WorldWideScience

Sample records for acids detection folding

  1. Folded Compact Range Development and Coherent Change Detection Measurement Project

    Energy Technology Data Exchange (ETDEWEB)

    Sorensen, K.W.

    1995-03-01

    A novel, folded compact range configuration has been developed at the Sandia National Laboratories compact range antenna and radar cross section measurement facility, operated by the Radar/Antenna Department 2343, as a means of performing indoor, environmentally-controlled, far-field simulations of synthetic aperture radar (SAR) coherent change detection (CCD) measurements. This report describes the development of the folded compact range configuration, as well as the initial set of coherent change detection measurements made with the system. These measurements have been highly successful, and have demonstrated the viability of the folded compact range concept in simulating SAR CCD measurements. It is felt that follow-on measurements have the potential of contributing significantly to the body of knowledge available to the scientific community involved in CCD image generation and processing, and that this tool will be a significant aid in the research and development of change detection methodologies.

  2. Linear Classifier with Reject Option for the Detection of Vocal Fold Paralysis and Vocal Fold Edema

    Science.gov (United States)

    Kotropoulos, Constantine; Arce, Gonzalo R.

    2009-12-01

    Two distinct two-class pattern recognition problems are studied, namely, the detection of male subjects who are diagnosed with vocal fold paralysis against male subjects who are diagnosed as normal and the detection of female subjects who are suffering from vocal fold edema against female subjects who do not suffer from any voice pathology. To do so, utterances of the sustained vowel "ah" are employed from the Massachusetts Eye and Ear Infirmary database of disordered speech. Linear prediction coefficients extracted from the aforementioned utterances are used as features. The receiver operating characteristic curve of the linear classifier, that stems from the Bayes classifier when Gaussian class conditional probability density functions with equal covariance matrices are assumed, is derived. The optimal operating point of the linear classifier is specified with and without reject option. First results using utterances of the "rainbow passage" are also reported for completeness. The reject option is shown to yield statistically significant improvements in the accuracy of detecting the voice pathologies under study.

  3. Kinetic Monte Carlo method applied to nucleic acid hairpin folding.

    Science.gov (United States)

    Sauerwine, Ben; Widom, Michael

    2011-12-01

    Kinetic Monte Carlo on coarse-grained systems, such as nucleic acid secondary structure, is advantageous for being able to access behavior at long time scales, even minutes or hours. Transition rates between coarse-grained states depend upon intermediate barriers, which are not directly simulated. We propose an Arrhenius rate model and an intermediate energy model that incorporates the effects of the barrier between simulated states without enlarging the state space itself. Applying our Arrhenius rate model to DNA hairpin folding, we demonstrate improved agreement with experiment compared to the usual kinetic Monte Carlo model. Further improvement results from including rigidity of single-stranded stacking.

  4. Building multiclass classifiers for remote homology detection and fold recognition

    Directory of Open Access Journals (Sweden)

    Karypis George

    2006-10-01

    Full Text Available Abstract Background Protein remote homology detection and fold recognition are central problems in computational biology. Supervised learning algorithms based on support vector machines are currently one of the most effective methods for solving these problems. These methods are primarily used to solve binary classification problems and they have not been extensively used to solve the more general multiclass remote homology prediction and fold recognition problems. Results We present a comprehensive evaluation of a number of methods for building SVM-based multiclass classification schemes in the context of the SCOP protein classification. These methods include schemes that directly build an SVM-based multiclass model, schemes that employ a second-level learning approach to combine the predictions generated by a set of binary SVM-based classifiers, and schemes that build and combine binary classifiers for various levels of the SCOP hierarchy beyond those defining the target classes. Conclusion Analyzing the performance achieved by the different approaches on four different datasets we show that most of the proposed multiclass SVM-based classification approaches are quite effective in solving the remote homology prediction and fold recognition problems and that the schemes that use predictions from binary models constructed for ancestral categories within the SCOP hierarchy tend to not only lead to lower error rates but also reduce the number of errors in which a superfamily is assigned to an entirely different fold and a fold is predicted as being from a different SCOP class. Our results also show that the limited size of the training data makes it hard to learn complex second-level models, and that models of moderate complexity lead to consistently better results.

  5. Detecção de receptor de ácido hialurônico em prega vocal humana por método imunohistoquímico Detection of hyaluronic acid receptor in human vocal folds by immunohistochemistry

    Directory of Open Access Journals (Sweden)

    Luiz Henrique Fonseca Barbosa

    2008-04-01

    Full Text Available O receptor do ácido Hialurônico é uma glicoproteína da membrana plasmática, sendo o principal o CD44, e está expresso em vários tipos de células onde possui a função de adesão celular. OBJETIVO: Estudar a possibilidade de empregar o método imunohistoquímico para identificar a distribuição dos receptores de ácido hialurônico ao longo da prega vocal humana. MATERIAL E MÉTODOS: Foram ressecadas as pregas vocais normais de um indivíduo de 23 anos, sexo masculino, cor negra. As lâminas foram analisadas por meio de estudo histomorfométrico, comparando-se a intensidade das cores nas camadas superficial, média e profunda da lâmina própria. Nas lâminas silanizadas foi utilizado método imunohistoquímico, sendo avaliadas através de microscopia óptica com aumento 40 vezes, obtendo coloração marrom onde houve a reação com receptor para ácido hialurônico. RESULTADOS: Os achados imunohistoquímicos mostraram presença de receptores para ácido hialurônico no epitélio de cobertura da prega vocal tendo maior concentração na região central da prega vocal. CONCLUSÃO: A técnica de imunohistoquímica, utilizada para avaliar a distribuição dos receptores para ácido hialurônico na pregas vocais humanas, mostrou sua disposição em epitélio da prega vocal e predomínio no terço médio, em relação às demais regiões na prega vocal estudada.Hyaluronic acid receptor is a glycoprotein of the plasmatic membrane, and the CD44 is its representative, expressed in many cell types where it has the task of cell adhesion. AIM: the goal of the present experimental study is to investigate the possibility of using immunohistochemistry to identify the distribution of hyaluronic acid along the vocal fold. MATERIALS AND METHODS: We resected the normal vocal folds from a normal 23 year-old male black individual. The slides were analyzed by means of a histomorphometric study, comparing the color intensity in the superficial, middle and

  6. pH-jump induced α-helix folding of poly-L-glutamic acid

    Energy Technology Data Exchange (ETDEWEB)

    Donten, Mateusz L. [Institute of Physical Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich (Switzerland); Hamm, Peter, E-mail: phamm@pci.uzh.ch [Institute of Physical Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zürich (Switzerland)

    2013-08-30

    Highlights: ► pH-jump as truly biomimetic tool to initiate non-equilibrium dynamics of biomolecules. ► Design criteria to widen the applicability of pH-jumps are developed. ► Folding of poly-L-Glu in dependence of starting pH, pH jump size and helix length. ► Length dependence provides strong evidence for a nucleation–propagation scenario. - Abstract: pH jumps are a truly biomimetic technique to initiate non-equilibrium dynamics of biomolecules. In this work, the pH jump induced α-helix folding of poly-L-glutamic acid is investigated upon proton release from o-nitrobenzaldehyde. The aim of this work is twofold: On the one hand, design criteria of pH jump experiments are discussed, on the other hand, the folding mechanism of poly-L-glutamic acid is clarified by probing the IR response of the amide I band. Its folding kinetics is studied in dependence of the starting pD, the size of the pD jump and the length of the helix. While no dependence on the first two parameters could be detected, the folding time varies from 0.6 μs to 1.8 μs for helix lengths of 20 residue to 440 residue, respectively. It converges to a long-length limit at about 50 residue, a result which is attributed to a nucleation–propagation mechanism.

  7. pH-jump induced α-helix folding of poly-L-glutamic acid

    Science.gov (United States)

    Donten, Mateusz L.; Hamm, Peter

    2013-08-01

    pH jumps are a truly biomimetic technique to initiate non-equilibrium dynamics of biomolecules. In this work, the pH jump induced α-helix folding of poly-L-glutamic acid is investigated upon proton release from o-nitrobenzaldehyde. The aim of this work is twofold: On the one hand, design criteria of pH jump experiments are discussed, on the other hand, the folding mechanism of poly-L-glutamic acid is clarified by probing the IR response of the amide I band. Its folding kinetics is studied in dependence of the starting pD, the size of the pD jump and the length of the helix. While no dependence on the first two parameters could be detected, the folding time varies from 0.6 μs to 1.8 μs for helix lengths of 20 residue to 440 residue, respectively. It converges to a long-length limit at about 50 residue, a result which is attributed to a nucleation-propagation mechanism.

  8. How the folding rates of two- and multistate proteins depend on the amino acid properties.

    Science.gov (United States)

    Huang, Jitao T; Huang, Wei; Huang, Shanran R; Li, Xin

    2014-10-01

    Proteins fold by either two-state or multistate kinetic mechanism. We observe that amino acids play different roles in different mechanism. Many residues that are easy to form regular secondary structures (α helices, β sheets and turns) can promote the two-state folding reactions of small proteins. Most of hydrophilic residues can speed up the multistate folding reactions of large proteins. Folding rates of large proteins are equally responsive to the flexibility of partial amino acids. Other properties of amino acids (including volume, polarity, accessible surface, exposure degree, isoelectric point, and phase transfer energy) have contributed little to folding kinetics of the proteins. Cysteine is a special residue, it triggers two-state folding reaction and but inhibits multistate folding reaction. These findings not only provide a new insight into protein structure prediction, but also could be used to direct the point mutations that can change folding rate.

  9. Computational simulations of protein folding to engineer amino acid sequences to encourage desired supersecondary structure formation.

    Science.gov (United States)

    Gerstman, Bernard S; Chapagain, Prem P

    2013-01-01

    The dynamics of protein folding are complicated because of the various types of amino acid interactions that create secondary, supersecondary, and tertiary interactions. Computational modeling can be used to simulate the biophysical and biochemical interactions that determine protein folding. Effective folding to a desired protein configuration requires a compromise between speed, stability, and specificity. If the primary sequence of amino acids emphasizes one of these characteristics, the others might suffer and the folding process may not be optimized. We provide an example of a model peptide whose primary sequence produces a highly stable supersecondary two-helix bundle structure, but at the expense of lower speed and specificity of the folding process. We show how computational simulations can be used to discover the configuration of the kinetic trap that causes the degradation in the speed and specificity of folding. We also show how amino acid sequences can be engineered by specific substitutions to optimize the folding to the desired supersecondary structure.

  10. Analysis of hyaluronic acid concentration in rat vocal folds during estral and gravidic puerperal cycles

    OpenAIRE

    Pedroso, José Eduardo de Sá [UNIFESP; Brasil,Osíris Camponês do; Martins, João Roberto Maciel [UNIFESP; Nader,Helena Bociane; Simões,Manuel de Jesus

    2009-01-01

    Hormone plays an important role in the larynx. Among other substances, vocal folds contain hyaluronic acid, which tissue concentration may vary according to hormone action. AIM: the objective of this study is to analyze hyaluronic acid concentration in the vocal folds during estral and gravidic-puerperal cycles. MATERIALS AND METHODS: Experimental study. 40 adult rats were divided into two groups. In the first group we used 20 rats to establish the concentration of hyaluronic acid during the ...

  11. The folding type of a protein is relevant to the amino acid composition

    OpenAIRE

    Nakashima, Hiroshi; Nishikawa, Ken; Ooi, Tatsuo

    1986-01-01

    The folding types of 135 proteins, the three-dimensional structures of which are known, were analyzed in terms of the amino acid composition. The amino acid composition of a protein was expressed as a point in a multidimensional space spanned with 20 axes, on which the corresponding contents of 20 amino acids in the protein were represented. The distribution pattern of proteins in this composition space was examined in relation to five folding types, , ß, /ß, +ß, and irregular type. The resul...

  12. Building Multiclass Classifiers for Remote Homology Detection and Fold Recognition

    Science.gov (United States)

    2006-04-05

    NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS...are thoroughly evaluated for both remote homology prediction and fold recognition using four differ- ent datasets derived from Astral [5]. Our...function may not be the most appropriate as it may lead to models where 5 Table 1: Dataset Statistics. Statistic DS1 DS2 DS3 DS4 ASTRAL filtering 90% 40% 25

  13. A Soluble, Folded Protein without Charged Amino Acid Residues

    DEFF Research Database (Denmark)

    Højgaard, Casper; Kofoed, Christian; Espersen, Roall

    2016-01-01

    Charges are considered an integral part of protein structure and function, enhancing solubility and providing specificity in molecular interactions. We wished to investigate whether charged amino acids are indeed required for protein biogenesis and whether a protein completely free of titratable...... side chains can maintain solubility, stability, and function. As a model, we used a cellulose-binding domain from Cellulomonas fimi, which, among proteins of more than 100 amino acids, presently is the least charged in the Protein Data Bank, with a total of only four titratable residues. We find...

  14. A Soluble, Folded Protein without Charged Amino Acid Residues

    DEFF Research Database (Denmark)

    Højgaard, Casper; Kofoed, Christian; Espersen, Roall;

    2016-01-01

    Charges are considered an integral part of protein structure and function, enhancing solubility and providing specificity in molecular interactions. We wished to investigate whether charged amino acids are indeed required for protein biogenesis and whether a protein completely free of titratable ...

  15. Efficient fold-change detection based on protein-protein interactions.

    Science.gov (United States)

    Buijsman, W; Sheinman, M

    2014-02-01

    Various biological sensory systems exhibit a response to a relative change of the stimulus, often referred to as fold-change detection. In the past few years, fold-change detecting mechanisms, based on transcriptional networks, have been proposed. Here we present a fold-change detecting mechanism, based on protein-protein interactions, consisting of two interacting proteins. This mechanism does not consume chemical energy and is not subject to transcriptional and translational noise, in contrast to previously proposed mechanisms. We show by analytical and numerical calculations that the mechanism is robust and can have a fast, precise, and efficient response for parameters that are relevant to eukaryotic cells.

  16. Efficient fold-change detection based on protein-protein interactions

    Science.gov (United States)

    Buijsman, W.; Sheinman, M.

    2014-02-01

    Various biological sensory systems exhibit a response to a relative change of the stimulus, often referred to as fold-change detection. In the past few years, fold-change detecting mechanisms, based on transcriptional networks, have been proposed. Here we present a fold-change detecting mechanism, based on protein-protein interactions, consisting of two interacting proteins. This mechanism does not consume chemical energy and is not subject to transcriptional and translational noise, in contrast to previously proposed mechanisms. We show by analytical and numerical calculations that the mechanism is robust and can have a fast, precise, and efficient response for parameters that are relevant to eukaryotic cells.

  17. The folding type of a protein is relevant to the amino acid composition.

    Science.gov (United States)

    Nakashima, H; Nishikawa, K; Ooi, T

    1986-01-01

    The folding types of 135 proteins, the three-dimensional structures of which are known, were analyzed in terms of the amino acid composition. The amino acid composition of a protein was expressed as a point in a multidimensional space spanned with 20 axes, on which the corresponding contents of 20 amino acids in the protein were represented. The distribution pattern of proteins in this composition space was examined in relation to five folding types, alpha, beta, alpha/beta, alpha + beta, and irregular type. The results show that amino acid compositions of the alpha, beta, and alpha/beta types are located in different regions in the composition space, thus allowing distinct separation of proteins depending on the folding types. The points representing proteins of the alpha + beta and irregular types, however, are widely scattered in the space, and the existing regions overlap with those of the other folding types. A simple method of utilizing the "distance" in the space was found to be convenient for classification of proteins into the five folding types. The assignment of the folding type with this method gave an accuracy of 70% in the coincidence with the experimental data.

  18. Dependence of α-helical and β-sheet amino acid propensities on the overall protein fold type

    Directory of Open Access Journals (Sweden)

    Fujiwara Kazuo

    2012-08-01

    Full Text Available Abstract Background A large number of studies have been carried out to obtain amino acid propensities for α-helices and β-sheets. The obtained propensities for α-helices are consistent with each other, and the pair-wise correlation coefficient is frequently high. On the other hand, the β-sheet propensities obtained by several studies differed significantly, indicating that the context significantly affects β-sheet propensity. Results We calculated amino acid propensities for α-helices and β-sheets for 39 and 24 protein folds, respectively, and addressed whether they correlate with the fold. The propensities were also calculated for exposed and buried sites, respectively. Results showed that α-helix propensities do not differ significantly by fold, but β-sheet propensities are diverse and depend on the fold. The propensities calculated for exposed sites and buried sites are similar for α-helix, but such is not the case for the β-sheet propensities. We also found some fold dependence on amino acid frequency in β-strands. Folds with a high Ser, Thr and Asn content at exposed sites in β-strands tend to have a low Leu, Ile, Glu, Lys and Arg content (correlation coefficient = −0.90 and to have flat β-sheets. At buried sites in β-strands, the content of Tyr, Trp, Gln and Ser correlates negatively with the content of Val, Ile and Leu (correlation coefficient = −0.93. "All-β" proteins tend to have a higher content of Tyr, Trp, Gln and Ser, whereas "α/β" proteins tend to have a higher content of Val, Ile and Leu. Conclusions The α-helix propensities are similar for all folds and for exposed and buried residues. However, β-sheet propensities calculated for exposed residues differ from those for buried residues, indicating that the exposed-residue fraction is one of the major factors governing amino acid composition in β-strands. Furthermore, the correlations we detected suggest that amino acid composition is related to folding

  19. Detection and mapping of delays in early cortical folding derived from in utero MRI

    Science.gov (United States)

    Habas, Piotr A.; Rajagopalan, Vidya; Scott, Julia A.; Kim, Kio; Roosta, Ahmad; Rousseau, Francois; Barkovich, A. James; Glenn, Orit A.; Studholme, Colin

    2011-03-01

    Understanding human brain development in utero and detecting cortical abnormalities related to specific clinical conditions is an important area of research. In this paper, we describe and evaluate methodology for detection and mapping of delays in early cortical folding from population-based studies of fetal brain anatomies imaged in utero. We use a general linear modeling framework to describe spatiotemporal changes in curvature of the developing brain and explore the ability to detect and localize delays in cortical folding in the presence of uncertainty in estimation of the fetal age. We apply permutation testing to examine which regions of the brain surface provide the most statistical power to detect a given folding delay at a given developmental stage. The presented methodology is evaluated using MR scans of fetuses with normal brain development and gestational ages ranging from 20.57 to 27.86 weeks. This period is critical in early cortical folding and the formation of the primary and secondary sulci. Finally, we demonstrate a clinical application of the framework for detection and localization of folding delays in fetuses with isolated mild ventriculomegaly.

  20. Two methods of Haustral fold detection from computed tomographic virtual colonoscopy images

    Science.gov (United States)

    Chowdhury, Ananda S.; Tan, Sovira; Yao, Jianhua; Linguraru, Marius G.; Summers, Ronald M.

    2009-02-01

    Virtual colonoscopy (VC) has gained popularity as a new colon diagnostic method over the last decade. VC is a new, less invasive alternative to the usually practiced optical colonoscopy for colorectal polyp and cancer screening, the second major cause of cancer related deaths in industrial nations. Haustral (colonic) folds serve as important landmarks for virtual endoscopic navigation in the existing computer-aided-diagnosis (CAD) system. In this paper, we propose and compare two different methods of haustral fold detection from volumetric computed tomographic virtual colonoscopy images. The colon lumen is segmented from the input using modified region growing and fuzzy connectedness. The first method for fold detection uses a level set that evolves on a mesh representation of the colon surface. The colon surface is obtained from the segmented colon lumen using the Marching Cubes algorithm. The second method for fold detection, based on a combination of heat diffusion and fuzzy c-means algorithm, is employed on the segmented colon volume. Folds obtained on the colon volume using this method are then transferred to the corresponding colon surface. After experimentation with different datasets, results are found to be promising. The results also demonstrate that the first method has a tendency of slight under-segmentation while the second method tends to slightly over-segment the folds.

  1. Efficient fold-change detection based on protein-protein interactions

    CERN Document Server

    Buijsman, Wouter

    2012-01-01

    Various biological sensory systems exhibit a response to the relative change of the stimulus, often reffered to as fold-change detection. Here, we present a mechanism consisting of two interacting proteins, able to detect a fold-change effectively. This mechanism, in contrast to other proposed mechanisms, does not consume chemical energy and is not subject to transcriptional and translational noise. We show by analytical and numerical calculations that the mechanism can have a fast, precise and efficient response for parameters that are relevant to eukaryotic cells.

  2. Identification of Amino Acid Sequences with Good Folding Properties in an Off-Lattice Model

    CERN Document Server

    Irbäck, Anders; Potthast, Frank

    2008-01-01

    Folding properties of a two-dimensional toy protein model containing only two amino-acid types, hydrophobic and hydrophilic, respectively, are analyzed. An efficient Monte Carlo procedure is employed to ensure that the ground states are found. The thermodynamic properties are found to be strongly sequence dependent in contrast to the kinetic ones. Hence, criteria for good folders are defined entirely in terms of thermodynamic fluctuations. With these criteria sequence patterns that fold well are isolated. For 300 chains with 20 randomly chosen binary residues approximately 10% meet these criteria. Also, an analysis is performed by means of statistical and artificial neural network methods from which it is concluded that the folding properties can be predicted to a certain degree given the binary numbers characterizing the sequences.

  3. n→π* Interactions in Poly(lactic acid) Suggest a Role in Protein Folding

    OpenAIRE

    Newberry, Robert W; Raines, Ronald T.

    2013-01-01

    Poly(lactic acid) (PLA) is a versatile synthetic polyester. We noted that this depsipeptide analog of polyalanine has a helical structure that resembles a polyproline II helix. Using natural bond orbital analysis, we find that n→π* interactions between sequential ester carbonyl groups contribute 0.44 kcal/mol per monomer to the conformational stability of PLA helices. We conclude that analogous n→π* interactions could direct the folding of a polypeptide chain into a polyproline II helix prior...

  4. Detecting Selection on Protein Stability through Statistical Mechanical Models of Folding and Evolution

    Directory of Open Access Journals (Sweden)

    Ugo Bastolla

    2014-03-01

    Full Text Available The properties of biomolecules depend both on physics and on the evolutionary process that formed them. These two points of view produce a powerful synergism. Physics sets the stage and the constraints that molecular evolution has to obey, and evolutionary theory helps in rationalizing the physical properties of biomolecules, including protein folding thermodynamics. To complete the parallelism, protein thermodynamics is founded on the statistical mechanics in the space of protein structures, and molecular evolution can be viewed as statistical mechanics in the space of protein sequences. In this review, we will integrate both points of view, applying them to detecting selection on the stability of the folded state of proteins. We will start discussing positive design, which strengthens the stability of the folded against the unfolded state of proteins. Positive design justifies why statistical potentials for protein folding can be obtained from the frequencies of structural motifs. Stability against unfolding is easier to achieve for longer proteins. On the contrary, negative design, which consists in destabilizing frequently formed misfolded conformations, is more difficult to achieve for longer proteins. The folding rate can be enhanced by strengthening short-range native interactions, but this requirement contrasts with negative design, and evolution has to trade-off between them. Finally, selection can accelerate functional movements by favoring low frequency normal modes of the dynamics of the native state that strongly correlate with the functional conformation change.

  5. Nucleic acid detection using MNAzymes.

    Science.gov (United States)

    Gerasimova, Yulia V; Kolpashchikov, Dmitry M

    2010-02-26

    Deoxyribozymes are promising biotechnological tools. In a recent JACS article, Mokany et al. reported on the design of multi-component deoxyribozyme (MNAzyme) sensors based on 10-23 and 8-17 DNA enzymes. The sensors can detect down to 5 pM of a specific nucleic acid. The versatility of MNAzyme platform allows the design of catalytic cascades for signal amplification. This work is a step forward to PCR-free molecular diagnostics.

  6. Nasal Alar Necrosis Following Hyaluronic Acid Injection into Nasolabial Folds: A Case Report

    Science.gov (United States)

    Manafi, Ali; Barikbin, Behrooz; Manafi, Amir; Hamedi, Zahra Sadat; Ahmadi Moghadam, Shokoofeh

    2015-01-01

    Injection of synthetic fillers for soft tissue augmentation is increasing over the last decade. One of the most common materials used is hyaluronic acid (HA) that is safe and temporary filler for soft tissue augmentation. We present a case of 54-year-old female who experienced vascular occlusion and nasal alar necrosis following HA injection to the nasolabial folds. She suffered from pain, necrosis, infection, and alar loss that finally required a reconstructive surgery for cosmetic appearance of the nose. The case highlights the importance of proper injection technique by an anesthesiologist, as well as the need for immediate recognition and treatment of vascular occlusion. PMID:25606480

  7. Natively unfolded human prothymosin alpha adopts partially folded collapsed conformation at acidic pH.

    Science.gov (United States)

    Uversky, V N; Gillespie, J R; Millett, I S; Khodyakova, A V; Vasiliev, A M; Chernovskaya, T V; Vasilenko, R N; Kozlovskaya, G D; Dolgikh, D A; Fink, A L; Doniach, S; Abramov, V M

    1999-11-09

    Prothymosin alpha has previously been shown to be unfolded at neutral pH, thus belonging to a growing family of "natively unfolded" proteins. The structural properties and conformational stability of recombinant human prothymosin alpha were characterized at neutral and acidic pH by gel filtration, SAXS, circular dichroism, ANS fluorescence, (1)H NMR, and resistance to urea-induced unfolding. Interestingly, prothymosin alpha underwent a cooperative transition from the unfolded state into a partially folded conformation on lowering the pH. This conformation of prothymosin alpha is a compact denatured state, with structural properties different from those of the molten globule. The formation of alpha-helical structure by the glutamic acid-rich elements of the protein accompanied by the partial hydrophobic collapse is expected at lower pH due to the neutralization of the negatively charged residues. It is possible that such conformational changes may be associated with the protein function.

  8. Quantification of vocal fold motion using echography: application to recurrent nerve paralysis detection

    Science.gov (United States)

    Cohen, Mike-Ely; Lefort, Muriel; Bergeret-Cassagne, Héloïse; Hachi, Siham; Li, Ang; Russ, Gilles; Lazard, Diane; Menegaux, Fabrice; Leenhardt, Laurence; Trésallet, Christophe; Frouin, Frédérique

    2015-03-01

    Recurrent nerve paralysis (RP) is one of the most frequent complications of thyroid surgery. It reduces vocal fold mobility. Nasal endoscopy, a mini-invasive procedure, is the conventional way to detect RP. We suggest a new approach based on laryngeal ultrasound and a specific data analysis was designed to help with the automated detection of RP. Ten subjects were enrolled for this feasibility study: four controls, three patients with RP and three patients without RP according to nasal endoscopy. The ultrasound protocol was based on a ten seconds B-mode acquisition in a coronal plane during normal breathing. Image processing included three steps: 1) automated detection of two consecutive closing and opening images, corresponding to extreme positions of vocal folds in the sequence of B-mode images, using principal component analysis of the image sequence; 2) positioning of three landmarks and robust tracking of these points using a multi-pyramidal refined optical flow approach; 3) estimation of quantitative parameters indicating left and right fractions of mobility, and motion symmetry. Results provided by automated image processing were compared to those obtained by an expert. Detection of extreme images was accurate; tracking of landmarks was reliable in 80% of cases. Motion symmetry indices showed similar values for controls and patients without RP. Fraction of mobility was reduced in cases of RP. Thus, our CAD system helped in the detection of RP. Laryngeal ultrasound combined with appropriate image processing helped in the diagnosis of recurrent nerve paralysis and could be proposed as a first-line method.

