer to a single high-coverage (mean: 220X) exome sequence file from a blood sample to simulate copy number profiles of 3 exemplar tumors from each of 10 tumor types at 5 tumor cellularity levels (20-100%, 150 BAM files in total). To demonstrate feasibility beyond exome data, we introduced read alignments to a targeted 5-gene cell-free DNA sequencing library to simulate EGFR amplifications at frequencies consistent with circulating tumor DNA (10, 1, 0.1 and 0.01%) while retaining the multimodal insert size distribution of the original data. We expect Bamgineer to be of use for development and systematic benchmarking of CNV calling algorithms by users using locally-generated data for a variety of applications. The source code is freely available at http://github.com/pughlab/bamgineer.

  2. Bamgineer: Introduction of simulated allele-specific copy number variants into exome and targeted sequence data sets.

    Directory of Open Access Journals (Sweden)

    Soroush Samadian

    2018-03-01

    Full Text Available Somatic copy number variations (CNVs play a crucial role in development of many human cancers. The broad availability of next-generation sequencing data has enabled the development of algorithms to computationally infer CNV profiles from a variety of data types including exome and targeted sequence data; currently the most prevalent types of cancer genomics data. However, systemic evaluation and comparison of these tools remains challenging due to a lack of ground truth reference sets. To address this need, we have developed Bamgineer, a tool written in Python to introduce user-defined haplotype-phased allele-specific copy number events into an existing Binary Alignment Mapping (BAM file, with a focus on targeted and exome sequencing experiments. As input, this tool requires a read alignment file (BAM format, lists of non-overlapping genome coordinates for introduction of gains and losses (bed file, and an optional file defining known haplotypes (vcf format. To improve runtime performance, Bamgineer introduces the desired CNVs in parallel using queuing and parallel processing on a local machine or on a high-performance computing cluster. As proof-of-principle, we applied Bamgineer to a single high-coverage (mean: 220X exome sequence file from a blood sample to simulate copy number profiles of 3 exemplar tumors from each of 10 tumor types at 5 tumor cellularity levels (20-100%, 150 BAM files in total. To demonstrate feasibility beyond exome data, we introduced read alignments to a targeted 5-gene cell-free DNA sequencing library to simulate EGFR amplifications at frequencies consistent with circulating tumor DNA (10, 1, 0.1 and 0.01% while retaining the multimodal insert size distribution of the original data. We expect Bamgineer to be of use for development and systematic benchmarking of CNV calling algorithms by users using locally-generated data for a variety of applications. The source code is freely available at http://github.com/pughlab/bamgineer.

  3. Studies of magnetic resonance in anemia of hematies falciformes

    International Nuclear Information System (INIS)

    Lores Guevara, Manuel Arsenio; Balcom, Bruce John; Cabal Mirabal, Carlos

    2012-01-01

    Magnetic Resonance applications to the study of Sickle Cell Disease are analyzed using classical procedures and Unilateral Magnetic Resonance. Hemoglobin and whole blood samples were obtained from healthy individual and patients with Sickle Cell Anemia to be used as samples. Classical pulse sequence as spin echo and inversion recovery were used in the experimental studies, the STEPR method was used for EPR spectrometric determinations. The results show the possibility of NMR methods to follow the molecular process causing the disease and allows to present quantitative procedures to estimate the clinical state of the patients and the results of clinical options. We present the Unilateral Magnetic Resonance as a new method to study Sickle Cell disease considering its portability and new possibilities as new image method

  4. Specific nuclear localizing sequence directs two myosin isoforms to the cell nucleus in calmodulin-sensitive manner.

    Science.gov (United States)

    Dzijak, Rastislav; Yildirim, Sukriye; Kahle, Michal; Novák, Petr; Hnilicová, Jarmila; Venit, Tomáš; Hozák, Pavel

    2012-01-01

    Nuclear myosin I (NM1) was the first molecular motor identified in the cell nucleus. Together with nuclear actin, they participate in crucial nuclear events such as transcription, chromatin movements, and chromatin remodeling. NM1 is an isoform of myosin 1c (Myo1c) that was identified earlier and is known to act in the cytoplasm. NM1 differs from the "cytoplasmic" myosin 1c only by additional 16 amino acids at the N-terminus of the molecule. This amino acid stretch was therefore suggested to direct NM1 into the nucleus. We investigated the mechanism of nuclear import of NM1 in detail. Using over-expressed GFP chimeras encoding for truncated NM1 mutants, we identified a specific sequence that is necessary for its import to the nucleus. This novel nuclear localization sequence is placed within calmodulin-binding motif of NM1, thus it is present also in the Myo1c. We confirmed the presence of both isoforms in the nucleus by transfection of tagged NM1 and Myo1c constructs into cultured cells, and also by showing the presence of the endogenous Myo1c in purified nuclei of cells derived from knock-out mice lacking NM1. Using pull-down and co-immunoprecipitation assays we identified importin beta, importin 5 and importin 7 as nuclear transport receptors that bind NM1. Since the NLS sequence of NM1 lies within the region that also binds calmodulin we tested the influence of calmodulin on the localization of NM1. The presence of elevated levels of calmodulin interfered with nuclear localization of tagged NM1. We have shown that the novel specific NLS brings to the cell nucleus not only the "nuclear" isoform of myosin I (NM1 protein) but also its "cytoplasmic" isoform (Myo1c protein). This opens a new field for exploring functions of this molecular motor in nuclear processes, and for exploring the signals between cytoplasm and the nucleus.

  5. The binding of TIA-1 to RNA C-rich sequences is driven by its C-terminal RRM domain.

    Science.gov (United States)

    Cruz-Gallardo, Isabel; Aroca, Ángeles; Gunzburg, Menachem J; Sivakumaran, Andrew; Yoon, Je-Hyun; Angulo, Jesús; Persson, Cecilia; Gorospe, Myriam; Karlsson, B Göran; Wilce, Jacqueline A; Díaz-Moreno, Irene

    2014-01-01

    T-cell intracellular antigen-1 (TIA-1) is a key DNA/RNA binding protein that regulates translation by sequestering target mRNAs in stress granules (SG) in response to stress conditions. TIA-1 possesses three RNA recognition motifs (RRM) along with a glutamine-rich domain, with the central domains (RRM2 and RRM3) acting as RNA binding platforms. While the RRM2 domain, which displays high affinity for U-rich RNA sequences, is primarily responsible for interaction with RNA, the contribution of RRM3 to bind RNA as well as the target RNA sequences that it binds preferentially are still unknown. Here we combined nuclear magnetic resonance (NMR) and surface plasmon resonance (SPR) techniques to elucidate the sequence specificity of TIA-1 RRM3. With a novel approach using saturation transfer difference NMR (STD-NMR) to quantify protein-nucleic acids interactions, we demonstrate that isolated RRM3 binds to both C- and U-rich stretches with micromolar affinity. In combination with RRM2 and in the context of full-length TIA-1, RRM3 significantly enhanced the binding to RNA, particularly to cytosine-rich RNA oligos, as assessed by biotinylated RNA pull-down analysis. Our findings provide new insight into the role of RRM3 in regulating TIA-1 binding to C-rich stretches, that are abundant at the 5' TOPs (5' terminal oligopyrimidine tracts) of mRNAs whose translation is repressed under stress situations.

  6. Magnetic resonance imaging of spinal plasmacytoma

    International Nuclear Information System (INIS)

    Shah, B.K.; Saifuddin, A.; Price, G.J.

    2000-01-01

    AIM: To describe the magnetic resonance imaging (MRI) features of spinal plasmacytoma. MATERIALS AND METHODS: The clinical records and MRI findings in six patients (five men, one woman; age range 41-61 years) with histologically proven plasmacytoma of the spine were reviewed. All studies included sagittal T1- and T2-weighted spin-echo sequences and axial T1-weighted spin-echo sequences. Intravenous gadolinium DTPA was administered in four cases. RESULTS: MRI showed a characteristic appearances in four cases of low signal intensity curvilinear areas within the vertebra or cortical irregularity. CONCLUSION: Recognition of these imaging features can initiate the appropriate investigation as the commonest differential diagnosis for such lesions is metastasis. Shah, B. K. (2000)

  7. Load characteristics of wireless power transfer system with different resonant types and resonator numbers

    Science.gov (United States)

    Zhang, Yiming; Zhao, Zhengming; Chen, Kainan; Fan, Jun

    2017-05-01

    Wireless Power Transfer (WPT) has been the research focus and applied in many fields. Normally power is transferred wirelessly to charge the battery, which requires specific load characteristics. The load characteristics are essential for the design and operation of the WPT system. This paper investigates the load characteristics of the WPT system with different resonant types and resonator numbers. It is found that in a WPT system with series or LCL resonance under a constant voltage source, the load characteristic is determined by the number of inductors. Even number of inductors results in a constant current characteristic and odd number constant voltage characteristic. Calculations, simulations, and experiments verify the analysis.

  8. The value of qualitative and quantitative assessment of lesion to cerebral cortex signal ratio on double inversion recovery sequence in the differentiation of demyelinating plaques from non-specific T2 hyperintensities

    Energy Technology Data Exchange (ETDEWEB)

    Hamcan, Salih; Battal, Bilal; Akgun, Veysel; Sari, Sebahattin; Tasar, Mustafa [Gulhane Military Medical School, Department of Radiology, Etlik, Ankara (Turkey); Oz, Oguzhan; Tasdemir, Serdar [Gulhane Military Medical School, Department of Neurology, Ankara (Turkey); Bozkurt, Yalcin [Golcuk Military Hospital, Department of Radiology, Kocaeli (Turkey)

    2017-02-15

    To assess the usefulness of the visual assessment and to determine diagnostic value of the lesion-to-cerebral cortex signal ratio (LCSR) measurement in the differentiation of demyelinating plaques and non-specific T2 hyperintensities on double inversion recovery (DIR) sequence. DIR and fluid-attenuated inversion recovery (FLAIR) sequences of 25 clinically diagnosed multiple sclerosis (MS) patients and 25 non-MS patients with non-specific T2-hyperintense lesions were evaluated visually and LCSRs were measured by two observers independently. On DIR sequence, the calculated mean LCSR ± SD for demyelinating plaques and non-specific T2-hyperintense lesions were 1.60 ± 0.26 and 0.75 ± 0.19 for observer1, and 1.61 ± 0.27 and 0.74 ± 0.19 for observer2. LCSRs of demyelinating plaques were significantly higher than other non-specific T2-hyperintense lesions on DIR sequence. By using the visual assessment demyelinating plaques were differentiated from non-specific T2-hyperintensities with 92.8 % sensitivity, 97.5 % specificity and 95.1 % accuracy for observer1 and 92.8 % sensitivity, 95 % specificity and 93.9 % accuracy for observer2. Visual assessment and LCSR measurement on DIR sequence seems to be useful for differentiating demyelinating MS plaques from supratentorial non-specific T2 hyperintensities. This feature can be used for diagnosis of MS particularly in patients with only supratentorial T2-hyperintense lesions who are categorized as radiologically possible MS. (orig.)

  9. SOLiD sequencing of four Vibrio vulnificus genomes enables comparative genomic analysis and identification of candidate clade-specific virulence genes

    Directory of Open Access Journals (Sweden)

    Telonis-Scott Marina

    2010-09-01

    Full Text Available Abstract Background Vibrio vulnificus is the leading cause of reported death from consumption of seafood in the United States. Despite several decades of research on molecular pathogenesis, much remains to be learned about the mechanisms of virulence of this opportunistic bacterial pathogen. The two complete and annotated genomic DNA sequences of V. vulnificus belong to strains of clade 2, which is the predominant clade among clinical strains. Clade 2 strains generally possess higher virulence potential in animal models of disease compared with clade 1, which predominates among environmental strains. SOLiD sequencing of four V. vulnificus strains representing different clades (1 and 2 and biotypes (1 and 2 was used for comparative genomic analysis. Results Greater than 4,100,000 bases were sequenced of each strain, yielding approximately 100-fold coverage for each of the four genomes. Although the read lengths of SOLiD genomic sequencing were only 35 nt, we were able to make significant conclusions about the unique and shared sequences among the genomes, including identification of single nucleotide polymorphisms. Comparative analysis of the newly sequenced genomes to the existing reference genomes enabled the identification of 3,459 core V. vulnificus genes shared among all six strains and 80 clade 2-specific genes. We identified 523,161 SNPs among the six genomes. Conclusions We were able to glean much information about the genomic content of each strain using next generation sequencing. Flp pili, GGDEF proteins, and genomic island XII were identified as possible virulence factors because of their presence in virulent sequenced strains. Genomic comparisons also point toward the involvement of sialic acid catabolism in pathogenesis.

  10. Unconventional abdominal uses of FIESTA (CISS) sequence

    International Nuclear Information System (INIS)

    Sen, Anitha

    2013-01-01

    The ability to provide cross-sectional imaging, combined with a lack of ionizing radiation has made magnetic resonance imaging (MRI) of abdomen popular. We report four interesting cases: Midgut malrotation with volvulus, sigmoid volvulus, biliary rupture of hydatid cyst, and small bowel lipomatosis, where fast imaging employing steady-state acquisition [FIESTA]/constructive interference into steady state [CISS] sequence helped in clinching the diagnosis

  11. Detection of cancer in cervical tissue biopsies using mobile lipid resonances measured with diffusion-weighted (1)H magnetic resonance spectroscopy.

    Science.gov (United States)

    Zietkowski, D; Davidson, R L; Eykyn, T R; De Silva, S S; Desouza, N M; Payne, G S

    2010-05-01

    The purpose of this study was to implement a diffusion-weighted sequence for visualisation of mobile lipid resonances (MLR) using high resolution magic angle spinning (HR-MAS) (1)H MRS and to evaluate its use in establishing differences between tissues from patients with cervical carcinoma that contain cancer from those that do not. A stimulated echo sequence with bipolar gradients was modified to allow T(1) and T(2) measurements and optimised by recording signal loss in HR-MAS spectra as a function of gradient strength in model lipids and tissues. Diffusion coefficients, T(1) and apparent T(2) relaxation times were measured in model lipid systems. MLR profiles were characterised in relation to T(1) and apparent T(2) relaxation in human cervical cancer tissue samples. Diffusion-weighted (DW) spectra of cervical biopsies were quantified and peak areas analysed using linear discriminant analysis (LDA). The optimised sequence reduced spectral overlap by suppressing signals originating from low molecular weight metabolites and non-lipid contributions. Significantly improved MLR visualisation allowed visualisation of peaks at 0.9, 1.3, 1.6, 2.0, 2.3, 2.8, 4.3 and 5.3 ppm. MLR analysis of DW spectra showed at least six peaks arising from saturated and unsaturated lipids and those arising from triglycerides. Significant differences in samples containing histologically confirmed cancer were seen for peaks at 0.9 (p Operating Characteristic (ROC) curves and calculated area under the curve (0.962) validated high sensitivity and specificity of the technique. Diffusion-weighting of HR-MAS spectroscopic sequences is a useful method for characterising MLR in cancer tissues and displays an accumulation of lipids arising during tumourigenesis and an increase in the unsaturated lipid and triglyceride peaks with respect to saturated MLR. Copyright © 2009 John Wiley & Sons, Ltd.

  12. A strand specific high resolution normalization method for chip-sequencing data employing multiple experimental control measurements

    DEFF Research Database (Denmark)

    Enroth, Stefan; Andersson, Claes; Andersson, Robin

    2012-01-01

    High-throughput sequencing is becoming the standard tool for investigating protein-DNA interactions or epigenetic modifications. However, the data generated will always contain noise due to e.g. repetitive regions or non-specific antibody interactions. The noise will appear in the form of a backg......, the background is only used to adjust peak calling and not as a pre-processing step that aims at discerning the signal from the background noise. A normalization procedure that extracts the signal of interest would be of universal use when investigating genomic patterns....

  13. Development of a functional cell-based assay that probes the specific interaction between influenza A virus NP and its packaging signal sequence RNA.

    Science.gov (United States)

    Woo, Jiwon; Yu, Kyung Lee; Lee, Sun Hee; You, Ji Chang

    2015-02-06

    Although cis-acting packaging signal RNA sequences for the influenza virus NP encoding vRNA have been identified recently though genetic studies, little is known about the interaction between NP and the vRNA packaging signals either in vivo or in vitro. Here, we provide evidence that NP is able to interact specifically with the vRNA packaging sequence RNA within living cells and that the specific RNA binding activity of NP in vivo requires both the N-terminal and central region of the protein. This assay established would be a valuable tool for further detailed studies of the NP-packaging signal RNA interaction in living cells. Copyright © 2014 Elsevier Inc. All rights reserved.