  9. Detection of the Vibration Signal from Human Vocal Folds Using a 94-GHz Millimeter-Wave Radar

    Science.gov (United States)

    Chen, Fuming; Li, Sheng; Zhang, Yang; Wang, Jianqi

    2017-01-01

    The detection of the vibration signal from human vocal folds provides essential information for studying human phonation and diagnosing voice disorders. Doppler radar technology has enabled the noncontact measurement of the human-vocal-fold vibration. However, existing systems must be placed in close proximity to the human throat and detailed information may be lost because of the low operating frequency. In this paper, a long-distance detection method, involving the use of a 94-GHz millimeter-wave radar sensor, is proposed for detecting the vibration signals from human vocal folds. An algorithm that combines empirical mode decomposition (EMD) and the auto-correlation function (ACF) method is proposed for detecting the signal. First, the EMD method is employed to suppress the noise of the radar-detected signal. Further, the ratio of the energy and entropy is used to detect voice activity in the radar-detected signal, following which, a short-time ACF is employed to extract the vibration signal of the human vocal folds from the processed signal. For validating the method and assessing the performance of the radar system, a vibration measurement sensor and microphone system are additionally employed for comparison. The experimental results obtained from the spectrograms, the vibration frequency of the vocal folds, and coherence analysis demonstrate that the proposed method can effectively detect the vibration of human vocal folds from a long detection distance. PMID:28282892

  10. Viscoelasticity of hyaluronic acid-gelatin hydrogels for vocal fold tissue engineering.

    Science.gov (United States)

    Kazemirad, Siavash; Heris, Hossein K; Mongeau, Luc

    2016-02-01

    Crosslinked injectable hyaluronic acid (HA)-gelatin (Ge) hydrogels have remarkable viscoelastic and biological properties for vocal fold tissue engineering. Patient-specific tuning of the viscoelastic properties of this injectable biomaterial could improve tissue regeneration. The frequency-dependent viscoelasticity of crosslinked HA-Ge hydrogels was measured as a function of the concentration of HA, Ge, and crosslinker. Synthetic extracellular matrix hydrogels were fabricated using thiol-modified HA and Ge, and crosslinked by poly(ethylene glycol) diacrylate. A recently developed characterization method based on Rayleigh wave propagation was used to quantify the frequency-dependent viscoelastic properties of these hydrogels, including shear storage and loss moduli, over a broad frequency range; that is, from 40 to 4000 Hz. The viscoelastic properties of the hydrogels increased with frequency. The storage and loss moduli values and the rate of increase with frequency varied with the concentrations of the constituents. The range of the viscoelastic properties of the hydrogels was within that of human vocal fold tissue obtained from in vivo and ex vivo measurements. Frequency-dependent parametric relations were obtained using a linear least-squares regression. The results are useful to better fine-tune the storage and loss moduli of HA-Ge hydrogels by varying the concentrations of the constituents for use in patient-specific treatments.

  11. Real-time apta-PCR for 20 000-fold improvement in detection limit.

    Science.gov (United States)

    Pinto, Alessandro; Bermudo Redondo, M Carmen; Ozalp, V Cengiz; O'Sullivan, Ciara K

    2009-05-01

    A real-time apta-PCR for the ultrasensitive detection of thrombin is reported, where the thrombin aptamer acts not only as a biomolecular recognition element, but also as a label for amplification via real-time PCR. Aptamers can be easily converted to a reporter agent for detection by real-time PCR, simply via flanking of the aptamer's recognition moiety with primer sequences. The reported technique has the advantage of the ultrasensitivity achievable with immuno-PCR, but without the complications of addition of a DNA label, and is a technique generically applicable to all aptamers. Here, we use a sandwich format, where two existing thrombin binding aptamers with distinct binding epitopes have been utilised to capture and detect thrombin in a streptavidin-coated microtiter plate. The amount of thrombin is calculated from real-time PCR analysis of eluted captured reporter aptamer. However, the technique can also be used for aptamer-antibody sandwiches, or simply with single aptamers. A greater than 20 000-fold increase in sensitivity is achieved, highlighting the potential of this approach for the detection of very low levels of target analytes. The use of the aptamer itself as the reporter molecule eliminates the necessity of laborious enzyme/DNA labelling, facilitating a significantly more straightforward assay with a vastly enhanced sensitivity.

  12. Folded Proteins Occur Frequently in Libraries of Random Amino Acid Sequences

    Science.gov (United States)

    Davidson, Alan R.; Sauer, Robert T.

    1994-03-01

    A library of synthetic genes encoding 80- to 100-residue proteins composed mainly of random combinations of glutamine (Q), leucine (L), and arginine (R) has been expressed in Escherichia coli. These genes also encode an epitope tag and six carboxyl-terminal histidines. Screening of this library by immunoblotting showed that 5% of these QLR proteins are expressed at readily detectable levels. Three well-expressed QLR proteins were purified and characterized. Each of these proteins has significant α-helical content, is largely resistant to degradation by Pronase, and has a distinct oligomeric structure. In addition, one protein unfolds in a highly cooperative manner. These properties of the QLR proteins demonstrate that they possess folded structures with some native-like properties. The QLR proteins differ from most natural proteins, however, in being remarkably resistant to denaturant-induced and thermal-induced unfolding and in being relatively insoluble in the absence of denaturants.

  13. Stochastic adaptation and fold-change detection: from single-cell to population behavior

    Directory of Open Access Journals (Sweden)

    Leier André

    2011-02-01

    Full Text Available Abstract Background In cell signaling terminology, adaptation refers to a system's capability of returning to its equilibrium upon a transient response. To achieve this, a network has to be both sensitive and precise. Namely, the system must display a significant output response upon stimulation, and later on return to pre-stimulation levels. If the system settles at the exact same equilibrium, adaptation is said to be 'perfect'. Examples of adaptation mechanisms include temperature regulation, calcium regulation and bacterial chemotaxis. Results We present models of the simplest adaptation architecture, a two-state protein system, in a stochastic setting. Furthermore, we consider differences between individual and collective adaptive behavior, and show how our system displays fold-change detection properties. Our analysis and simulations highlight why adaptation needs to be understood in terms of probability, and not in strict numbers of molecules. Most importantly, selection of appropriate parameters in this simple linear setting may yield populations of cells displaying adaptation, while single cells do not. Conclusions Single cell behavior cannot be inferred from population measurements and, sometimes, collective behavior cannot be determined from the individuals. By consequence, adaptation can many times be considered a purely emergent property of the collective system. This is a clear example where biological ergodicity cannot be assumed, just as is also the case when cell replication rates are not homogeneous, or depend on the cell state. Our analysis shows, for the first time, how ergodicity cannot be taken for granted in simple linear examples either. The latter holds even when cells are considered isolated and devoid of replication capabilities (cell-cycle arrested. We also show how a simple linear adaptation scheme displays fold-change detection properties, and how rupture of ergodicity prevails in scenarios where transitions between

  14. Nucleic acid detection system and method for detecting influenza

    Science.gov (United States)

    Cai, Hong; Song, Jian

    2015-03-17

    The invention provides a rapid, sensitive and specific nucleic acid detection system which utilizes isothermal nucleic acid amplification in combination with a lateral flow chromatographic device, or DNA dipstick, for DNA-hybridization detection. The system of the invention requires no complex instrumentation or electronic hardware, and provides a low cost nucleic acid detection system suitable for highly sensitive pathogen detection. Hybridization to single-stranded DNA amplification products using the system of the invention provides a sensitive and specific means by which assays can be multiplexed for the detection of multiple target sequences.

  15. Nucleic acid detection system and method for detecting influenza

    Energy Technology Data Exchange (ETDEWEB)

    Cai, Hong; Song, Jian

    2015-03-17

    The invention provides a rapid, sensitive and specific nucleic acid detection system which utilizes isothermal nucleic acid amplification in combination with a lateral flow chromatographic device, or DNA dipstick, for DNA-hybridization detection. The system of the invention requires no complex instrumentation or electronic hardware, and provides a low cost nucleic acid detection system suitable for highly sensitive pathogen detection. Hybridization to single-stranded DNA amplification products using the system of the invention provides a sensitive and specific means by which assays can be multiplexed for the detection of multiple target sequences.

  16. Thermal Contrast Amplification Reader Yielding 8-Fold Analytical Improvement for Disease Detection with Lateral Flow Assays.

    Science.gov (United States)

    Wang, Yiru; Qin, Zhenpeng; Boulware, David R; Pritt, Bobbi S; Sloan, Lynne M; González, Iveth J; Bell, David; Rees-Channer, Roxanne R; Chiodini, Peter; Chan, Warren C W; Bischof, John C

    2016-12-06

    There is an increasing need for highly sensitive and quantitative diagnostics at the point-of-care. The lateral flow immunoassay (LFA) is one of the most widely used point-of-care diagnostic tests; however, LFAs generally suffer from low sensitivity and lack of quantification. To overcome these limitations, thermal contrast amplification (TCA) is a new method that is based on the laser excitation of gold nanoparticles (GNPs), the most commonly used visual signature, to evoke a thermal signature. To facilitate the clinical translation of the TCA technology, we present the development of a TCA reader, a platform technology that significantly improves the limit of detection and provides quantification of disease antigens in LFAs. This TCA reader provides enhanced sensitivity over visual detection by the human eye or by a colorimetric reader (e.g., BD Veritor System Reader). More specifically, the TCA reader demonstrated up to an 8-fold enhanced analytical sensitivity and quantification among LFAs for influenza, malaria, and Clostridium difficile. Systematic characterization of the laser, infrared camera, and other components of the reader and their integration into a working reader instrument are described. The development of the TCA reader enables simple, highly sensitive quantification of LFAs at the point-of-care.

  17. Cooperative folding near the downhill limit determined with amino acid resolution by hydrogen exchange.

    Science.gov (United States)

    Yu, Wookyung; Baxa, Michael C; Gagnon, Isabelle; Freed, Karl F; Sosnick, Tobin R

    2016-04-26

    The relationship between folding cooperativity and downhill, or barrier-free, folding of proteins under highly stabilizing conditions remains an unresolved topic, especially for proteins such as λ-repressor that fold on the microsecond timescale. Under aqueous conditions where downhill folding is most likely to occur, we measure the stability of multiple H bonds, using hydrogen exchange (HX) in a λYA variant that is suggested to be an incipient downhill folder having an extrapolated folding rate constant of 2 × 10(5) s(-1) and a stability of 7.4 kcal·mol(-1) at 298 K. At least one H bond on each of the three largest helices (α1, α3, and α4) breaks during a common unfolding event that reflects global denaturation. The use of HX enables us to both examine folding under highly stabilizing, native-like conditions and probe the pretransition state region for stable species without the need to initiate the folding reaction. The equivalence of the stability determined at zero and high denaturant indicates that any residual denatured state structure minimally affects the stability even under native conditions. Using our ψ analysis method along with mutational ϕ analysis, we find that the three aforementioned helices are all present in the folding transition state. Hence, the free energy surface has a sufficiently high barrier separating the denatured and native states that folding appears cooperative even under extremely stable and fast folding conditions.

  18. Logarithmic and power law input-output relations in sensory systems with fold-change detection.

    Science.gov (United States)

    Adler, Miri; Mayo, Avi; Alon, Uri

    2014-08-01

    Two central biophysical laws describe sensory responses to input signals. One is a logarithmic relationship between input and output, and the other is a power law relationship. These laws are sometimes called the Weber-Fechner law and the Stevens power law, respectively. The two laws are found in a wide variety of human sensory systems including hearing, vision, taste, and weight perception; they also occur in the responses of cells to stimuli. However the mechanistic origin of these laws is not fully understood. To address this, we consider a class of biological circuits exhibiting a property called fold-change detection (FCD). In these circuits the response dynamics depend only on the relative change in input signal and not its absolute level, a property which applies to many physiological and cellular sensory systems. We show analytically that by changing a single parameter in the FCD circuits, both logarithmic and power-law relationships emerge; these laws are modified versions of the Weber-Fechner and Stevens laws. The parameter that determines which law is found is the steepness (effective Hill coefficient) of the effect of the internal variable on the output. This finding applies to major circuit architectures found in biological systems, including the incoherent feed-forward loop and nonlinear integral feedback loops. Therefore, if one measures the response to different fold changes in input signal and observes a logarithmic or power law, the present theory can be used to rule out certain FCD mechanisms, and to predict their cooperativity parameter. We demonstrate this approach using data from eukaryotic chemotaxis signaling.

  19. Targeting folded RNA: A branched peptide boronic acid that binds to a large surface area of HIV-1 RRE RNA†

    Science.gov (United States)

    Zhang, Wenyu; Bryson, David I.; Crumpton, Jason B.; Wynn, Jessica; Santos, Webster L.

    2013-01-01

    On-bead high throughput screening of a medium sized (1000–2000 Da) branched peptide boronic acid (BPBA) library consisting of 46,656 unique sequences against HIV-1 RRE RNA generated peptides with binding affinities in the low micromolar range. In particular, BPBA1 had a Kd of 1.4 µM with RRE IIB, preference for RNA over DNA (27 fold), and selectivity of up to >75 fold against a panel of RRE IIB variants. Structure-activity studies suggest that the boronic acid moiety and “branching” in peptides are key structural features for efficient binding and selectivity for the folded RNA target. BPBA1 was efficiently taken up by HeLa and A2780 cells. RNA-footprinting studies revealed that the BPBA1 binding site encompasses a large surface area that spans both the upper stem as well as the internal loop regions of RRE IIB. PMID:23925474

  20. Transient dynamic phenotypes as criteria for model discrimination: fold-change detection in Rhodobacter sphaeroides chemotaxis.

    Science.gov (United States)

    Hamadeh, Abdullah; Ingalls, Brian; Sontag, Eduardo

    2013-03-01

    The chemotaxis pathway of the bacterium Rhodobacter sphaeroides shares many similarities with that of Escherichia coli. It exhibits robust adaptation and has several homologues of the latter's chemotaxis proteins. Recent theoretical results have correctly predicted that the E. coli output behaviour is unchanged under scaling of its ligand input signal; this property is known as fold-change detection (FCD). In the light of recent experimental results suggesting that R. sphaeroides may also show FCD, we present theoretical assumptions on the R. sphaeroides chemosensory dynamics that can be shown to yield FCD behaviour. Furthermore, it is shown that these assumptions make FCD a property of this system that is robust to structural and parametric variations in the chemotaxis pathway, in agreement with experimental results. We construct and examine models of the full chemotaxis pathway that satisfy these assumptions and reproduce experimental time-series data from earlier studies. We then propose experiments in which models satisfying our theoretical assumptions predict robust FCD behaviour where earlier models do not. In this way, we illustrate how transient dynamic phenotypes such as FCD can be used for the purposes of discriminating between models that reproduce the same experimental time-series data.

  1. Be an acid rain detective

    Energy Technology Data Exchange (ETDEWEB)

    Atwill, L.

    1982-07-01

    Acid rain is discussed in a question and answer format. The article is aimed at educating sport fishermen on the subject, and also to encourage them to write their congressmen, senators, and the President about the acid rain problem. The article also announces the availability of an acid rain test kit available through the magazine, ''Sports Afield.'' The kit consists of pH-test paper that turns different shades of pink and blue according to the pH of the water tested. The color of the test paper is then compared to a color chart furnished in the kit and an approximate pH can be determined.

  2. An Evolutionary Strategy for All-Atom Folding of the 60-Amino-Acid Bacterial Ribosomal Protein L20

    Science.gov (United States)

    Schug, A.; Wenzel, W.

    2006-01-01

    We have investigated an evolutionary algorithm for de novo all-atom folding of the bacterial ribosomal protein L20. We report results of two simulations that converge to near-native conformations of this 60-amino-acid, four-helix protein. We observe a steady increase of “native content” in both simulated ensembles and a large number of near-native conformations in their final populations. We argue that these structures represent a significant fraction of the low-energy metastable conformations, which characterize the folding funnel of this protein. These data validate our all-atom free-energy force field PFF01 for tertiary structure prediction of a previously inaccessible structural family of proteins. We also compare folding simulations of the evolutionary algorithm with the basin-hopping technique for the Trp-cage protein. We find that the evolutionary algorithm generates a dynamic memory in the simulated population, which leads to faster overall convergence. PMID:16565067

  3. G-rich VEGF aptamer with locked and unlocked nucleic acid modifications exhibits a unique G-quadruplex fold

    DEFF Research Database (Denmark)

    Marusic, Maja; Veedu, Rakesh N; Wengel, Jesper

    2013-01-01

    The formation of a single G-quadruplex structure adopted by a promising 25 nt G-rich vascular endothelial growth factor aptamer in a K(+) rich environment was facilitated by locked nucleic acid modifications. An unprecedented all parallel-stranded monomeric G-quadruplex with three G-quartet planes...... residues contribute to thermal stabilization of the adopted structure and formation of structurally pre-organized intermediates that facilitate folding into a single G-quadruplex. Understanding the impact of chemical modifications on folding, thermal stability and structural polymorphism of G...... exhibits several unique structural features. Five consecutive guanine residues are all involved in G-quartet formation and occupy positions in adjacent DNA strands, which are bridged with a no-residue propeller-type loop. A two-residue D-shaped loop facilitates inclusion of an isolated guanine residue...

  4. Scale-free behaviour of amino acid pair interactions in folded proteins

    DEFF Research Database (Denmark)

    Petersen, Steffen B.; Neves-Petersen, Maria Teresa; Mortensen, Rasmus J.

    2012-01-01

    that they are in buried a-helices or b-strands, in a spatial distance of 3.8–4.3A° and in a sequence distance .4 residues. We speculate that the scale free organization of the amino acid pair interactions in the 8D protein structure combined with the clear dominance of pairs of Ala, Ile, Leu and Val is important......The protein structure is a cumulative result of interactions between amino acid residues interacting with each other through space and/or chemical bonds. Despite the large number of high resolution protein structures, the ‘‘protein structure code’’ has not been fully identified. Our manuscript...... presents a novel approach to protein structure analysis in order to identify rules for spatial packing of amino acid pairs in proteins. We have investigated 8706 high resolution non-redundant protein chains and quantified amino acid pair interactions in terms of solvent accessibility, spatial and sequence...

  5. Safety and persistence of non-animal stabilized hyaluronic acid fillers for nasolabial folds correction in 30 Indian patients

    Directory of Open Access Journals (Sweden)

    Shehnaz Z Arsiwala

    2010-01-01

    Full Text Available Background: Correction of nasolabial creases through minimally invasive procedures is increasingly being sought by patients. Injecting non-animal stabilized hyaluronic acid filler is a highly effective method to achieve an optimal and persistent cosmetic result. Aims: To evaluate the efficacy, persistence and safety of Restylane and Perlane (Q-Med, Sweden for correction of nasolabial folds in Indian patients. Materials and Methods: Thirty Indian patients with mild, moderate and severe nasolabial folds (based on Wrinkle Assessment Scale were recruited in the study after informed consent for correction of their folds with Restylane or Perlane or both. Injections were administered in a single sitting after global assessment of the patient′s face using Wrinkle assessment scale (WAS.Optimal filling was performed by using appropriate techniques and its safety and efficacy assessed independently by the investigator as well as by patients at immediately, 3, 6 and 9 months post-procedure. Any adverse reactions were noted. Results: Twenty two females and 8 males (age range 45-55 years, mean age 52 years were recruited in the study. An optimum cosmetic correction was obtained in all patients. The efficacy increased with time and was greatest at 3 months after the treatment. Grade 2 improvement was maintained at 9 months in mild and moderate folds, and grade 3 improvement for severe folds. Minor post injection side effects like erythema at puncture site, needle marks and bruising were seen. Conclusion: Restylane and Perlane are safe and effective dermal fillers for correction of nasolabial creases and offer immediate effect.

  6. Amplification-free In Situ KRAS Point Mutation Detection at 60 copies/mL in Urine in a Background of 1000-fold Wild Type

    Science.gov (United States)

    KirimLi, Ceyhun E.; Shih, Wei-Heng; Shih, Wan Y.

    2016-01-01

    We have examined in situ detection of single-nucleotide KRAS mutation in urine using a (Pb(Mg1/3Nb2/3)O3)0.65(PbTiO3)0.35 (PMN-PT) piezoelectric plate sensor (PEPS) coated with a 17-nucleotide (nt) locked nucleic acid (LNA) probe DNA complementary to the KRAS mutation. To enhance in situ mutant (MT) DNA detection specificity against the wild type (WT), the detection was carried out in a flow with a flow rate of 4 mL/min and at 63°C with the PEPS vertically situated at the center of the flow in which both the temperature and the flow impingement force discriminated the wild type. Under such conditions, PEPS was shown to specifically detect KRAS MT in situ with 60 copies/mL analytical sensitivity in a background of clinically-relevant 1000-fold more WT in 30 min without DNA isolation, amplification, or labeling. For validation, the detection was followed with detection in a mixture of blue MT fluorescent reporter microspheres (FRMs) (MT FRMs) that bound to only the captured MT and orange WT FRMs that bound to only the captured WT. Microscopic examinations showed that the captured blue MT FRMs still outnumbered the orange WT FRMs by a factor of 4 to 1 even though WT was 1000-fold of MT in urine. Finally, multiplexed specific mutation detection was demonstrated using a 6-PEPS array each with a probe DNA targeting one of the 6 codon-12 KRAS mutations. PMID:26783561

  7. Amino acid empirical contact energy definitions for fold recognition in the space of contact maps

    Directory of Open Access Journals (Sweden)

    Fogolari Federico

    2003-02-01

    Full Text Available Abstract Background Contradicting evidence has been presented in the literature concerning the effectiveness of empirical contact energies for fold recognition. Empirical contact energies are calculated on the basis of information available from selected protein structures, with respect to a defined reference state, according to the quasi-chemical approximation. Protein-solvent interactions are estimated from residue solvent accessibility. Results In the approach presented here, contact energies are derived from the potential of mean force theory, several definitions of contact are examined and their performance in fold recognition is evaluated on sets of decoy structures. The best definition of contact is tested, on a more realistic scenario, on all predictions including sidechains accepted in the CASP4 experiment. In 30 out of 35 cases the native structure is correctly recognized and best predictions are usually found among the 10 lowest energy predictions. Conclusion The definition of contact based on van der Waals radii of alpha carbon and side chain heavy atoms is seen to perform better than other definitions involving only alpha carbons, only beta carbons, all heavy atoms or only backbone atoms. An important prerequisite for the applicability of the approach is that the protein structure under study should not exhibit anomalous solvent accessibility, compared to soluble proteins whose structure is deposited in the Protein Data Bank. The combined evaluation of a solvent accessibility parameter and contact energy allows for an effective gross screening of predictive models.

  8. Comparative study of the folding/unfolding dynamics of poly(glutamic acid) in light and heavy water.

    Science.gov (United States)

    Mendonça, Lucille; Steinbacher, Andreas; Bouganne, Raphaël; Hache, François

    2014-05-22

    The folding/unfolding equilibrium is investigated in poly(glutamic acid) (PGA) by two complementary sets of experiments: temperature-dependent steady-state circular dichroism spectra on the one hand and time-resolved circular dichroism measurements coupled with a T-jump experiment on the other hand. The experiments are performed for PGA dissolved in water for various pH values, as well as in heavy water. The kinetic and thermodynamic parameters extracted from these measurements are shown to be markedly different between light and heavy water, which is assigned to the difference in hydrogen bond energies in both solvents.

  9. An In Vivo Study of Composite Microgels Based on Hyaluronic Acid and Gelatin for the Reconstruction of Surgically Injured Rat Vocal Folds

    Science.gov (United States)

    Coppoolse, Jiska M. S.; Van Kooten, T. G.; Heris, Hossein K.; Mongeau, Luc; Li, Nicole Y. K.; Thibeault, Susan L.; Pitaro, Jacob; Akinpelu, Olubunm; Daniel, Sam J.

    2014-01-01

    Purpose: The objective of this study was to investigate local injection with a hierarchically microstructured hyaluronic acid-gelatin (HA-Ge) hydrogel for the treatment of acute vocal fold injury using a rat model. Method: Vocal fold stripping was performed unilaterally in 108 Sprague-Dawley rats. A volume of 25 µl saline (placebo controls),…

  10. Prediction of the Occurrence of the ADP-binding βαβ-fold in Proteins, Using an Amino Acid Sequence Fingerprint

    NARCIS (Netherlands)

    Wierenga, Rik K.; Terpstra, Peter; Hol, Wim G.J.

    1986-01-01

    An amino acid sequence "fingerprint” has been derived that can be used to test if a particular sequence will fold into a βαβ-unit with ADP-binding properties. It was deduced from a careful analysis of the known three-dimensional structures of ADP-binding βαβ-folds. This fingerprint is in fact a set

  11. Determination of acetylsalicylic acid and salicylic acid in foods, using HPLC with fluorescence detection.

    OpenAIRE

    Venema, D.P.; Hollman, P.C.H.; Janssen, P.L.T.M.K.; Katan, M B

    1996-01-01

    We developed a specific and sensitive HPLC method with fluorescence detection for the determination of free acetylsalicylic acid, free salicylic acid, and free salicylic acid plus salicylic acid after alkaline hydrolysis (free-plus-bound) in foods. Acetylsalicylic acid was detected after postcolumn hydrolysis to salicylic acid. With the method for free acetylsalicylic acid and salicylic acid, recovery was 95-98␏or acetylsalicylic acid added to foods and 92-102␏or salicylic acid. Recovery of a...

  12. The exchangeable yeast ribosomal acidic protein YP2beta shows characteristics of a partly folded state under physiological conditions.

    Science.gov (United States)

    Zurdo, J; Sanz, J M; González, C; Rico, M; Ballesta, J P

    1997-08-05

    The eukaryotic acidic ribosomal P proteins, contrary to the standard r-proteins which are rapidly degraded in the cytoplasm, are found forming a large cytoplasmic pool that exchanges with the ribosome-bound proteins during translation. The native structure of the P proteins in solution is therefore an essential determinant of the protein-protein interactions that take place in the exchange process. In this work, the structure of the ribosomal acidic protein YP2beta from Saccharomyces cerevisiae has been investigated by fluorescence spectroscopy, circular dichroism (CD), nuclear magnetic resonance (NMR), and sedimentation equilibrium techniques. We have established the fact that YP2beta bears a 22% alpha-helical secondary structure and a noncompact tertiary structure under physiological conditions (pH 7.0 and 25 degrees C); the hydrophobic core of the protein appears to be solvent-exposed, and very low cooperativity is observed for heat- or urea-induced denaturation. Moreover, the 1H-NMR spectra show a small signal dispersion, and virtually all the amide protons exchange with the solvent on a very short time scale, which is characteristic of an open structure. At low pH, YP2beta maintains its secondary structure content, but there is no evidence for tertiary structure. 2,2,2-Trifluoroethanol (TFE) induces a higher amount of alpha-helical structure but also disrupts any trace of the remaining tertiary fold. These results indicate that YP2beta may have a flexible structure in the cytoplasmic pool, with some of the characteristics of a "molten globule", and also point out the physiological relevance of such flexible protein states in processes other than protein folding.

  13. How Does Your Protein Fold? Elucidating the Apomyoglobin Folding Pathway.

    Science.gov (United States)

    Dyson, H Jane; Wright, Peter E

    2017-01-17

    Although each type of protein fold and in some cases individual proteins within a fold classification can have very different mechanisms of folding, the underlying biophysical and biochemical principles that operate to cause a linear polypeptide chain to fold into a globular structure must be the same. In an aqueous solution, the protein takes up the thermodynamically most stable structure, but the pathway along which the polypeptide proceeds in order to reach that structure is a function of the amino acid sequence, which must be the final determining factor, not only in shaping the final folded structure, but in dictating the folding pathway. A number of groups have focused on a single protein or group of proteins, to determine in detail the factors that influence the rate and mechanism of folding in a defined system, with the hope that hypothesis-driven experiments can elucidate the underlying principles governing the folding process. Our research group has focused on the folding of the globin family of proteins, and in particular on the monomeric protein apomyoglobin. Apomyoglobin (apoMb) folds relatively slowly (∼2 s) via an ensemble of obligatory intermediates that form rapidly after the initiation of folding. The folding pathway can be dissected using rapid-mixing techniques, which can probe processes in the millisecond time range. Stopped-flow measurements detected by circular dichroism (CD) or fluorescence spectroscopy give information on the rates of folding events. Quench-flow experiments utilize the differential rates of hydrogen-deuterium exchange of amide protons protected in parts of the structure that are folded early; protection of amides can be detected by mass spectrometry or proton nuclear magnetic resonance spectroscopy (NMR). In addition, apoMb forms an intermediate at equilibrium at pH ∼ 4, which is sufficiently stable for it to be structurally characterized by solution methods such as CD, fluorescence and NMR spectroscopies, and the

  14. Folding Landscape of Mutant Huntingtin Exon1: Diffusible Multimers, Oligomers and Fibrils, and No Detectable Monomer.

    Directory of Open Access Journals (Sweden)

    Bankanidhi Sahoo

    Full Text Available Expansion of the polyglutamine (polyQ track of the Huntingtin (HTT protein above 36 is associated with a sharply enhanced risk of Huntington's disease (HD. Although there is general agreement that HTT toxicity resides primarily in N-terminal fragments such as the HTT exon1 protein, there is no consensus on the nature of the physical states of HTT exon1 that are induced by polyQ expansion, nor on which of these states might be responsible for toxicity. One hypothesis is that polyQ expansion induces an alternative, toxic conformation in the HTT exon1 monomer. Alternative hypotheses posit that the toxic species is one of several possible aggregated states. Defining the nature of the toxic species is particularly challenging because of facile interconversion between physical states as well as challenges to identifying these states, especially in vivo. Here we describe the use of fluorescence correlation spectroscopy (FCS to characterize the detailed time and repeat length dependent self-association of HTT exon1-like fragments both with chemically synthesized peptides in vitro and with cell-produced proteins in extracts and in living cells. We find that, in vitro, mutant HTT exon1 peptides engage in polyQ repeat length dependent dimer and tetramer formation, followed by time dependent formation of diffusible spherical and fibrillar oligomers and finally by larger, sedimentable amyloid fibrils. For expanded polyQ HTT exon1 expressed in PC12 cells, monomers are absent, with tetramers being the smallest molecular form detected, followed in the incubation time course by small, diffusible aggregates at 6-9 hours and larger, sedimentable aggregates that begin to build up at 12 hrs. In these cell cultures, significant nuclear DNA damage appears by 6 hours, followed at later times by caspase 3 induction, mitochondrial dysfunction, and cell death. Our data thus defines limits on the sizes and concentrations of different physical states of HTT exon1 along the

  15. Reproducible In-Silico Folding of a Four Helix 60 Amino Acid Protein in a Transferable All-Atom Forcefield

    Science.gov (United States)

    Schug, Alexander

    2005-03-01

    For predicting the protein tertiary structure one approach describes the native state of a protein as the global minimum of an appropiate free-energy forcefield. We have recently developed such a all-atom protein forcefield (PFF01). As major challenge remains the search for the global minimum for which we developed efficient methods. Using these we were able to predict the structure of helical proteins from different families ranging in size from 20 to 60 amino acids starting with random configurations. For the four helix 60 amino acid protein Bacterial Ribosomal Protein L20 (pdb code: 1GYZ) we used a simple client-master model for distributed computing. Starting from a set of random structures three phases of different folding simulations refined this set to a final one with 50 configurations. During this process the amount of native-like structures increased strongly. Six out of the ten structures best in energy approached the native structure within 5 åbackbone rmsd. The conformation with the lowest energy had a backbone rmsd value of 4.6 åtherefore correctly predicting the tertiary structure of 1GYZ.ReferencesA. Schug et al, Phys. Rev. Letters, 91:158102, 2003A. Schug et al, J. Am. Chem. Soc. (in press), 2004

  16. SCOWLP update: 3D classification of protein-protein, -peptide, -saccharide and -nucleic acid interactions, and structure-based binding inferences across folds

    Directory of Open Access Journals (Sweden)

    Schreiber Sven

    2011-10-01

    Full Text Available Abstract Background Protein interactions are essential for coordinating cellular functions. Proteomic studies have already elucidated a huge amount of protein-protein interactions that require detailed functional analysis. Understanding the structural basis of each individual interaction through their structural determination is necessary, yet an unfeasible task. Therefore, computational tools able to predict protein binding regions and recognition modes are required to rationalize putative molecular functions for proteins. With this aim, we previously created SCOWLP, a structural classification of protein binding regions at protein family level, based on the information obtained from high-resolution 3D protein-protein and protein-peptide complexes. Description We present here a new version of SCOWLP that has been enhanced by the inclusion of protein-nucleic acid and protein-saccharide interactions. SCOWLP takes interfacial solvent into account for a detailed characterization of protein interactions. In addition, the binding regions obtained per protein family have been enriched by the inclusion of predicted binding regions, which have been inferred from structurally related proteins across all existing folds. These inferences might become very useful to suggest novel recognition regions and compare structurally similar interfaces from different families. Conclusions The updated SCOWLP has new functionalities that allow both, detection and comparison of protein regions recognizing different types of ligands, which include other proteins, peptides, nucleic acids and saccharides, within a solvated environment. Currently, SCOWLP allows the analysis of predicted protein binding regions based on structure-based inferences across fold space. These predictions may have a unique potential in assisting protein docking, in providing insights into protein interaction networks, and in guiding rational engineering of protein ligands. The newly designed

  17. Determination of acetylsalicylic acid and salicylic acid in foods, using HPLC with fluorescence detection.

    NARCIS (Netherlands)

    Venema, D.P.; Hollman, P.C.H.; Janssen, P.L.T.M.K.; Katan, M.B.

    1996-01-01

    We developed a specific and sensitive HPLC method with fluorescence detection for the determination of free acetylsalicylic acid, free salicylic acid, and free salicylic acid plus salicylic acid after alkaline hydrolysis (free-plus-bound) in foods. Acetylsalicylic acid was detected after postcolumn

  18. Determination of acetylsalicylic acid and salicylic acid in foods, using HPLC with fluorescence detection.

    NARCIS (Netherlands)

    Venema, D.P.; Hollman, P.C.H.; Janssen, P.L.T.M.K.; Katan, M.B.

    1996-01-01

    We developed a specific and sensitive HPLC method with fluorescence detection for the determination of free acetylsalicylic acid, free salicylic acid, and free salicylic acid plus salicylic acid after alkaline hydrolysis (free-plus-bound) in foods. Acetylsalicylic acid was detected after postcolumn

  19. Extreme Folding

    Science.gov (United States)

    Demaine, Erik

    2012-02-01

    Our understanding of the mathematics and algorithms behind paper folding, and geometric folding in general, has increased dramatically over the past several years. These developments have found a surprisingly broad range of applications. In the art of origami, it has helped spur the technical origami revolution. In engineering and science, it has helped solve problems in areas such as manufacturing, robotics, graphics, and protein folding. On the recreational side, it has led to new kinds of folding puzzles and magic. I will give an overview of the mathematics and algorithms of folding, with a focus on new mathematics and sculpture.

  20. Fluorescent hybridization probes for nucleic acid detection.

    Science.gov (United States)

    Guo, Jia; Ju, Jingyue; Turro, Nicholas J

    2012-04-01

    Due to their high sensitivity and selectivity, minimum interference with living biological systems, and ease of design and synthesis, fluorescent hybridization probes have been widely used to detect nucleic acids both in vivo and in vitro. Molecular beacons (MBs) and binary probes (BPs) are two very important hybridization probes that are designed based on well-established photophysical principles. These probes have shown particular applicability in a variety of studies, such as mRNA tracking, single nucleotide polymorphism (SNP) detection, polymerase chain reaction (PCR) monitoring, and microorganism identification. Molecular beacons are hairpin oligonucleotide probes that present distinctive fluorescent signatures in the presence and absence of their target. Binary probes consist of two fluorescently labeled oligonucleotide strands that can hybridize to adjacent regions of their target and generate distinctive fluorescence signals. These probes have been extensively studied and modified for different applications by modulating their structures or using various combinations of fluorophores, excimer-forming molecules, and metal complexes. This review describes the applicability and advantages of various hybridization probes that utilize novel and creative design to enhance their target detection sensitivity and specificity.

  1. Tween 20-stabilized gold nanoparticles combined with adenosine triphosphate-BODIPY conjugates for the fluorescence detection of adenosine with more than 1000-fold selectivity

    Energy Technology Data Exchange (ETDEWEB)

    Hung, Szu-Ying; Shih, Ya-Chen [Department of Chemistry, National Sun Yat-sen University, Taiwan (China); Tseng, Wei-Lung, E-mail: tsengwl@mail.nsysu.edu.tw [Department of Chemistry, National Sun Yat-sen University, Taiwan (China); School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Taiwan (China); Center for Nanoscience and Nanotechnology, National Sun Yat-sen University, Taiwan (China); Center for Stem Cell Research, Kaohsiung Medical University, Taiwan (China)

    2015-02-01

    Graphical abstract: A simple, enzyme-free, label-free, sensitive and selective system was developed for detecting adenosine based on the use of Tween 20-stabilized gold nanoparticles as an efficient quencher for boron dipyrromethene-conjugated adenosine 5′-triphosphate and as a recognition element for adenosine. - Highlights: • The proposed method can detect adenosine with more than 1000-fold selectivity. • The analysis of adenosine is rapid (∼6 min) using the proposed method. • This method provided better sensitivity for adenosine as compared to aptamer-based sensors. • This method can be applied for the determination of adenosine in urine. - Abstract: This study describes the development of a simple, enzyme-free, label-free, sensitive, and selective system for detecting adenosine based on the use of Tween 20-stabilized gold nanoparticles (Tween 20-AuNPs) as an efficient fluorescence quencher for boron dipyrromethene-conjugated adenosine 5′-triphosphate (BODIPY-ATP) and as a recognition element for adenosine. BODIPY-ATP can interact with Tween 20-AuNPs through the coordination between the adenine group of BODIPY-ATP and Au atoms on the NP surface, thereby causing the fluorescence quenching of BODIPY-ATP through the nanometal surface energy transfer (NSET) effect. When adenosine attaches to the NP surface, the attached adenosine exhibits additional electrostatic attraction to BODIPY-ATP. As a result, the presence of adenosine enhances the efficiency of AuNPs in fluorescence quenching of BODIPY-ATP. The AuNP-induced fluorescence quenching of BODIPY-ATP progressively increased with an increase in the concentration of adenosine; the detection limit at a signal-to-noise ratio of 3 for adenosine was determined to be 60 nM. The selectivity of the proposed system was more than 1000-fold for adenosine over any adenosine analogs and other nucleotides. The proposed system combined with a phenylboronic acid-containing column was successfully applied to the

  2. A hydrogel actuator with flexible folding deformation and shape programming via using sodium carboxymethyl cellulose and acrylic acid.

    Science.gov (United States)

    Wu, Shuiping; Yu, Feng; Dong, Hua; Cao, Xiaodong

    2017-10-01

    Hydrogel actuator is an intelligent material, which can work as artificial muscle. However, most present hydrogel actuators, due to the inferior mechanical property and uncontrolled folding property, have always resulted in slipping off or the failure of grasping an object with specific shape and required weight. In order to solve this problem, here a tough hydrogel actuator with programmable folding deformation has been prepared by combining the "selective implanting method" and "ionic coordination". The shape and folding angle (from 0 to 180 (o)) of hydrogel actuator can be precisely controlled by altering the location and size of the implanting parts that seems like the joints of finger. The ionic coordination is not only the force to trigger the folding of hydrogel, but also utilized to reinforce the mechanical property. We believed the superior mechanical and shape-programmable property can endow the hydrogel actuator with great application prospect in soft machine. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. Effects of two mutations detected in medium chain acyl-CoA dehydrogenase (MCAD)-deficient patients on folding, oligomer assembly, and stability of MCAD enzyme

    DEFF Research Database (Denmark)

    Bross, P; Jespersen, C; Jensen, T G

    1995-01-01

    We have used expression of human medium chain acyl-CoA dehydrogenase (MCAD) in Escherichia coli as a model system for dissecting the molecular effects of two mutations detected in patients with MCAD deficiency. We demonstrate that the R28C mutation predominantly affects polypeptide folding...

  4. GANDivAWeb: A web server for detecting early folding units ("foldons" from protein 3D structures

    Directory of Open Access Journals (Sweden)

    Krishnan Arun

    2008-03-01

    Full Text Available Abstract Background It has long been known that small regions of proteins tend to fold independently and are then stabilized by interactions between these distinct subunits or modules. Such units, also known as autonomous folding units (AFUs or"foldons" play a key role in protein folding. A knowledge of such early folding units has diverse applications in protein engineering as well as in developing an understanding of the protein folding process. Such AFUs can also be used as model systems in order to study the structural organization of proteins. Results In an earlier work, we had utilized a global network partitioning algorithm to identify modules in proteins. We had shown that these modules correlate well with AFUs. In this work, we have developed a webserver, GANDivAWeb, to identify early folding units or "foldons" in networks using the algorithm described earlier. The website has three functionalities: (a It is able to display information on the modularity of a database of 1420 proteins used in the original work, (b It can take as input an uploaded PDB file, identify the modules using the GANDivA algorithm and email the results back to the user and (c It can take as input an uploaded PDB file and a results file (obtained from functionality (b and display the results using the embedded viewer. The results include the module decomposition of the protein, plots of cartoon representations of the protein colored by module identity and connectivity as well as contour plots of the hydrophobicity and relative accessible surface area (RASA distributions. Conclusion We believe that the GANDivAWeb server, will be a useful tool for scientists interested in the phenomena of protein folding as well as in protein engineering. Our tool not only provides a knowledge of the AFUs through a natural graph partitioning approach but is also able to identify residues that are critical during folding. It is our intention to use this tool to study the topological

  5. Monitoring Homovanillic Acid and Vanillylmandelic Acid in Human Urine by Capillary Electrophoresis with Electrochemical Detection

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    A simple, rapid and low-cost method of separation and determination of homovanillic acid and vanillylmandelic acid in human urine was developed based on capillary zone electrophoresis / amperometric detection with high sensitivity and good resolution.

  6. Transition Path Times for Nucleic Acid Folding Determined from Energy-Landscape Analysis of Single-Molecule Trajectories

    Science.gov (United States)

    Neupane, Krishna; Ritchie, Dustin B.; Yu, Hao; Foster, Daniel A. N.; Wang, Feng; Woodside, Michael T.

    2012-08-01

    The duration of structural transitions in biopolymers is only a fraction of the time spent searching diffusively over the configurational energy landscape. We found the transition time, τTP, and the diffusion constant, D, for DNA and RNA folding using energy landscapes obtained from single-molecule trajectories under tension in optical traps. DNA hairpins, RNA pseudoknots, and a riboswitch all had τTP˜10μs and D˜10-13-14m2/s, despite widely differing unfolding rates. These results show how energy-landscape analysis can be harnessed to characterize brief but critical events during folding reactions.

  7. Early kinetic intermediate in the folding of acyl-CoA binding protein detected by fluorescence labeling and ultrarapid mixing

    DEFF Research Database (Denmark)

    Teilum, Kaare; Maki, Kosuke; Kragelund, Birthe B

    2002-01-01

    Early conformational events during folding of acyl-CoA binding protein (ACBP), an 86-residue alpha-helical protein, were explored by using a continuous-flow mixing apparatus with a dead time of 70 micros to measure changes in intrinsic tryptophan fluorescence and tryptophan-dansyl fluorescence en...

  8. The Next Generation MOD: A Microchip Amino Acid Analyzer for Detecting Extraterrestrial Life

    Science.gov (United States)

    Mathies, R. A.; Hutt, L. D.; Bada, J. L.; Glavin, D.; Grunthaner, F. J.; Grunthaner, P. J.

    2000-01-01

    The MOD (Mars Organic Detector) instrument which has selected for the definition phase of the BEDS package on the 2005 Mars Explorer Program spacecraft is designed to simply detect the presence of amino acids in Martian surface samples at a sensitivity of a few parts per billion (ppb). An additional important aspect of amino acid analyses of Martian samples is identifying and quantifying which compounds are present, and also distinguishing those produced abiotically from those synthesized by either extinct or extant life. Amino acid homochirality provides an unambiguous way of distinguishing between abiotic vs. biotic origins. Proteins made up of mixed D- and L-amino acids would not likely have been efficient catalysts in early organisms because they could not fold into bioactive configurations such as the a-helix. However, enzymes made up of all D-amino acids function just as well as those made up of only L-amino acids, but the two enzymes use the opposite stereoisomeric substrates. There are no biochemical reasons why L-amino acids would be favored over Damino acids. On Earth, the use of only L-amino acids in proteins by life is probably simply a matter of chance. We assume that if proteins and enzymes were a component of extinct or extant life on Mars, then amino acid homochirality would have been a requirement. However, the possibility that Martian life was (or is) based on D-amino acids would be equal to that based on L-amino acids. The detection of a nonracemic mixture of amino acids in a Martian sample would be strong evidence for the presence of an extinct or extant biota on Mars. The finding of an excess of D-amino acids would provide irrefutable evidence of unique Martian life that could not have been derived from seeding the planet with terrestrial life (or the seeding of the Earth with Martian life). In contrast, the presence of racemic amino acids, along with non-protein amino acids such as alpha-aminoisobutyric acid and isovaline, would be indicative

  9. The Next Generation MOD: A Microchip Amino Acid Analyzer for Detecting Extraterrestrial Life

    Science.gov (United States)

    Mathies, R. A.; Hutt, L. D.; Bada, J. L.; Glavin, D.; Grunthaner, F. J.; Grunthaner, P. J.

    2000-01-01

    The MOD (Mars Organic Detector) instrument which has selected for the definition phase of the BEDS package on the 2005 Mars Explorer Program spacecraft is designed to simply detect the presence of amino acids in Martian surface samples at a sensitivity of a few parts per billion (ppb). An additional important aspect of amino acid analyses of Martian samples is identifying and quantifying which compounds are present, and also distinguishing those produced abiotically from those synthesized by either extinct or extant life. Amino acid homochirality provides an unambiguous way of distinguishing between abiotic vs. biotic origins. Proteins made up of mixed D- and L-amino acids would not likely have been efficient catalysts in early organisms because they could not fold into bioactive configurations such as the a-helix. However, enzymes made up of all D-amino acids function just as well as those made up of only L-amino acids, but the two enzymes use the opposite stereoisomeric substrates. There are no biochemical reasons why L-amino acids would be favored over Damino acids. On Earth, the use of only L-amino acids in proteins by life is probably simply a matter of chance. We assume that if proteins and enzymes were a component of extinct or extant life on Mars, then amino acid homochirality would have been a requirement. However, the possibility that Martian life was (or is) based on D-amino acids would be equal to that based on L-amino acids. The detection of a nonracemic mixture of amino acids in a Martian sample would be strong evidence for the presence of an extinct or extant biota on Mars. The finding of an excess of D-amino acids would provide irrefutable evidence of unique Martian life that could not have been derived from seeding the planet with terrestrial life (or the seeding of the Earth with Martian life). In contrast, the presence of racemic amino acids, along with non-protein amino acids such as alpha-aminoisobutyric acid and isovaline, would be indicative

  10. 4-mercaptophenylboronic acid functionalized gold nanoparticles for colorimetric sialic acid detection.

    Science.gov (United States)

    Sankoh, Supannee; Thammakhet, Chongdee; Numnuam, Apon; Limbut, Warakorn; Kanatharana, Proespichaya; Thavarungkul, Panote

    2016-11-15

    A simple and selective colorimetric sensor for sialic acid detection, based on the aggregation of 4-mercaptophenylboronic acid functionalized gold nanoparticles (4-MPBA-AuNPs) was developed. The color of the solution changed from wine-red to blue after binding with sialic acid. The colorimetric sensor provided good analytical performances with a linear dynamic range of 80µM to 2.00mM and a 68±2µM limit of detection without any effect from possible interferences and sample matrix. In addition, the quantitative results were obtained within only 10min. This developed sensor was used to detect sialic acid in blood serum samples and the results were in good agreement with those from the current periodate-resorcinol method (P>0.05) thus indicating that this developed colorimetric sensor can be used as an alternative method for sialic acid detection with a shorter analysis time and a high accuracy.

  11. Nanopore-based sequencing and detection of nucleic acids.

    Science.gov (United States)

    Ying, Yi-Lun; Zhang, Junji; Gao, Rui; Long, Yi-Tao

    2013-12-09

    Nanopore-based techniques, which mimic the functions of natural ion channels, have attracted increasing attention as unique methods for single-molecule detection. The technology allows the real-time, selective, high-throughput analysis of nucleic acids through both biological and solid-state nanopores. In this Minireview, the background and latest progress in nanopore-based sequencing and detection of nucleic acids are summarized, and light is shed on a novel platform for nanopore-based detection. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Structure of LP2179, the first representative of Pfam family PF08866, suggests a new fold with a role in amino-acid metabolism

    Energy Technology Data Exchange (ETDEWEB)

    Bakolitsa, Constantina; Kumar, Abhinav; Carlton, Dennis; Miller, Mitchell D.; Krishna, S.Sri; Abdubek, Polat; Astakhova, Tamara; Axelrod, Herbert L.; Chiu, Hsiu-Ju; Clayton, Thomas; Deller, Marc C.; Duan, Lian; Elsliger, Marc-André; Feuerhelm, Julie; Grzechnik, Slawomir K.; Grant, Joanna C.; Han, Gye Won; Jaroszewski, Lukasz; Jin, Kevin K.; Klock, Heath E.; Knuth, Mark W.; Kozbial, Piotr; Marciano, David; McMullan, Daniel; Morse, Andrew T.; Nigoghossian, Edward; Okach, Linda; Oommachen, Silvya; Paulsen, Jessica; Reyes, Ron; Rife, Christopher L.; Tien, Henry J.; Trout, Christina V.; van den Bedem, Henry; Weekes, Dana; Xu, Qingping; Hodgson, Keith O.; Wooley, John; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Wilson, Ian A. (Burnham)

    2011-08-17

    The structure of LP2179, a member of the PF08866 (DUF1831) family, suggests a novel {alpha} + {beta} fold comprising two {beta}-sheets packed against a single helix. A remote structural similarity to two other uncharacterized protein families specific to the Bacillus genus (PF08868 and PF08968), as well as to prokaryotic S-adenosylmethionine decarboxylases, is consistent with a role in amino-acid metabolism. Genomic neighborhood analysis of LP2179 supports this functional assignment, which might also then be extended to PF08868 and PF08968.

  13. Investigation of the Viability, Adhesion, and Migration of Human Fibroblasts in a Hyaluronic Acid/Gelatin Microgel-Reinforced Composite Hydrogel for Vocal Fold Tissue Regeneration.

    Science.gov (United States)

    Heris, Hossein K; Daoud, Jamal; Sheibani, Sara; Vali, Hojatollah; Tabrizian, Maryam; Mongeau, Luc

    2016-01-21

    The potential use of a novel scaffold biomaterial consisting of cross-linked hyaluronic acid (HA)-gelatin (Ge) composite microgels is investigated for use in treating vocal fold injury and scarring. Cell adhesion integrins and kinematics of cell motion are investigated in 2D and 3D culture conditions, respectively. Human vocal fold fibroblast (hVFF) cells are seeded on HA-Ge microgels attached to a HA hydrogel thin film. The results show that hVFF cells establish effective adhesion to HA-Ge microgels through the ubiquitous expression of β1 integrin in the cell membrane. The microgels are then encapsulated in a 3D HA hydrogel for the study of cell migration. The cells within the HA-Ge microgel-reinforced composite hydrogel (MRCH) scaffold have an average motility speed of 0.24 ± 0.08 μm min(-1) . The recorded microscopic images reveal features that are presumably associated with lobopodial and lamellipodial cell migration modes within the MRCH scaffold. Average cell speed during lobopodial migration is greater than that during lamellipodial migration. The cells move faster in the MRCH than in the HA-Ge gel without microgels. These findings support the hypothesis that HA-Ge MRCH promotes cell adhesion and migration; thereby they constitute a promising biomaterial for vocal fold repair.