  14. Complete resonance assignment for the polypeptide backbone of interleukin 1β using three-dimensional heteronuclear NMR spectroscopy

    International Nuclear Information System (INIS)

    Driscoll, P.C.; Clore, G.M.; Marion, D.; Gronenborn, A.M.; Wingfield, P.T.

    1990-01-01

    The complete sequence-specific assignment of the 15 N and 1 H backbone resonances of the NMR spectrum of recombinant human interleukin 1β has been obtained by using primarily 15 N- 1 H heteronuclear three-dimensional (3D) NMR techniques in combination with 15 N- 1 H heteronuclear and 1 H homonuclear two-dimensional NMR. The fingerprint region of the spectrum was analyzed by using a combination of 3D heteronuclear 1 H Hartmann-Hahn 15 N- 1 H multiple quantum coherence (3D HOHAHA-HMQC) and 3D heteronuclear 1 H nuclear Overhauser 15 N- 1 H multiple quantum coherence (3D NOESY-HMQC) spectroscopies. The authors show that the problems of amide NH and C α H chemical shift degeneracy that are prevalent for proteins of the size are readily overcome by using the 3D heteronuclear NMR technique. A doubling of some peaks in the spectrum was found to be due to N-terminal heterogeneity of the 15 N-labeled protein, corresponding to a mixture of wild-type and des-Ala-1-interleukin 1β. The complete list of 15 N and 1 H assignments is given for all the amide NH and C α H resonances of all non-proline residues, as well as the 1 H assignments for some of the amino acid side chains. This first example of the sequence-specific assignment of a protein using heteronuclear 3D NMR provides a basis for further conformational and dynamic studies of interleukin 1β

  15. Is there an added value of T1-weighted contrast-enhanced fat-suppressed spin-echo MR sequences compared to STIR sequences in MRI of the foot and ankle?

    Energy Technology Data Exchange (ETDEWEB)

    Zubler, Veronika; Zanetti, Marco; Dietrich, Tobias J.; Pfirrmann, Christian W.; Mamisch-Saupe, Nadja [University of Zurich, Faculty of Medicine, Zurich (Switzerland); Orthopedic University Hospital Balgrist, Department of Radiology, Zurich (Switzerland); Espinosa, Norman [University of Zurich, Faculty of Medicine, Zurich (Switzerland); Orthopedic University Hospital Balgrist, Orthopedic Surgery, Zurich (Switzerland)

    2017-08-15

    To prospectively compare T1-weighted fat-suppressed spin-echo magnetic resonance (MR) sequences after gadolinium application (T1wGdFS) to STIR sequences in patients with acute and chronic foot pain. In 51 patients referred for MRI of the foot and ankle, additional transverse and sagittal T1wGdFS sequences were obtained. Two sets of MR images (standard protocol with STIR or T1wGdFS) were analysed. Diagnosis, diagnostic confidence, and localization of the abnormality were noted. Standard of reference was established by an expert panel of two experienced MSK radiologists and one experienced foot surgeon based on MR images, clinical charts and surgical reports. Patients reported prospectively localization of pain. Descriptive statistics, McNemar test and Kappa test were used. Diagnostic accuracy with STIR protocol was 80% for reader 1, 67% for reader 2, with contrast-protocol 84%, both readers. Significance was found for reader 2. Diagnostic confidence for reader 1 was 1.7 with STIR, 1.3 with contrast-protocol; reader 2: 2.1/1.7. Significance was found for reader 1. Pain location correlated with STIR sequences in 64% and 52%, with gadolinium sequences in 70% and 71%. T1-weighted contrast material-enhanced fat-suppressed spin-echo magnetic resonance sequences improve diagnostic accuracy, diagnostic confidence and correlation of MR abnormalities with pain location in MRI of the foot and ankle. However, the additional value is small. (orig.)

  16. Is there an added value of T1-weighted contrast-enhanced fat-suppressed spin-echo MR sequences compared to STIR sequences in MRI of the foot and ankle?

    International Nuclear Information System (INIS)

    Zubler, Veronika; Zanetti, Marco; Dietrich, Tobias J.; Pfirrmann, Christian W.; Mamisch-Saupe, Nadja; Espinosa, Norman

    2017-01-01

    To prospectively compare T1-weighted fat-suppressed spin-echo magnetic resonance (MR) sequences after gadolinium application (T1wGdFS) to STIR sequences in patients with acute and chronic foot pain. In 51 patients referred for MRI of the foot and ankle, additional transverse and sagittal T1wGdFS sequences were obtained. Two sets of MR images (standard protocol with STIR or T1wGdFS) were analysed. Diagnosis, diagnostic confidence, and localization of the abnormality were noted. Standard of reference was established by an expert panel of two experienced MSK radiologists and one experienced foot surgeon based on MR images, clinical charts and surgical reports. Patients reported prospectively localization of pain. Descriptive statistics, McNemar test and Kappa test were used. Diagnostic accuracy with STIR protocol was 80% for reader 1, 67% for reader 2, with contrast-protocol 84%, both readers. Significance was found for reader 2. Diagnostic confidence for reader 1 was 1.7 with STIR, 1.3 with contrast-protocol; reader 2: 2.1/1.7. Significance was found for reader 1. Pain location correlated with STIR sequences in 64% and 52%, with gadolinium sequences in 70% and 71%. T1-weighted contrast material-enhanced fat-suppressed spin-echo magnetic resonance sequences improve diagnostic accuracy, diagnostic confidence and correlation of MR abnormalities with pain location in MRI of the foot and ankle. However, the additional value is small. (orig.)

  17. Coherence Phenomena in Coupled Optical Resonators

    Science.gov (United States)

    Smith, D. D.; Chang, H.

    2004-01-01

    We predict a variety of photonic coherence phenomena in passive and active coupled ring resonators. Specifically, the effective dispersive and absorptive steady-state response of coupled resonators is derived, and used to determine the conditions for coupled-resonator-induced transparency and absorption, lasing without gain, and cooperative cavity emission. These effects rely on coherent photon trapping, in direct analogy with coherent population trapping phenomena in atomic systems. We also demonstrate that the coupled-mode equations are formally identical to the two-level atom Schrodinger equation in the rotating-wave approximation, and use this result for the analysis of coupled-resonator photon dynamics. Notably, because these effects are predicted directly from coupled-mode theory, they are not unique to atoms, but rather are fundamental to systems of coherently coupled resonators.

  18. Magnetic resonance angiography of fetal vasculature at 3.0 T

    Science.gov (United States)

    Krishnamurthy, Uday; Jella, Pavan K.; Mody, Swati S.; Yadav, Brijesh K.; Hendershot, Kelly; Hernandez-Andrade, Edgar; Yeo, Lami; Cabrera, Maria D.; Haacke, Ewart M.; Hassan, Sonia S.; Romero, Roberto

    2016-01-01

    Magnetic resonance angiography has not been used much previously for visualizing fetal vessels in utero for reasons that include a contraindication for the use of exogenous contrast agents, maternal respiratory motion and fetal motion. In this work, we report the feasibility of using an appropriately modified clinical time-of-flight magnetic resonance imaging sequence for non-contrast angiography of human fetal and placental vessels at 3.0 T. Using this 2D angiography technique, it is possible to visualize fetal vascular networks in late pregnancy. PMID:27189488

  19. Magnetic resonance angiography of fetal vasculature at 3.0 T

    International Nuclear Information System (INIS)

    Neelavalli, Jaladhar; Krishnamurthy, Uday; Yadav, Brijesh K.; Haacke, Ewart M.; Jella, Pavan K.; Hendershot, Kelly; Cabrera, Maria D.; Mody, Swati S.; Hernandez-Andrade, Edgar; Yeo, Lami; Hassan, Sonia S.; Romero, Roberto

    2016-01-01

    Magnetic resonance angiography has not been used much previously for visualizing fetal vessels in utero for reasons that include a contraindication for the use of exogenous contrast agents, maternal respiratory motion and fetal motion. In this work, we report the feasibility of using an appropriately modified clinical time-of-flight magnetic resonance imaging sequence for non-contrast angiography of human fetal and placental vessels at 3.0 T. Using this 2D angiography technique, it is possible to visualize fetal vascular networks in late pregnancy. (orig.)

  20. Magnetic resonance angiography of fetal vasculature at 3.0 T

    Energy Technology Data Exchange (ETDEWEB)

    Neelavalli, Jaladhar; Krishnamurthy, Uday; Yadav, Brijesh K.; Haacke, Ewart M. [Wayne State University School of Medicine, Department of Radiology, Detroit, MI (United States); Wayne State University, Department of Biomedical Engineering, Detroit, MI (United States); Jella, Pavan K.; Hendershot, Kelly; Cabrera, Maria D. [Wayne State University School of Medicine, Department of Radiology, Detroit, MI (United States); Mody, Swati S. [Wayne State University School of Medicine, Department of Radiology, Detroit, MI (United States); Children' s Hospital of Michigan, Department of Radiology, Detroit, MI (United States); Hernandez-Andrade, Edgar; Yeo, Lami; Hassan, Sonia S. [Wayne State University, Department of Obstetrics and Gynecology, Detroit, MI (United States); Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, MD, and Detroit, MI (United States); Romero, Roberto [Perinatology Research Branch, NICHD/NIH/DHHS, Bethesda, MD, and Detroit, MI (United States); University of Michigan, Department of Obstetrics and Gynecology, Ann Arbor, MI (United States); Michigan State University, Department of Epidemiology and Biostatistics, East Lansing, MI (United States); Wayne State University, Center for Molecular Medicine and Genetics, Detroit, MI (United States)

    2016-12-15

    Magnetic resonance angiography has not been used much previously for visualizing fetal vessels in utero for reasons that include a contraindication for the use of exogenous contrast agents, maternal respiratory motion and fetal motion. In this work, we report the feasibility of using an appropriately modified clinical time-of-flight magnetic resonance imaging sequence for non-contrast angiography of human fetal and placental vessels at 3.0 T. Using this 2D angiography technique, it is possible to visualize fetal vascular networks in late pregnancy. (orig.)

  1. Hybrid PET/MR imaging: an algorithm to reduce metal artifacts from dental implants in Dixon-based attenuation map generation using a multiacquisition variable-resonance image combination sequence.

    Science.gov (United States)

    Burger, Irene A; Wurnig, Moritz C; Becker, Anton S; Kenkel, David; Delso, Gaspar; Veit-Haibach, Patrick; Boss, Andreas

    2015-01-01

    It was the aim of this study to implement an algorithm modifying Dixon-based MR imaging datasets for attenuation correction in hybrid PET/MR imaging with a multiacquisition variable resonance image combination (MAVRIC) sequence to reduce metal artifacts. After ethics approval, in 8 oncologic patients with dental implants data were acquired in a trimodality setup with PET/CT and MR imaging. The protocol included a whole-body 3-dimensional dual gradient-echo sequence (Dixon) used for MR imaging-based PET attenuation correction and a high-resolution MAVRIC sequence, applied in the oral area compromised by dental implants. An algorithm was implemented correcting the Dixon-based μ maps using the MAVRIC in areas of Dixon signal voids. The artifact size of the corrected μ maps was compared with the uncorrected MR imaging μ maps. The algorithm was robust in all patients. There was a significant reduction in mean artifact size of 70.5% between uncorrected and corrected μ maps from 697 ± 589 mm(2) to 202 ± 119 mm(2) (P = 0.016). The proposed algorithm could improve MR imaging-based attenuation correction in critical areas, when standard attenuation correction is hampered by metal artifacts, using a MAVRIC. © 2015 by the Society of Nuclear Medicine and Molecular Imaging, Inc.

  2. In vivo MR detection of fluorine-labeled human MSC using the bSSFP sequence.

    Science.gov (United States)

    Ribot, Emeline J; Gaudet, Jeffrey M; Chen, Yuhua; Gilbert, Kyle M; Foster, Paula J

    2014-01-01

    Mesenchymal stem cells (MSC) are used to restore deteriorated cell environments. There is a need to specifically track these cells following transplantation in order to evaluate different methods of implantation, to follow their migration within the body, and to quantify their accumulation at the target. Cellular magnetic resonance imaging (MRI) using fluorine-based nanoemulsions is a great means to detect these transplanted cells in vivo because of the high specificity for fluorine detection and the capability for precise quantification. This technique, however, has low sensitivity, necessitating improvement in MR sequences. To counteract this issue, the balanced steady-state free precession (bSSFP) imaging sequence can be of great interest due to the high signal-to-noise ratio (SNR). Furthermore, it can be applied to obtain 3D images within short acquisition times. In this paper, bSSFP provided accurate quantification of samples of the perfluorocarbon Cell Sense-labeled cells in vitro. Cell Sense was internalized by human MSC (hMSC) without adverse alterations in cell viability or differentiation into adipocytes/osteocytes. The bSSFP sequence was applied in vivo to track and quantify the signals from both Cell Sense-labeled and iron-labeled hMSC after intramuscular implantation. The fluorine signal was observed to decrease faster and more significantly than the volume of iron-associated voids, which points to the advantage of quantifying the fluorine signal and the complexity of quantifying signal loss due to iron.

  3. Significantly improving nuclear resonance fluorescence non-destructive assay by using the integral resonance transmission method and photofission

    International Nuclear Information System (INIS)

    Angell, Christopher T.; Hayakawa, Takehito; Shizuma, Toshiyuki; Hajima, Ryoichi

    2013-01-01

    Non-destructive assay (NDA) of 239 Pu in spent nuclear fuel or melted fuel using a γ-ray beam is possible using self absorption and the integral resonance transmission method. The method uses nuclear resonance absorption where resonances in 239 Pu remove photons from the beam, and the selective absorption is detected by measuring the decrease in scattering in a witness target placed in the beam after the fuel, consisting of the isotope of interest, namely 239 Pu. The method is isotope specific, and can use photofission or scattered γ-rays to assay the 239 Pu. It overcomes several problems related to NDA of melted fuel, including the radioactivity of the fuel, and the unknown composition and geometry. This talk will explain the general method, and how photofission can be used to assay specific isotopes, and present example calculations. (author)

  4. Selection of diethylstilbestrol-specific single-chain antibodies from a non-immunized mouse ribosome display library.

    Directory of Open Access Journals (Sweden)

    Yanan Sun

    Full Text Available Single chain variable fragments (scFvs against diethylstilbestrol (DES were selected from the splenocytes of non-immunized mice by ribosome display technology. A naive library was constructed and engineered to allow in vitro transcription and translation using an E. coli lysate system. Alternating selection in solution and immobilization in microtiter wells was used to pan mRNA-ribosome-antibody (ARM complexes. After seven rounds of ribosome display, the expression vector pTIG-TRX containing the selected specific scFv DNAs were transformed into Escherichia coli BL21 (DE3 for expression. Twenty-six positive clones were screened and five clones had high antibody affinity and specificity to DES as evidenced by indirect competitive ELISA. Sequence analysis showed that these five DES-specific scFvs had different amino acid sequences, but the CDRs were highly similar. Surface plasmon resonance (SPR analysis was used to determine binding kinetics of one clone (30-1. The measured K(D was 3.79 µM. These results indicate that ribosome display technology can be used to efficiently isolate hapten-specific antibody (Ab fragments from a naive library; this study provides a methodological framework for the development of novel immunoassays for multiple environmental pollutants with low molecular weight detection using recombinant antibodies.