  14. Developing nucleic acid-based electrical detection systems

    Directory of Open Access Journals (Sweden)

    Gabig-Ciminska Magdalena

    2006-03-01

    Full Text Available Abstract Development of nucleic acid-based detection systems is the main focus of many research groups and high technology companies. The enormous work done in this field is particularly due to the broad versatility and variety of these sensing devices. From optical to electrical systems, from label-dependent to label-free approaches, from single to multi-analyte and array formats, this wide range of possibilities makes the research field very diversified and competitive. New challenges and requirements for an ideal detector suitable for nucleic acid analysis include high sensitivity and high specificity protocol that can be completed in a relatively short time offering at the same time low detection limit. Moreover, systems that can be miniaturized and automated present a significant advantage over conventional technology, especially if detection is needed in the field. Electrical system technology for nucleic acid-based detection is an enabling mode for making miniaturized to micro- and nanometer scale bio-monitoring devices via the fusion of modern micro- and nanofabrication technology and molecular biotechnology. The electrical biosensors that rely on the conversion of the Watson-Crick base-pair recognition event into a useful electrical signal are advancing rapidly, and recently are receiving much attention as a valuable tool for microbial pathogen detection. Pathogens may pose a serious threat to humans, animal and plants, thus their detection and analysis is a significant element of public health. Although different conventional methods for detection of pathogenic microorganisms and their toxins exist and are currently being applied, improvements of molecular-based detection methodologies have changed these traditional detection techniques and introduced a new era of rapid, miniaturized and automated electrical chip detection technologies into pathogen identification sector. In this review some developments and current directions in

  15. Nucleic acid in-situ hybridization detection of infectious agents

    Science.gov (United States)

    Thompson, Curtis T.

    2000-04-01

    Limitations of traditional culture methods and newer polymerase chain reaction (PCR)-based methods for detection and speciation of infectious agents demonstrate the need for more rapid and better diagnostics. Nucleic acid hybridization is a detection technology that has gained wide acceptance in cancer and prenatal cytogenetics. Using a modification of the nucleic acid hybridization technique known as fluorescence in-situ hybridization, infectious agents can be detected in a variety of specimens with high sensitivity and specificity. The specimens derive from all types of human and animal sources including body fluids, tissue aspirates and biopsy material. Nucleic acid hybridization can be performed in less than one hour. The result can be interpreted either using traditional fluorescence microscopy or automated platforms such as micro arrays. This paper demonstrates proof of concept for nucleic acid hybridization detection of different infectious agents. Interpretation within a cytologic and histologic context is possible with fluorescence microscopic analysis, thereby providing confirmatory evidence of hybridization. With careful probe selection, nucleic acid hybridization promises to be a highly sensitive and specific practical diagnostic alternative to culture, traditional staining methods, immunohistochemistry and complicated nucleic acid amplification tests.

  16. Plasmonics-based SERS nanobiosensor for homogeneous nucleic acid detection.

    Science.gov (United States)

    Wang, Hsin-Neng; Fales, Andrew M; Vo-Dinh, Tuan

    2015-05-01

    Developing a simple and efficient nucleic acid detection technology is essential for clinical diagnostics. Here, we describe a new conceptually simple and selective "turn on" plasmonics-based nanobiosensor, which integrates non-enzymatic DNA strand-displacement hybridization for specific nucleic acid target identification with surface-enhanced Raman scattering (SERS) detection. This SERS nanobiosensor is a target label-free, and rapid nanoparticle-based biosensing system using a homogeneous assay format that offers a simple and efficient tool for nucleic acid diagnostics. Our results showed that the nanobiosensor provided a limit of detection of ~0.1nM (200amol) in the current bioassay system, and exhibited high specificity for single nucleotide mismatch discrimination. Surface-enhanced Raman scattering (SERS) is a sensitive technique that enhances Raman scattering by molecules adsorbed on rough metal surfaces. The enhancement means that the technique may even detect single molecules. In this article, the authors describe a simple and efficient nucleic acid detection technology using SERS, with "OFF-to-ON" signal switch upon nucleic acid target identification and capture, which provides high sensitivity and specificity for single nucleotide mismatch discrimination. This new technology will be most welcomed in clinical diagnostics. Copyright © 2015 Elsevier Inc. All rights reserved.

  17. Selective detection of sub-atto-molar Streptavidin in 10(13)-fold impure sample using photonic crystal nanolaser sensors.

    Science.gov (United States)

    Hachuda, Shoji; Otsuka, Shota; Kita, Shota; Isono, Toshinari; Narimatsu, Michimasa; Watanabe, Keisuke; Goshima, Yoshio; Baba, Toshihiko

    2013-05-20

    Biosensors selectively detecting a very small amount of biomarker protein in human blood are desired for early and reliable diagnoses of severe diseases. This paper reports the detection of protein (streptavidin: SA) in ultra-low concentration, with an ultra-high selectivity against contaminants, using photonic crystal nanolasers. For biotin-modified nanolasers in pure water with SA, an extremely-low detection limit of 16 zM is evaluated. Even in a mixture with 1 μM bovine serum albumin as the contaminant, 100 zM SA is detected, meaning a selectivity of 10(13). These are remarkable capabilities that are promising for practical biosensing in the medical applications mentioned above.

  18. Evolutionary relationship between 5+5 and 7+7 inverted repeat folds within the amino acid-polyamine-organocation superfamily.

    Science.gov (United States)

    Västermark, Åke; Saier, Milton H

    2014-02-01

    Evidence has been presented that 5+5 TMS and 7+7 TMS inverted repeat fold transporters are members of a single superfamily named the Amino acid-Polyamine-organoCation (APC) superfamily. However, the evolutionary relationship between the 5+5 and the 7+7 topological types has not been established. We have identified a common fold, consisting of a spiny membrane helix/sheet, followed by a U-like structure and a V-like structure that is recurrent between domain duplicated units of 5+5 and 7+7 inverted repeat folds. This fold is found in the following protein structures: AdiC, ApcT, LeuT, Mhp1, BetP, CaiT, and SglT (all 5+5 TMS repeats), as well as UraA and SulP (7+7 TMS repeats). AdiC, LeuT and Mhp1 have two extra TMSs after the second duplicated domain, SglT has four extra C-terminal TMSs, and BetP has two extra TMSs before the first duplicated domain. UraA and SulP on the other hand have two extra TMSs at the N-terminus of each duplicated domain unit. These observations imply that multiple hairpin and domain duplication events occurred during the evolution of the APC superfamily. We suggest that the five TMS architecture was primordial and that families gained two TMSs on either side of this basic structure via dissimilar hairpin duplications either before or after intragenic duplication. Evidence for homology between TMSs 1-2 of AdiC and TMSs 1-2 and 3-4 of UraA suggests that the 7+7 topology arose via an internal duplication of the N-terminal hairpin loop within the five TMS repeat unit followed by duplication of the 7 TMS domain.

  19. Integrated sample-to-detection chip for nucleic acid test assays.

    Science.gov (United States)

    Prakash, R; Pabbaraju, K; Wong, S; Tellier, R; Kaler, K V I S

    2016-06-01

    Nucleic acid based diagnostic techniques are routinely used for the detection of infectious agents. Most of these assays rely on nucleic acid extraction platforms for the extraction and purification of nucleic acids and a separate real-time PCR platform for quantitative nucleic acid amplification tests (NATs). Several microfluidic lab on chip (LOC) technologies have been developed, where mechanical and chemical methods are used for the extraction and purification of nucleic acids. Microfluidic technologies have also been effectively utilized for chip based real-time PCR assays. However, there are few examples of microfluidic systems which have successfully integrated these two key processes. In this study, we have implemented an electro-actuation based LOC micro-device that leverages multi-frequency actuation of samples and reagents droplets for chip based nucleic acid extraction and real-time, reverse transcription (RT) PCR (qRT-PCR) amplification from clinical samples. Our prototype micro-device combines chemical lysis with electric field assisted isolation of nucleic acid in a four channel parallel processing scheme. Furthermore, a four channel parallel qRT-PCR amplification and detection assay is integrated to deliver the sample-to-detection NAT chip. The NAT chip combines dielectrophoresis and electrostatic/electrowetting actuation methods with resistive micro-heaters and temperature sensors to perform chip based integrated NATs. The two chip modules have been validated using different panels of clinical samples and their performance compared with standard platforms. This study has established that our integrated NAT chip system has a sensitivity and specificity comparable to that of the standard platforms while providing up to 10 fold reduction in sample/reagent volumes.

  20. Metal-ion rescue revisited: biochemical detection of site-bound metal ions important for RNA folding.

    Science.gov (United States)

    Frederiksen, John K; Li, Nan-Sheng; Das, Rhiju; Herschlag, Daniel; Piccirilli, Joseph A

    2012-06-01

    Within the three-dimensional architectures of RNA molecules, divalent metal ions populate specific locations, shedding their water molecules to form chelates. These interactions help the RNA adopt and maintain specific conformations and frequently make essential contributions to function. Defining the locations of these site-bound metal ions remains challenging despite the growing database of RNA structures. Metal-ion rescue experiments have provided a powerful approach to identify and distinguish catalytic metal ions within RNA active sites, but the ability of such experiments to identify metal ions that contribute to tertiary structure acquisition and structural stability is less developed and has been challenged. Herein, we use the well-defined P4-P6 RNA domain of the Tetrahymena group I intron to reevaluate prior evidence against the discriminatory power of metal-ion rescue experiments and to advance thermodynamic descriptions necessary for interpreting these experiments. The approach successfully identifies ligands within the RNA that occupy the inner coordination sphere of divalent metal ions and distinguishes them from ligands that occupy the outer coordination sphere. Our results underscore the importance of obtaining complete folding isotherms and establishing and evaluating thermodynamic models in order to draw conclusions from metal-ion rescue experiments. These results establish metal-ion rescue as a rigorous tool for identifying and dissecting energetically important metal-ion interactions in RNAs that are noncatalytic but critical for RNA tertiary structure.

  1. Nucleic Acid-Based Approaches for Detection of Viral Hepatitis

    OpenAIRE

    BEHZADI, Payam; Ranjbar, Reza; Alavian, Seyed Moayed

    2014-01-01

    Context: To determining suitable nucleic acid diagnostics for individual viral hepatitis agent, an extensive search using related keywords was done in major medical library and data were collected, categorized, and summarized in different sections. Results: Various types of molecular biology tools can be used to detect and quantify viral genomic elements and analyze the sequences. These molecular assays are proper technologies for rapidly detecting viral agents with high accuracy, high sensit...

  2. Induced Folding Under Membrane Mimetic and Acidic Conditions Implies Undiscovered Biological Roles of Prokaryotic Ubiquitin-Like Protein Pup.

    Science.gov (United States)

    Ye, Kaiqin; Tu, Xiaoming; Zhang, Xuecheng; Shang, Qiang; Liao, Shanhui; Yu, Jigang; Zhang, Jiahai

    2016-01-01

    Ubiquitin-like proteins play important roles in diverse biological processes. In Mycobacterium tuberculosis, Pup (prokaryotic ubiquitin-like protein), a functional homologue of eukaryotic ubiquitin, interacts with the proteasome ATPase subunit Mpa to recognize and unfold substrates, and then translocate them into the proteasome core for degradation. Previous studies revealed that, Pup, an intrinsically disordered protein (IDP), adopts a helical structure upon binding to the N-terminal coiled-coil domain of Mpa, at its disordered C-terminal region. In the present study, using circular dichroism (CD), surface plasmon resonance (SPR) and nuclear magnetic resonance (NMR), we show that membrane mimetic and acidic conditions also induce Pup to adopt helical conformations. Moreover, at low pH, Pup, via both of its N- and C-terminal regions, binds to Mpa on sites from the N-terminal region in addition to the C-terminal region of the coiled-coil domain. Our results imply Pup may play undiscovered roles in some biological processes e.g. those involve in membrane.

  3. Detecting acid precipitation impacts on lake water quality

    Science.gov (United States)

    Loftis, Jim C.; Taylor, Charles H.

    1989-09-01

    The United States Environmental Protection Agency is planning to expand its long-term monitoring of lakes that are sensitive to acid deposition effects. Effective use of resources will require a careful definition of the statistical objectives of monitoring, a network design which balances spatial and temporal coverage, and a sound approach to data analysis. This study examines the monitoring objective of detecting trends in water quality for individual lakes and small groups of lakes. Appropriate methods of trend analysis are suggested, and the power of trend detection under seasonal (quarterly) sampling is compared to that of annual sampling. The effects of both temporal and spatial correlation on trend detection ability are described.

  4. Fast hybridization solution for the detection of immobilized nucleic acids.

    Science.gov (United States)

    Yang, T T; Kain, S R

    1995-03-01

    We have developed a fast hybridization solution, termed ExpressHyb, for the rapid and sensitive detection of nucleic acids immobilized on membrane supports. This solution reduces typical hybridization times of 12-24 h to as little as 1 h while simultaneously increasing the sensitivity of detection in many applications. Using ExpressHyb, human beta-actin mRNA was detected on a human multiple tissue Northern (MTN) blot following a 30-min hybridization, with optimal detection occurring with a 1-h hybridization interval. The moderately abundant human glyceraldehyde-3-phosphate dehydrogenase (G3PDH) mRNA was detected using similar hybridization conditions and yielded improved signal-to-background characteristics relative to overnight hybridizations in conventional solutions. ExpressHyb can be used with either 32P- or digoxigenin-labeled probes and works effectively with both cDNA and oligonucleotide probes. For non-isotopic detection in particular, ExpressHyb reduces the nonspecific background commonly encountered with this technique. In cDNA library screening, ExpressHyb was found to both reduce the time required for effective hybridizations and to increase the number of positive colonies obtained relative to conventional overnight procedures. Taken together, these results illustrate the broad capability of ExpressHyb Hybridization Solution to improve nucleic acid detection in a variety of important techniques.

  5. X-ray structure of Pur-alpha reveals a Whirly-like fold and an unusual nucleic-acid binding surface.

    Science.gov (United States)

    Graebsch, Almut; Roche, Stéphane; Niessing, Dierk

    2009-11-03

    The PUR protein family is a distinct and highly conserved class that is characterized by its sequence-specific RNA- and DNA-binding. Its best-studied family member, Pur-alpha, acts as a transcriptional regulator, as host factor for viral replication, and as cofactor for mRNP localization in dendrites. Pur-alpha-deficient mice show severe neurologic defects and die after birth. Nucleic-acid binding by Pur-alpha is mediated by its central core region, for which no structural information is available. We determined the x-ray structure of residues 40 to 185 from Drosophila melanogaster Pur-alpha, which constitutes a major part of the core region. We found that this region contains two almost identical structural motifs, termed "PUR repeats," which interact with each other to form a PUR domain. DNA- and RNA-binding studies confirmed that PUR domains are indeed functional nucleic-acid binding domains. Database analysis show that PUR domains share a fold with the Whirly class of nucleic-acid binding proteins. Structural analysis combined with mutational studies suggest that a PUR domain binds nucleic acids through two independent surface regions involving concave beta-sheets. Structure-based sequence alignment revealed that the core region harbors a third PUR repeat at its C terminus. Subsequent characterization by small-angle x-ray scattering (SAXS) and size-exclusion chromatography indicated that PUR repeat III mediates dimerization of Pur-alpha. Surface envelopes calculated from SAXS data show that the Pur-alpha dimer consisting of repeats I to III is arranged in a Z-like shape. This unexpected domain organization of the entire core domain of Pur-alpha has direct implications for ssDNA/ssRNA and dsDNA binding.

  6. Clinical comparison between two hyaluronic acid-derived fillers in the treatment of nasolabial folds in Chinese subjects: BioHyalux versus Restylane.

    Science.gov (United States)

    Wu, Yan; Sun, Nan; Xu, Yue; Liu, Huixian; Zhong, Shaomin; Chen, Liyang; Li, Dong

    2016-04-01

    Hyaluronic acid fillers are used to improve the appearance of nasolabial folds (NLF). This study aimed to compare the efficacy, safety, and durability of a new hyaluronic acid gel (BioHyalux) versus Restylane for the correction of NLF. This was a multicenter, double-blinded, randomized, controlled, non-inferiority clinical trial involving 88 subjects with moderate to severe NLF. Subjects were randomized to BioHyalux and Restylane on either sides of the NLF. NLF was assessed before and right after injection, and at 1 week, 1, 3, and 6 months. Patients were followed up for 13-15 months to evaluate the durability and long-term safety. A clinically meaningful response was predefined as at least one-point improvement on the Wrinkle Severity Rating Scale, which is a five-point scale. At 6 months, the response rate of BioHyalux was not inferior to that of Restylane (P  0.05) at all time points. At 6 months, 100 % reported improvements on both side; at 13-15 months, 60 % of subjects reported improvements with BioHyalux versus 64 % with Restylane. Adverse events were transient and predominantly mild or moderate in severity including injection site swelling, pain, itching, bruising, and tenderness. BioHyalux had reliable safety and tolerance, and could be an effective injectable filler for correcting NLF.

  7. Complex folding and misfolding effects of deer-specific amino acid substitutions in the β2-α2 loop of murine prion protein

    Science.gov (United States)

    Agarwal, Sonya; Döring, Kristina; Gierusz, Leszek A.; Iyer, Pooja; Lane, Fiona M.; Graham, James F.; Goldmann, Wilfred; Pinheiro, Teresa J. T.; Gill, Andrew C.

    2015-10-01

    The β2-α2 loop of PrPC is a key modulator of disease-associated prion protein misfolding. Amino acids that differentiate mouse (Ser169, Asn173) and deer (Asn169, Thr173) PrPC appear to confer dramatically different structural properties in this region and it has been suggested that amino acid sequences associated with structural rigidity of the loop also confer susceptibility to prion disease. Using mouse recombinant PrP, we show that mutating residue 173 from Asn to Thr alters protein stability and misfolding only subtly, whilst changing Ser to Asn at codon 169 causes instability in the protein, promotes oligomer formation and dramatically potentiates fibril formation. The doubly mutated protein exhibits more complex folding and misfolding behaviour than either single mutant, suggestive of differential effects of the β2-α2 loop sequence on both protein stability and on specific misfolding pathways. Molecular dynamics simulation of protein structure suggests a key role for the solvent accessibility of Tyr168 in promoting molecular interactions that may lead to prion protein misfolding. Thus, we conclude that ‘rigidity’ in the β2-α2 loop region of the normal conformer of PrP has less effect on misfolding than other sequence-related effects in this region.

  8. Loop-mediated isothermal amplification for detection of nucleic acids.

    Science.gov (United States)

    Tanner, Nathan A; Evans, Thomas C

    2014-01-06

    Sequence-specific isothermal nucleic acid amplification techniques are ideally suited for use in molecular diagnostic applications because they do not require thermal cycling equipment and the reactions are typically fast. One of the most widely cited isothermal techniques is termed loop-mediated isothermal amplification (LAMP). This protocol allows amplification times as fast as 5 to 10 min. Furthermore, various methodologies to detect amplification have been applied to LAMP to increase its utility for the point-of-care market. Basic LAMP protocols are provided herein for detection of specific DNA and RNA targets, along with a method to perform multiplex LAMP reactions, permitting even greater flexibility from this powerful technique.

  9. Developing nucleic acid-based electrical detection systems

    OpenAIRE

    Gabig-Ciminska Magdalena

    2006-01-01

    Abstract Development of nucleic acid-based detection systems is the main focus of many research groups and high technology companies. The enormous work done in this field is particularly due to the broad versatility and variety of these sensing devices. From optical to electrical systems, from label-dependent to label-free approaches, from single to multi-analyte and array formats, this wide range of possibilities makes the research field very diversified and competitive. New challenges and r...

  10. Developing nucleic acid-based electrical detection systems

    OpenAIRE

    Gabig-Ciminska Magdalena

    2006-01-01

    Abstract Development of nucleic acid-based detection systems is the main focus of many research groups and high technology companies. The enormous work done in this field is particularly due to the broad versatility and variety of these sensing devices. From optical to electrical systems, from label-dependent to label-free approaches, from single to multi-analyte and array formats, this wide range of possibilities makes the research field very diversified and competitive. New challenges and r...

  11. Nucleic acid sequence detection using multiplexed oligonucleotide PCR

    Science.gov (United States)

    Nolan, John P.; White, P. Scott

    2006-12-26

    Methods for rapidly detecting single or multiple sequence alleles in a sample nucleic acid are described. Provided are all of the oligonucleotide pairs capable of annealing specifically to a target allele and discriminating among possible sequences thereof, and ligating to each other to form an oligonucleotide complex when a particular sequence feature is present (or, alternatively, absent) in the sample nucleic acid. The design of each oligonucleotide pair permits the subsequent high-level PCR amplification of a specific amplicon when the oligonucleotide complex is formed, but not when the oligonucleotide complex is not formed. The presence or absence of the specific amplicon is used to detect the allele. Detection of the specific amplicon may be achieved using a variety of methods well known in the art, including without limitation, oligonucleotide capture onto DNA chips or microarrays, oligonucleotide capture onto beads or microspheres, electrophoresis, and mass spectrometry. Various labels and address-capture tags may be employed in the amplicon detection step of multiplexed assays, as further described herein.

  12. Photodynamic Detection of Peritoneal Metastases Using 5-Aminolevulinic Acid (ALA

    Directory of Open Access Journals (Sweden)

    Yutaka Yonemura

    2017-03-01

    Full Text Available In the past, peritoneal metastasis (PM was considered as a terminal stage of cancer. From the early 1990s, however, a new comprehensive treatment consisting of cytoreductive surgery and perioperative chemotherapy has been established to improve long-term survival for selected patients with PM. Among prognostic indicators after the treatment, completeness of cytoreduction is the most independent predictors of survival. However, peritoneal recurrence is a main cause of recurrence, even after complete cytoreduction. As a cause of peritoneal recurrence, small PM may be overlooked at the time of cytoreductive surgery (CRS, therefore, development of a new method to detect small PM is desired. Recently, photodynamic diagnosis (PDD was developed for detection of PM. The objectives of this review were to evaluate whether PDD using 5-aminolevulinic acid (ALA could improve detection of small PM.

  13. The structure of a purple acid phosphatase involved in plant growth and pathogen defence exhibits a novel immunoglobulin-like fold

    Directory of Open Access Journals (Sweden)

    Svetlana Vladimirovna Antonyuk

    2014-03-01

    Full Text Available Phosphatases function in the production, transport and recycling of inorganic phosphorus, which is crucial for cellular metabolism and bioenergetics, as well as in bacterial killing, since they are able to generate reactive oxygen species via Fenton chemistry. Diphosphonucleotide phosphatase/phosphodiesterase (PPD1, a glycoprotein plant purple acid phosphatase (PAP from yellow lupin seeds, contains a bimetallic Fe–Mn catalytic site which is most active at acidic pH. Unlike other plant PAPs, PPD1 cleaves the pyrophosphate bond in diphosphonucleotides and the phosphodiester bond in various phosphodiesters. The homohexameric organization of PPD1, as revealed by a 1.65 Å resolution crystal structure and confirmed by solution X-ray scattering, is unique among plant PAPs, for which only homodimers have previously been reported. A phosphate anion is bound in a bidentate fashion at the active site, bridging the Fe and Mn atoms in a binding mode similar to that previously reported for sweet potato PAP, which suggests that common features occur in their catalytic mechanisms. The N-terminal domain of PPD1 has an unexpected and unique fibronectin type III-like fold that is absent in other plant PAPs. Here, the in vitro DNA-cleavage activity of PPD1 is demonstrated and it is proposed that the fibronectin III-like domain, which `overhangs' the active site, is involved in DNA selectivity, binding and activation. The degradation of DNA by PPD1 implies a role for PPD1 in plant growth and repair and in pathogen defence.

  14. Detection of biologically active diterpenoic acids by Raman Spectroscopy

    DEFF Research Database (Denmark)

    Talian, Ivan; Orinak, Andrej; Efremov, Evtim V.

    2010-01-01

    Three poorly detectable, biologically active diterpenoic acids, kaurenoic, abietic, and gibberellic acid, were studied by using different modes of Raman spectroscopy. Because of their structural similarities, in the absence of strongly polarizable groups, conventional Raman spectroscopy...... is not suitable for their unambiguous identification, especially not in solution. We attempted to increase the sensitivity by applying UV-resonance Raman spectroscopy and surface-enhanced Raman spectroscopy (SERS) techniques. The UV-Raman spectra of the three compounds in ethanol/water 50 : 50 showed only very...... few enhanced Raman lines. SERS spectra with 514-nm excitation with Ag colloids were also relatively weak. The best SERS spectrawere obtained with 785-nm excitation on a novel nanostructured substrate, 'black silicon' coated with a 400-nm gold layer. The spectra showed clear differences...

  15. Conformational Transition of Poly (Acrylic Acid) Detected by Microcantilever Sensing

    Institute of Scientific and Technical Information of China (English)

    LI Kai; LIU Hong; ZHANG Qing-Chuan; XUE Chang-Guo; WU Xiao-Ping

    2007-01-01

    Poly (acrylic acid) (PAA) chains are grafted on one side of a microcantilever by the self-assembled method and the deflections of the microcantilever are detected as a function of medium pH from 3 to 11. It is found that when the pH varies, the microcantilever deflects because of the changing surface stress. By analysing the electrostatic repulsive effect, the surface stress change is related to the conformation transition of PAA from a collapse state to a swelling state. This method offers the interaction information among the polymer chains during the conformational transition and affords an alternative way to study conformational change of polymers.

  16. Methodology for detecting residual phosphoric acid in polybenzoxazole fibers.

    Science.gov (United States)

    Park, Eun Su; Sieber, John; Guttman, Charles; Rice, Kirk; Flynn, Kathleen; Watson, Stephanie; Holmes, Gale

    2009-12-01

    Because of the premature failure of in-service soft-body armor containing the ballistic fiber poly[(benzo-[1,2-d:5,4-d']-benzoxazole-2,6-diyl)-1,4-phenylene] (PBO), the Office of Law Enforcement Standards (OLES) at the National Institute of Standards and Technology (NIST) initiated a research program to investigate the reasons for this failure and to develop testing methodologies and protocols to ensure that these types of failures do not reoccur. In a report that focused on the stability of the benzoxazole ring that is characteristic of PBO fibers, Holmes, G. A.; Rice, K.; Snyder, C. R. J. Mater. Sci. 2006, 41, 4105-4116, showed that the benzoxazole ring was susceptible to hydrolytic degradation under acid conditions. Because of the processing conditions for the fibers, it is suspected by many researchers that residual phosphoric acid may cause degradation of the benzoxazole ring resulting in a reduction of ballistic performance. Prior to this work, no definitive data have indicated the presence of phosphoric acid since the residual phosphorus is not easily extracted and the processed fibers are known to incorporate phosphorus containing processing aids. Methods to efficiently extract phosphorus from PBO are described in this article. Further, characterization determined that the majority of the extractable phosphorus in PBO was attributed to the octyldecyl phosphate processing aid with some phosphoric acid being detected. Analysis by matrix assisted laser desorption ionization of model PBO oligomers indicates that the nonextractable phosphorus is attached to the PBO polymer chain as a monoaryl phosphate ester. The response of model aryl phosphates to NaOH exposure indicates that monoaryl phosphate ester is stable to NaOH washes used in the manufacturing process to neutralize the phosphoric acid reaction medium and to extract residual phosphorus impurities.

  17. Detection of formaldehyde in textiles by chromotropic acid method

    Directory of Open Access Journals (Sweden)

    Rao Sanath

    2004-11-01

    Full Text Available BACKGROUND: The common causes of textile dermatitis are formaldehyde resins and disperse dyes. There are various methods to detect the presence of formaldehyde in clothing. AIM: To detect the presence of formaldehyde in various types of textiles by the chromotropic acid method and to assess the effect of washing on the formaldehyde content. METHODS: Twenty randomly selected textiles from a local cloth store were tested for formaldehyde by the chromotropic acid method. A purple ring indicated a positive reaction. The intensity of the purple ring was graded from 1+ to 3+ and reassessed after washing the clothes. RESULTS: Eleven out of the 20 textiles tested positive for formaldehyde. The fully synthetic clothes were free from formaldehyde. After the first and second washes the majority did not show a reduction in the formaldehyde content. CONCLUSIONS: This is a simple and rapid test which can be used in the practical management of patients with textile allergy. Washing the clothes may not have an effect on the formaldehyde content.

  18. HMMerThread: detecting remote, functional conserved domains in entire genomes by combining relaxed sequence-database searches with fold recognition.

    Directory of Open Access Journals (Sweden)

    Charles Richard Bradshaw

    Full Text Available Conserved domains in proteins are one of the major sources of functional information for experimental design and genome-level annotation. Though search tools for conserved domain databases such as Hidden Markov Models (HMMs are sensitive in detecting conserved domains in proteins when they share sufficient sequence similarity, they tend to miss more divergent family members, as they lack a reliable statistical framework for the detection of low sequence similarity. We have developed a greatly improved HMMerThread algorithm that can detect remotely conserved domains in highly divergent sequences. HMMerThread combines relaxed conserved domain searches with fold recognition to eliminate false positive, sequence-based identifications. With an accuracy of 90%, our software is able to automatically predict highly divergent members of conserved domain families with an associated 3-dimensional structure. We give additional confidence to our predictions by validation across species. We have run HMMerThread searches on eight proteomes including human and present a rich resource of remotely conserved domains, which adds significantly to the functional annotation of entire proteomes. We find ∼4500 cross-species validated, remotely conserved domain predictions in the human proteome alone. As an example, we find a DNA-binding domain in the C-terminal part of the A-kinase anchor protein 10 (AKAP10, a PKA adaptor that has been implicated in cardiac arrhythmias and premature cardiac death, which upon stress likely translocates from mitochondria to the nucleus/nucleolus. Based on our prediction, we propose that with this HLH-domain, AKAP10 is involved in the transcriptional control of stress response. Further remotely conserved domains we discuss are examples from areas such as sporulation, chromosome segregation and signalling during immune response. The HMMerThread algorithm is able to automatically detect the presence of remotely conserved domains in

  19. Electrochemical microfluidic biosensor for the detection of nucleic acid sequences.

    Science.gov (United States)

    Goral, Vasiliy N; Zaytseva, Natalya V; Baeumner, Antje J

    2006-03-01

    A microfluidic biosensor with electrochemical detection for the quantification of nucleic acid sequences was developed. In contrast to most microbiosensors that are based on fluorescence for signal generation, it takes advantage of the simplicity and high sensitivity provided by an amperometric and coulorimetric detection system. An interdigitated ultramicroelectrode array (IDUA) was fabricated in a glass chip and integrated directly with microchannels made of poly(dimethylsiloxane) (PDMS). The assembly was packaged into a Plexiglas housing providing fluid and electrical connections. IDUAs were characterized amperometrically and using cyclic voltammetry with respect to static and dynamic responses for the presence of a reversible redox couple-potassium hexacyanoferrate (ii)/hexacyanoferrate (iii) (ferri/ferrocyanide). A combined concentration of 0.5 microM of ferro/ferricyanide was determined as lower limit of detection with a dynamic range of 5 orders of magnitude. Background signals were negligible and the IDUA responded in a highly reversible manner to the injection of various volumes and various concentrations of the electrochemical marker. For the detection of nucleic acid sequences, liposomes entrapping the electrochemical marker were tagged with a DNA probe, and superparamagnetic beads were coated with a second DNA probe. A single stranded DNA target sequence hybridized with both probes. The sandwich was captured in the microfluidic channel just upstream of the IDUA via a magnet located in the outside housing. Liposomes were lysed using a detergent and the amount of released ferro/ferricyanide was quantified while passing by the IDUA. Optimal location of the magnet with respect to the IDUA was investigated, the effect of dextran sulfate on the hybridization reaction was studied and the amount of magnetic beads used in the assay was optimized. A dose response curve using varying concentrations of target DNA molecules was carried out demonstrating a limit of

  20. Detecting coevolving amino acid sites using Bayesian mutational mapping

    DEFF Research Database (Denmark)

    Dimmic, Matthew W.; Hubisz, Melissa J.; Bustamente, Carlos D.

    2005-01-01

    Motivation: The evolution of protein sequences is constrained by complex interactions between amino acid residues. Because harmful substitutions may be compensated for by other substitutions at neighboring sites, residues can coevolve. We describe a Bayesian phylogenetic approach to the detection...... of coevolving residues in protein families. This method, Bayesian mutational mapping (BMM), assigns mutations to the branches of the evolutionary tree stochastically, and then test statistics are calculated to determine whether a coevolutionary signal exists in the mapping. Posterior predictive P-values provide...... of eukaryotic proteins from the phosphoglycerate kinase (PGK) family, interdomain site contacts yield a significantly greater coevolutionary signal than interdomain non-contacts, an indication that the method provides information about interacting sites. Failure to account for the heterogeneity in rates across...

  1. Detect and exploit hidden structure in fatty acid signature data

    Science.gov (United States)

    Budge, Suzanne; Bromaghin, Jeffrey; Thiemann, Gregory

    2017-01-01

    Estimates of predator diet composition are essential to our understanding of their ecology. Although several methods of estimating diet are practiced, methods based on biomarkers have become increasingly common. Quantitative fatty acid signature analysis (QFASA) is a popular method that continues to be refined and extended. Quantitative fatty acid signature analysis is based on differences in the signatures of prey types, often species, which are recognized and designated by investigators. Similarly, predator signatures may be structured by known factors such as sex or age class, and the season or region of sample collection. The recognized structure in signature data inherently influences QFASA results in important and typically beneficial ways. However, predator and prey signatures may contain additional, hidden structure that investigators either choose not to incorporate into an analysis or of which they are unaware, being caused by unknown ecological mechanisms. Hidden structure also influences QFASA results, most often negatively. We developed a new method to explore signature data for hidden structure, called divisive magnetic clustering (DIMAC). Our DIMAC approach is based on the same distance measure used in diet estimation, closely linking methods of data exploration and parameter estimation, and it does not require data transformation or distributional assumptions, as do many multivariate ordination methods in common use. We investigated the potential benefits of the DIMAC method to detect and subsequently exploit hidden structure in signature data using two prey signature libraries with quite different characteristics. We found that the existence of hidden structure in prey signatures can increase the confusion between prey types and thereby reduce the accuracy and precision of QFASA diet estimates. Conversely, the detection and exploitation of hidden structure represent a potential opportunity to improve predator diet estimates and may lead to new

  2. A split-face comparison of a new hyaluronic acid facial filler containing pre-incorporated lidocaine versus a standard hyaluronic acid facial filler in the treatment of naso-labial folds.

    Science.gov (United States)

    Levy, Phillip M; De Boulle, Koenraad; Raspaldo, Herve

    2009-09-01

    This split-face, single-blind study compared the comfort and ease of injection of a new hyaluronic acid facial filler containing pre-incorporated lidocaine (Juvederm ULTRA 3) versus the established hyaluronic acid facial filler Restylane-Perlane. A total of 126 individuals were treated with both products, randomly assigned to the right or left naso-labial fold. Injector assessment-indicated mean injection pain, pain of massaging the injected area and post-injection discomfort (based on a scale of 0=no pain to 10=extreme pain) were 2.1, 0.9 and 0.4 for Juvederm ULTRA 3, and 4.1, 3.3 and 1.7 for Restylane-Perlane, respectively (p<0.0001). Patient assessment of the same parameters were 2.8, 1.3 and 0.4 for Juvederm ULTRA 3, and 4.9, 3.6 and 1.8 for Restylane-Perlane (p<0.0001). Injectors indicated that 92% of Juvederm ULTRA 3 injections were 'very easy', compared with 21% for Restylane-Perlane. Post-treatment smoothness was comparable, but 95% of individuals preferred Juvederm ULTRA 3 for overall injection comfort. A total of 95% of individuals indicated that Juvederm ULTRA 3 was a more comfortable and gentle experience.

  3. Covering folded shapes

    Directory of Open Access Journals (Sweden)

    Oswin Aichholzer

    2014-05-01

    Full Text Available Can folding a piece of paper flat make it larger? We explore whether a shape S must be scaled to cover a flat-folded copy of itself. We consider both single folds and arbitrary folds (continuous piecewise isometries \\(S\\to\\mathbb{R}^2\\. The underlying problem is motivated by computational origami, and is related to other covering and fixturing problems, such as Lebesgue's universal cover problem and force closure grasps. In addition to considering special shapes (squares, equilateral triangles, polygons and disks, we give upper and lower bounds on scale factors for single folds of convex objects and arbitrary folds of simply connected objects.

  4. Mesoscale Modeling of Chromatin Folding

    Science.gov (United States)

    Schlick, Tamar

    2009-03-01

    Eukaryotic chromatin is the fundamental protein/nucleic acid unit that stores the genetic material. Understanding how chromatin fibers fold and unfold in physiological conditions is important for interpreting fundamental biological processes like DNA replication and transcription regulation. Using a mesoscopic model of oligonucleosome chains and tailored sampling protocols, we elucidate the energetics of oligonucleosome folding/unfolding and the role of each histone tail, linker histones, and divalent ions in regulating chromatin structure. The resulting compact topologies reconcile features of the zigzag model with straight linker DNAs with the solenoid model with bent linker DNAs for optimal fiber organization and reveal dynamic and energetic aspects involved.

  5. Sensitive monitoring of humic acid in various aquatic environments with acidic cerium chemiluminescence detection.

    Science.gov (United States)

    Cheng, Xianglei; Zhao, Lixia; Wang, Xu; Lin, Jin-Ming

    2007-10-01

    In this research, a simple, sensitive chemiluminescence (CL) method for the determination of humic acid (HA) in water samples was first developed based on the redox reaction between humic acid and cerium(IV) in the acidic condition. Different with the former redox CL reaction which occurred in alkaline solution, no enhancers were needed and neither precipitation nor a second contamination would occur in the present CL system. Comparing with other spectrometric methods, we find that the proposed analysis system had better applicability and accuracy. Under the optimal experiment conditions, the CL peak height was linear with the concentration of HA in the range of 0.03 to 10.0 microg mL(-1). The detection limit is 0.01 microg mL(-1) (S/N = 3), and the relative standard deviation was 2.3% for 0.5 microg mL(-1) HA solution with eleven repeated measurements. The present CL method was successfully applied to the determination of HA in tap water, spring water and river water samples with good recovery from 90.0 to 110.0%. A possible CL mechanism was proposed based on the results of UV and fluorescence spectrometry and the CL spectrum of HA. It was speculated that the semi-quinone radicals in the excited state were the emitters.

  6. Fe-nitrilotriacetic acid coordination polymer nanowires: an effective sensing platform for fluorescence-enhanced nucleic acid detection

    Science.gov (United States)

    Zhou, Yunchun; Liu, Qian; Sun, Xuping; Kong, Rongmei

    2017-02-01

    The determination of specific nucleic acid sequences is key in identifying disease-causing pathogens and genetic diseases. In this paper we report the utilization of Fe-nitrilotriacetic acid coordination polymer nanowires as an effective nanoquencher for fluorescence-enhanced nucleic acid detection. The detection is fast and the whole process can be completed within 15 min. This nanosensor shows a low detection limit of 0.2 nM with selectivity down to single-base mismatch. This work provides us with an attractive sensing platform for applications.

  7. Label-free amino acid detection based on nanocomposites of graphene oxide hybridized with gold nanoparticles.

    Science.gov (United States)

    Zhang, Qian; Zhang, Diming; Lu, Yanli; Xu, Gang; Yao, Yao; Li, Shuang; Liu, Qingjun

    2016-03-15

    Nanocomposites of graphene oxide and gold nanoparticles (GO/GNPs) were synthesized for label-free detections of amino acids. Interactions between the composites and amino acids were investigated by both naked-eye observation and optical absorption spectroscopy. The GO/GNPs composites displayed apparent color changes and absorption spectra changes in presences of amino acids including glutamate, aspartate, and cysteine. The interaction mechanisms of the composites and amino acids were discussed and explored with sulfhydryl groups and non-α-carboxylic groups on the amino acids. Sensing properties of the composites were tested, while pure gold particles were used as the control. The results suggested that the GO/GNPs composites had better linearity and stability in dose-dependent responses to the amino acids than those of the particles, especially in detections for acidic amino acids. Therefore, the nanocomposites platform can provide a convenient and efficient approach for label-free optical detections of important molecules such as amino acids.

  8. Origami - Folded Plate Structures

    OpenAIRE

    Buri, Hans Ulrich

    2010-01-01

    This research investigates new methods of designing folded plate structures that can be built with cross-laminated timber panels. Folded plate structures are attractive to both architects and engineers for their structural, spatial, and plastic qualities. Thin surfaces can be stiffened by a series of folds, and thus not only cover space, but also act as load bearing elements. The variation of light and shadow along the folded faces emphasizes the plas...

  9. The Folded t Distribution

    OpenAIRE

    Psarakis, Stelios; Panaretos, John

    1990-01-01

    Measurements are frequently recorder without their algebraic sign. As a consequence the underlying distribution of measurements is replaced by a distribution of absolute measurements. When the underlying distribution is t the resulting distribution is called the “folded-t distribution”. Here we study this distribution, we find the relationship between the folded-t distribution and a special case of the folded normal distribution and we derive relationships of the folded-t distribution to othe...

  10. MODELS OF PROTEIN FOLDING

    Directory of Open Access Journals (Sweden)

    Unnati Ahluwalia

    2012-12-01

    Full Text Available In an attempt to explore the understanding of protein folding mechanism, various models have been proposed in the literature. Advances in recent experimental and computational techniques rationalized our understanding on some of the fundamental features of the protein folding pathways. The goal of this review is to revisit the various models and outline the essential aspects of the folding reaction.

  11. Detection of target DNA using fluorescent cationic polymer and peptide nucleic acid probes on solid support

    Directory of Open Access Journals (Sweden)

    Leclerc Mario

    2005-04-01

    Full Text Available Abstract Background Nucleic acids detection using microarrays requires labelling of target nucleic acids with fluorophores or other reporter molecules prior to hybridization. Results Using surface-bound peptide nucleic acids (PNA probes and soluble fluorescent cationic polythiophenes, we show a simple and sensitive electrostatic approach to detect and identify unlabelled target nucleic acid on microarray. Conclusion This simple methodology opens exciting possibilities for applied genetic analysis for the diagnosis of infections, identification of genetic mutations, and forensic inquiries. This electrostatic strategy could also be used with other nucleic acid detection methods such as electrochemistry, silver staining, metallization, quantum dots, or electrochemical dyes.

  12. A novel nanocomposites sensor for epinephrine detection in the presence of uric acids and ascorbic acids

    Energy Technology Data Exchange (ETDEWEB)

    Lu Xiaoquan, E-mail: luxq@nwnu.edu.cn [Key Laboratory of Bioelectrochemistry and Environmental Analysis of Gansu Province, College of Chemistry and Chemical Engineering, Northwest Normal University, LanZhou, 730070 (China); Li Yaya; Du Jie; Zhou Xibin; Xue Zhonghua; Liu Xiuhui; Wang Zhihua [Key Laboratory of Bioelectrochemistry and Environmental Analysis of Gansu Province, College of Chemistry and Chemical Engineering, Northwest Normal University, LanZhou, 730070 (China)

    2011-08-30

    Highlights: {center_dot} A novel PPy/AuNPs/SWCNTs nanomaterials biosensor was prepared to the selective determination of EP. {center_dot} The methods we employed to prepare PPy/AuNPs/SWCNTs nanomaterials are extremely simple. {center_dot} The PPy/AuNPs/SWCNTs nanocomposites biosensor we got from the results of experiments can totally eliminate the interference from AA and distinguish EP from UA. - Abstract: A novel nanocomposites film of conducting polymers including single-walled carbon nanotubes (SWCNTs), polypyrrole (PPy) and gold nanoparticles (AuNPs) modified electrode has been applied in voltammetric sensors to detect epinephrine (EP) sensitively when ascorbic acids (AA) and uric acids (UA) exist. The nanocomposites film of conducting polymers which show an excellent electrocatalystic activity for the oxidation of EP and UA was characterized by scanning electron microscopy (SEM) and electrochemical methods. The catalytic peak currents obtained from differential pulse voltammetry (DPV) increased linearly with increasing EP concentrations in the range of 4.0 x 10{sup -9}-1.0 x 10{sup -7} M with a detection limit of 2.0 x 10{sup -9} M (S/N = 3), respectively. The results showed that the nanocomposites of conducting polymers can selectively determine EP in the coexistence of a large amount of UA and AA. In addition, the sensor exhibited excellent sensitivity, selectivity and stability. The PPy/AuNPs/SWCNTs nanocomposites film can also be satisfactorily used for detecting EP in epinephrine hydrochloride injection when contain AA and UA, which also shows good recovery for determination of EP in some biological fluids.

  13. Electrochemistry of folded graphene edges.

    Science.gov (United States)

    Ambrosi, Adriano; Bonanni, Alessandra; Pumera, Martin

    2011-05-01

    There is enormous interest in the investigation of electron transfer rates at the edges of graphene due to possible energy storage and sensing applications. While electrochemistry at the edges and the basal plane of graphene has been studied in the past, the new frontier is the electrochemistry of folded graphene edges. Here we describe the electrochemistry of folded graphene edges and compare it to that of open graphene edges. The materials were characterized in detail by high-resolution transmission electron microscopy, Raman spectroscopy, high-resolution X-ray photoelectron spectroscopy, electrochemical impedance spectroscopy and cyclic voltammetry. We found that the heterogeneous electron transfer rate is significantly lower on folded graphene edges compared to open edge sites for ferro/ferricyanide, and that electrochemical properties of open edges offer lower potential detection of biomarkers than the folded ones. It is apparent, therefore, that for sensing and biosensing applications the folded edges are less active than open edges, which should then be preferred for such applications. As folded edges are the product of thermal treatment of multilayer graphene, such thermal procedures should be avoided when fabricating graphene for electrochemical applications.

  14. Simultaneous detection of seven phenolic acids in Danshen injection using HPLC with ultraviolet detector

    Institute of Scientific and Technical Information of China (English)

    Jin-zhong XU; Jie SHEN; Yi-yu CHENG; Hai-bin QU

    2008-01-01

    A high-performance liquid chromatographic (HPLC) method with ultraviolet (UV) detector had been developed for simultaneous quantification of danshensu, protocatechuie aldehyde, caffeic acid, salvianolic acid D, rosmarinic acid, salvianolic acid B and salvianolic acid A in Danshen injection. According to the UV spectra of these components, three detection wavelengths have been selected as follows: 280 nm for danshensu and protocatechuic aldehyde, 326 nm for caffeic acid, salvianolic acid D and rosmarinic acid, 286 nm for salvianolic acid B and salvianolic acid A. The limit of detection (LOD) was improved to be in the range of 0.008~0.160 μg/ml. Moreover, excellent linear behavior over the investigated concentration range was observed, with R>0.999 for all the analytes.

  15. Structure-property study of the Raman spectroscopy detection of fusaric acid and analogs

    Science.gov (United States)

    Food security can benefit from the development of selective methods to detect toxins. Fusaric acid is a mycotoxin produced by certain fungi occasionally found in agricultural commodities. Raman spectroscopy allows selective detection of analytes associated with certain spectral characteristics relat...

  16. Detecting to secret folded composite lamina package pairs in cores related slump dump structures and seismites with high resolution sampling of physical parameters

    Science.gov (United States)

    Acar, Dursun; Cagatay, Namik; Feray Meydan, Aysegul; Eris, Kadir; Sari, Erol; Akcer, Sena; Makaroglu, Ozlem; Alkislar, Hakan; Biltekin, Demet; Nagehan Arslan, Tugce

    2016-04-01

    The core retrieved from Lake Van consists of seismites that were possibly deposited during the earthquakes around the Van region. Deformed parts of the core sediments display folded laminations that can be attributed to seismites. The problem arises that if the fold axis is deposited perpendicular to the liner and, if the hinge line is far enough, describing the true laminations might be impossible related to real age of basin evolution because extra laminae seem deposited to the area. Scientist must pay attention such problem that dating method like varve counting and basin evolution estimates can totally change due to extra laminae that explained before. For eliminate to wrong interpretations considering reversal reflected anomalies even with angularity effects to one package of pair can show significant difference than other symmetric one due to angle of the hinge line or soft sediment deformation. Considering the situation explained, p-wave is not enough to support the idea however; chemical analyses (x-ray florescence), ICP-MS (asdasd) analysis can provide appropriate results to identify laminae that appear on the limbs of the reversed micro folds. New easy designed extra U-Channel drive tray framework prepared by us. U-Channels are prepared well conditioned, saturated enough to well contact between sediment surface and plastic shield of u-channel samples from cores. Physical parameters are measured by Multi sensor core logger (MSCL) with high resolution step ratio fixed to 1mm. At the p- wave and gamma ray results, we observed together stair upwards form and reverse reflected downward data graphics, thus our interpretation of identifying the fold limbs are now visible. We understand that laminae packages are exactly the same. XRF and MSCL are totally supporting to origin of pairs generated after their sedimentation age with mechanical forces. For this reason, in this study, we attended to solve such problem to analyze deformed folded laminations that must be

  17. Using RNA nanoparticles with thermostable motifs and fluorogenic modules for real-time detection of RNA folding and turnover in prokaryotic and eukaryotic cells.

    Science.gov (United States)

    Zhang, Hui; Pi, Fengmei; Shu, Dan; Vieweger, Mario; Guo, Peixuan

    2015-01-01

    RNA nanotechnology is an emerging field at the interface of biochemistry and nanomaterials that shows immense promise for applications in nanomedicines, therapeutics and nanotechnology. Noncoding RNAs, such as siRNA, miRNA, ribozymes, and riboswitches, play important roles in the regulation of cellular processes. They carry out highly specific functions on a compact and efficient footprint. The properties of specificity and small size make them excellent modules in the construction of multifaceted RNA nanoparticles for targeted delivery and therapy. Biological activity of RNA molecules, however, relies on their proper folding. Therefore their thermodynamic and biochemical stability in the cellular environment is critical. Consequently, it is essential to assess global fold and intracellular lifetime of multifaceted RNA nanoparticles to optimize their therapeutic effectiveness. Here, we describe a method to express and assemble stable RNA nanoparticles in cells, and to assess the folding and turnover rate of RNA nanoparticles in vitro as well as in vivo in real time using a thermostable core motif derived from pRNA of bacteriophage Phi29 DNA packaging motor and fluorogenic RNA modules.

  18. Rapid detection method for fusaric acid-producing species of Fusarium by PCR

    Science.gov (United States)

    Fusaric acid is a mycotoxin produced by species of the fungus Fusarium and can act synergistically with other Fusarium toxins. In order to develop a specific detection method for fusaric acid-producing fungus, PCR prim¬ers were designed to amplify FUB10, a transcription factor gene in fusaric acid ...

  19. (S)-1-(4-Dimethylaminophenylcarbonyl)-3-aminopyrrolidine: a derivatization reagent for enantiomeric separation and sensitive detection of chiral carboxylic acids by LC/ESI-MS/MS.

    Science.gov (United States)

    Ogawa, Shoujiro; Tadokoro, Hiroaki; Sato, Maho; Hanawa, Takehisa; Higashi, Tatsuya

    2013-12-01

    A novel derivatization reagent, (S)-1-(4-dimethylaminophenylcarbonyl)-3-aminopyrrolidine (1-DAPAP), was developed for increasing the detection sensitivity and enantiomeric separation of chiral carboxylic acids by liquid chromatography/electrospray ionization-tandem mass spectrometry (LC/ESI-MS/MS). 1-DAPAP reacted with carboxylic acids at room temperature within 5min in the presence of 4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium chloride. The epimerization (racemization) during the derivatization reaction was negligible. The resulting derivatives were highly responsive during the ESI-MS operating in the positive-ion mode and gave a characteristic product ion during the MS/MS, which enabled the sensitive detection using selected reaction monitoring; the detection responses of the 1-DAPAP-derivatives were increased by 10-1100-fold over the intact carboxylic acids and the limits of detection ranged from 0.97 and 5.2fmol on the column. The 1-DAPAP-derivatization was also effective for the enantiomeric separation of chiral carboxylic acids; the resolution values were 1.2-4.3 for the evaluated carboxylic acids. The derivatization procedure was successfully applied to biological sample analyses; the derivatization followed by LC/ESI-MS/MS enabled the separation and detection of trace amounts of ibuprofen and naproxen in human saliva with a simple pretreatment and small sample volume.

  20. Fast protein folding kinetics

    Science.gov (United States)

    Gelman, Hannah; Gruebele, Martin

    2014-01-01

    Fast folding proteins have been a major focus of computational and experimental study because they are accessible to both techniques: they are small and fast enough to be reasonably simulated with current computational power, but have dynamics slow enough to be observed with specially developed experimental techniques. This coupled study of fast folding proteins has provided insight into the mechanisms which allow some proteins to find their native conformation well less than 1 ms and has uncovered examples of theoretically predicted phenomena such as downhill folding. The study of fast folders also informs our understanding of even “slow” folding processes: fast folders are small, relatively simple protein domains and the principles that govern their folding also govern the folding of more complex systems. This review summarizes the major theoretical and experimental techniques used to study fast folding proteins and provides an overview of the major findings of fast folding research. Finally, we examine the themes that have emerged from studying fast folders and briefly summarize their application to protein folding in general as well as some work that is left to do. PMID:24641816

  1. A galaxy of folds.

    Science.gov (United States)

    Alva, Vikram; Remmert, Michael; Biegert, Andreas; Lupas, Andrei N; Söding, Johannes

    2010-01-01

    Many protein classification systems capture homologous relationships by grouping domains into families and superfamilies on the basis of sequence similarity. Superfamilies with similar 3D structures are further grouped into folds. In the absence of discernable sequence similarity, these structural similarities were long thought to have originated independently, by convergent evolution. However, the growth of databases and advances in sequence comparison methods have led to the discovery of many distant evolutionary relationships that transcend the boundaries of superfamilies and folds. To investigate the contributions of convergent versus divergent evolution in the origin of protein folds, we clustered representative domains of known structure by their sequence similarity, treating them as point masses in a virtual 2D space which attract or repel each other depending on their pairwise sequence similarities. As expected, families in the same superfamily form tight clusters. But often, superfamilies of the same fold are linked with each other, suggesting that the entire fold evolved from an ancient prototype. Strikingly, some links connect superfamilies with different folds. They arise from modular peptide fragments of between 20 and 40 residues that co-occur in the connected folds in disparate structural contexts. These may be descendants of an ancestral pool of peptide modules that evolved as cofactors in the RNA world and from which the first folded proteins arose by amplification and recombination. Our galaxy of folds summarizes, in a single image, most known and many yet undescribed homologous relationships between protein superfamilies, providing new insights into the evolution of protein domains.