  5. Fast MR arthrography using VIBE sequences to evaluate the rotator cuff

    Energy Technology Data Exchange (ETDEWEB)

    Vandevenne, Jan E. [Ziekenhuizen Oost-Limburg, Department of Radiology, Genk (Belgium); Universitair Ziekenhuis Antwerpen, University of Antwerp, Department of Radiology, Edegem (Belgium); Vanhoenacker, Filip; Parizel, Paul M. [Universitair Ziekenhuis Antwerpen, University of Antwerp, Department of Radiology, Edegem (Belgium); Mahachie John, Jestinah M. [University of Hasselt, Centre for Statistics, Diepenbeek (Belgium); Gelin, Geert [Ziekenhuizen Oost-Limburg, Department of Radiology, Genk (Belgium)

    2009-07-15

    The purpose of this paper was to evaluate if short volumetric interpolated breath-hold examination (VIBE) sequences can be used as a substitute for T1-weighted with fat saturation (T1-FS) sequences when performing magnetic resonance (MR) arthrography to diagnose rotator cuff tears. Eighty-two patients underwent direct MR arthrography of the shoulder joint using VIBE (acquisition time of 13 s) and T1-FS (acquisition time of 5 min) sequences in the axial and paracoronal plane on a 1.0-T MR unit. Two radiologists scored rotator cuff tendons on VIBE and T1-FS images separately as normal, small/large partial thickness and full thickness tears with or without geyser sign. T1-FS sequences were considered the gold standard. Surgical correlation was available in a small sample. Sensitivity, specificity, and positive and negative predictive values of VIBE were greater than 92% for large articular-sided partial thickness and full thickness tears. For detecting fraying and articular-sided small partial thickness tears, these parameters were 55%, 94%, 94%, and 57%, respectively. The simple kappa value was 0.76, and the weighted kappa value was 0.86 for agreement between T1-FS and VIBE scores. All large partial and full thickness tears at surgery were correctly diagnosed using VIBE or T1-FS MR images. Fast MR arthrography of the shoulder joint using VIBE sequences showed good concordance with the classically used T1-FS sequences for the appearance of the rotator cuff, in particular for large articular-sided partial thickness tears and for full thickness tears. Due to its very short acquisition time, VIBE may be especially useful when performing MR arthrography in claustrophobic patients or patients with a painful shoulder. (orig.)

  6. Value of fat-suppressed PD-weighted TSE-sequences for detection of anterior and posterior cruciate ligament lesions-Comparison to arthroscopy

    International Nuclear Information System (INIS)

    Schaefer, Fritz K.W.; Schaefer, Philipp J.; Brossmann, Joachim; Frahm, Christian; Muhle, Claus; Hilgert, Ralf Erik; Heller, Martin; Jahnke, Thomas

    2006-01-01

    Objective: To evaluate fat-suppressed (FS) proton-density-weighted (PDw) turbo spin-echo (TSE) magnetic resonance imaging for the detection of anterior and posterior cruciate ligament lesions in comparison to arthroscopy. Materials and methods: In a prospective study 31 knee joints were imaged on a 1.5 T MR scanner (Vision[reg], Siemens, Erlangen) prior to arthroscopy using following sequences: (a) sagittal FS-PDw/T2w TSE (TR/TE: 4009/15/105 ms); (b) sagittal PDw/T2w TSE (TR/TE:3800/15/105 ms). Further imaging parameters: slice thickness 3 mm, FOV 160 mm, matrix 256 x 256. A total of 62 anterior and posterior cruciate ligaments (ACL/PCL) were evaluated, standard of reference was arthroscopy. Sensitivity, specificity, positive (ppv) and negative predictive value (npv) and accuracy were calculated. Results: Twenty-one cruciate ligament ruptures were detected in arthroscopy, 19 ACL- and 2 PCL-ruptures (on MRI 34/124, 25/62 ACL, 9/62 PCL lesions). For all four sequences in the 31 patients with arthroscopic correlation sensitivity, specificity, ppv, npv and accuracy were 86%, 98%, 95%, 93% and 94% for detection of tears, and 84%, 100%, 100%, 80% and 90% for ACL-ruptures respectively. The two PCL-ruptures were true positive in all sequences, one intact PCL was diagnosed as torn (false positive). Conclusions: Fat-suppressed PDw/T2w TSE-MR sequences are comparable to PDw TSE sequences for the detection of ACL/PCL-lesions

  7. SWANS: A Prototypic SCALE Criticality Sequence for Automated Optimization Using the SWAN Methodology

    International Nuclear Information System (INIS)

    Greenspan, E.

    2001-01-01

    SWANS is a new prototypic analysis sequence that provides an intelligent, semi-automatic search for the maximum k eff of a given amount of specified fissile material, or of the minimum critical mass. It combines the optimization strategy of the SWAN code with the composition-dependent resonance self-shielded cross sections of the SCALE package. For a given system composition arrived at during the iterative optimization process, the value of k eff is as accurate and reliable as obtained using the CSAS1X Sequence of SCALE-4.4. This report describes how SWAN is integrated within the SCALE system to form the new prototypic optimization sequence, describes the optimization procedure, provides a user guide for SWANS, and illustrates its application to five different types of problems. In addition, the report illustrates that resonance self-shielding might have a significant effect on the maximum k eff value a given fissile material mass can have

  8. SWANS: A Prototypic SCALE Criticality Sequence for Automated Optimization Using the SWAN Methodology

    Energy Technology Data Exchange (ETDEWEB)

    Greenspan, E.

    2001-01-11

    SWANS is a new prototypic analysis sequence that provides an intelligent, semi-automatic search for the maximum k{sub eff} of a given amount of specified fissile material, or of the minimum critical mass. It combines the optimization strategy of the SWAN code with the composition-dependent resonance self-shielded cross sections of the SCALE package. For a given system composition arrived at during the iterative optimization process, the value of k{sub eff} is as accurate and reliable as obtained using the CSAS1X Sequence of SCALE-4.4. This report describes how SWAN is integrated within the SCALE system to form the new prototypic optimization sequence, describes the optimization procedure, provides a user guide for SWANS, and illustrates its application to five different types of problems. In addition, the report illustrates that resonance self-shielding might have a significant effect on the maximum k{sub eff} value a given fissile material mass can have.

  9. Assessment of structural lesions in sacroiliac joints enhances diagnostic utility of magnetic resonance imaging in early spondylarthritis

    DEFF Research Database (Denmark)

    Weber, Ulrich; Lambert, Robert G W; Pedersen, Susanne J

    2010-01-01

    To compare the diagnostic utility of T1-weighted and STIR magnetic resonance imaging (MRI) sequences in early spondylarthritis (SpA) using a standardized approach to the evaluation of sacroiliac (SI) joints, and to test whether systematic calibration of readers directed at recognition of abnormal......To compare the diagnostic utility of T1-weighted and STIR magnetic resonance imaging (MRI) sequences in early spondylarthritis (SpA) using a standardized approach to the evaluation of sacroiliac (SI) joints, and to test whether systematic calibration of readers directed at recognition...

  10. Direct Lymph Node Vaccination of Lentivector/Prostate-Specific Antigen is Safe and Generates Tissue-Specific Responses in Rhesus Macaques

    Directory of Open Access Journals (Sweden)

    Bryan C. Au

    2016-02-01

    Full Text Available Anti-cancer immunotherapy is emerging from a nadir and demonstrating tangible benefits to patients. A variety of approaches are now employed. We are invoking antigen (Ag-specific responses through direct injections of recombinant lentivectors (LVs that encode sequences for tumor-associated antigens into multiple lymph nodes to optimize immune presentation/stimulation. Here we first demonstrate the effectiveness and antigen-specificity of this approach in mice challenged with prostate-specific antigen (PSA-expressing tumor cells. Next we tested the safety and efficacy of this approach in two cohorts of rhesus macaques as a prelude to a clinical trial application. Our vector encodes the cDNA for rhesus macaque PSA and a rhesus macaque cell surface marker to facilitate vector titering and tracking. We utilized two independent injection schemas demarcated by the timing of LV administration. In both cohorts we observed marked tissue-specific responses as measured by clinical evaluations and magnetic resonance imaging of the prostate gland. Tissue-specific responses were sustained for up to six months—the end-point of the study. Control animals immunized against an irrelevant Ag were unaffected. We did not observe vector spread in test or control animals or perturbations of systemic immune parameters. This approach thus offers an “off-the-shelf” anti-cancer vaccine that could be made at large scale and injected into patients—even on an out-patient basis.

  11. Direct Lymph Node Vaccination of Lentivector/Prostate-Specific Antigen is Safe and Generates Tissue-Specific Responses in Rhesus Macaques.

    Science.gov (United States)

    Au, Bryan C; Lee, Chyan-Jang; Lopez-Perez, Orlay; Foltz, Warren; Felizardo, Tania C; Wang, James C M; Huang, Ju; Fan, Xin; Madden, Melissa; Goldstein, Alyssa; Jaffray, David A; Moloo, Badru; McCart, J Andrea; Medin, Jeffrey A

    2016-02-19

    Anti-cancer immunotherapy is emerging from a nadir and demonstrating tangible benefits to patients. A variety of approaches are now employed. We are invoking antigen (Ag)-specific responses through direct injections of recombinant lentivectors (LVs) that encode sequences for tumor-associated antigens into multiple lymph nodes to optimize immune presentation/stimulation. Here we first demonstrate the effectiveness and antigen-specificity of this approach in mice challenged with prostate-specific antigen (PSA)-expressing tumor cells. Next we tested the safety and efficacy of this approach in two cohorts of rhesus macaques as a prelude to a clinical trial application. Our vector encodes the cDNA for rhesus macaque PSA and a rhesus macaque cell surface marker to facilitate vector titering and tracking. We utilized two independent injection schemas demarcated by the timing of LV administration. In both cohorts we observed marked tissue-specific responses as measured by clinical evaluations and magnetic resonance imaging of the prostate gland. Tissue-specific responses were sustained for up to six months-the end-point of the study. Control animals immunized against an irrelevant Ag were unaffected. We did not observe vector spread in test or control animals or perturbations of systemic immune parameters. This approach thus offers an "off-the-shelf" anti-cancer vaccine that could be made at large scale and injected into patients-even on an out-patient basis.

  12. Load characteristics of wireless power transfer system with different resonant types and resonator numbers

    Directory of Open Access Journals (Sweden)

    Yiming Zhang

    2017-05-01

    Full Text Available Wireless Power Transfer (WPT has been the research focus and applied in many fields. Normally power is transferred wirelessly to charge the battery, which requires specific load characteristics. The load characteristics are essential for the design and operation of the WPT system. This paper investigates the load characteristics of the WPT system with different resonant types and resonator numbers. It is found that in a WPT system with series or LCL resonance under a constant voltage source, the load characteristic is determined by the number of inductors. Even number of inductors results in a constant current characteristic and odd number constant voltage characteristic. Calculations, simulations, and experiments verify the analysis.

  13. Alu polymerase chain reaction: A method for rapid isolation of human-specific sequences from complex DNA sources

    International Nuclear Information System (INIS)

    Nelson, D.L.; Ledbetter, S.A.; Corbo, L.; Victoria, M.F.; Ramirez-Solis, R.; Webster, T.D.; Ledbetter, D.H.; Caskey, C.T.

    1989-01-01

    Current efforts to map the human genome are focused on individual chromosomes or smaller regions and frequently rely on the use of somatic cell hybrids. The authors report the application of the polymerase chain reaction to direct amplification of human DNA from hybrid cells containing regions of the human genome in rodent cell backgrounds using primers directed to the human Alu repeat element. They demonstrate Alu-directed amplification of a fragment of the human HPRT gene from both hybrid cell and cloned DNA and identify through sequence analysis the Alu repeats involved in this amplification. They also demonstrate the application of this technique to identify the chromosomal locations of large fragments of the human X chromosome cloned in a yeast artificial chromosome and the general applicability of the method to the preparation of DNA probes from cloned human sequences. The technique allows rapid gene mapping and provides a simple method for the isolation and analysis of specific chromosomal regions

  14. Modeling of supermodes in coupled unstable resonators

    International Nuclear Information System (INIS)

    Townsend, S.S.

    1986-01-01

    A general formalism describing the supermodes of an array of N identical, circulantly coupled resonators is presented. The symmetry of the problem results in a reduction of the N coupled integral equations to N decoupled integral equations. Each independent integral equation defines a set of single-resonator modes derived for a hypothetical resonator whose geometry resembles a member of the real array with the exception that all coupling beams are replaced by feedback beams, each with a prescribed constant phase. A given array supermode consists of a single equivalent resonator mode appearing repetitively in each resonator with a prescribed relative phase between individual resonators. The specific array design chosen for example is that of N adjoint coupled confocal unstable resonators. The impact of coupling on the computer modeling of this system is discussed and computer results for the cases of two- and four-laser coupling are presented

  15. Evaluation of the Subscapularis Tendon Tears on 3T Magnetic Resonance Arthrography: Comparison of Diagnostic Performance of T1-Weighted Spectral Presaturation with Inversion-Recovery and T2-Weighted Turbo Spin-Echo Sequences.

    Science.gov (United States)

    Lee, Hoseok; Ahn, Joong Mo; Kang, Yusuhn; Oh, Joo Han; Lee, Eugene; Lee, Joon Woo; Kang, Heung Sik

    2018-01-01

    To compare the T1-weighted spectral presaturation with inversion-recovery sequences (T1 SPIR) with T2-weighted turbo spin-echo sequences (T2 TSE) on 3T magnetic resonance arthrography (MRA) in the evaluation of the subscapularis (SSC) tendon tear with arthroscopic findings as the reference standard. This retrospective study included 120 consecutive patients who had undergone MRA within 3 months between April and December 2015. Two musculoskeletal radiologists blinded to the arthroscopic results evaluated T1 SPIR and T2 TSE images in separate sessions for the integrity of the SSC tendon, examining normal/articular-surface partial-thickness tear (PTTa)/full-thickness tear (FTT). Diagnostic performance of T1 SPIR and T2 TSE was calculated with arthroscopic results as the reference standard, and sensitivity, specificity, and accuracy were compared using the McNemar test. Interobserver agreement was measured with kappa (κ) statistics. There were 74 SSC tendon tears (36 PTTa and 38 FTT) confirmed by arthroscopy. Significant differences were found in the sensitivity and accuracy between T1 SPIR and T2 TSE using the McNemar test, with respective rates of 95.9-94.6% vs. 71.6-75.7% and 90.8-91.7% vs. 79.2-83.3% for detecting tear; 55.3% vs. 31.6-34.2% and 85.8% vs. 78.3-79.2%, respectively, for FTT; and 91.7-97.2% vs. 58.3-61.1% and 89% vs. 78-79.3%, respectively, for PTTa. Interobserver agreement for T1 SPIR was almost perfect for T1 SPIR (κ = 0.839) and substantial for T2 TSE (κ = 0.769). T1-weighted spectral presaturation with inversion-recovery sequences is more sensitive and accurate compared to T2 TSE in detecting SSC tendon tear on 3T MRA.

  16. Rapid profiling of the antigen regions recognized by serum antibodies using massively parallel sequencing of antigen-specific libraries.

    KAUST Repository

    Domina, Maria; Lanza Cariccio, Veronica; Benfatto, Salvatore; D'Aliberti, Deborah; Venza, Mario; Borgogni, Erica; Castellino, Flora; Biondo, Carmelo; D'Andrea, Daniel; Grassi, Luigi; Tramontano, Anna; Teti, Giuseppe; Felici, Franco; Beninati, Concetta

    2014-01-01

    There is a need for techniques capable of identifying the antigenic epitopes targeted by polyclonal antibody responses during deliberate or natural immunization. Although successful, traditional phage library screening is laborious and can map only some of the epitopes. To accelerate and improve epitope identification, we have employed massive sequencing of phage-displayed antigen-specific libraries using the Illumina MiSeq platform. This enabled us to precisely identify the regions of a model antigen, the meningococcal NadA virulence factor, targeted by serum antibodies in vaccinated individuals and to rank hundreds of antigenic fragments according to their immunoreactivity. We found that next generation sequencing can significantly empower the analysis of antigen-specific libraries by allowing simultaneous processing of dozens of library/serum combinations in less than two days, including the time required for antibody-mediated library selection. Moreover, compared with traditional plaque picking, the new technology (named Phage-based Representation OF Immuno-Ligand Epitope Repertoire or PROFILER) provides superior resolution in epitope identification. PROFILER seems ideally suited to streamline and guide rational antigen design, adjuvant selection, and quality control of newly produced vaccines. Furthermore, this method is also susceptible to find important applications in other fields covered by traditional quantitative serology.

  17. Rapid profiling of the antigen regions recognized by serum antibodies using massively parallel sequencing of antigen-specific libraries.

    Directory of Open Access Journals (Sweden)

    Maria Domina

    Full Text Available There is a need for techniques capable of identifying the antigenic epitopes targeted by polyclonal antibody responses during deliberate or natural immunization. Although successful, traditional phage library screening is laborious and can map only some of the epitopes. To accelerate and improve epitope identification, we have employed massive sequencing of phage-displayed antigen-specific libraries using the Illumina MiSeq platform. This enabled us to precisely identify the regions of a model antigen, the meningococcal NadA virulence factor, targeted by serum antibodies in vaccinated individuals and to rank hundreds of antigenic fragments according to their immunoreactivity. We found that next generation sequencing can significantly empower the analysis of antigen-specific libraries by allowing simultaneous processing of dozens of library/serum combinations in less than two days, including the time required for antibody-mediated library selection. Moreover, compared with traditional plaque picking, the new technology (named Phage-based Representation OF Immuno-Ligand Epitope Repertoire or PROFILER provides superior resolution in epitope identification. PROFILER seems ideally suited to streamline and guide rational antigen design, adjuvant selection, and quality control of newly produced vaccines. Furthermore, this method is also susceptible to find important applications in other fields covered by traditional quantitative serology.

  18. Rapid profiling of the antigen regions recognized by serum antibodies using massively parallel sequencing of antigen-specific libraries.

    KAUST Repository

    Domina, Maria

    2014-12-04

    There is a need for techniques capable of identifying the antigenic epitopes targeted by polyclonal antibody responses during deliberate or natural immunization. Although successful, traditional phage library screening is laborious and can map only some of the epitopes. To accelerate and improve epitope identification, we have employed massive sequencing of phage-displayed antigen-specific libraries using the Illumina MiSeq platform. This enabled us to precisely identify the regions of a model antigen, the meningococcal NadA virulence factor, targeted by serum antibodies in vaccinated individuals and to rank hundreds of antigenic fragments according to their immunoreactivity. We found that next generation sequencing can significantly empower the analysis of antigen-specific libraries by allowing simultaneous processing of dozens of library/serum combinations in less than two days, including the time required for antibody-mediated library selection. Moreover, compared with traditional plaque picking, the new technology (named Phage-based Representation OF Immuno-Ligand Epitope Repertoire or PROFILER) provides superior resolution in epitope identification. PROFILER seems ideally suited to streamline and guide rational antigen design, adjuvant selection, and quality control of newly produced vaccines. Furthermore, this method is also susceptible to find important applications in other fields covered by traditional quantitative serology.

  19. Chaotic parametric soliton-like pulses in ferromagnetic-film active ring resonators

    International Nuclear Information System (INIS)

    Grishin, S. V.; Golova, T. M.; Morozova, M. A.; Romanenko, D. V.; Seleznev, E. P.; Sysoev, I. V.; Sharaevskii, Yu. P.

    2015-01-01

    The generation of quasi-periodic sequences of parametric soliton-like pulses in an active ring resonator with a ferromagnetic film via the three-wave parametric instability of a magnetostatic surface wave is studied theoretically and experimentally. These dissipative structures form in time due to the competition between the cubic nonlinearity caused by parametric coupling between spin waves and the time dispersion caused by the resonant cavity that is present in a self-oscillatory system. The development of dynamic chaos due to the parametric instability of a magnetostatic surface wave results in irregular behavior of a phase. However, this behavior does not break a quasi-periodic pulse sequence when the gain changes over a wide range. The generated soliton-like pulses have a chaotic nature, which is supported by the maximum Lyapunov exponent estimated from experimental time series

  20. Nitrogen-detected CAN and CON experiments as alternative experiments for main chain NMR resonance assignments

    International Nuclear Information System (INIS)

    Takeuchi, Koh; Heffron, Gregory; Sun, Zhen-Yu J.; Frueh, Dominique P.; Wagner, Gerhard

    2010-01-01

    Heteronuclear direct-detection experiments, which utilize the slower relaxation properties of low γ nuclei, such as 13 C have recently been proposed for sequence-specific assignment and structural analyses of large, unstructured, and/or paramagnetic proteins. Here we present two novel 15 N direct-detection experiments. The CAN experiment sequentially connects amide 15 N resonances using 13 C α chemical shift matching, and the CON experiment connects the preceding 13 C' nuclei. When starting from the same carbon polarization, the intensities of nitrogen signals detected in the CAN or CON experiments would be expected four times lower than those of carbon resonances observed in the corresponding 13 C-detecting experiment, NCA-DIPAP or NCO-IPAP (Bermel et al. 2006b; Takeuchi et al. 2008). However, the disadvantage due to the lower γ is counteracted by the slower 15 N transverse relaxation during detection, the possibility for more efficient decoupling in both dimensions, and relaxation optimized properties of the pulse sequences. As a result, the median S/N in the 15 N observe CAN experiment is 16% higher than in the 13 C observe NCA-DIPAP experiment. In addition, significantly higher sensitivity was observed for those residues that are hard to detect in the NCA-DIPAP experiment, such as Gly, Ser and residues with high-field C α resonances. Both CAN and CON experiments are able to detect Pro resonances that would not be observed in conventional proton-detected experiments. In addition, those experiments are free from problems of incomplete deuterium-to-proton back exchange in amide positions of perdeuterated proteins expressed in D 2 O. Thus, these features and the superior resolution of 15 N-detected experiments provide an attractive alternative for main chain assignments. The experiments are demonstrated with the small model protein GB1 at conditions simulating a 150 kDa protein, and the 52 kDa glutathione S-transferase dimer, GST.

  1. Herpes simplex virus latency-associated transcript sequence downstream of the promoter influences type-specific reactivation and viral neurotropism.

    Science.gov (United States)

    Bertke, Andrea S; Patel, Amita; Krause, Philip R

    2007-06-01

    Herpes simplex virus (HSV) establishes latency in sensory nerve ganglia during acute infection and may later periodically reactivate to cause recurrent disease. HSV type 1 (HSV-1) reactivates more efficiently than HSV-2 from trigeminal ganglia while HSV-2 reactivates more efficiently than HSV-1 from lumbosacral dorsal root ganglia (DRG) to cause recurrent orofacial and genital herpes, respectively. In a previous study, a chimeric HSV-2 that expressed the latency-associated transcript (LAT) from HSV-1 reactivated similarly to wild-type HSV-1, suggesting that the LAT influences the type-specific reactivation phenotype of HSV-2. To further define the LAT region essential for type-specific reactivation, we constructed additional chimeric HSV-2 viruses by replacing the HSV-2 LAT promoter (HSV2-LAT-P1) or 2.5 kb of the HSV-2 LAT sequence (HSV2-LAT-S1) with the corresponding regions from HSV-1. HSV2-LAT-S1 was impaired for reactivation in the guinea pig genital model, while its rescuant and HSV2-LAT-P1 reactivated with a wild-type HSV-2 phenotype. Moreover, recurrences of HSV-2-LAT-S1 were frequently fatal, in contrast to the relatively mild recurrences of the other viruses. During recurrences, HSV2-LAT-S1 DNA increased more in the sacral cord compared to its rescuant or HSV-2. Thus, the LAT sequence region, not the LAT promoter region, provides essential elements for type-specific reactivation of HSV-2 and also plays a role in viral neurotropism. HSV-1 DNA, as quantified by real-time PCR, was more abundant in the lumbar spinal cord, while HSV-2 DNA was more abundant in the sacral spinal cord, which may provide insights into the mechanism for type-specific reactivation and different patterns of central nervous system infection of HSV-1 and HSV-2.

  2. Basic principles of nuclear magnetic resonance imaging

    International Nuclear Information System (INIS)

    Valk, J.; MacLean, C.; Algra, P.R.

    1985-01-01

    The intent of this book is to help clinicians understand the basic physical principles of magnetic resonance (MR) imaging. The book consists of the following: a discussion of elementary considerations; pulse sequencing; localization of MR signals in space; MR equipment; MR contrast agents; clinical applications; MR spectroscopy; and biological effects of MR imaging; a set of appendixes; and a bibliography. Illustrations and images are included

  3. Determination of the shear impedance of viscoelastic liquids using cylindrical piezoceramic resonators.

    Science.gov (United States)

    Kiełczyński, Piotr; Pajewski, Wincenty; Szalewski, Marek

    2003-03-01

    In this paper, a new method for determining the rheological parameters of viscoelastic liquids is presented. To this end, we used the perturbation method applied to shear vibrations of cylindrical piezoceramic resonators. The resonator was viscoelastically loaded on the outer cylindrical surface. Due to this loading, the resonant frequency and quality factor of the resonator changed. According to the perturbation method, the change in the complex resonant frequency deltaomega = deltaomega(re) + jdeltaomega(im) is directly proportional to the specific acoustic impedance for cylindrical waves Zc of a viscoelastic liquid surrounding the resonator, i.e., deltaomega is approximately equal to jZc, where j = (-1)1/2. Hence, the measurement of the real and imaginary parts of the complex resonant frequency deltaomega determines the real part, Rc, and imaginary part, Xc, of the complex acoustic impedance for cylindrical waves Zc of an investigated liquid. Furthermore, the specific impedance ZL for plane waves was related to the specific impedance Zc for cylindrical waves. Using theoretical formulas established and the results of the experiments performed, the shear storage modulus mu and the viscosity eta for various liquids (e.g., epoxy resins) were determined. Moreover, the authors derived for cylindrical resonators a formula that relates the shift in resonant frequency to the viscosity of the liquid. This formula is analogous to the Kanazawa-Gordon formula that was derived for planar resonators and Newtonian liquids.

  4. Ion-channel genosensor for the detection of specific DNA sequences derived from Plum Pox Virus in plant extracts.

    Science.gov (United States)

    Malecka, Kamila; Michalczuk, Lech; Radecka, Hanna; Radecki, Jerzy

    2014-10-09

    A DNA biosensor for detection of specific oligonucleotides sequences of Plum Pox Virus (PPV) in plant extracts and buffer is proposed. The working principles of a genosensor are based on the ion-channel mechanism. The NH2-ssDNA probe was deposited onto a glassy carbon electrode surface to form an amide bond between the carboxyl group of oxidized electrode surface and amino group from ssDNA probe. The analytical signals generated as a result of hybridization were registered in Osteryoung square wave voltammetry in the presence of [Fe(CN)6]3-/4- as a redox marker. The 22-mer and 42-mer complementary ssDNA sequences derived from PPV and DNA samples from plants infected with PPV were used as targets. Similar detection limits of 2.4 pM (31.0 pg/mL) and 2.3 pM (29.5 pg/mL) in the concentration range 1-8 pM were observed in the presence of the 22-mer ssDNA and 42-mer complementary ssDNA sequences of PPV, respectively. The genosensor was capable of discriminating between samples consisting of extracts from healthy plants and leaf extracts from infected plants in the concentration range 10-50 pg/mL. The detection limit was 12.8 pg/mL. The genosensor displayed good selectivity and sensitivity. The 20-mer partially complementary DNA sequences with four complementary bases and DNA samples from healthy plants used as negative controls generated low signal.

  5. A powerful method for transcriptional profiling of specific cell types in eukaryotes: laser-assisted microdissection and RNA sequencing.

    Directory of Open Access Journals (Sweden)

    Marc W Schmid

    Full Text Available The acquisition of distinct cell fates is central to the development of multicellular organisms and is largely mediated by gene expression patterns specific to individual cells and tissues. A spatially and temporally resolved analysis of gene expression facilitates the elucidation of transcriptional networks linked to cellular identity and function. We present an approach that allows cell type-specific transcriptional profiling of distinct target cells, which are rare and difficult to access, with unprecedented sensitivity and resolution. We combined laser-assisted microdissection (LAM, linear amplification starting from <1 ng of total RNA, and RNA-sequencing (RNA-Seq. As a model we used the central cell of the Arabidopsis thaliana female gametophyte, one of the female gametes harbored in the reproductive organs of the flower. We estimated the number of expressed genes to be more than twice the number reported previously in a study using LAM and ATH1 microarrays, and identified several classes of genes that were systematically underrepresented in the transcriptome measured with the ATH1 microarray. Among them are many genes that are likely to be important for developmental processes and specific cellular functions. In addition, we identified several intergenic regions, which are likely to be transcribed, and describe a considerable fraction of reads mapping to introns and regions flanking annotated loci, which may represent alternative transcript isoforms. Finally, we performed a de novo assembly of the transcriptome and show that the method is suitable for studying individual cell types of organisms lacking reference sequence information, demonstrating that this approach can be applied to most eukaryotic organisms.

  6. [Isolation and identification of specific sequences correlated to cytoplasmic male sterility and fertile maintenance in cauliflower (Brassica oleracea var. botrytis)].

    Science.gov (United States)

    Wang, Chun Guo; Chen, Xiao Qiang; Li, Hui; Zhao, Qian Cheng; Sun, De Ling; Song, Wen Qin

    2008-02-01

    Analysis of ISSR (Inter-Simple Sequence Repeat) and DDRT-PCR (Differential Display Reverse Transcriptase Polymerase Chain Reaction) was performed between cytoplasmic male sterility cauliflower ogura-A and its corresponding maintainer line ogura-B. Totally, 306 detectable bands were obtained by ISSR using thirty oligonucleotide primers. Commonly, six to twelve bands were produced per primer. Among all these primers only the amplification of primer ISSR3 was polymorphic, an 1100 bp specific band was only detected in maintainer line, named ISSR3(1100). Analysis of this sequence indicated that ISSR3(1100) was high homologous with the corresponding sequences of mitochondrial genome in Brassica napus and Arabidopsis thaliana,which suggested that ISSR3(1100) may derive from mitochondrial genome in cauliflower. To carry out DDRT-PCR analysis, three anchor primers and fifteen random primers were selected to combine. Totally, 1122 bands from 1 000 bp to 50 bp were detected. However, only four bands, named ogura-A 205, ogura-A383, ogura-B307 and ogura-B352, were confirmed to be different display in both lines. This result was further identified by reverse Northern dot blotting analysis. Among these four bands, ogura-A205 and ogura-A383 only express in cytoplasmic male sterility line, while ogura-B307 and ogura-B352 were only detected in maintainer line. Analysis of these sequences indicated that it was the first time that these four sequences were reported in cauliflower. Interestingly, ogura-A205 and ogura-B307 did not exhibit any similarities to other reported sequences in other species, more investigations were required to obtain further information. ogura-A383 and ogura-B352 were also two new sequences, they showed high similarities to corresponding chloroplast sequences of Arabidopsis thaliana and Brassica rapa subsp. pekinensis. So we speculated that these two sequences may derive from chloroplast genome. All these results obtained in this study offer new and

  7. Specific proof of various stages of Osler's disease of the brain via high field magnetic resonance tomography (1. 5 Tesla)

    Energy Technology Data Exchange (ETDEWEB)

    Billet, F; Bluemm, R G; Beyer, H K

    1988-08-01

    MR is a sensitive noninvasive examination method for diagnosing parenchymatous cryptic arteriovenous malformations and sequels of cerebral haemorrhage. In a patient with recurring nosebleed and brain stem syndrome eleven so-called cryptic arteriovenous malformations or their haemorrhage sequels were diagnosed via magnetic resonance tomography. Basing on these specific findings, nosebleeding, and a positive family anamnesis, the findings could be classified as belonging to manifestations of Osler's disease (hereditary haemorrhagic telangiectasia). This rare disease is characterised by a triad of signs: telangiectasias, recurring bleeding, and heredity. In this article the specific MR image is compared with the CT pattern and the results are discussed against the background of literature on Osler's disease which is also known as Rendu-Osler-Weber disease.

  8. High resolution spectroscopy in solids by nuclear magnetic resonance; Espectroscopia de alta resolucao em solidos por ressonancia magnetica nuclear

    Energy Technology Data Exchange (ETDEWEB)

    Bonagamba, T J

    1991-07-01

    The nuclear magnetic resonance (NMR) techniques for High Resolution Spectroscopy in Solids are described. Also the construction project of a partially home made spectrometer and its applications in the characterization of solid samples are shown in detail. The high resolution spectrometer used is implemented with the double resonance multiple pulses sequences and magic angle spinning (MAS) and can be used with solid and liquid samples. The maximum spinning frequency for the MAS experiment is in excess of 5 Khz, the double resonance sequences can be performed with any type of nucleus, in the variable temperature operating range with nitrogen gas: -120{sup 0} C to +160{sup 0} C, and is fully controlled by a Macintosh IIci microcomputer. (author).

  9. Theory and applications of maps on SO(3) in nuclear magnetic resonance

    International Nuclear Information System (INIS)

    Cho, H.M.