  2. Uniform chromatographic conditions for quantifying urinary catecholamines, metanephrines, vanillylmandelic acid, 5-hydroxyindoleacetic acid, by liquid chromatography, with electrochemical detection.

    Science.gov (United States)

    Parker, N C; Levtzow, C B; Wright, P W; Woodard, L L; Chapman, J F

    1986-08-01

    Uniform liquid-chromatographic conditions were developed such that we could quantify norepinephrine, epinephrine, normetanephrine, metanephrine, vanillylmandelic acid, and 5-hydroxyindoleacetic acid in urine by using a single mobile phase of monochloroacetic acid and citric acid, 0.1 mol/L each. All compounds were separated on a C18 column and detected electrochemically at a potential of +0.800 V. Optimization of these uniform chromatographic conditions significantly shortens the changeover time required from one assay to another, resulting in a substantial savings of time and cost to the laboratory.

  3. Analysis of hyaluronic acid concentration in rat vocal folds during estral and gravidic puerperal cycles Análise da concentração do ácido hialurônico nas pregas vocais de ratas durante o ciclo estral e ciclo gravídico-puerperal

    OpenAIRE

    José Eduardo de Sá Pedroso; Osíris Camponês do Brasil; João Roberto Maciel Martins; Helena Bociane Nader; Manuel de Jesus Simões

    2009-01-01

    Hormone plays an important role in the larynx. Among other substances, vocal folds contain hyaluronic acid, which tissue concentration may vary according to hormone action. AIM: the objective of this study is to analyze hyaluronic acid concentration in the vocal folds during estral and gravidic-puerperal cycles. MATERIALS AND METHODS: Experimental study. 40 adult rats were divided into two groups. In the first group we used 20 rats to establish the concentration of hyaluronic acid during the ...

  4. Folding RaCe: a robust method for predicting changes in protein folding rates upon point mutations.

    Science.gov (United States)

    Chaudhary, Priyashree; Naganathan, Athi N; Gromiha, M Michael

    2015-07-01

    Protein engineering methods are commonly employed to decipher the folding mechanism of proteins and enzymes. However, such experiments are exceedingly time and resource intensive. It would therefore be advantageous to develop a simple computational tool to predict changes in folding rates upon mutations. Such a method should be able to rapidly provide the sequence position and chemical nature to modulate through mutation, to effect a particular change in rate. This can be of importance in protein folding, function or mechanistic studies. We have developed a robust knowledge-based methodology to predict the changes in folding rates upon mutations formulated from amino and acid properties using multiple linear regression approach. We benchmarked this method against an experimental database of 790 point mutations from 26 two-state proteins. Mutants were first classified according to secondary structure, accessible surface area and position along the primary sequence. Three prime amino acid features eliciting the best relationship with folding rates change were then shortlisted for each class along with an optimized window length. We obtained a self-consistent mean absolute error of 0.36 s(-1) and a mean Pearson correlation coefficient (PCC) of 0.81. Jack-knife test resulted in a MAE of 0.42 s(-1) and a PCC of 0.73. Moreover, our method highlights the importance of outlier(s) detection and studying their implications in the folding mechanism. A web server 'Folding RaCe' has been developed and is available at http://www.iitm.ac.in/bioinfo/proteinfolding/foldingrace.html. gromiha@iitm.ac.in Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  5. Optimization of Chromatographic Conditions for Detecting Ellagic Acid in Pomegranate Peels Using HPLC Method

    Institute of Scientific and Technical Information of China (English)

    2012-01-01

    [Objective] This study aimed to optimize the chromatographic conditions for detecting ellagic acid in pomegranate peels using HPLC method. [Method] By using 0.2 mg/ml ellagic acid standard solution, on the basis of single-factor experiment and orthogonal experiment, chromatographic conditions (mobile phase ratio, flow rate, col- umn temperature) for detecting ellagic acid using HPLC were optimized. Based on the optimal chromatographic conditions, the ellagic acid content in experimental pomegranate peels was determined. [Resull] The optimal chromatographic conditions for detecting ellagic acid in pomegranate peels using HPLC method are: 1.2% phos- phoric acid:acetonitrile=85:15, column temperature of 35 ℃, and flow rate of 1.0 ml/min. The linear regression equation of ellagic acid is: y=2.9e+0.6x+4.4e+5 (FF=9 999). Ac- cording to the standard addition recovery test, the average recovery rate of ellagic acid is 98.20%, and RSD is 0.60%. Under above optimized chromatographic condi- tions, ellagic acid can be well separated from other interfering components in pomegranate peels, with shorter peak time and ideal effect, which is convenient for the detection in production practices. [Conclusion] This study laid the foundation for detecting ellagic acid in pomegranate peels using HPLC method.

  6. On Safe Folding

    NARCIS (Netherlands)

    Bossi, Annalisa; Cocco, Nicoletta; Etalle, Sandro; Bruynooghe, Maurice; Wirsing, Martin

    1993-01-01

    In [3] a general fold operation has been introduced for definite programs wrt computed answer substitution semantics. It differs from the fold operation defined by Tamaki and Sato in [26,25] because its application does not depend on the transformation history. This paper extends the results in [3

  7. Fast protein folding kinetics.

    Science.gov (United States)

    Gelman, Hannah; Gruebele, Martin

    2014-05-01

    Fast-folding proteins have been a major focus of computational and experimental study because they are accessible to both techniques: they are small and fast enough to be reasonably simulated with current computational power, but have dynamics slow enough to be observed with specially developed experimental techniques. This coupled study of fast-folding proteins has provided insight into the mechanisms, which allow some proteins to find their native conformation well fast folders also informs our understanding of even 'slow' folding processes: fast folders are small; relatively simple protein domains and the principles that govern their folding also govern the folding of more complex systems. This review summarizes the major theoretical and experimental techniques used to study fast-folding proteins and provides an overview of the major findings of fast-folding research. Finally, we examine the themes that have emerged from studying fast folders and briefly summarize their application to protein folding in general, as well as some work that is left to do.

  8. Folding by Design

    Science.gov (United States)

    Dodd, Paul; Damasceno, Pablo; Glotzer, Sharon

    2014-03-01

    A form of self-assembly, ``self-folding'' presents an alternative approach to the creation of reconfigurable, responsive materials with applications ranging from robotics to drug design. However, the complexity of interactions present in biological and engineered systems that undergo folding makes it challenging to isolate the main factors controlling their assembly and dis-assembly. Here we use computer simulations of simple, minimalistic self-foldable structures and investigate their stochastic folding process. By dynamically accessing all the states that lead to, or inhibit, successful folding, we show that the mechanisms by which general stochastic systems can achieve their ``native'' structures can be identified and used to design rules for optimized folding propensity. Research supported by the National Science Foundation, Emerging Frontiers in Research and Innovation Award # EFRI-1240264.

  9. Nanopore biosensors for detection of proteins and nucleic acids

    NARCIS (Netherlands)

    Maglia, Giovanni; Soskine, Mikhael

    2014-01-01

    Described herein are nanopore biosensors based on a modified cytolysin protein. The nanopore biosensors accommodate macromoiecules including proteins and nucleic acids, and may additionally comprise ligands with selective binding properties.

  10. Detection of COL III in Parchment by Amino Acid Analysis

    DEFF Research Database (Denmark)

    Vestergaard Poulsen Sommer, Dorte; Larsen, René

    2016-01-01

    Cultural heritage parchments made from the reticular dermis of animals have been subject to studies of deterioration and conservation by amino acid analysis. The reticular dermis contains a varying mixture of collagen I and III (COL I and III). When dealing with the results of the amino acid...... analyses, till now the COL III content has not been taken into account. Based on the available amino acid sequences we present a method for determining the amount of COL III in the reticular dermis of new and historical parchments calculated from the ratio of Ile/Val. We find COL III contents between 7...... and 32 % in new parchments and between 0.2 and 40 % in the historical parchments. This is consistent with results in the literature. The varying content of COL III has a significant influence on the uncertainty of the amino acid analysis. Although we have not found a simple correlation between the COL...

  11. Nanopore biosensors for detection of proteins and nucleic acids

    NARCIS (Netherlands)

    Maglia, Giovanni; Soskine, Mikhael

    2014-01-01

    Described herein are nanopore biosensors based on a modified cytolysin protein. The nanopore biosensors accommodate macromoiecules including proteins and nucleic acids, and may additionally comprise ligands with selective binding properties.

  12. Optical methods for measuring DNA folding

    Science.gov (United States)

    Smith, Adam D.; Ukogu, Obinna A.; Devenica, Luka M.; White, Elizabeth D.; Carter, Ashley R.

    2017-03-01

    One of the most important biological processes is the dynamic folding and unfolding of deoxyribonucleic acid (DNA). The folding process is crucial for DNA to fit within the boundaries of the cell, while the unfolding process is essential for DNA replication and transcription. To accommodate both processes, the cell employs a highly active folding mechanism that has been the subject of intense study over the last few decades. Still, many open questions remain. What are the pathways for folding or unfolding? How does the folding equilibrium shift? And, what is the energy landscape for a particular process? Here, we review these emerging questions and the in vitro, optical methods that have provided answers, introducing the topic for those physicists seeking to step into biology. Specifically, we discuss two iconic experiments for DNA folding, the tethered particle motion (TPM) experiment and the optical tweezers experiment.

  13. Structural features of protein folding nuclei.

    Science.gov (United States)

    Garbuzynskiy, S O; Kondratova, M S

    2008-03-05

    A crucial event of protein folding is the formation of a folding nucleus. We demonstrate the presence of a considerable coincidence between the location of folding nuclei and the location of so-called "root structural motifs", which have unique overall folds and handedness. In the case of proteins with a single root structural motif, the involvement in the formation of a folding nucleus is in average significantly higher for amino acids residues that are in root structural motifs, compared to residues in other parts of the protein. The tests carried out revealed that the observed difference is statistically reliable. Thus, a structural feature that corresponds to the protein folding nucleus is now found.

  14. Applications of Luminex xMAP technology for rapid, high-throughput multiplexed nucleic acid detection.

    Science.gov (United States)

    Dunbar, Sherry A

    2006-01-01

    As we enter the post-genome sequencing era and begin to sift through the enormous amount of genetic information now available, the need for technologies that allow rapid, cost-effective, high-throughput detection of specific nucleic acid sequences becomes apparent. Multiplexing technologies, which allow for simultaneous detection of multiple nucleic acid sequences in a single reaction, can greatly reduce the time, cost and labor associated with single reaction detection technologies. The Luminex xMAP system is a multiplexed microsphere-based suspension array platform capable of analyzing and reporting up to 100 different reactions in a single reaction vessel. This technology provides a new platform for high-throughput nucleic acid detection and is being utilized with increasing frequency. Here we review specific applications of xMAP technology for nucleic acid detection in the areas of single nucleotide polymorphism (SNP) genotyping, genetic disease screening, gene expression profiling, HLA DNA typing and microbial detection. These studies demonstrate the speed, efficiency and utility of xMAP technology for simultaneous, rapid, sensitive and specific nucleic acid detection, and its capability to meet the current and future requirements of the molecular laboratory for high-throughput nucleic acid detection.

  15. Ultrasensitive electrochemical immunosensor based on horseradish peroxidase (HRP)-loaded silica-poly(acrylic acid) brushes for protein biomarker detection.

    Science.gov (United States)

    Zhao, Yan; Zheng, Yiqun; Kong, Rongmei; Xia, Lian; Qu, Fengli

    2016-01-15

    We report an ultrasensitive electrochemical immunosensor designed for the detection of protein biomarkers using horseradish peroxidase (HRP)-loaded silica-poly(acrylic acid) brushes (SiO2-SPAABs) as labels. HRP could be efficiently and stably accommodated in the three-dimensional architecture of the SiO2-SPAABs and the SiO2-SPAABs-HRP exhibited high catalytic performance towards o-phenylenediamine (OPD) oxidation in the presence of H2O2, which resulted in significant differential pulse voltammetric (DPV) response change and color change. Using human IgG (HIgG) as a model analyte, a sandwich-type immunosensor was constructed. In particular, graphene oxide (GO) and SiO2-SPAABs-HRP were used to immobilize capture antibody (Ab1) and bind a layer of detection antibody (Ab2), respectively. The current biosensor exhibited a good linear response of HIgG from 100pg/mL to 100μg/mL with a detection limit of 50pg/mL (S/N=5). The sensitivity was 6.70-fold higher than the conventional enzyme-linked immunosorbent assays. The immunosensor results were validated through the detection of HIgG in serum samples.

  16. Absolute quantitation of proteins by Acid hydrolysis combined with amino Acid detection by mass spectrometry

    DEFF Research Database (Denmark)

    Mirgorodskaya, Olga A; Körner, Roman; Kozmin, Yuri P;

    2012-01-01

    Amino acid analysis is among the most accurate methods for absolute quantification of proteins and peptides. Here, we combine acid hydrolysis with the addition of isotopically labeled standard amino acids and analysis by mass spectrometry for accurate and sensitive protein quantitation...

  17. Detection of COL III in parchment by amino acid analysis.

    Science.gov (United States)

    Sommer, Dorte V P; Larsen, René

    2016-01-01

    Cultural heritage parchments made from the reticular dermis of animals have been subject to studies of deterioration and conservation by amino acid analysis. The reticular dermis contains a varying mixture of collagen I and III (COL I and III). When dealing with the results of the amino acid analyses, till now the COL III content has not been taken into account. Based on the available amino acid sequences, we present a method for determining the amount of COL III in the reticular dermis of new and historical parchments calculated from the ratio of Ile/Val. We find COL III contents between 7 and 32 % in new parchments and between 0.2 and 40 % in the historical parchments. This is consistent with results in the literature. The varying content of COL III has a significant influence on the uncertainty of the amino acid analysis. Although we have not found a simple correlation between the COL III content and the degree of deterioration, our results show that this question must be taken into consideration in future studies of the chemical and physical deterioration of parchment measured by amino acid analysis and other analytical methods.

  18. Selective fluorescent detection of aspartic acid and glutamic acid employing dansyl hydrazine dextran conjugate.

    Science.gov (United States)

    Nasomphan, Weerachai; Tangboriboonrat, Pramuan; Tanapongpipat, Sutipa; Smanmoo, Srung

    2014-01-01

    Highly water soluble polymer (DD) was prepared and evaluated for its fluorescence response towards various amino acids. The polymer consists of dansyl hydrazine unit conjugated into dextran template. The conjugation enhances higher water solubility of dansyl hydrazine moiety. Of screened amino acids, DD exhibited selective fluorescence quenching in the presence of aspartic acid (Asp) and glutamic acid (Glu). A plot of fluorescence intensity change of DD against the concentration of corresponding amino acids gave a good linear relationship in the range of 1 × 10(-4) M to 25 × 10(-3) M. This establishes DD as a potential polymeric sensor for selective sensing of Asp and Glu.

  19. An Optical Test Strip for the Detection of Benzoic Acid in Food

    Directory of Open Access Journals (Sweden)

    Fatimah Abu Bakar

    2011-07-01

    Full Text Available Fabrication of a test strip for detection of benzoic acid was successfully implemented by immobilizing tyrosinase, phenol and 3-methyl-2-benzothiazolinone hydrazone (MBTH onto filter paper using polystyrene as polymeric support. The sensing scheme was based on the decreasing intensity of the maroon colour of the test strip when introduced into benzoic acid solution. The test strip was characterized using optical fiber reflectance and has maximum reflectance at 375 nm. It has shown a highly reproducible measurement of benzoic acid with a calculated RSD of 0.47% (n = 10. The detection was optimized at pH 7. A linear response of the biosensor was obtained in 100 to 700 ppm of benzoic acid with a detection limit (LOD of 73.6 ppm. At 1:1 ratio of benzoic acid to interfering substances, the main interfering substance is boric acid. The kinetic analyses show that, the inhibition of benzoic is competitive inhibitor and the inhibition constant (Ki is 52.9 ppm. The activity of immobilized tyrosinase, phenol, and MBTH in the test strip was fairly sustained during 20 days when stored at 3 °C. The developed test strip was used for detection of benzoic acid in food samples and was observed to have comparable results to the HPLC method, hence the developed test strip can be used as an alternative to HPLC in detecting benzoic acid in food products.

  20. Understanding the folding process of synthetic polymers by small-molecule folding agents

    Indian Academy of Sciences (India)

    S G Ramkumar; S Ramakrishnan

    2008-01-01

    Two acceptor containing polyimides PDI and NDI carrying pyromellitic diimide units and 1,4,5,8-naphthalene tetracarboxy diimide units, respectively, along with hexa(oxyethylene) (EO6) segments as linkers, were prepared from the corresponding dianhydrides and diamines. These polyimides were made to fold by interaction with specifically designed folding agents containing a dialkoxynaphthalene (DAN) donor linked to a carboxylic acid group. The alkali-metal counter-ion of the donor carboxylic acid upon complexation with the EO6 segment brings the DAN unit in the right location to induce a charge-transfer complex formation with acceptor units in the polymer backbone. This two-point interaction between the folding agent and the polymer backbone leads to a folding of the polymer chain, which was readily monitored by NMR titrations. The effect of various parameters, such as structures of the folding agent and polymer, and the solvent composition, on the folding propensities of the polymer was studied.

  1. Evolution of Substrate Specificity within a Diverse Family of [beta/alpha]-Barrel-fold Basic Amino Acid Decarboxylases X-ray Structure Determination of Enzymes with Specificity for L-Arginine and Carboxynorspermidine

    Energy Technology Data Exchange (ETDEWEB)

    Deng, Xiaoyi; Lee, Jeongmi; Michael, Anthony J.; Tomchick, Diana R.; Goldsmith, Elizabeth J.; Phillips, Margaret A. (Sungkyunkwan); (UTSMC)

    2010-08-26

    Pyridoxal 5{prime}-phosphate (PLP)-dependent basic amino acid decarboxylases from the {beta}/{alpha}-barrel-fold class (group IV) exist in most organisms and catalyze the decarboxylation of diverse substrates, essential for polyamine and lysine biosynthesis. Herein we describe the first x-ray structure determination of bacterial biosynthetic arginine decarboxylase (ADC) and carboxynorspermidine decarboxylase (CANSDC) to 2.3- and 2.0-{angstrom} resolution, solved as product complexes with agmatine and norspermidine. Despite low overall sequence identity, the monomeric and dimeric structures are similar to other enzymes in the family, with the active sites formed between the {beta}/{alpha}-barrel domain of one subunit and the {beta}-barrel of the other. ADC contains both a unique interdomain insertion (4-helical bundle) and a C-terminal extension (3-helical bundle) and it packs as a tetramer in the asymmetric unit with the insertions forming part of the dimer and tetramer interfaces. Analytical ultracentrifugation studies confirmed that the ADC solution structure is a tetramer. Specificity for different basic amino acids appears to arise primarily from changes in the position of, and amino acid replacements in, a helix in the {beta}-barrel domain we refer to as the 'specificity helix.' Additionally, in CANSDC a key acidic residue that interacts with the distal amino group of other substrates is replaced by Leu{sup 314}, which interacts with the aliphatic portion of norspermidine. Neither product, agmatine in ADC nor norspermidine in CANSDC, form a Schiff base to pyridoxal 5{prime}-phosphate, suggesting that the product complexes may promote product release by slowing the back reaction. These studies provide insight into the structural basis for the evolution of novel function within a common structural-fold.

  2. Detection of cyclopiazonic acid (CPA) in maize by immunoassay

    Science.gov (United States)

    Cyclopiazonic acid (a-CPA) is a tremorgenic mycotoxin that is commonly produced by certain of the Aspergilli, in particular A. flavus, which is more widely known for production of the aflatoxins. Despite the fact that a-CPA may co-occur with aflatoxins, immunoassay-based methods for monitoring for C...

  3. Suitable combination of promoter and micellar catalyst for kilo fold rate acceleration on benzaldehyde to benzoic acid conversion in aqueous media at room temperature: a kinetic approach.

    Science.gov (United States)

    Ghosh, Aniruddha; Saha, Rumpa; Ghosh, Sumanta K; Mukherjee, Kakali; Saha, Bidyut

    2013-05-15

    The kinetics of oxidation of benzaldehyde by chromic acid in aqueous and aqueous surfactant (sodium dodecyl sulfate, SDS, alkyl phenyl polyethylene glycol, Triton X-100 and N-cetylpyridinium chloride, CPC) media have been investigated in the presence of promoter at 303 K. The pseudo-first-order rate constants (kobs) were determined from a logarithmic plot of absorbance as a function time. The rate constants were found to increase with introduction of heteroaromatic nitrogen base promoters such as Picolinic acid (PA), 2,2'-bipyridine (bipy) and 1,10-phenanthroline (phen). The product benzoic acid has been characterized by conventional melting point experiment, NMR, HRMS and FTIR spectral analysis. The mechanism of both unpromoted and promoted reaction path has been proposed for the reaction. In presence of the anionic surfactant SDS, cationic surfactant CPC and neutral surfactant TX-100 the reaction can undergo simultaneously in both aqueous and micellar phase with an enhanced rate of oxidation in the micellar phase. Both SDS and TX-100 produce normal micellar effect whereas CPC produce reverse micellar effect in the presence of benzaldehyde. The observed net enhancement of rate effects has been explained by considering the hydrophobic and electrostatic interaction between the surfactants and reactants. SDS and bipy combination is the suitable one for benzaldehyde oxidation.

  4. Determination of selected fatty acids in dried sweat spot using gas chromatography with flame ionization detection.

    Science.gov (United States)

    Kanďár, Roman; Drábková, Petra; Andrlová, Lenka; Kostelník, Adam; Čegan, Alexander

    2016-11-01

    A method is described for the determination of fatty acids in dried sweat spot and plasma samples using gas chromatography with flame ionization detection. Plasma and dried sweat spot samples were obtained from a group of blood donors. The sweat was collected from each volunteer during exercise. Sweat was spotted onto collection paper containing butylated hydroxytoluene. Fatty acids were derivatized with acetyl chloride in methanol to form methyl esters of fatty acids. The fatty acids in dried sweat spot samples treated with butylated hydroxytoluene and stored at -20°C were stable for 3 months. Our results indicate that sweat contains, among fatty acids with short chain, also fatty acids with long chain and unsaturated fatty acids. Linear relationships between percentage content of selected fatty acids in dried sweat spot and plasma were observed. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Nucleic Acid-based Detection of Bacterial Pathogens Using Integrated Microfluidic Platform Systems

    Directory of Open Access Journals (Sweden)

    Carl A. Batt

    2009-05-01

    Full Text Available The advent of nucleic acid-based pathogen detection methods offers increased sensitivity and specificity over traditional microbiological techniques, driving the development of portable, integrated biosensors. The miniaturization and automation of integrated detection systems presents a significant advantage for rapid, portable field-based testing. In this review, we highlight current developments and directions in nucleic acid-based micro total analysis systems for the detection of bacterial pathogens. Recent progress in the miniaturization of microfluidic processing steps for cell capture, DNA extraction and purification, polymerase chain reaction, and product detection are detailed. Discussions include strategies and challenges for implementation of an integrated portable platform.

  6. CRISPR Spacer Arrays for Detection of Viral Signatures from Acidic Hot Springs

    Science.gov (United States)

    Snyder, J. C.; Bateson, M. M.; Suciu, D.; Young, M. J.

    2010-04-01

    Viruses are the most abundant life-like entities on the planet Earth. Using CRISPR spacer sequences, we have developed a microarray-based approach to detecting viral signatures in the acidic hot springs of Yellowstone.

  7. Quantitative detection of single amino acid polyrnorphisms by targeted proteornics

    Institute of Scientific and Technical Information of China (English)

    Zhi-Duan Su; Jia-Rui Wu; Liang Sun; Dan-Xia Yu; Rong-Xia Li; Huai-Xing Li; Zhi-Jie Yu; Quan-Hu Sheng; Xu Lin; RongZeng

    2011-01-01

    Single-nucleotide polymorphisms (SNPs) are recognized as one kind of major genetic variants in population scale. However, polymorphisms at the proteome level in population scale remain elusive. In the present study, we named amino acid variances derived from SNPs within coding regions as single amino acid polymorphisms (SAPs) at the proteome level, and developed a pipeline of non-targeted and targeted proteomics to identify and quantify SAP peptides in human plasma. The absolute concentrations of three selected SAP-peptide pairs among 290 Asian individuals were measured by selected reaction monitoring (SRM) approach, and their associations with both obesity and diabetes were further analyzed. This work revealed that heterozygotes and homozygotes with various SAPs in a population could have different associations with particular traits. In addition, the SRM approach allows us for the first time to separately measure the absolute concentration of each SAP peptide in the heterozygotes, which also shows different associations with particular traits.%Single-nucleotide polymorphisms (SNPs) are recognized as one kind of major genetic variants in population scale.However,polymorphisms at the proteome level in population scale remain elusive.In the present study,we named amino acid variances derived from SNPs within coding regions as single amino acid polymorphisms (SAPs) at the proteome level,and developed a pipeline of non-targeted and targeted proteomics to identify and quantify SAP peptides in human plasma.The absolute concentrations of three selected SAP-peptide pairs among 290 Asian individuals were measured by selected reaction monitoring (SRM) approach,and their associations with both obesity and diabetes were further analyzed.This work revealed that heterozygotes and homozygotes with various SAPs in a population could have different associations with particular traits.In addition,the SRM approach allows us for the first time to separately measure the absolute

  8. JAWS: Just Add Water System - A device for detection of nucleic acids in Martian ice caps

    DEFF Research Database (Denmark)

    Hansen, Anders J.; Willerslev, Eske; Mørk, Søren

    2002-01-01

    The design of a device for nucleic acid detection in the Martian ice caps is presented; the Just Add Water System (JAWS). It is based on fiber-optic PNA (peptide nucleic acid) light up probe random microsphere universal array technology. JAWS is designed to be part of a larger system with a regul...