    1987-02-01

    Theoretical approaches and experimental work in the design of multiple pulse sequences in Nuclear Magnetic Resonance (NMR) are the subjects of this dissertation. Sequences of discrete pulses which reproduce the nominal effect of single pulses, but over substantially broader, narrower, or more selective ranges of transition frequencies, radiofrequency field amplitudes, and spin-spin couplings than the single pulses they replace, are developed and demonstrated. 107 refs., 86 figs., 6 tabs

  10. Diagnostic value of T1 and T2 * relaxation times and off-resonance saturation effects in the evaluation of Achilles tendinopathy by MRI at 3T.

    Science.gov (United States)

    Grosse, Ulrich; Syha, Roland; Hein, Tobias; Gatidis, Sergios; Grözinger, Gerd; Schabel, Christoph; Martirosian, Petros; Schick, Fritz; Springer, Fabian

    2015-04-01

    To evaluate and compare the diagnostic value of T1 , T2 * relaxation times and off-resonance saturation ratios (OSR) in healthy controls and patients with different clinical and morphological stages of Achilles tendinopathy. Forty-two healthy Achilles tendons and 34 tendons of 17 patients with symptomatic and asymptomatic tendinopathy were investigated clinically with conventional magnetic resonance imaging (MRI) sequences on a 3T whole-body MR scanner and a dynamic ultrasound examination. In addition, T1 and T2 * relaxation times were assessed using an ultrashort echo time (UTE) imaging sequence with flip angle and echo time variation. For the calculation of OSR values a Gaussian off-resonance saturation pulse (frequency offset: 750-5000 Hz) was used. The diagnostic value of the derived MR values was assessed and compared using receiver operating characteristic (ROC) curves. ROC curves demonstrate the highest overall test performance for OSR values at 2000 Hz off-resonance in differentiating slightly (OSR-2000 [AUC: 0.930] > T2 * [AUC: 0.884] > T1 [AUC: 0.737]) and more severe pathologically altered tendon areas (OSR-2000 [AUC: 0.964] > T2 * [AUC: 0.917] > T1 [AUC: 0.819]) from healthy ones. OSR values at a frequency offset of 2000 Hz demonstrated a better sensitivity and specificity for detecting mild and severe stages of tendinopathy compared to T2 * and particularly when compared to T1 relaxation times. © 2014 Wiley Periodicals, Inc.

  11. Structure and Sequence Search on Aptamer-Protein Docking

    Science.gov (United States)

    Xiao, Jiajie; Bonin, Keith; Guthold, Martin; Salsbury, Freddie

    2015-03-01

    Interactions between proteins and deoxyribonucleic acid (DNA) play a significant role in the living systems, especially through gene regulation. However, short nucleic acids sequences (aptamers) with specific binding affinity to specific proteins exhibit clinical potential as therapeutics. Our capillary and gel electrophoresis selection experiments show that specific sequences of aptamers can be selected that bind specific proteins. Computationally, given the experimentally-determined structure and sequence of a thrombin-binding aptamer, we can successfully dock the aptamer onto thrombin in agreement with experimental structures of the complex. In order to further study the conformational flexibility of this thrombin-binding aptamer and to potentially develop a predictive computational model of aptamer-binding, we use GPU-enabled molecular dynamics simulations to both examine the conformational flexibility of the aptamer in the absence of binding to thrombin, and to determine our ability to fold an aptamer. This study should help further de-novo predictions of aptamer sequences by enabling the study of structural and sequence-dependent effects on aptamer-protein docking specificity.

  12. Viewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV).

    Science.gov (United States)

    Martin, Andrew C R

    2014-01-01

    The JavaScript Sequence Alignment Viewer (JSAV) is designed as a simple-to-use JavaScript component for displaying sequence alignments on web pages. The display of sequences is highly configurable with options to allow alternative coloring schemes, sorting of sequences and 'dotifying' repeated amino acids. An option is also available to submit selected sequences to another web site, or to other JavaScript code. JSAV is implemented purely in JavaScript making use of the JQuery and JQuery-UI libraries. It does not use any HTML5-specific options to help with browser compatibility. The code is documented using JSDOC and is available from http://www.bioinf.org.uk/software/jsav/.

  13. Tissue discrimination in magnetic resonance imaging of the rotator cuff

    International Nuclear Information System (INIS)

    Meschino, G J; Comas, D S; González, M A; Ballarin, V L; Capiel, C

    2016-01-01

    Evaluation and diagnosis of diseases of the muscles within the rotator cuff can be done using different modalities, being the Magnetic Resonance the method more widely used. There are criteria to evaluate the degree of fat infiltration and muscle atrophy, but these have low accuracy and show great variability inter and intra observer. In this paper, an analysis of the texture features of the rotator cuff muscles is performed to classify them and other tissues. A general supervised classification approach was used, combining forward-search as feature selection method with kNN as classification rule. Sections of Magnetic Resonance Images of the tissues of interest were selected by specialist doctors and they were considered as Gold Standard. Accuracies obtained were of 93% for T1-weighted images and 92% for T2-weighted images. As an immediate future work, the combination of both sequences of images will be considered, expecting to improve the results, as well as the use of other sequences of Magnetic Resonance Images. This work represents an initial point for the classification and quantification of fat infiltration and muscle atrophy degree. From this initial point, it is expected to make an accurate and objective system which will result in benefits for future research and for patients’ health. (paper)

  14. Tissue discrimination in magnetic resonance imaging of the rotator cuff

    Science.gov (United States)

    Meschino, G. J.; Comas, D. S.; González, M. A.; Capiel, C.; Ballarin, V. L.

    2016-04-01

    Evaluation and diagnosis of diseases of the muscles within the rotator cuff can be done using different modalities, being the Magnetic Resonance the method more widely used. There are criteria to evaluate the degree of fat infiltration and muscle atrophy, but these have low accuracy and show great variability inter and intra observer. In this paper, an analysis of the texture features of the rotator cuff muscles is performed to classify them and other tissues. A general supervised classification approach was used, combining forward-search as feature selection method with kNN as classification rule. Sections of Magnetic Resonance Images of the tissues of interest were selected by specialist doctors and they were considered as Gold Standard. Accuracies obtained were of 93% for T1-weighted images and 92% for T2-weighted images. As an immediate future work, the combination of both sequences of images will be considered, expecting to improve the results, as well as the use of other sequences of Magnetic Resonance Images. This work represents an initial point for the classification and quantification of fat infiltration and muscle atrophy degree. From this initial point, it is expected to make an accurate and objective system which will result in benefits for future research and for patients’ health.

  15. Violation of an evolutionarily conserved immunoglobulin diversity gene sequence preference promotes production of dsDNA-specific IgG antibodies.

    Directory of Open Access Journals (Sweden)

    Aaron Silva-Sanchez

    Full Text Available Variability in the developing antibody repertoire is focused on the third complementarity determining region of the H chain (CDR-H3, which lies at the center of the antigen binding site where it often plays a decisive role in antigen binding. The power of VDJ recombination and N nucleotide addition has led to the common conception that the sequence of CDR-H3 is unrestricted in its variability and random in its composition. Under this view, the immune response is solely controlled by somatic positive and negative clonal selection mechanisms that act on individual B cells to promote production of protective antibodies and prevent the production of self-reactive antibodies. This concept of a repertoire of random antigen binding sites is inconsistent with the observation that diversity (DH gene segment sequence content by reading frame (RF is evolutionarily conserved, creating biases in the prevalence and distribution of individual amino acids in CDR-H3. For example, arginine, which is often found in the CDR-H3 of dsDNA binding autoantibodies, is under-represented in the commonly used DH RFs rearranged by deletion, but is a frequent component of rarely used inverted RF1 (iRF1, which is rearranged by inversion. To determine the effect of altering this germline bias in DH gene segment sequence on autoantibody production, we generated mice that by genetic manipulation are forced to utilize an iRF1 sequence encoding two arginines. Over a one year period we collected serial serum samples from these unimmunized, specific pathogen-free mice and found that more than one-fifth of them contained elevated levels of dsDNA-binding IgG, but not IgM; whereas mice with a wild type DH sequence did not. Thus, germline bias against the use of arginine enriched DH sequence helps to reduce the likelihood of producing self-reactive antibodies.

  16. Bone marrow blood supply in gadolinium-enhanced magnetic resonance imaging

    International Nuclear Information System (INIS)

    Saifuddin, A.; Bann, K.; Ridgway, J.P.; Butt, W.P.

    1994-01-01

    A retrospective study was performed to determine whether bone blood supply can be assessed on gadolinium-enhanced magnetic resonance imaging. Lumbar spine magnetic resonance imaging (MRI) examinations of 49 patients attending for post-laminectomy examination were reviewed (30 male, 19 female, mean age 46.4 years, age range 23-84 years). Each study included sagittal T1-weighted spin echo sequences before and after gadolinium administration. Regions of interest were drawn within the L3 vertebral body from a parasagittal slice from each sequence. Signal intensity (SI) values were ascertained and the percentage increase in SI was calculated. For each patient, changes in receiver gain for pre- and post-gadolinium images were corrected by an image scaling factor. In all cases, a measurable increase in SI was found (mean 15.3%, range 4.4-55.7) due to bone vascularity. The results give no indication of the quantity or timing of blood supply but provide a basis for further work. (orig.)

  17. Selective ligand activity at Nur/retinoid X receptor complexes revealed by dimer-specific bioluminescence resonance energy transfer-based sensors

    Science.gov (United States)

    Giner, Xavier C; Cotnoir-White, David; Mader, Sylvie; Lévesque, Daniel

    2017-01-01

    Retinoid X receptors (RXR) play a role as master regulators due to their capacity to form heterodimers with other nuclear receptors. Accordingly, retinoid signaling is involved in multiple biological processes, including development, cell differentiation, metabolism and cell death. However, the role and functions of RXR in different heterodimer complexes remain unsolved, mainly because most RXR drugs (called rexinoids) are not selective to specific heterodimer complexes. This also strongly limits the use of rexinoids for specific therapeutic approaches. In order to better characterize rexinoids at specific nuclear receptor complexes, we have developed and optimized luciferase protein complementation-based Bioluminescence Resonance Energy Transfer (BRET) assays, which can directly measure recruitment of a co-activator motif fused to yellow fluorescent protein (YFP) by specific nuclear receptor dimers. To validate the assays, we compared rexinoid modulation of co-activator recruitment by RXR homodimer, and heterodimers Nur77/RXR and Nurr1/RXR. Results reveal that some rexinoids display selective co-activator recruitment activities with homo- or hetero-dimer complexes. In particular, SR11237 (BMS649) has increased potency for recruitment of co-activator motif and transcriptional activity with the Nur77/RXR heterodimer compared to other complexes. This technology should prove useful to identify new compounds with specificity for individual dimeric species formed by nuclear receptors. PMID:26148973

  18. Coherent control through near-resonant Raman transitions

    International Nuclear Information System (INIS)

    Dai Xingcan; Lerch, Eliza-Beth W.; Leone, Stephen R.

    2006-01-01

    The phase of an electronic wave function is shown to play an important role in coherent control experiments. By using a pulse shaping system with a femtosecond laser, we explore the phase relationships among resonant and off-resonant Raman transitions in Li 2 by measuring the phases of the resulting wave packets, or quantum beats. Specific pixels in a liquid-crystal spatial light modulator are used to isolate the resonant and off-resonant portions of the Raman transitions in Li 2 . The off-resonant Raman transitions have an approximately 90 degree sign phase shift with respect to the resonant Raman transition, and there is an approximately 180 degree sign phase shift between the blue-detuned and the red-detuned off-resonant Raman transitions. Calculations using second-order time-dependent perturbation theory for the electronic transitions agree with the experimental results for the laser pulse intensities used here. Interferences between the off-resonant Raman transitions as a function of detuning are used to demonstrate coherent control of the Raman quantum wave packet

  19. Generic and sequence-variant specific molecular assays for the detection of the highly variable Grapevine leafroll-associated virus 3.

    Science.gov (United States)

    Chooi, Kar Mun; Cohen, Daniel; Pearson, Michael N

    2013-04-01

    Grapevine leafroll-associated virus 3 (GLRaV-3) is an economically important virus, which is found in all grapevine growing regions worldwide. Its accurate detection in nursery and field samples is of high importance for certification schemes and disease management programmes. To reduce false negatives that can be caused by sequence variability, a new universal primer pair was designed against a divergent sequence data set, targeting the open reading frame 4 (heat shock protein 70 homologue gene), and optimised for conventional one-step RT-PCR and one-step SYBR Green real-time RT-PCR assays. In addition, primer pairs for the simultaneous detection of specific GLRaV-3 variants from groups 1, 2, 6 (specifically NZ-1) and the outlier NZ2 variant, and the generic detection of variants from groups 1 to 5 were designed and optimised as a conventional one-step multiplex RT-PCR assay using the plant nad5 gene as an internal control (i.e. one-step hexaplex RT-PCR). Results showed that the generic and variant specific assays detected in vitro RNA transcripts from a range of 1×10(1)-1×10(8) copies of amplicon per μl diluted in healthy total RNA from Vitis vinifera cv. Cabernet Sauvignon. Furthermore, the assays were employed effectively to screen 157 germplasm and 159 commercial field samples. Thus results demonstrate that the GLRaV-3 generic and variant-specific assays are prospective tools that will be beneficial for certification schemes and disease management programmes, as well as biological and epidemiological studies of the divergent GLRaV-3 populations. Copyright © 2013 Elsevier B.V. All rights reserved.

  20. Technical aspects of contrast-enhanced magnetic resonance imaging of the breast: literature review

    International Nuclear Information System (INIS)

    Leopoldino, Denise de Deus; Gracio, Tatiana Schiller; D'Ippolito, Giuseppe; Bezerra, Alexandre Sergio de Araujo; Gracio, Tatiana Schiller

    2005-01-01

    With the advances in surface coil technology and the development of new imaging protocols in addition to the increase of the use of contrast agents, contrast enhanced magnetic resonance imaging (MRI) has emerged as a promising modality for detection, diagnosis and staging of breast cancer. Despite these advances, there are some unresolved issues, including no defined standard technique for contrast-enhanced breast MRI and no standard criteria of interpretation for the evaluation of such studies. In this article, we review the literature and discuss the general requirements and recommendations for contrast agent-enhanced breast MRI, including image interpretation criteria, MR equipment, dedicated radiofrequency coils, use of paramagnetic contrast agents, fat-suppression techniques, planes of acquisition, pulse sequence specifications and artifact sources. (author)

  1. Quantitative magnetic resonance micro-imaging methods for pharmaceutical research.

    Science.gov (United States)

    Mantle, M D

    2011-09-30

    The use of magnetic resonance imaging (MRI) as a tool in pharmaceutical research is now well established and the current literature covers a multitude of different pharmaceutically relevant research areas. This review focuses on the use of quantitative magnetic resonance micro-imaging techniques and how they have been exploited to extract information that is of direct relevance to the pharmaceutical industry. The article is divided into two main areas. The first half outlines the theoretical aspects of magnetic resonance and deals with basic magnetic resonance theory, the effects of nuclear spin-lattice (T(1)), spin-spin (T(2)) relaxation and molecular diffusion upon image quantitation, and discusses the applications of rapid magnetic resonance imaging techniques. In addition to the theory, the review aims to provide some practical guidelines for the pharmaceutical researcher with an interest in MRI as to which MRI pulse sequences/protocols should be used and when. The second half of the article reviews the recent advances and developments that have appeared in the literature concerning the use of quantitative micro-imaging methods to pharmaceutically relevant research. Copyright © 2010 Elsevier B.V. All rights reserved.

  2. Direct, rapid RNA sequence analysis

    International Nuclear Information System (INIS)

    Peattie, D.A.

    1987-01-01

    The original methods of RNA sequence analysis were based on enzymatic production and chromatographic separation of overlapping oligonucleotide fragments from within an RNA molecule followed by identification of the mononucleotides comprising the oligomer. Over the past decade the field of nucleic acid sequencing has changed dramatically, however, and RNA molecules now can be sequenced in a variety of more streamlined fashions. Most of the more recent advances in RNA sequencing have involved one-dimensional electrophoretic separation of 32 P-end-labeled oligoribonucleotides on polyacrylamide gels. In this chapter the author discusses two of these methods for determining the nucleotide sequences of RNA molecules rapidly: the chemical method and the enzymatic method. Both methods are direct and degradative, i.e., they rely on fragmatic and chemical approaches should be utilized. The single-strand-specific ribonucleases (A, T 1 , T 2 , and S 1 ) provide an efficient means to locate double-helical regions rapidly, and the chemical reactions provide a means to determine the RNA sequence within these regions. In addition, the chemical reactions allow one to assign interactions to specific atoms and to distinguish secondary interactions from tertiary ones. If the RNA molecule is small enough to be sequenced directly by the enzymatic or chemical method, the probing reactions can be done easily at the same time as sequencing reactions

  3. Use of the Frank sequence in pulsed EPR

    DEFF Research Database (Denmark)

    Tseitlin, Mark; Quine, Richard W.; Eaton, Sandra S.

    2011-01-01

    The Frank polyphase sequence has been applied to pulsed EPR of triarylmethyl radicals at 256MHz (9.1mT magnetic field), using 256 phase pulses. In EPR, as in NMR, use of a Frank sequence of phase steps permits pulsed FID signal acquisition with very low power microwave/RF pulses (ca. 1.5m......W in the application reported here) relative to standard pulsed EPR. A 0.2mM aqueous solution of a triarylmethyl radical was studied using a 16mm diameter cross-loop resonator to isolate the EPR signal detection system from the incident pulses. Keyword: Correlation spectroscopy,Multi-pulse EPR,Low power pulses,NMR,EPR...

  4. High resolution T{sub 2}{sup *}-weighted magnetic resonance imaging at 3 Tesla using PROPELLER-EPI

    Energy Technology Data Exchange (ETDEWEB)

    Kraemer, Martin; Reichenbach, Juergen R. [Jena University Hospital (Germany). Medical Physics Group

    2014-09-01

    We report the application of PROPELLER-EPI for high resolution T{sub 2}{sup *}-weighted imaging with sub-millimeter in-plane resolution on a clinical 3 Tesla scanner. Periodically rotated blades of a long-axis PROPELLER-EPI sequence were acquired with fast gradient echo readout and acquisition matrix of 320 x 50 per blade. Images were reconstructed by using 2D-gridding, phase and geometric distortion correction and compensation of resonance frequency drifts that occurred during extended measurements. To characterize these resonance frequency offsets, short FID calibration measurements were added to the PROPELLER-EPI sequence. Functional PROPELLER-EPI was performed with volunteers using a simple block design of right handed finger tapping. Results indicate that PROPELLER-EPI can be employed for fast, high resolution T{sub 2}{sup *}-weighted imaging provided geometric distortions and possible resonance frequency drifts are properly corrected. Even small resonance frequency drifts below 10 Hz as well as non-corrected geometric distortions degraded image quality substantially. In the initial fMRI experiment image quality and signal-to-noise ratio was sufficient for obtaining high resolution functional activation maps. (orig.)

  5. Optimized protocols for cardiac magnetic resonance imaging in patients with thoracic metallic implants.

    Science.gov (United States)

    Olivieri, Laura J; Cross, Russell R; O'Brien, Kendall E; Ratnayaka, Kanishka; Hansen, Michael S

    2015-09-01

    Cardiac magnetic resonance (MR) imaging is a valuable tool in congenital heart disease; however patients frequently have metal devices in the chest from the treatment of their disease that complicate imaging. Methods are needed to improve imaging around metal implants near the heart. Basic sequence parameter manipulations have the potential to minimize artifact while limiting effects on image resolution and quality. Our objective was to design cine and static cardiac imaging sequences to minimize metal artifact while maintaining image quality. Using systematic variation of standard imaging parameters on a fluid-filled phantom containing commonly used metal cardiac devices, we developed optimized sequences for steady-state free precession (SSFP), gradient recalled echo (GRE) cine imaging, and turbo spin-echo (TSE) black-blood imaging. We imaged 17 consecutive patients undergoing routine cardiac MR with 25 metal implants of various origins using both standard and optimized imaging protocols for a given slice position. We rated images for quality and metal artifact size by measuring metal artifact in two orthogonal planes within the image. All metal artifacts were reduced with optimized imaging. The average metal artifact reduction for the optimized SSFP cine was 1.5+/-1.8 mm, and for the optimized GRE cine the reduction was 4.6+/-4.5 mm (P metal artifact reduction for the optimized TSE images was 1.6+/-1.7 mm (P metal artifact are easily created by modifying basic sequence parameters, and images are superior to standard imaging sequences in both quality and artifact size. Specifically, for optimized cine imaging a GRE sequence should be used with settings that favor short echo time, i.e. flow compensation off, weak asymmetrical echo and a relatively high receiver bandwidth. For static black-blood imaging, a TSE sequence should be used with fat saturation turned off and high receiver bandwidth.

  6. Magnetic resonance imaging of central nervous system haemorrhage

    International Nuclear Information System (INIS)

    Silberstein, M.; Hennessy, O.

    1993-01-01

    The variable magnetic resonance imaging appearances of central nervous system haemorrhage, both intra- and extra-axial, are described. These will vary with the type of image contrast (T1 or T2 weighting), the nature of the imaging sequence (spin-echo or gradient-echo) and the time from onset of haemorrhage. Magnetic resonance imaging is a useful technique for imaging haemorrhage in the central nervous system as it yields temporal information about haematoma development, and it is the only non-invasive means of imaging intraspinal haemorrhage. However, in the imaging of haematomas within 24 h of onset and in subarachnoid haemorrhage computed tomography is the investigation of choice. 13 refs., 6 figs

  7. Magnetic resonance imaging of the sacroiliac joints in patients with suspected spondyloarthritis. Comparison of turbo spin-echo and gradient-echo sequences for the detection of structural alterations

    International Nuclear Information System (INIS)

    Dornia, C.; Hoffstetter, P.; Asklepios Klinikum, Bad Abbach; Fleck, M.; Asklepios Klinikum, Bad Abbach; Hartung, W.; Niessen, C.; Stroszczynski, C.

    2015-01-01

    Magnetic resonance imaging (MRI) is the method of choice for the evaluation of spondyloarthritis (SpA). According to the guidelines of the Assessment of Spondyloarthritis International Society (ASAS) and Outcome Measures in Rheumatology (OMERACT), MRI findings in SpA of the spine and the sacroiliac joints (SIJ) are classified as inflammatory and structural alterations. Modern gradient-echo sequences (GRE) are recommended for optimized detection of structural alterations of the SIJ. We assess the benefit of GRE in the detection of structural alterations of the SIJ in comparison to conventional turbo spin-echo sequences (TSE). Retrospective study of 114 patients who received MRI of the SIJ for the evaluation of SpA. Structural alterations of the SIJ were assessed by two blinded readers separately for T1 TSE and T2 * GRE. The findings were classified according to a previously published chronicity score separately for both sides and sequences. Interobserver reliability was calculated with Cohen's Kappa, and the significance of findings was assessed with the Wilcoxon test. P-values * GRE showed a high interobserver reliability in the detection of structural alterations in patients with SpA. However, T2 * GRE detected significantly more structural alterations than T1 TSE and should be an integral part of a modern MRI protocol for the diagnostic workup of patients with suspected SpA.

  8. Magnetic resonance tomography for focal lesions in the liver using the para-magnetic contrast medium gadolinium DTPA

    International Nuclear Information System (INIS)

    Hamm, B.; Roemer, T.; Felix, R.; Wolf, K.J.; Klinikum Charlottenburg, Berlin

    1986-01-01

    The use of the para-magnetic contrast medium gadolinium DTPA for magnetic resonance tomography of focal lesions in the liver was investigated in 31 patients. Two dosage schedules of the contrast medium (0.1 and 0.2 mmol/kg body weight) were used with field strengths of 0.35 and 0.5 Tesla. Using T 1 sequences, gadolinium DTPA showed increased signal intensity in the liver and in tumours, but this was significantly more marked in the tumour. On T 1 spin-echo sequences, previously iso-intense lesions became visible after administration of contrast. On the other hand, contrast-enhanced lesions were less well seen on inversion recovery sequences because of a reduction in the contrast between tumour and liver tissue. The contrast between tumour and liver tissue was not improved by gadolinium DTPA in comparison with precontrast inversion recovery sequences and T 2 spin-echo sequences. The perfusion of intra-hepatic tumours could be elucidated by magnetic resonance tomography after the administration of gadolinium DTPA. (orig.) [de

  9. Further technical development in magnetic resonance imaging of the brain in children

    International Nuclear Information System (INIS)

    Young, I.R.; Dubowitz, L.M.S.; Pennock, J.M.; Bydder, G.M.

    1988-01-01

    Further technical developments implemented in magnetic resonance imaging (MRI) of the brain in children are described. These include the use of longer data collection periods, T2-dependent field echoes, susceptibility mapping, short inversion time inversion recovery sequences, very long echo time spin-echo sequences, and phase mapping techniques to detect tissue perfusion. These techniques are illustrated in selected cases and have increased the range of options available in MR examinations of children. (author)

  10. Developing market class specific InDel markers from next generation sequence data in Phaseolus vulgaris L.

    Directory of Open Access Journals (Sweden)

    Samira eMafi Moghaddam

    2014-05-01

    Full Text Available Next generation sequence data provides valuable information and tools for genetic and genomic research and offers new insights useful for marker development. This data is useful for the design of accurate and user-friendly molecular tools. Common bean (Phaseolus vulgaris L. is a diverse crop in which separate domestication events happened in each gene pool followed by race and market class diversification that has resulted in different morphological characteristics in each commercial market class. This has led to essentially independent breeding programs within each market class which in turn has resulted in limited within market class sequence variation. Sequence data from selected genotypes of five bean market classes (pinto, black, navy, and light and dark red kidney were used to develop InDel-based markers specific to each market class. Design of the InDel markers was conducted through a combination of assembly, alignment and primer design software using 1.6x to 5.1x coverage of Illumina GAII sequence data for each of the selected genotypes. The procedure we developed for primer design is fast, accurate, less error prone, and higher throughput than when they are designed manually. All InDel markers are easy to run and score with no need for PCR optimization. A total of 2,687 InDel markers distributed across the genome were developed. To highlight their usefulness, they were employed to construct a phylogenetic tree and a genetic map, showing that InDel markers are reliable, simple, and accurate.

  11. Short sequence motifs, overrepresented in mammalian conservednon-coding sequences

    Energy Technology Data Exchange (ETDEWEB)

    Minovitsky, Simon; Stegmaier, Philip; Kel, Alexander; Kondrashov,Alexey S.; Dubchak, Inna

    2007-02-21

    Background: A substantial fraction of non-coding DNAsequences of multicellular eukaryotes is under selective constraint. Inparticular, ~;5 percent of the human genome consists of conservednon-coding sequences (CNSs). CNSs differ from other genomic sequences intheir nucleotide composition and must play important functional roles,which mostly remain obscure.Results: We investigated relative abundancesof short sequence motifs in all human CNSs present in the human/mousewhole-genome alignments vs. three background sets of sequences: (i)weakly conserved or unconserved non-coding sequences (non-CNSs); (ii)near-promoter sequences (located between nucleotides -500 and -1500,relative to a start of transcription); and (iii) random sequences withthe same nucleotide composition as that of CNSs. When compared tonon-CNSs and near-promoter sequences, CNSs possess an excess of AT-richmotifs, often containing runs of identical nucleotides. In contrast, whencompared to random sequences, CNSs contain an excess of GC-rich motifswhich, however, lack CpG dinucleotides. Thus, abundance of short sequencemotifs in human CNSs, taken as a whole, is mostly determined by theiroverall compositional properties and not by overrepresentation of anyspecific short motifs. These properties are: (i) high AT-content of CNSs,(ii) a tendency, probably due to context-dependent mutation, of A's andT's to clump, (iii) presence of short GC-rich regions, and (iv) avoidanceof CpG contexts, due to their hypermutability. Only a small number ofshort motifs, overrepresented in all human CNSs are similar to bindingsites of transcription factors from the FOX family.Conclusion: Human CNSsas a whole appear to be too broad a class of sequences to possess strongfootprints of any short sequence-specific functions. Such footprintsshould be studied at the level of functional subclasses of CNSs, such asthose which flank genes with a particular pattern of expression. Overallproperties of CNSs are affected by

  12. Real time magnetic resonance guided endomyocardial local delivery

    Science.gov (United States)

    Corti, R; Badimon, J; Mizsei, G; Macaluso, F; Lee, M; Licato, P; Viles-Gonzalez, J F; Fuster, V; Sherman, W

    2005-01-01

    Objective: To investigate the feasibility of targeting various areas of left ventricle myocardium under real time magnetic resonance (MR) imaging with a customised injection catheter equipped with a miniaturised coil. Design: A needle injection catheter with a mounted resonant solenoid circuit (coil) at its tip was designed and constructed. A 1.5 T MR scanner with customised real time sequence combined with in-room scan running capabilities was used. With this system, various myocardial areas within the left ventricle were targeted and injected with a gadolinium-diethylenetriaminepentaacetic acid (DTPA) and Indian ink mixture. Results: Real time sequencing at 10 frames/s allowed clear visualisation of the moving catheter and its transit through the aorta into the ventricle, as well as targeting of all ventricle wall segments without further image enhancement techniques. All injections were visualised by real time MR imaging and verified by gross pathology. Conclusion: The tracking device allowed real time in vivo visualisation of catheters in the aorta and left ventricle as well as precise targeting of myocardial areas. The use of this real time catheter tracking may enable precise and adequate delivery of agents for tissue regeneration. PMID:15710717

  13. On Resonance: A Critical Pluralistic Inquiry into Advertising Rhetoric.

    OpenAIRE

    McQuarrie, Edward F; Mick, David Glen

    1992-01-01

    Print ads exhibit resonance when they combine wordplay with a relevant picture to create ambiguity and incongruity. This article uses multiple perspectives and methods within a framework of critical pluralism to investigate advertising resonance. Semiotic text analyses, a content analysis of contemporary magazine ads, two experiments, and phenomenological interviews combine to yield insights into the operation, prevalence, impact and experience of resonance. Specifically, the two experiments ...

  14. Detection of nucleic acid sequences by invader-directed cleavage

    Science.gov (United States)

    Brow, Mary Ann D.; Hall, Jeff Steven Grotelueschen; Lyamichev, Victor; Olive, David Michael; Prudent, James Robert

    1999-01-01

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The 5' nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof. The present invention further relates to methods and devices for the separation of nucleic acid molecules based by charge.

  15. Evaluation of magnetic resonance velocimetry for steady flow.

    Science.gov (United States)

    Ku, D N; Biancheri, C L; Pettigrew, R I; Peifer, J W; Markou, C P; Engels, H

    1990-11-01

    Whole body magnetic resonance (MR) imaging has recently become an important diagnostic tool for cardiovascular diseases. The technique of magnetic resonance phase velocity encoding allows the quantitative measurement of velocity for an arbitrary component direction. A study was initiated to determine the ability and accuracy of MR velocimetry to measure a wide range of flow conditions including flow separation, three-dimensional secondary flow, high velocity gradients, and turbulence. A steady flow system pumped water doped with manganese chloride through a variety of test sections. Images were produced using gradient echo sequences on test sections including a straight tube, a curved tube, a smoothly converging-diverging nozzle, and an orifice. Magnetic resonance measurements of laminar and turbulent flows were depicted as cross-sectional velocity profiles. MR velocity measurements revealed such flow behavior as spatially varying velocity, recirculation and secondary flows over a wide range of conditions. Comparisons made with published experimental laser Doppler anemometry measurements and theoretical calculations for similar flow conditions revealed excellent accuracy and precision levels. The successful measurement of velocity profiles for a variety of flow conditions and geometries indicate that magnetic resonance imaging is an accurate, non-contacting velocimeter.

  16. Strain-specific and pooled genome sequences for populations of Drosophila melanogaster from three continents.

    Science.gov (United States)

    Bergman, Casey M; Haddrill, Penelope R

    2015-01-01

    To contribute to our general understanding of the evolutionary forces that shape variation in genome sequences in nature, we have sequenced genomes from 50 isofemale lines and six pooled samples from populations of Drosophila melanogaster on three continents. Analysis of raw and reference-mapped reads indicates the quality of these genomic sequence data is very high. Comparison of the predicted and experimentally-determined Wolbachia infection status of these samples suggests that strain or sample swaps are unlikely to have occurred in the generation of these data. Genome sequences are freely available in the European Nucleotide Archive under accession ERP009059. Isofemale lines can be obtained from the Drosophila Species Stock Center.