  9. Apparatus for point-of-care detection of nucleic acid in a sample

    Science.gov (United States)

    Bearinger, Jane P.; Dugan, Lawrence C.

    2016-04-19

    Provided herein are methods and apparatus for detecting a target nucleic acid in a sample and related methods and apparatus for diagnosing a condition in an individual. The condition is associated with presence of nucleic acid produced by certain pathogens in the individual.

  10. Detection of cancer cells using a peptide nanotube–folic acid modified graphene electrode

    DEFF Research Database (Denmark)

    Castillo, John J.; Svendsen, Winnie Edith; Rozlosnik, Noemi

    2013-01-01

    This article describes the preparation of a graphene electrode modified with a new conjugate of peptide nanotubes and folic acid for the selective detection of human cervical cancer cells over-expressing folate receptors. The functionalization of peptide nanotubes with folic acid was confirmed by...

  11. Methods for point-of-care detection of nucleic acid in a sample

    Science.gov (United States)

    Bearinger, Jane P.; Dugan, Lawrence C.

    2015-12-29

    Provided herein are methods and apparatus for detecting a target nucleic acid in a sample and related methods and apparatus for diagnosing a condition in an individual. The condition is associated with presence of nucleic acid produced by certain pathogens in the individual.

  12. Capillary electrophoresis of FITC labeled amino acids with laser-induced fluorescence detection

    Institute of Scientific and Technical Information of China (English)

    党福全; 陈义

    1999-01-01

    FITC labeled amino acids have been separated using a home-huilt capillary electrophoresis with a laserinduced fluorescence detection (CE-LIF) system. Seventeen peaks can now be generated from the twenty common amino acids. The key conditions lie in the optimization of pH, buffer electrolytes and buffer additives.

  13. Selective detection of uric acid in the presence of ascorbic acid at physiological pH by using a beta-cyclodextrin modified copolymer of sulfanilic acid and N-acetylaniline.

    Science.gov (United States)

    Wu, Shouguo; Wang, Taoling; Gao, Zongyong; Xu, Haihong; Zhou, Baineng; Wang, Chuanqin

    2008-07-15

    A beta-cyclodextrin (CD) modified copolymer membrane of sulfanilic acid (p-ASA) and N-acetylaniline (SPNAANI) on glassy carbon electrode (GCE) was prepared and used to determine uric acid (UA) in the presence of a large excess of ascorbic acid (AA) by differential pulse voltammetry (DPV). The properties of the copolymer were characterized by X-ray photoelectron spectra (XPS) and Raman spectroscopy. The oxidation peaks of AA and UA were well separated at the composite membrane modified electrode in phosphate buffer solution (PBS, pH 7.4). A linear relationship between the peak current and the concentration of UA was obtained in the range from 1.0 x 10(-5) to 3.5 x 10(-4)mol L(-1), and the detection limit was 2.7 x 10(-6)mol L(-1) at a signal-to-noise ratio of 3. Two hundred and fifty-fold excess of AA did not interfere with the determination of UA. The application of the prepared electrode was demonstrated by measuring UA in human serum samples without any pretreatment, and the results were comparatively in agreement with the spectrometric clinical assay method.

  14. Vocal Fold Collision Modeling

    DEFF Research Database (Denmark)

    Granados, Alba; Brunskog, Jonas; Misztal, M. K.

    2015-01-01

    When vocal folds vibrate at normal speaking frequencies, collisions occurs. The numerics and formulations behind a position-based continuum model of contact is an active field of research in the contact mechanics community. In this paper, a frictionless three-dimensional finite element model...... of the vocal fold collision is proposed, which incorporates different procedures used in contact mechanics and mathematical optimization theories. The penalty approach and the Lagrange multiplier method are investigated. The contact force solution obtained by the penalty formulation is highly dependent...

  15. Simulations of Protein Folding

    CERN Document Server

    Cahill, M; Cahill, K E; Cahill, Michael; Fleharty, Mark; Cahill, Kevin

    2000-01-01

    We have developed a simple, phenomenological, Monte-Carlo code that predicts the three-dimensional structure of globular proteins from the DNA sequences that define them. We have applied this code to two small proteins, the villin headpiece (1VII) and cole1 rop (1ROP). Our code folded the 36-residue villin headpiece to a mean rms distance of less than 5 A from its native structure as revealed by NMR; it folded a 56-residue fragment of the protein cole1 rop to within 11 A of its native structure. The denatured starting configurations of these two proteins were, respectively, 29 A and 55 A distant from their native structures.

  16. Protein folding, protein homeostasis, and cancer

    Institute of Scientific and Technical Information of China (English)

    John H. Van Drie

    2011-01-01

    Proteins fold into their functional 3-dimensional structures from a linear amino acid sequence. In vitro this process is spontaneous; while in vivo it is orchestrated by a specialized set of proteins, called chaperones. Protein folding is an ongoing cellular process, as cellular proteins constantly undergo synthesis and degradation. Here emerging links between this process and cancer are reviewed. This perspective both yields insights into the current struggle to develop novel cancer chemotherapeutics and has implications for future chemotherapy discovery.

  17. RFLP analysis in rice by using ECL direct nucleic acid labeling and detection system

    Institute of Scientific and Technical Information of China (English)

    ZHANGShanhong; LIUBin; LUOLin; ZHUXiaoyuan; YANGQiyun; WUShangzhong

    1998-01-01

    ECL (Enhanced Chemiluminescence) direct nu cleic acid labeling and detection syslem were used for RFLP analysis in rice. The system involved directly labeling DNA probe with the enzyme horseradish peroxidase (HRP), and the detection of non-radioactive signal based on chemiluminescence, that was the generation of light via enzyme (HRP)-catalyzed reactions. It was a simple, safe,

  18. Sensitive Monitoring of Humic Acid in Various Aquatic Environments with Acidic Cerium Chemiluminescence Detection

    National Research Council Canada - National Science Library

    CHENG, Xianglei; ZHAO, Lixia; WANG, Xu; LIN, Jin-Ming

    2007-01-01

    ...(IV) in the acidic condition. Different with the former redox CL reaction which occurred in alkaline solution, no enhancers were needed and neither precipitation nor a second contamination would occur in the present CL system...

  19. Preparation of MIP-based QCM nanosensor for detection of caffeic acid.

    Science.gov (United States)

    Gültekin, Aytaç; Karanfil, Gamze; Kuş, Mahmut; Sönmezoğlu, Savaş; Say, Rıdvan

    2014-02-01

    In the present work, a new caffeic acid imprinted quartz crystal microbalance (QCM) nanosensor has been designed for selective assignation of caffeic acid in plant materials. Methacrylamidoantipyrine-iron(III) [MAAP-Fe(III)] as metal-chelating monomer has been used to prepare selective molecular imprinted polymer (MIP). MIP film for detection of caffeic acid has been developed on QCM electrode and selectivity experiments and analytical performance of caffeic acid imprinted QCM nanosensor has been studied. The caffeic acid imprinted QCM nanosensor has been characterized by AFM. After the characterization studies, imprinted and non-imprinted nanosensors was connected to QCM system for studies of connection of the target molecule, selectivity and the detection of amount of target molecule in real samples. The detection limit was found to be 7.8 nM. The value of Langmuir constant (b) (4.06 × 10(6)) that was acquired using Langmuir graph demonstrated that the affinity of binding sites was strong. Also, selectivity of prepared caffeic acid imprinted nanosensor was found as being high compared to chlorogenic acid. Finally, the caffeic acid levels in plant materials was determined by the prepared QCM nanosensor.

  20. Polyfunctional Lewis acids: intriguing solid-state structure and selective detection and discrimination of nitroaromatic explosives.

    Science.gov (United States)

    Swamy P, Chinna Ayya; Thilagar, Pakkirisamy

    2015-06-08

    Synthesis and crystal structures of three porphyrin-based polyfunctional Lewis acids 1-3 are reported. Intermolecular HgCl⋅⋅⋅HgCl (linear and μ-type) interactions in the solid state of the peripherally ArHgCl-decorated compound 3 lead to a fascinating 3D supramolecular architecture. Compound 3 shows a selective fluorescence quenching response to picric acid and discriminates other nitroaromatic-based explosives. For the first time, an electron-deficient polyfunctional Lewis acid is shown to be useful for the selective detection and discrimination of nitroaromatic explosives. The Stern-Volmer quenching constant and detection limits of compound 3 for picric acid are the best among the reported small-molecular receptors for nitroaromatic explosives. The electronic structure, Lewis acidity, and selective sensing characteristics of 3 are well corroborated by DFT calculations. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Determination of urinary vanillylmandelic acid by direct injection and coupled-column chromatography with electrochemical detection.

    Science.gov (United States)

    Eriksson, B M; Persson, B A; Wikström, M

    1990-04-27

    An automated column-switching system for determination of vanillylmandelic acid in urine is described. The liquid chromatographic system was composed of two separation columns with different selectivity properties, an octadecyl column coated with tributyl phosphate as stationary liquid phase and a silica-based anion exchanger. Urine samples were injected directly onto the first column, where vanillylmandelic acid was separated from the main part of the sample matrix. The internal standard isovanillylmandelic acid was co-eluting with vanillylmandelic acid, and a fraction of the eluate containing both substances was switched to the second column, where separation was performed. To assess peak purity, detection was performed with dual working electrodes in parallel mode. A relative standard deviation of 3.5% was obtained for determination of human urine samples containing 3 microM vanillylmandelic acid, and less than 0.1 microM could be detected.

  2. Detection and quantification of protein adduction by electrophilic fatty acids: mitochondrial generation of fatty acid nitroalkene derivatives.

    Science.gov (United States)

    Schopfer, F J; Batthyany, C; Baker, P R S; Bonacci, G; Cole, M P; Rudolph, V; Groeger, A L; Rudolph, T K; Nadtochiy, S; Brookes, P S; Freeman, B A

    2009-05-01

    Nitroalkene fatty acid derivatives manifest a strong electrophilic nature, are clinically detectable, and induce multiple transcriptionally regulated anti-inflammatory responses. At present, the characterization and quantification of endogenous electrophilic lipids are compromised by their Michael addition with protein and small-molecule nucleophilic targets. Herein, we report a trans-nitroalkylation reaction of nitro-fatty acids with beta-mercaptoethanol (BME) and apply this reaction to the unbiased identification and quantification of reaction with nucleophilic targets. Trans-nitroalkylation yields are maximal at pH 7 to 8 and occur with physiological concentrations of target nucleophiles. This reaction is also amenable to sensitive mass spectrometry-based quantification of electrophilic fatty acid-protein adducts upon electrophoretic resolution of proteins. In-gel trans-nitroalkylation reactions also permit the identification of protein targets without the bias and lack of sensitivity of current proteomic approaches. Using this approach, it was observed that fatty acid nitroalkenes are rapidly metabolized in vivo by a nitroalkene reductase activity and mitochondrial beta-oxidation, yielding a variety of electrophilic and nonelectrophilic products that could be structurally characterized upon BME-based trans-nitroalkylation reaction. This strategy was applied to the detection and quantification of fatty acid nitration in mitochondria in response to oxidative inflammatory conditions induced by myocardial ischemia-reoxygenation.

  3. Folding worlds between pages

    CERN Multimedia

    Meier, Matthias

    2010-01-01

    "We all remember pop-up books form our childhood. As fascinated as we were back then, we probably never imagined how much engineering know-how went into these books. Pop-up engineer Anton Radevsky has even managed to fold a 27-kilometre particle accelerator into a book" (4 pages)

  4. Folds and Etudes

    Science.gov (United States)

    Bean, Robert

    2007-01-01

    In this article, the author talks about "Folds" and "Etudes" which are images derived from anonymous typing exercises that he found in a used copy of "Touch Typing Made Simple". "Etudes" refers to the musical tradition of studies for a solo instrument, which is a typewriter. Typing exercises are repetitive attempts to type words and phrases…

  5. ProbFold

    DEFF Research Database (Denmark)

    Sahoo, Sudhakar; Świtnicki, Michał P; Pedersen, Jakob Skou

    2016-01-01

    ) with probabilistic graphical models. This approach allows rapid adaptation and integration of new probing data types. AVAILABILITY AND IMPLEMENTATION: ProbFold is implemented in C ++. Models are specified using simple textual formats. Data reformatting is done using separate C ++ programs. Source code, statically...

  6. Zirconia based nucleic acid sensor for Mycobacterium tuberculosis detection

    Science.gov (United States)

    Das, Maumita; Sumana, Gajjala; Nagarajan, R.; Malhotra, B. D.

    2010-03-01

    Nanostructured zirconium oxide (ZrO2) film (particle size˜35 nm), electrochemically deposited onto gold(Au) surface, has been used to immobilize 21-mer oligonucleotide probe (ssDNA) specific to Mycobacterium tuberculosis by utilizing affinity between oxygen atom of phosphoric group and zirconium to fabricate DNA biosensor. This DNA-ZrO2/Au bioelectrode, characterized using x-ray diffraction, Fourier transform infrared spectroscopy, cyclic voltammetry, and scanning electron microscopy techniques, can be used for early and rapid diagnosis of M. tuberculosis with detection limit of 0.065 ng/μL within 60s.

  7. Detection of D-amino acids in purified proteins synthesized in Escherichia coli.

    Science.gov (United States)

    Miyamoto, Tetsuya; Sekine, Masae; Ogawa, Tetsuhiro; Hidaka, Makoto; Homma, Hiroshi; Masaki, Haruhiko

    2010-05-01

    It has long been believed that amino acids comprising proteins of all living organisms are only of the L-configuration, except for Gly. However, peptidyl D-amino acids were observed in hydrolysates of soluble high molecular weight fractions extracted from cells or tissues of various organisms. This strongly suggests that significant amounts of D-amino acids are naturally present in usual proteins. Thus we analyzed the D-amino acid contents of His-tag-purified beta-galactosidase and human urocortin, which were synthesized by Escherichia coli grown in controlled synthetic media. After acidic hydrolysis for various times at 110 degrees C, samples were derivatized with 4-fluoro-7-nitro-2, 1, 3-benzoxadiazole (NBD-F) and separated on a reverse-phase column followed by a chiral column into D- and L-enantiomers. The contents of D-enantiomers of Ala, Leu, Phe, Val, Asp, and Glu were determined by plotting index D/(D + L) against the incubation time for hydrolysis and extrapolating the linear regression line to 0 h to eliminate the effect of racemization of amino acids during the incubation. Significant contents of D-amino acids were reproducibly detected, the D-amino acid profile being specific to an individual protein. This finding indicated the likelihood that D-amino acids are in fact present in the purified proteins. On the other hand, the D-amino acid contents of proteins were hardly influenced by the addition of D- or L-amino acids to the cultivation medium, whereas intracellular free D-amino acids sensitively varied according to the extracellular conditions. The origin of these D-amino acids detected in proteins was discussed.

  8. Detection of domoic acid in northern anchovies and California sea lions associated with an unusual mortality event.

    Science.gov (United States)

    Lefebvre, K A; Powell, C L; Busman, M; Doucette, G J; Moeller, P D; Silver, J B; Miller, P E; Hughes, M P; Singaram, S; Silver, M W; Tjeerdema, R S

    1999-01-01

    The occurrence of an unusual mortality event involving California sea lions (Zalophus californianus) along the central California coast in May 1998 was recently reported. The potent neurotoxin domoic acid (DA), produced naturally by the diatom Pseudo-nitzschia australis and transmitted to the sea lions via planktivorous northern anchovies (Engraulis mordax), was identified as the probable causative agent. Details of DA analyses for anchovy tissues and sea lion feces are described. Domoic acid levels were estimated in anchovy samples by HPLC-UV, and in sea lion feces using the same method as well as a microplate receptor binding assay, with absolute confirmation by tandem mass spectrometry. The highest DA concentrations in anchovies occurred in the viscera (223 +/- 5 microg DA g(-1)), exceeding values in the body tissues by seven-fold and suggesting minimal bioaccumulation of DA in anchovy tissue. HPLC values for DA in sea lion fecal material (ranging from 152 to 136.5 microg DA g(-1)) required correction for interference from an unidentified compound. Inter-laboratory comparisons of HPLC data showed close quantitative agreement. Fecal DA activity determined using the receptor binding assay corresponded with HPLC values to within a factor of two. Finally, our detection of P. australis frustules, via scanning electron microscopy, in both anchovy viscera and fecal material from sea lions exhibiting seizures provides corroborating evidence that this toxic algal species was involved in this unusual sea lion mortality event.

  9. The Folding of de Novo Designed Protein DS119 via Molecular Dynamics Simulations.

    Science.gov (United States)

    Wang, Moye; Hu, Jie; Zhang, Zhuqing

    2016-04-26

    As they are not subjected to natural selection process, de novo designed proteins usually fold in a manner different from natural proteins. Recently, a de novo designed mini-protein DS119, with a βαβ motif and 36 amino acids, has folded unusually slowly in experiments, and transient dimers have been detected in the folding process. Here, by means of all-atom replica exchange molecular dynamics (REMD) simulations, several comparably stable intermediate states were observed on the folding free-energy landscape of DS119. Conventional molecular dynamics (CMD) simulations showed that when two unfolded DS119 proteins bound together, most binding sites of dimeric aggregates were located at the N-terminal segment, especially residues 5-10, which were supposed to form β-sheet with its own C-terminal segment. Furthermore, a large percentage of individual proteins in the dimeric aggregates adopted conformations similar to those in the intermediate states observed in REMD simulations. These results indicate that, during the folding process, DS119 can easily become trapped in intermediate states. Then, with diffusion, a transient dimer would be formed and stabilized with the binding interface located at N-terminals. This means that it could not quickly fold to the native structure. The complicated folding manner of DS119 implies the important influence of natural selection on protein-folding kinetics, and more improvement should be achieved in rational protein design.

  10. Determination of Monochloroacetic Acid in Swimming Pool Water by Ion Chromatography-Conductivity Detection

    Directory of Open Access Journals (Sweden)

    Maria Pythias B. Espino

    2013-02-01

    Full Text Available In this study, an analytical method involving ion chromatography with conductivity detection was developed and optimized for the determination of monochloroacetic acid in swimming pool water. The ion chromatographic method has a detection limit of 0.02 mg L-1 and linear range of 0.05 to 1.0 mg L-1 with correlation coeff icient of 0.9992. The method is reproducible with percent RSD of 0.052% (n=10. The recovery of monochloroacetic acid spiked in different water types (bottled, tap and swimming pool water ranged from 28 to 122%. In dilute solutions, chloride and bromide were simultaneously analyzed along with monochloroacetic acid using the optimized method. Chloride and bromide have detection limits of 0.01 to 0.05 mg L-1, respectively. The usefulness of the ion chromatographic method was demonstrated in the analysis of monochloroacetic acid in swimming pool water samples. In such highly-chlorinated samples, an Ag/H cartridge was used prior to the ion chromatographic determination so as to minimize the signal due to chloride ion. Monochloroacetic acid was detected in concentrations between 0.020 and 0.093 mg L-1 in three of the six swimming pool water samples studied. The presence of monochloroacetic acid in the swimming pool water samples suggests the possible occurrence of other disinfection by-products in these waters.

  11. Determination of Monochloroacetic Acid in Swimming Pool Water by Ion Chromatography-Conductivity Detection

    Directory of Open Access Journals (Sweden)

    Maria Pythias B. Espino

    2013-12-01

    Full Text Available In this study, an analytical method involving ion chromatography with conductivity detection was developed and optimized for the determination of monochloroacetic acid in swimming pool water. The ion chromatographic method has a detection limit of 0.02 mg L-1 and linear range of 0.05 to 1.0 mg L-1 with correlation coeff icient of 0.9992. The method is reproducible with percent RSD of 0.052% (n=10. The recovery of monochloroacetic acid spiked in different water types (bottled, tap and swimming pool water ranged from 28 to 122%. In dilute solutions, chloride and bromide were simultaneously analyzed along with monochloroacetic acid using the optimized method. Chloride and bromide have detection limits of 0.01 to 0.05 mg L-1, respectively. The usefulness of the ion chromatographic method was demonstrated in the analysis of monochloroacetic acid in swimming pool water samples. In such highly-chlorinated samples, an Ag/H cartridge was used prior to the ion chromatographic determination so as to minimize the signal due to chloride ion. Monochloroacetic acid was detected in concentrations between 0.020 and 0.093 mg L-1 in three of the six swimming pool water samples studied. The presence of monochloroacetic acid in the swimming pool water samples suggests the possible occurrence of other disinfection by-products in these waters.

  12. [Determination of amino acids in honey by capillary electrophoresis with indirect ultraviolet detection].

    Science.gov (United States)

    Zhou, Xianjing; Shi, Yanping

    2013-07-01

    A method of capillary electrophoresis with indirect ultraviolet (UV) detection was developed for the separation and determination of nine amino acids such as lysine, tryptophan, glutamic acid, etc. The effects of sodium dihydrogen phosphates concentration, pH of buffer and sample injection type and time on the reproducibility and efficiency were investigated. The optimum injection time was 5 s at 5 kPa. The optimum electrophoretic conditions were as follow: 10 mmol/L sodium dihydrogen phosphates (pH 10. 2) containing 0. 5 mmol/L cetrimonium bromide, 20 mmol/L nicotinic acid and 10% (v/v) methanol as running buffer, applied voltage of - 15 kV, detection wavelength of 220 nm. The base line separation of the nine amino acids was achieved successfully within 11 min. The lowest detection limit was 0. 3 mg/L. All of the nine analytes showed good linearities within 1. 0 - 1000 mg/L. The relative standard deviations of migration time and peak area were 0. 64% - 5. 83%. The recoveries of the eight amino acids spiked in a real sample were between 60. 00% and 118.37%. The method was applied in the determination of the amino acids in honey samples from different nectar plants and origins. Prolin, serine and aspartic acid were found in five honey samples, and tryptophan was only found in a litchi honey sample. This method can provide good reference to the evaluation of the quality and nectar origin of honey.

  13. Combined gadoxetic acid and gadofosveset enhanced liver MRI for detection and characterization of liver metastases

    Energy Technology Data Exchange (ETDEWEB)

    Bannas, Peter [University of Wisconsin-Madison, Department of Radiology, Madison, WI (United States); University Medical Center Hamburg-Eppendorf, Department of Radiology, University Hospital, Hamburg (Germany); Bookwalter, Candice A.; Ziemlewicz, Tim; Munoz del Rio, Alejandro; Potretzke, Theodora A. [University of Wisconsin-Madison, Department of Radiology, Madison, WI (United States); Motosugi, Utaroh [University of Wisconsin-Madison, Department of Radiology, Madison, WI (United States); University of Yamanashi, Department of Radiology, Yamanashi (Japan); Nagle, Scott K. [University of Wisconsin-Madison, Department of Radiology, Madison, WI (United States); University of Wisconsin-Madison, Department of Medical Physics, Madison, WI (United States); University of Wisconsin-Madison, Department of Pediatrics, Madison, WI (United States); Reeder, Scott B. [University of Wisconsin-Madison, Department of Radiology, Madison, WI (United States); University of Wisconsin-Madison, Department of Medical Physics, Madison, WI (United States); University of Wisconsin-Madison, Department of Biomedical Engineering, Madison, WI (United States); University of Wisconsin-Madison, Department of Medicine, Madison, WI (United States); University of Wisconsin-Madison, Department of Emergency Medicine, Madison, WI (United States)

    2017-01-15

    To compare gadoxetic acid alone and combined gadoxetic acid/gadofosveset trisodium-enhanced liver MRI for detection of metastases and differentiation of metastases from haemangiomas. Ninety-one patients underwent gadoxetic acid-enhanced liver MRI before and after additional injection of gadofosveset. First, two readers retrospectively identified metastases on gadoxetic acid alone enhanced delayed hepatobiliary phase T1-weighted images together with all other MR images (dynamic images, T2-weighted images, diffusion-weighted images). Second, readers assessed additional T1-weighted images obtained after administration of gadofosveset trisodium. For both interpretations, readers rated lesion conspicuity and confidence in differentiating metastases from haemangiomas. Results were compared using alternative free-response receiver-operating characteristic (AFROC) and conventional ROC methods. Histology and follow-up served as reference standard. There were 145 metastases and 16 haemangiomas. Both readers detected more metastases using combined gadoxetic acid/gadofosveset (reader 1 = 130; reader 2 = 124) compared to gadoxetic acid alone (reader 1 = 104; reader 2 = 103). Sensitivity of combined gadoxetic acid/gadofosveset (reader 1 = 90 %; reader 2 = 86 %) was higher than that of gadoxetic acid alone (reader 1 = 72 %; reader 2 = 71 %, both P < 0.01). AFROC-AUC was higher for the combined technique (0.92 vs. 0.86, P < 0.001). Sensitivity for correct differentiation of metastases from haemangiomas was higher for the combined technique (reader 1 = 98 %; reader 2 = 99 % vs. reader 1 = 86 %; reader 2 = 91 %, both P < 0.01). ROC-AUC was significantly higher for the combined technique (reader 1 = 1.00; reader 2 = 1.00 vs. reader 1 = 0.87; reader 2 = 0.92, both P < 0.01). Combined gadoxetic acid/gadofosveset-enhanced MRI improves detection and characterization of liver metastases compared to gadoxetic acid alone. (orig.)

  14. Development of a bacterial bioassay for atrazine and cyanuric acid detection

    Directory of Open Access Journals (Sweden)

    Anna eHUA

    2015-03-01

    Full Text Available The s-triazine herbicides are compounds which can disseminate into soils and water. Due to their toxic effects on living organisms, their concentrations in drinking water are legislated by WHO recommendations. Here we have developed for the first time, to the best of our knowledge, an alternative method for physicochemical quantification using two bioluminescent bacterial biosensors: E. coli SM003 for cyanuric acid detection and E. coli SM004 for both atrazine and cyanuric acid detection. The concentration of cyanuric acid detection for E. coli SM003 ranges from 7.83 µM to 2.89 mM, and for E. coli SM004 ranges from 0.22 µM to 15 µM. Moreover, atrazine detection by E. coli SM004 ranges from 1.08 µM to 15 µM. According to WHO recommendations, the cyanuric acid detection range is sensitive enough to discriminate between polluted and drinking water. Nevertheless, the detection of atrazine by E. coli SM004 is only applicable for high concentrations of contaminants.