  17. Prebiopsy magnetic resonance spectroscopy and imaging in the diagnosis of prostate cancer

    International Nuclear Information System (INIS)

    Kumar, V.; Jagannathan, N.R.; Thulkar, S.; Kumar, R.

    2012-01-01

    Existing screening investigations for the diagnosis of early prostate cancer lack specificity, resulting in a high negative biopsy rate. There is increasing interest in the use of various magnetic resonance methods for improving the yield of transrectal ultrasound-guided biopsies of the prostate in men suspected to have prostate cancer. We review the existing status of such investigations. A literature search was carried out using the Pubmed database to identify articles related to magnetic resonance methods for diagnosing prostate cancer. References from these articles were also extracted and reviewed. Recent studies have focused on prebiopsy magnetic resonance investigations using conventional magnetic resonance imaging, dynamic contrast enhanced magnetic resonance imaging, diffusion weighted magnetic resonance imaging, magnetization transfer imaging and magnetic resonance spectroscopy of the prostate. This marks a shift from the earlier strategy of carrying out postbiopsy magnetic resonance investigations. Prebiopsy magnetic resonance investigations has been useful in identifying patients who are more likely to have a biopsy positive for malignancy. Prebiopsy magnetic resonance investigations has a potential role in increasing specificity of screening for early prostate cancer. It has a role in the targeting of biopsy sites, avoiding unnecessary biopsies and predicting the outcome of biopsies. (author)

  18. MRI to delineate the gross tumor volume of nasopharyngeal cancers: which sequences and planes should be used?

    Science.gov (United States)

    Popovtzer, Aron; Ibrahim, Mohannad; Tatro, Daniel; Feng, Felix Y; Ten Haken, Randall K; Eisbruch, Avraham

    2014-09-01

    Magnetic resonance imaging (MRI) has been found to be better than computed tomography for defining the extent of primary gross tumor volume (GTV) in advanced nasopharyngeal cancer. It is routinely applied for target delineation in planning radiotherapy. However, the specific MRI sequences/planes that should be used are unknown. Twelve patients with nasopharyngeal cancer underwent primary GTV evaluation with gadolinium-enhanced axial T1 weighted image (T1) and T2 weighted image (T2), coronal T1, and sagittal T1 sequences. Each sequence was registered with the planning computed tomography scans. Planning target volumes (PTVs) were derived by uniform expansions of the GTVs. The volumes encompassed by the various sequences/planes, and the volumes common to all sequences/planes, were compared quantitatively and anatomically to the volume delineated by the commonly used axial T1-based dataset. Addition of the axial T2 sequence increased the axial T1-based GTV by 12% on average (p = 0.004), and composite evaluations that included the coronal T1 and sagittal T1 planes increased the axial T1-based GTVs by 30% on average (p = 0.003). The axial T1-based PTVs were increased by 20% by the additional sequences (p = 0.04). Each sequence/plane added unique volume extensions. The GTVs common to all the T1 planes accounted for 38% of the total volumes of all the T1 planes. Anatomically, addition of the coronal and sagittal-based GTVs extended the axial T1-based GTV caudally and cranially, notably to the base of the skull. Adding MRI planes and sequences to the traditional axial T1 sequence yields significant quantitative and anatomically important extensions of the GTVs and PTVs. For accurate target delineation in nasopharyngeal cancer, we recommend that GTVs be outlined in all MRI sequences/planes and registered with the planning computed tomography scans.

  19. A new technique for MR elastography of the supraspinatus muscle: A gradient-echo type multi-echo sequence.

    Science.gov (United States)

    Ito, Daiki; Numano, Tomokazu; Mizuhara, Kazuyuki; Takamoto, Koichi; Onishi, Takaaki; Nishijo, Hisao

    2016-10-01

    Magnetic resonance elastography (MRE) can measure tissue stiffness quantitatively and noninvasively. Supraspinatus muscle injury is a significant problem among throwing athletes. The purpose of this study was to develop an MRE technique for application to the supraspinatus muscle by using a conventional magnetic resonance imaging (MRI). MRE acquisitions were performed with a gradient-echo type multi-echo MR sequence at 100Hz pneumatic vibration. A custom-designed vibration pad was used as a pneumatic transducer in order to adapt to individual shoulder shapes. In a gradient-echo type multi-echo MR sequence, without motion encoding gradient (MEG) that synchronizes with vibrations, bipolar readout gradient lobes achieved a similar function to MEG (MEG-like effect). In other words, a dedicated MRE sequence (built-in MEG) is not always necessary for MRE. In this study, 7 healthy volunteers underwent MRE. We investigated the effects of direction of the MEG-like effect and selected imaging planes on the patterns of wave propagation (wave image). The results indicated that wave images showed clear wave propagation on a condition that the direction of the MEG-like effect was nearly perpendicular to the long axis of the supraspinatus muscle, and that the imaging plane was superior to the proximal supraspinatus muscle. This limited condition might be ascribed to specific features of fibers in the supraspinatus muscle and wave reflection from the boundaries of the supraspinous fossa. The mean stiffness of the supraspinatus muscle was 10.6±3.17kPa. Our results demonstrated that using MRE, our method can be applied to the supraspinatus muscle by using conventional MRI. Copyright © 2016 Elsevier Inc. All rights reserved.

  20. Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes

    Directory of Open Access Journals (Sweden)

    Blackmon Barbara P

    2011-07-01

    Full Text Available Abstract Background BAC-based physical maps provide for sequencing across an entire genome or a selected sub-genomic region of biological interest. Such a region can be approached with next-generation whole-genome sequencing and assembly as if it were an independent small genome. Using the minimum tiling path as a guide, specific BAC clones representing the prioritized genomic interval are selected, pooled, and used to prepare a sequencing library. Results This pooled BAC approach was taken to sequence and assemble a QTL-rich region, of ~3 Mbp and represented by twenty-seven BACs, on linkage group 5 of the Theobroma cacao cv. Matina 1-6 genome. Using various mixtures of read coverages from paired-end and linear 454 libraries, multiple assemblies of varied quality were generated. Quality was assessed by comparing the assembly of 454 reads with a subset of ten BACs individually sequenced and assembled using Sanger reads. A mixture of reads optimal for assembly was identified. We found, furthermore, that a quality assembly suitable for serving as a reference genome template could be obtained even with a reduced depth of sequencing coverage. Annotation of the resulting assembly revealed several genes potentially responsible for three T. cacao traits: black pod disease resistance, bean shape index, and pod weight. Conclusions Our results, as with other pooled BAC sequencing reports, suggest that pooling portions of a minimum tiling path derived from a BAC-based physical map is an effective method to target sub-genomic regions for sequencing. While we focused on a single QTL region, other QTL regions of importance could be similarly sequenced allowing for biological discovery to take place before a high quality whole-genome assembly is completed.

  1. Gated magnetic resonance imaging of congenital cardiac malformations

    International Nuclear Information System (INIS)

    Fletcher, B.D.; Jocobstein, M.D.; Nelson, A.D.; Riemenschneider, T.A.; Alfidi, R.J.

    1984-01-01

    Magnetic resonance (MR) images of a variety of cardiac malformations in 19 patients aged 1 week to 33 years were obtained using pulse plethysmographic- or ECG-gated spin echo pulse sequences. Coronal, axial, and sagittal images displaying intracardiac structures with excellent spatial and contrast resolution were acquired during systole or diastole. It is concluded that MR will be a valuable noninvasive method of diagnosing congenital heart disease

  2. Ring-Resonator/Sol-Gel Interferometric Immunosensor

    Science.gov (United States)

    Bearman, Gregory; Cohen, David

    2007-01-01

    A proposed biosensing system would be based on a combination of (1) a sensing volume containing antibodies immobilized in a sol-gel matrix and (2) an optical interferometer having a ring resonator configuration. The antibodies would be specific to an antigen species that one seeks to detect. In the ring resonator of the proposed system, light would make multiple passes through the sensing volume, affording greater interaction length and, hence, greater antibody- detection sensitivity.

  3. Sequence-specific 1H NMR assignments, secondary structure, and location of the calcium binding site in the first epidermal growth factor like domain of blood coagulation factor IX

    International Nuclear Information System (INIS)

    Huang, L.H.; Cheng, H.; Sweeney, W.V.; Pardi, A.; Tam, J.P.

    1991-01-01

    Factor IX is a blood clotting protein that contains three regions, including a γ-carboxyglutamic acid (Gla) domain, two tandemly connected epidermal growth factor like (EGF-like) domains, and a serine protease region. The protein exhibits a high-affinity calcium binding site in the first EGF0like domain, in addition to calcium binding in the Gla domain. The first EGF-like domain, factor IX (45-87), has been synthesized. Sequence-specific resonance assignment of the peptide has been made by using 2D NMR techniques, and its secondary structure has been determined. The protein is found to have two antiparallel β-sheets, and preliminary distance geometry calculations indicate that the protein has two domains, separated by Trp 28 , with the overall structure being similar to that of EGF. An NMR investigation of the calcium-bound first EGF-like domain indicates the presence and location of a calcium binding site involving residues on both strands of one of the β-sheets as well as the N-terminal region of the peptide. These results suggest that calcium binding in the first EGF-like domain could induce long-range (possibly interdomain) conformational changes in factor IX, rather than causing structural alterations in the EGF-like domain itself

  4. Improved switching using Fano resonances in photonic crystal structures

    DEFF Research Database (Denmark)

    Heuck, Mikkel; Kristensen, Philip Trøst; Elesin, Yuriy

    2013-01-01

    difference time domain simulations taking into account the signal bandwidth. The results suggest a significant energy reduction by employing Fano resonances compared to more well established Lorentzian resonance structures. A specific example of a Kerr nonlinearity shows an order of magnitude energy...

  5. Global Transcriptome Sequencing Identifies Chlamydospore Specific Markers in Candida albicans and Candida dubliniensis

    LENUS (Irish Health Repository)

    Palige, Katja

    2013-04-15

    Candida albicans and Candida dubliniensis are pathogenic fungi that are highly related but differ in virulence and in some phenotypic traits. During in vitro growth on certain nutrient-poor media, C. albicans and C. dubliniensis are the only yeast species which are able to produce chlamydospores, large thick-walled cells of unknown function. Interestingly, only C. dubliniensis forms pseudohyphae with abundant chlamydospores when grown on Staib medium, while C. albicans grows exclusively as a budding yeast. In order to further our understanding of chlamydospore development and assembly, we compared the global transcriptional profile of both species during growth in liquid Staib medium by RNA sequencing. We also included a C. albicans mutant in our study which lacks the morphogenetic transcriptional repressor Nrg1. This strain, which is characterized by its constitutive pseudohyphal growth, specifically produces masses of chlamydospores in Staib medium, similar to C. dubliniensis. This comparative approach identified a set of putatively chlamydospore-related genes. Two of the homologous C. albicans and C. dubliniensis genes (CSP1 and CSP2) which were most strongly upregulated during chlamydospore development were analysed in more detail. By use of the green fluorescent protein as a reporter, the encoded putative cell wall related proteins were found to exclusively localize to C. albicans and C. dubliniensis chlamydospores. Our findings uncover the first chlamydospore specific markers in Candida species and provide novel insights in the complex morphogenetic development of these important fungal pathogens.

  6. Children's (Pediatric) Magnetic Resonance Imaging

    Medline Plus

    Full Text Available ... MRI) exam. View full size with caption Pediatric Content Some imaging tests and treatments have special pediatric considerations. The teddy bear denotes child-specific content. Related Articles and Media Catheter Angiography Magnetic Resonance, ...

  7. Added value of gadoxetic acid-enhanced T1-weighted magnetic resonance cholangiography for the diagnosis of post-transplant biliary complications

    Energy Technology Data Exchange (ETDEWEB)

    Kinner, Sonja [University of Wisconsin School of Medicine and Public Health, Department of Radiology, Madison, WI (United States); University Hospital Essen, Department of Diagnostic and Interventional Radiology and Neuroradiology, Essen (Germany); Schubert, Tilman B. [University of Wisconsin School of Medicine and Public Health, Department of Radiology, Madison, WI (United States); Basel University Hospital, Clinic of Radiology and Nuclear Medicine, Basel (Switzerland); Said, Adnan [University of Wisconsin-Madison, Department of Medicine, Madison, WI (United States); Mezrich, Joshua D. [University of Wisconsin-Madison, Department of Surgery, Madison, WI (United States); Reeder, Scott B. [University of Wisconsin School of Medicine and Public Health, Department of Radiology, Madison, WI (United States); University of Wisconsin-Madison, Department of Medicine, Madison, WI (United States); University of Wisconsin-Madison, Department of Biomedical Engineering, Madison, WI (United States); University of Wisconsin-Madison, Department of Medical Physics, Madison, WI (United States); University of Wisconsin-Madison, Department of Emergency Medicine, Madison, WI (United States)

    2017-10-15

    Biliary complications after liver transplantation (LT) are common. This study aimed to ascertain the value of gadoxetic acid-enhanced T1-weighted (T1w) magnetic resonance cholangiography (MRC) to evaluate anastomotic strictures (AS), non-anastomotic strictures (NAS) and biliary casts (BC). Sixty liver-transplanted patients with suspicion of biliary complications and T2w-MRCP and T1w-MRC followed by endoscopic retrograde cholangiopancreatography (ERCP) or percutaneous transhepatic cholangiography (PTC) were analysed. Two readers reviewed the MRCs and rated image quality (IQ) and likelihood for AS/NAS/BC on Likert scales. Sensitivity, specificity and predictive values were calculated, ROC curve analysis performed, and inter-reader variability assessed. The subjective added value of T1w-MRC was rated. IQ was high for all sequences without significant differences (2.83-2.88). In 39 patients ERCP/PTC detected a complication. Sensitivity and specificity for AS were 64-96 using T2w-MRCP, increasing to 79-100 using all sequences. Use of all sequences increased the sensitivity of detecting NAS/BC from 72-92% to 88-100% and 67-89% to 72-94%, respectively. Kappa values were substantial (0.45-0.62). T1w-MRC was found to be helpful in 75-83.3%. Combining T1w-MRC and T2w-MRCP increased sensitivity and specificity and diagnostic confidence in patients after LT with suspected biliary complications. T1w-MRC is a valuable tool for evaluating post-transplant biliary complications. (orig.)

  8. Molecular dynamics simulations shed light on the enthalpic and entropic driving forces that govern the sequence specific recognition between netropsin and DNA.

    Science.gov (United States)

    Dolenc, Jozica; Gerster, Sarah; van Gunsteren, Wilfred F

    2010-09-02

    With the aim to gain a better understanding of the various driving forces that govern sequence specific DNA minor groove binding, we performed a thermodynamic analysis of netropsin binding to an AT-containing and to a set of six mixed AT/GC-containing binding sequences in the DNA minor groove. The relative binding free energies obtained using molecular dynamics simulations and free energy calculations show significant variations with the binding sequence. While the introduction of a GC base pair in the middle or close to the middle of the binding site is unfavorable for netropsin binding, a GC base pair at the end of the binding site appears to have no negative influence on the binding. The results of the structural and energetic analyses of the netropsin-DNA complexes reveal that the differences in the calculated binding affinities cannot be explained solely in terms of netropsin-DNA hydrogen-bonding or interaction energies. In addition, solvation effects and entropic contributions to the relative binding free energy provide a more complete picture of the various factors determining binding. Analysis of the relative binding entropy indicates that its magnitude is highly sequence-dependent, with the ratio |TDeltaDeltaS|/|DeltaDeltaH| ranging from 0.07 for the AAAGA to 1.7 for the AAGAG binding sequence, respectively.

  9. Protein structure analysis using the resonant recognition model and wavelet transforms

    International Nuclear Information System (INIS)

    Fang, Q.; Cosic, I.

    1998-01-01

    An approach based on the resonant recognition model and the discrete wavelet transform is introduced here for characterising proteins' biological function. The protein sequence is converted into a numerical series by assigning the electron-ion interaction potential to each amino acid from N-terminal to C-terminal. A set of peaks is found after performing a wavelet transform onto a numerical series representing a group of homologous proteins. These peaks are related to protein structural and functional properties and named characteristic vector of that protein group. Further more, the amino acids contributing mostly to a protein's biological functions, the so-called 'hot spots' amino acids, are predicted by the continuous wavelet transform. It is found that the hot spots are clustered around the protein's cleft structure. The wavelets approach provides a novel methods for amino acid sequence analysis as well as an expansion for the newly established macromolecular interaction model: the resonant recognition model. Copyright (1998) Australasian Physical and Engineering Sciences in Medicine

  10. Sequence-specific assignments in the 1H NMR spectrum of the human inflammatory protein C5a

    International Nuclear Information System (INIS)

    Zuiderweg, E.R.P.; Mollison, K.W.; Henkin, J.; Carter, G.W.

    1988-01-01

    Full sequence-specific assignments for the 1 H NMR lines of the backbone protons of the human complement factor C5a are described and documented. The results were obtained by largely following the methodology developed by Wuethrich et al. Assignments for the majority of the amino acid side chain protons were obtained by using a comparison of double- and triple-quantum-filtered two-dimensional correlated experiments together with the analysis of relayed coherence transfer spectra. The assignments provide the basis for the determination of the thus far unknown three-dimensional structure of C5a from nuclear Overhauser enhancement distance constraints

  11. Sequencing Information Management System (SIMS). Final report

    Energy Technology Data Exchange (ETDEWEB)

    Fields, C.

    1996-02-15

    A feasibility study to develop a requirements analysis and functional specification for a data management system for large-scale DNA sequencing laboratories resulted in a functional specification for a Sequencing Information Management System (SIMS). This document reports the results of this feasibility study, and includes a functional specification for a SIMS relational schema. The SIMS is an integrated information management system that supports data acquisition, management, analysis, and distribution for DNA sequencing laboratories. The SIMS provides ad hoc query access to information on the sequencing process and its results, and partially automates the transfer of data between laboratory instruments, analysis programs, technical personnel, and managers. The SIMS user interfaces are designed for use by laboratory technicians, laboratory managers, and scientists. The SIMS is designed to run in a heterogeneous, multiplatform environment in a client/server mode. The SIMS communicates with external computational and data resources via the internet.

  12. Analysis and Visualization Tool for Targeted Amplicon Bisulfite Sequencing on Ion Torrent Sequencers.

    Directory of Open Access Journals (Sweden)

    Stephan Pabinger

    Full Text Available Targeted sequencing of PCR amplicons generated from bisulfite deaminated DNA is a flexible, cost-effective way to study methylation of a sample at single CpG resolution and perform subsequent multi-target, multi-sample comparisons. Currently, no platform specific protocol, support, or analysis solution is provided to perform targeted bisulfite sequencing on a Personal Genome Machine (PGM. Here, we present a novel tool, called TABSAT, for analyzing targeted bisulfite sequencing data generated on Ion Torrent sequencers. The workflow starts with raw sequencing data, performs quality assessment, and uses a tailored version of Bismark to map the reads to a reference genome. The pipeline visualizes results as lollipop plots and is able to deduce specific methylation-patterns present in a sample. The obtained profiles are then summarized and compared between samples. In order to assess the performance of the targeted bisulfite sequencing workflow, 48 samples were used to generate 53 different Bisulfite-Sequencing PCR amplicons from each sample, resulting in 2,544 amplicon targets. We obtained a mean coverage of 282X using 1,196,822 aligned reads. Next, we compared the sequencing results of these targets to the methylation level of the corresponding sites on an Illumina 450k methylation chip. The calculated average Pearson correlation coefficient of 0.91 confirms the sequencing results with one of the industry-leading CpG methylation platforms and shows that targeted amplicon bisulfite sequencing provides an accurate and cost-efficient method for DNA methylation studies, e.g., to provide platform-independent confirmation of Illumina Infinium 450k methylation data. TABSAT offers a novel way to analyze data generated by Ion Torrent instruments and can also be used with data from the Illumina MiSeq platform. It can be easily accessed via the Platomics platform, which offers a web-based graphical user interface along with sample and parameter storage

  13. Impact of cadmium, cobalt and nickel on sequence-specific DNA binding of p63 and p73 in vitro and in cells

    Czech Academy of Sciences Publication Activity Database

    Adámik, Matěj; Bažantová, Pavla; Navrátilová, Lucie; Polášková, Alena; Pečinka, Petr; Holanová, L.; Tichý, Vlastimil; Brázdová, Marie

    2015-01-01

    Roč. 456, č. 1 (2015), s. 29-34 ISSN 0006-291X R&D Projects: GA ČR(CZ) GA13-36108S Institutional support: RVO:68081707 Keywords : p53 protein family * Sequence-specific DNA binding * Heavy metals Subject RIV: BO - Biophysics Impact factor: 2.371, year: 2015

  14. Magnetic nanoparticle imaging using multiple electron paramagnetic resonance activation sequences

    International Nuclear Information System (INIS)

    Coene, A.; Dupré, L.; Crevecoeur, G.

    2015-01-01

    Magnetic nanoparticles play an important role in several biomedical applications such as hyperthermia, drug targeting, and disease detection. To realize an effective working of these applications, the spatial distribution of the particles needs to be accurately known, in a non-invasive way. Electron Paramagnetic Resonance (EPR) is a promising and sensitive measurement technique for recovering these distributions. In the conventional approach, EPR is applied with a homogeneous magnetic field. In this paper, we employ different heterogeneous magnetic fields that allow to stabilize the solution of the associated inverse problem and to obtain localized spatial information. A comparison is made between the two approaches and our novel adaptation shows an average increase in reconstruction quality by 5% and is 12 times more robust towards noise. Furthermore, our approach allows to speed up the EPR measurements while still obtaining reconstructions with an improved accuracy and noise robustness compared to homogeneous EPR

  15. Integrated sequence analysis. Final report

    International Nuclear Information System (INIS)

    Andersson, K.; Pyy, P.

    1998-02-01

    The NKS/RAK subprojet 3 'integrated sequence analysis' (ISA) was formulated with the overall objective to develop and to test integrated methodologies in order to evaluate event sequences with significant human action contribution. The term 'methodology' denotes not only technical tools but also methods for integration of different scientific disciplines. In this report, we first discuss the background of ISA and the surveys made to map methods in different application fields, such as man machine system simulation software, human reliability analysis (HRA) and expert judgement. Specific event sequences were, after the surveys, selected for application and testing of a number of ISA methods. The event sequences discussed in the report were cold overpressure of BWR, shutdown LOCA of BWR, steam generator tube rupture of a PWR and BWR disturbed signal view in the control room after an external event. Different teams analysed these sequences by using different ISA and HRA methods. Two kinds of results were obtained from the ISA project: sequence specific and more general findings. The sequence specific results are discussed together with each sequence description. The general lessons are discussed under a separate chapter by using comparisons of different case studies. These lessons include areas ranging from plant safety management (design, procedures, instrumentation, operations, maintenance and safety practices) to methodological findings (ISA methodology, PSA,HRA, physical analyses, behavioural analyses and uncertainty assessment). Finally follows a discussion about the project and conclusions are presented. An interdisciplinary study of complex phenomena is a natural way to produce valuable and innovative results. This project came up with structured ways to perform ISA and managed to apply the in practice. The project also highlighted some areas where more work is needed. In the HRA work, development is required for the use of simulators and expert judgement as

  16. Integrated sequence analysis. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Andersson, K.; Pyy, P

    1998-02-01

    The NKS/RAK subprojet 3 `integrated sequence analysis` (ISA) was formulated with the overall objective to develop and to test integrated methodologies in order to evaluate event sequences with significant human action contribution. The term `methodology` denotes not only technical tools but also methods for integration of different scientific disciplines. In this report, we first discuss the background of ISA and the surveys made to map methods in different application fields, such as man machine system simulation software, human reliability analysis (HRA) and expert judgement. Specific event sequences were, after the surveys, selected for application and testing of a number of ISA methods. The event sequences discussed in the report were cold overpressure of BWR, shutdown LOCA of BWR, steam generator tube rupture of a PWR and BWR disturbed signal view in the control room after an external event. Different teams analysed these sequences by using different ISA and HRA methods. Two kinds of results were obtained from the ISA project: sequence specific and more general findings. The sequence specific results are discussed together with each sequence description. The general lessons are discussed under a separate chapter by using comparisons of different case studies. These lessons include areas ranging from plant safety management (design, procedures, instrumentation, operations, maintenance and safety practices) to methodological findings (ISA methodology, PSA,HRA, physical analyses, behavioural analyses and uncertainty assessment). Finally follows a discussion about the project and conclusions are presented. An interdisciplinary study of complex phenomena is a natural way to produce valuable and innovative results. This project came up with structured ways to perform ISA and managed to apply the in practice. The project also highlighted some areas where more work is needed. In the HRA work, development is required for the use of simulators and expert judgement as

  17. Targeted assembly of short sequence reads.

    Directory of Open Access Journals (Sweden)

    René L Warren

    Full Text Available As next-generation sequence (NGS production continues to increase, analysis is becoming a significant bottleneck. However, in situations where information is required only for specific sequence variants, it is not necessary to assemble or align whole genome data sets in their entirety. Rather, NGS data sets can be mined for the presence of sequence variants of interest by localized assembly, which is a faster, easier, and more accurate approach. We present TASR, a streamlined assembler that interrogates very large NGS data sets for the presence of specific variants by only considering reads within the sequence space of input target sequences provided by the user. The NGS data set is searched for reads with an exact match to all possible short words within the target sequence, and these reads are then assembled stringently to generate a consensus of the target and flanking sequence. Typically, variants of a particular locus are provided as different target sequences, and the presence of the variant in the data set being interrogated is revealed by a successful assembly outcome. However, TASR can also be used to find unknown sequences that flank a given target. We demonstrate that TASR has utility in finding or confirming genomic mutations, polymorphisms, fusions and integration events. Targeted assembly is a powerful method for interrogating large data sets for the presence of sequence variants of interest. TASR is a fast, flexible and easy to use tool for targeted assembly.

  18. Adaptive bulk motion exclusion for improved robustness of abdominal magnetic resonance imaging

    NARCIS (Netherlands)

    Stemkens, Bjorn; Benkert, Thomas; Chandarana, Hersh; Bittman, Mark E.; Van den Berg, Cornelis A.T.; Lagendijk, Jan J.W.; Sodickson, Daniel K.; Tijssen, Rob H.N.; Block, Kai Tobias

    2017-01-01

    Non-Cartesian magnetic resonance imaging (MRI) sequences have shown great promise for abdominal examination during free breathing, but break down in the presence of bulk patient motion (i.e. voluntary or involuntary patient movement resulting in translation, rotation or elastic deformations of the

  19. Parenchymal abnormalities in cerebral venous thrombosis: findings of magnetic resonance imaging and magnetic resonance angiography

    International Nuclear Information System (INIS)

    Ferreira, Clecia Santos; Pellini, Marcos; Boasquevisque, Edson; Souza, Luis Alberto M. de

    2006-01-01

    Objective: to determine the frequency and localization of parenchymal abnormalities in cerebral venous thrombosis on magnetic resonance imaging and magnetic resonance angiography as well as their correlation with the territory and affected venous drainage. Materials and methods: retrospective analysis (1996 to 2004) of 21 patients (3 male and 18 female) age range between 3 and 82 years (mean 40 years, median 36 years) with clinical and radiological diagnosis of cerebral venous thrombosis on magnetic resonance imaging and magnetic resonance angiography in 2D PC, 3D PC and contrast-enhanced 3D TOF sequences. The statistical analysis was performed with the qui-square test. Four patients had follow-up exams and three patients underwent digital subtraction angiography. Results: main predisposing factors were: infection, use of oral contraceptives, hormone replacement therapy and collagenosis. Predominant symptoms included: focal deficit, headache, alteration of consciousness level and seizures. Most frequent parenchymal manifestations were: cortical/subcortical edema or infarct, venous congestion and collateral circulation, meningeal enhancement and thalamic and basal ganglia edema or infarct. Occlusion occurred mainly in superior sagittal, left transverse, left sigmoid and straight sinuses. Cavernous sinus and cortical veins thrombosis are uncommon events. Conclusion: cerebral venous thrombosis is an uncommon cause of stroke, with favorable prognosis because of its reversibility. Diagnosis is highly dependent on the radiologist capacity to recognize the presentations of this disease, principally in cases where the diagnosis is suggested by parenchymal abnormalities rather than necessarily by visualization of the thrombus itself. An accurate and rapid diagnosis allows an immediate treatment, reducing the morbidity and mortality rates. (author)

  20. Off-resonance artifacts correction with convolution in k-space (ORACLE).

    Science.gov (United States)

    Lin, Wei; Huang, Feng; Simonotto, Enrico; Duensing, George R; Reykowski, Arne

    2012-06-01

    Off-resonance artifacts hinder the wider applicability of echo-planar imaging and non-Cartesian MRI methods such as radial and spiral. In this work, a general and rapid method is proposed for off-resonance artifacts correction based on data convolution in k-space. The acquired k-space is divided into multiple segments based on their acquisition times. Off-resonance-induced artifact within each segment is removed by applying a convolution kernel, which is the Fourier transform of an off-resonance correcting spatial phase modulation term. The field map is determined from the inverse Fourier transform of a basis kernel, which is calibrated from data fitting in k-space. The technique was demonstrated in phantom and in vivo studies for radial, spiral and echo-planar imaging datasets. For radial acquisitions, the proposed method allows the self-calibration of the field map from the imaging data, when an alternating view-angle ordering scheme is used. An additional advantage for off-resonance artifacts correction based on data convolution in k-space is the reusability of convolution kernels to images acquired with the same sequence but different contrasts. Copyright © 2011 Wiley-Liss, Inc.

  1. Use of PCR with Sequence-specific Primers for High-Resolution Human Leukocyte Antigen Typing of Patients with Narcolepsy

    Science.gov (United States)

    Woo, Hye In; Joo, Eun Yeon; Lee, Kyung Wha

    2012-01-01

    Background Narcolepsy is a neurologic disorder characterized by excessive daytime sleepiness, symptoms of abnormal rapid eye movement (REM) sleep, and a strong association with HLA-DRB1*1501, -DQA1*0102, and -DQB1*0602. Here, we investigated the clinico-physical characteristics of Korean patients with narcolepsy, their HLA types, and the clinical utility of high-resolution PCR with sequence-specific primers (PCR-SSP) as a simple typing method for identifying DRB1*15/16, DQA1, and DQB1 alleles. Methods The study population consisted of 67 consecutively enrolled patients having unexplained daytime sleepiness and diagnosed narcolepsy based on clinical and neurological findings. Clinical data and the results of the multiple sleep latency test and polysomnography were reviewed, and HLA typing was performed using both high-resolution PCR-SSP and sequence-based typing (SBT). Results The 44 narcolepsy patients with cataplexy displayed significantly higher frequencies of DRB1*1501 (Pc= 0.003), DQA1*0102 (Pc=0.001), and DQB1*0602 (Pc=0.014) than the patients without cataplexy. Among patients carrying DRB1*1501-DQB1*0602 or DQA1*0102, the frequencies of a mean REM sleep latency of less than 20 min in nocturnal polysomnography and clinical findings, including sleep paralysis and hypnagogic hallucination were significantly higher. SBT and PCR-SSP showed 100% concordance for high-resolution typing of DRB1*15/16 alleles and DQA1 and DQB1 loci. Conclusions The clinical characteristics and somnographic findings of narcolepsy patients were associated with specific HLA alleles, including DRB1*1501, DQA1*0102, and DQB1*0602. Application of high-resolution PCR-SSP, a reliable and simple method, for both allele- and locus-specific HLA typing of DRB1*15/16, DQA1, and DQB1 would be useful for characterizing clinical status among subjects with narcolepsy. PMID:22259780

  2. Extended RF shimming: Sequence-level parallel transmission optimization applied to steady-state free precession MRI of the heart.

    Science.gov (United States)

    Beqiri, Arian; Price, Anthony N; Padormo, Francesco; Hajnal, Joseph V; Malik, Shaihan J

    2017-06-01

    Cardiac magnetic resonance imaging (MRI) at high field presents challenges because of the high specific absorption rate and significant transmit field (B 1 + ) inhomogeneities. Parallel transmission MRI offers the ability to correct for both issues at the level of individual radiofrequency (RF) pulses, but must operate within strict hardware and safety constraints. The constraints are themselves affected by sequence parameters, such as the RF pulse duration and TR, meaning that an overall optimal operating point exists for a given sequence. This work seeks to obtain optimal performance by performing a 'sequence-level' optimization in which pulse sequence parameters are included as part of an RF shimming calculation. The method is applied to balanced steady-state free precession cardiac MRI with the objective of minim