  15. Ab initio RNA folding.

    Science.gov (United States)

    Cragnolini, Tristan; Derreumaux, Philippe; Pasquali, Samuela

    2015-06-17

    RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, the experimental determination of RNA structures through x-ray crystallography and NMR seems to have reached a plateau in the number of structures resolved each year, but as more and more RNA sequences are being discovered, the need for structure prediction tools to complement experimental data is strong. Theoretical approaches to RNA folding have been developed since the late nineties, when the first algorithms for secondary structure prediction appeared. Over the last 10 years a number of prediction methods for 3D structures have been developed, first based on bioinformatics and data-mining, and more recently based on a coarse-grained physical representation of the systems. In this review we are going to present the challenges of RNA structure prediction and the main ideas behind bioinformatic approaches and physics-based approaches. We will focus on the description of the more recent physics-based phenomenological models and on how they are built to include the specificity of the interactions of RNA bases, whose role is critical in folding. Through examples from different models, we will point out the strengths of physics-based approaches, which are able not only to predict equilibrium structures, but also to investigate dynamical and thermodynamical behavior, and the open challenges to include more key interactions ruling RNA folding.

  16. Urinary 4-hydroxy-3-methoxymandelic (vanillylmandelic) acid, 4-hydroxy-3-methoxyphenylacetic (homovanillic) acid, and 5-hydroxy-3-indoleacetic acid determined by liquid chromatography with electrochemical detection.

    Science.gov (United States)

    Fujita, K; Maruta, K; Ito, S; Nagatsu, T

    1983-05-01

    We describe a simple liquid-chromatographic assay of urinary 4-hydroxy-3-methoxymandelic (vanillylmandelic) acid, 4-hydroxy-3-methoxyphenylacetic (homovanillic) acid, and 5-hydroxy-3-indoleacetic acid with electrochemical detection, with direct injection of the sample. The first two analytes are measured simultaneously; 5-hydroxy-3-indoleacetic acid is measured separately. Chromatographic conditions for assay of the three were: column temperature, 65 and 60 degrees C; mobile phase, potassium phosphate buffer (0.2 mol/L, pH 3.0) for 6 min, then potassium phosphate buffer plus acetonitrile (9/1 by vol) for 20 min; flow rate, 0.7 mL/min; oxidation potential, 600 and 450 mV vs an Ag/AgCl reference electrode; and sensitivity, 40 and 160 nA at full scale. Values so obtained agreed well with those obtained for samples that were first solvent-extracted.

  17. Simultaneous liquid chromatographic determination of vanillylmandelic acid, homovanillic acid, and 5-hydroxy-3-indoleacetic acid in urine, using isocratic elution and electrochemical detection.

    Science.gov (United States)

    Richards, D A; Titheradge, A C

    1987-01-01

    A method for the simultaneous measurement of vanillylmandelic acid, homovanillic acid and 5-hydroxyindoleacetic acid in urine is described. Based on reversed-phase liquid chromatography with electrochemical detection, the procedure employs isocratic elution, thus making it suitable for use in the less well-equipped clinical or research laboratory. A simple extraction of the acids from acidified urine into ethyl acetate, is followed by evaporating to dryness a portion of the organic layer, and redissolving the residue in chromatographic mobile phase. Up to 20 samples can be analysed in a single working day. The method is validated and the results obtained are compared with reference methods. The cause of contamination of the glassy carbon surface of the working electrode is investigated, and a simple electrochemical pretreatment is described that overcomes this problem. Finally, the extra clinical information that can be derived from multi-metabolite assays is considered.

  18. Association of amino acids embedded in helium droplets detected by mass spectrometry

    Science.gov (United States)

    Lalanne, Matthieu R.; Achazi, Georg; Reichwald, Sebastian; Lindinger, Albrecht

    2015-12-01

    Amino acids were embedded in helium droplets. The electron impact ionization allows for detecting positively charged glycine, valine, histidine, tryptophan and their principal fragments. Monomers and polymers with up to four amino acids are reported. Heterodimers of tryptophan and valine or histidine are observed as well as heterodimers of included fragments. The ability of these associations of molecules to form complexes with water is examined.

  19. Uric acid, an important screening tool to detect inborn errors of metabolism: a case series.

    Science.gov (United States)

    Jasinge, Eresha; Kularatnam, Grace Angeline Malarnangai; Dilanthi, Hewa Warawitage; Vidanapathirana, Dinesha Maduri; Jayasena, Kandana Liyanage Subhashinie Priyadarshika Kapilani Menike; Chandrasiri, Nambage Dona Priyani Dhammika; Indika, Neluwa Liyanage Ruwan; Ratnayake, Pyara Dilani; Gunasekara, Vindya Nandani; Fairbanks, Lynette Dianne; Stiburkova, Blanka

    2017-09-06

    Uric acid is the metabolic end product of purine metabolism in humans. Altered serum and urine uric acid level (both above and below the reference ranges) is an indispensable marker in detecting rare inborn errors of metabolism. We describe different case scenarios of 4 Sri Lankan patients related to abnormal uric acid levels in blood and urine. CASE 1: A one-and-half-year-old boy was investigated for haematuria and a calculus in the bladder. Xanthine crystals were seen in microscopic examination of urine sediment. Low uric acid concentrations in serum and low urinary fractional excretion of uric acid associated with high urinary excretion of xanthine and hypoxanthine were compatible with xanthine oxidase deficiency. CASE 2: An 8-month-old boy presented with intractable seizures, feeding difficulties, screaming episodes, microcephaly, facial dysmorphism and severe neuro developmental delay. Low uric acid level in serum, low fractional excretion of uric acid and radiological findings were consistent with possible molybdenum cofactor deficiency. Diagnosis was confirmed by elevated levels of xanthine, hypoxanthine and sulfocysteine levels in urine. CASE 3: A 3-year-10-month-old boy presented with global developmental delay, failure to thrive, dystonia and self-destructive behaviour. High uric acid levels in serum, increased fractional excretion of uric acid and absent hypoxanthine-guanine phosphoribosyltransferase enzyme level confirmed the diagnosis of Lesch-Nyhan syndrome. CASE 4: A 9-year-old boy was investigated for lower abdominal pain, gross haematuria and right renal calculus. Low uric acid level in serum and increased fractional excretion of uric acid pointed towards hereditary renal hypouricaemia which was confirmed by genetic studies. Abnormal uric acid level in blood and urine is a valuable tool in screening for clinical conditions related to derangement of the nucleic acid metabolic pathway.

  20. Facile synthesis of graphene hybrid tube-like structure for simultaneous detection of ascorbic acid, dopamine, uric acid and tryptophan

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Wen [Education Ministry Key Laboratory on Luminescence and Real-Time Analysis, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715 (China); Chai Yaqin, E-mail: yqchai@swu.edu.cn [Education Ministry Key Laboratory on Luminescence and Real-Time Analysis, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715 (China); Yuan Ruo, E-mail: yuanruo@swu.edu.cn [Education Ministry Key Laboratory on Luminescence and Real-Time Analysis, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715 (China); Chen Shihong; Han Jing; Yuan Dehua [Education Ministry Key Laboratory on Luminescence and Real-Time Analysis, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715 (China)

    2012-12-05

    Graphical abstract: A tube-like structure of graphene hybrid (GS-PTCA) was synthesized via {pi}-{pi} stacking interaction, and was used as modifier to fabricate electrode for simultaneous detection of ascorbic acid (AA), dopamine (DA), uric acid (UA) and tryptophan (Trp). SEM images of GS, PTCA and GS-PTCA were presented. Under the synergistic effects between GS and PTCA, the modified electrode displayed high catalytic activity and selectivity toward the oxidation of AA, DA, UA, and Trp. Highlights: Black-Right-Pointing-Pointer A simple strategy for simultaneous detection of AA, DA, UA and Trp has been constructed. Black-Right-Pointing-Pointer The tube-like structure of graphene hybrid (GS-PTCA) was synthesized. Black-Right-Pointing-Pointer The GS-PTCA provided a selective interface for discrimination of AA, DA, UA and Trp. - Abstract: In the present work, a tube-like structure of graphene hybrid as modifier to fabricate electrode for simultaneous detection of ascorbic acid (AA), dopamine (DA), uric acid (UA) and tryptophan (Trp) was reported. The hybrid was synthesized by a simple method based on graphene sheets (GS) and 3,4,9,10-perylenetetracarboxylic acid (PTCA) via {pi}-{pi} stacking interaction under ultrasonic condition. The combination of GS and PTCA could effectively improve the dispersion of GS, owing to PTCA with the carboxylic-functionalized interface. Comparing with pure GS or PTCA modified electrode, GS-PTCA displayed high catalytic activity and selectivity toward the oxidation of AA, DA, UA, and Trp. Moreover, cyclic voltammetry, different pulse voltammetry and scanning electron microscopy were employed to characterize the sensors. The experiment results showed that the linear response range for simultaneous detection of AA, DA, UA, and Trp were 20-420 {mu}M, 0.40-374 {mu}M, 4-544 {mu}M and 0.40-138 {mu}M, respectively, and the detection limits were 5.60 {mu}M, 0.13 {mu}M, 0.92 {mu}M and 0.06 {mu}M (S/N = 3). Importantly, the proposed method offers

  1. Acetic Acid Detection Threshold in Synthetic Wine Samples of a Portable Electronic Nose

    Directory of Open Access Journals (Sweden)

    Miguel Macías Macías

    2012-12-01

    Full Text Available Wine quality is related to its intrinsic visual, taste, or aroma characteristics and is reflected in the price paid for that wine. One of the most important wine faults is the excessive concentration of acetic acid which can cause a wine to take on vinegar aromas and reduce its varietal character. Thereby it is very important for the wine industry to have methods, like electronic noses, for real-time monitoring the excessive concentration of acetic acid in wines. However, aroma characterization of alcoholic beverages with sensor array electronic noses is a difficult challenge due to the masking effect of ethanol. In this work, in order to detect the presence of acetic acid in synthetic wine samples (aqueous ethanol solution at 10% v/v we use a detection unit which consists of a commercial electronic nose and a HSS32 auto sampler, in combination with a neural network classifier (MLP. To find the characteristic vector representative of the sample that we want to classify, first we select the sensors, and the section of the sensors response curves, where the probability of detecting the presence of acetic acid will be higher, and then we apply Principal Component Analysis (PCA such that each sensor response curve is represented by the coefficients of its first principal components. Results show that the PEN3 electronic nose is able to detect and discriminate wine samples doped with acetic acid in concentrations equal or greater than 2 g/L.

  2. Method for rapid detection and identification of chaetomium and evaluation of resistance to peracetic acid.

    Science.gov (United States)

    Nakayama, Motokazu; Hosoya, Kouichi; Tomiyama, Daisuke; Tsugukuni, Takashi; Matsuzawa, Tetsuhiro; Imanishi, Yumi; Yaguchi, Takashi

    2013-06-01

    In the beverage industry, peracetic acid has been increasingly used as a disinfectant for the filling machinery and environment due to merits of leaving no residue, it is safe for humans, and its antiseptic effect against fungi and endospores of bacteria. Recently, Chaetomium globosum and Chaetomium funicola were reported resistant to peracetic acid; however, little is known concerning the detail of peracetic acid resistance. Therefore, we assessed the peracetic acid resistance of the species of Chaetomium and related genera under identical conditions and made a thorough observation of the microstructure of their ascospores by transmission electron microscopy. The results of analyses revealed that C. globosum and C. funicola showed the high resistance to peracetic acid (a 1-D antiseptic effect after 900 s and 3-D antiseptic effect after 900 s) and had thick cell walls of ascospores that can impede the action mechanism of peracetic acid. We also developed specific primers to detect the C. globosum clade and identify C. funicola by using PCR to amplify the β-tubulin gene. PCR with the primer sets designed for C. globosum (Chae 4F/4R) and C. funicola (Cfu 2F/2R) amplified PCR products specific for the C. globosum clade and C. funicola, respectively. PCR with these two primer sets did not detect other fungi involved in food spoilage and environmental contamination. This detection and identification method is rapid and simple, with extremely high specificity.

  3. Determination of urinary vanillylmandelic acid by liquid chromatography with electrochemical detection.

    Science.gov (United States)

    Moleman, P; Borstrok, J J

    1983-05-01

    We describe an improved method for the assay of urinary vanillylmandelic acid by "high-performance" liquid chromatography, with electrochemical detection. A 1-mL aliquot of urine is acidified and extracted with ethyl acetate, then the ethyl acetate extract is extracted with phosphate buffer, pH 8.5. An acidified aliquot of the phosphate extract is injected into a reversed-phase column and vanillylmandelic acid is detected electrochemically. The between-day CV is 5-6% for concentrations ranging from 10 to 75 mumol/L. We also discuss the critical steps for extraction and calibration.

  4. Highly sensitive analysis of nucleic acids using capillary gel electrophoresis with ultraviolet detection based on the combination of matrix field-amplified and head-column field-amplified stacking injection.

    Science.gov (United States)

    Lian, Dong-Sheng; Zhao, Shu-Jin

    2015-01-26

    To develop a highly sensitive method for analyzing nucleic acids using capillary gel electrophoresis with ultraviolet detection (CGE-UV), we combined matrix field-amplified with head-column field-amplified stacking injection (C-FASI) to employ the advantages of two methods. Without diminishing the resolution, a limit of detection of 0.13 ng/ml (signal/noise=3) in a 300,000-fold diluted sample was obtained, the sensitivity is 102,308 times higher than that achieved with normal pressure injection, 3077 times that with normal electrokinetic injection, 154 times that with pressure field-amplified sample stacking injection, and 31 times that with matrix field-amplified stacking injection. After establishing the method, we tested the detection of a φX174-Hae III digest DNA product without purification and with a high ionic strength. At the lowest dilution of 5000-fold, sample at a concentration of 10 ng/ml was enriched and detected. The relative standard deviations for migration time and peak area (n=3) were 0.03-1.15 and 0.72-6.42, respectively. To further validate C-FASI was applicable for real sample, a 400 bp PCR product without purification was directly detected with a limit of detection at the concentration of 6000-fold dilution (signal/noise=3), The relative standard deviations for migration time and peak area (n=6) were 0.44 and 4.8, respectively. These results indicated that C-FASI had good qualitative and quantitative detection abilities and CGE-UV based on C-FASI is easy to perform, practical, highly-sensitive and robust for nucleic acid detection, which makes it a highly valuable tool for genetic diagnostics based on nucleic acid analysis. Copyright © 2014 Elsevier B.V. All rights reserved.

  5. Species-specific protein sequence and fold optimizations

    Directory of Open Access Journals (Sweden)

    Michalickova Katerina

    2002-12-01

    Full Text Available Abstract Background An organism's ability to adapt to its particular environmental niche is of fundamental importance to its survival and proliferation. In the largest study of its kind, we sought to identify and exploit the amino-acid signatures that make species-specific protein adaptation possible across 100 complete genomes. Results Environmental niche was determined to be a significant factor in variability from correspondence analysis using the amino acid composition of over 360,000 predicted open reading frames (ORFs from 17 archae, 76 bacteria and 7 eukaryote complete genomes. Additionally, we found clusters of phylogenetically unrelated archae and bacteria that share similar environments by amino acid composition clustering. Composition analyses of conservative, domain-based homology modeling suggested an enrichment of small hydrophobic residues Ala, Gly, Val and charged residues Asp, Glu, His and Arg across all genomes. However, larger aromatic residues Phe, Trp and Tyr are reduced in folds, and these results were not affected by low complexity biases. We derived two simple log-odds scoring functions from ORFs (CG and folds (CF for each of the complete genomes. CF achieved an average cross-validation success rate of 85 ± 8% whereas the CG detected 73 ± 9% species-specific sequences when competing against all other non-redundant CG. Continuously updated results are available at http://genome.mshri.on.ca. Conclusion Our analysis of amino acid compositions from the complete genomes provides stronger evidence for species-specific and environmental residue preferences in genomic sequences as well as in folds. Scoring functions derived from this work will be useful in future protein engineering experiments and possibly in identifying horizontal transfer events.

  6. DNA tetrahedron and star trigon nanostructures for target recycling detection of nucleic acid.

    Science.gov (United States)

    Li, Yueran; Chen, Xifeng; Wang, Bidou; Liu, Guangxing; Tang, Yuguo; Miao, Peng

    2016-06-01

    Human immunodeficiency virus (HIV) is a retrovirus which attacks the human body's immune system and further leads to acquired immunodeficiency syndrome (AIDS). Nucleic acid detection is of great importance in the medical diagnosis of such diseases. Herein, we develop a simple and enzyme-free electrochemical method for the target recycling detection of nuclei acid. DNA tetrahedron and star trigon nanostructures are designed and constructed on the electrode interface for target capture and signal enrichment. This strategy is convenient and sensitive, with a limit of detection as low as 1 fM, and can also successfully distinguish single-base mismatched DNA. Therefore, the proposed method has a promising potential application for HIV DNA detection.

  7. Isothermal amplification detection of nucleic acids by a double-nicked beacon.

    Science.gov (United States)

    Shi, Chao; Zhou, Meiling; Pan, Mei; Zhong, Guilin; Ma, Cuiping

    2016-03-01

    Isothermal and rapid amplification detection of nucleic acids is an important technology in environmental monitoring, foodborne pathogen detection, and point-of-care clinical diagnostics. Here we have developed a novel method of isothermal signal amplification for single-stranded DNA (ssDNA) detection. The ssDNA target could be used as an initiator, coupled with a double-nicked molecular beacon, to originate amplification cycles, achieving cascade signal amplification. In addition, the method showed good specificity and strong anti-jamming capability. Overall, it is a one-pot and isothermal strand displacement amplification method without the requirement of a stepwise procedure, which greatly simplifies the experimental procedure and decreases the probability of contamination of samples. With its advantages, the method would be very useful to detect nucleic acids in point-of-care or field use.

  8. The Fold of Commitment

    DEFF Research Database (Denmark)

    Raastrup Kristensen, Anders; Pedersen, Michael

    2016-01-01

    This paper serves two purposes. First, a rereading of Douglas McGregor’s An uneasy look at performance appraisal serves to show how McGregor’s conceptualization of commitment as a question of integrating personal goals with organizational purpose has helped shape founding the modern understanding...... of corporate community representation. Second, we suggest that French philosopher Gilles Deleuze’s concepts of fold, desire and interests can be useful in comprehending this modern form of corporate representation already present in McGregor’s text....

  9. Folding of Pollen Grains

    Science.gov (United States)

    Katifori, Eleni; Alben, Silas; Cerda, Enrique; Nelson, David; Dumais, Jacques

    2008-03-01

    At dehiscence, which occurs when the anther reaches maturity and opens, pollen grains dehydrate and their volume is reduced. The pollen wall deforms to accommodate the volume loss, and the deformation pathway depends on the initial turgid pollen grain geometry and the mechanical properties of the pollen wall. We demonstrate, using both experimental and theoretical approaches, that the design of the apertures (areas on the pollen wall where the stretching and the bending modulus are reduced) is critical for controlling the folding pattern, and ensures the pollen grain viability. An excellent fit to the experiments is obtained using a discretized version of the theory of thin elastic shells.

  10. Detection of Boronic Acids through Excited-State Intramolecular Proton-Transfer Fluorescence

    Science.gov (United States)

    Aronoff, Matthew R.; VanVeller, Brett

    2013-01-01

    Boronic acids are versatile reagents for the chemical synthesis of organic molecules. They and other boron-containing compounds can be detected readily by the interruption of the excited-state intramolecular proton transfer (ESIPT) of 10-hydroxybenzo[h]quinolone. This method is highly sensitive and selective, and useful for monitoring synthetic reactions and detecting boron-containing compounds on a solid support. PMID:24099104

  11. Contemporary nucleic acid-based molecular techniques for detection, identification, and characterization of Bifidobacterium.

    Science.gov (United States)

    Mianzhi, Yao; Shah, Nagendra P

    2017-03-24

    Bifidobacteria are one of the most important bacterial groups found in the gastrointestinal tract of humans. Medical and food industry researchers have focused on bifidobacteria because of their health-promoting properties. Researchers have historically relied on classic phenotypic approaches (culture and biochemical tests) for detection and identification of bifidobacteria. Those approaches still have values for the identification and detection of some bifidobacterial species, but they are often labor-intensive and time-consuming and can be problematic in differentiating closely related species. Rapid, accurate, and reliable methods for detection, identification, and characterization of bifidobacteria in a mixed bacterial population have become a major challenge. The advent of nucleic acid-based molecular techniques has significantly advanced isolation and detection of bifidobacteria. Diverse nucleic acid-based molecular techniques have been employed, including hybridization, target amplification, and fingerprinting. Certain techniques enable the detection, characterization, and identification at genus-, species-, and strains-levels, whereas others allow typing of species or strains of bifidobacteria. In this review, an overview of methodological principle, technique complexity, and application of various nucleic acid-based molecular techniques for detection, identification, and characterization of bifidobacteria is presented. Advantages and limitations of each technique are discussed, and significant findings based on particular techniques are also highlighted.

  12. Simultaneous Detection of Dopamine and Uric Acid under Coexistence of Ascorbic Acid with DNA/Pt Nanocluster Modified Electrode

    Institute of Scientific and Technical Information of China (English)

    ZHENG Yu; LIN Xiang-Qin

    2008-01-01

    A novel biosensor by electrochemically codeposited Pt nanoclusters and DNA film was constructed and applied to detection of dopamine(DA)and uric acid(UA)in the presence of high concentration ascorbic acid(AA).Scanning electron microscopy and X-ray photoelectron spectroscopy were used for characterization.This electrode was successfully used to resolve the overlapping voltammetric response of DA,UA and AA into three well-defined peaks with a large anodic peak difference(△Epa)of about 184 mV for DA and 324 mV for UA.The catalytic peak current obtained from differential pulse voltammetry was linearly dependent on the DA concentration from 1.1×10-7 to 3.8×10-5 mol·L-1 with a detection limit of 3.6 X 10-8 mol·L-1(S/N=3)and on the UA concentration from 3.0X 10-7 to 5.7X 10-5 mol·L-1 with a detection limit of 1.0×10-7 mol·L-1 with coexistence of 1.0X 10-3 mol·L-1 AA.The modified electrode shows good sensitivity and selectivity.

  13. Capillary electrophoresis method with UV-detection for analysis of free amino acids concentrations in food.

    Science.gov (United States)

    Omar, Mei Musa Ali; Elbashir, Abdalla Ahmed; Schmitz, Oliver J

    2017-01-01

    Simple and inexpensive capillary electrophoresis with UV-detection method (CE-UV) was optimized and validated for determination of six amino acids namely (alanine, asparagine, glutamine, proline, serine and valine) for Sudanese food. Amino acids in the samples were derivatized with 4-chloro-7-nitro-2,1,3-benzoxadiazole (NBD-Cl) prior to CE-UV analysis. Labeling reaction conditions (100mM borate buffer at pH 8.5, labeling reaction time 60min, temperature 70°C and NBD-Cl concentration 40mM) were systematically investigated. The optimal conditions for the separation were 100mM borate buffer at pH 9.7 and detected at 475nm. The method was validated in terms of linearity, limit of detection (LOD), limit of quantification (LOQ), precision (repeatability) (RSD%) and accuracy (recovery). Good linearity was achieved for all amino acids (r(2)>0.9981) in the concentration range of 2.5-40mg/L. The LODs in the range of 0.32-0.56mg/L were obtained. Recoveries of amino acids ranging from 85% to 108%, (n=3) were obtained. The validated method was successfully applied for the determination of amino acids for Sudanese food samples.

  14. Application of RP-HPLC in Detecting Content of Ferulic Acid in Fuke Qianjin Capsule

    Directory of Open Access Journals (Sweden)

    Ming-zhi WANG

    2015-09-01

    Full Text Available Objective: To establish a method for the determination of ferulic acid content in Fuke Qianjin Capsule. Methods: Reversed phase high performance liquid chromatography (RP-HPLC was applied in this study, with the detection conditions as follows: chromatographic column: Boston green ODS·min-1, detection wavelength: 316 nm, and column temperature: 30℃. C18 (250 mm × 4.6 mm, 5 μm, mobile phase: methanol-0.1% phosphoric acid (25:75, flow velocity: 1.0 mLResults: Ferulic acid, whose sample size was 0.017760-0.10656 μg, was in favorable linear relationship with the integral value of peak area, with correlation coefficient r=0.9998. The average sample-injecting recovery rate and degree of precision (RSD were 97.6% (n=6 and 1.6%, respectively. The results of this study also showed that the specificity of RP-HPLC in this study was excellent; negative samples had no interference on chromatographic peak of target substance (ferulic acid; and RSD of accuracy, repeatability, stability and recovery rate were 1.1%, 1.4%, 1.2% and 1.6%, respectively.Conclusion: RP-HPLC is accurate, rapid, stable and convenient, so it can be used as an optimal method for the detection of ferulic acid content in Fuke Qianjin Capsule.

  15. Sulfuric acid-ammonium sulfate aerosol: optical detection in the St. Louis region.

    Science.gov (United States)

    Charlson, R J; Vanderpol, A H; Covert, D S; Waggnoner, A P; Ahlquist, N C

    1974-04-12

    Nephelometric sensing of the deliquescence of ammonium sulfate produced by the reaction of sulfuric acid or ammonium bisulfate aerosol with ammonia provides a means for detecting these substances in air. Field experiments show them to be the dominant substances in the submicrometer, light-scattering aerosol in the St. Louis region.

  16. Analysis of Ascorbic Acid in Single Human Neutrophils by Electrochemical Detection

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Ascorbic acid in individual human neutrophils was determined by capillary zone electrophoresis with electrochemical detection. In order to overcome the influence of the adsorption of the substances in cells on the inner surface wall of the capillary on the migration time and the number of theoretical plates, a procedure for treating capillaries has been described.

  17. Graphene-carbon nanotube composite aerogel for selective detection of uric acid

    Science.gov (United States)

    Zhang, Feifei; Tang, Jie; Wang, Zonghua; Qin, Lu-Chang

    2013-12-01

    Graphene and single-walled carbon nanotube (SWNT) composite aerogel has been prepared by hydrothermal synthesis. The restacking of graphene is effectively reduced by SWNTs inserted in between graphene layers in order to make available more active sites and reactive surface area. Electrochemical experiments show that the graphene-SWNT composite electrode has superior catalytic performance in selective detection of uric acid (UA).

  18. Monitoring the Hydrolysis of Olive Oil Catalyzed by Lipase via Acid Value Detection

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Hydrolysis of olive oil catalyzed by Candida lipolytica lipase was investigated. The relative concentration of the components in the product was determined by using high performance liquid chromatography(HPLC). Furthermore, a novel rapid method to detect the hydrolytic process of olive oil was developed based on the relationship between the acid value and the relative concentration of the different components.

  19. [Micro-droplet characterization and its application for amino acid detection in droplet microfluidic system].

    Science.gov (United States)

    Yuan, Huiling; Dong, Libing; Tu, Ran; Du, Wenbin; Ji, Shiru; Wang, Qinhong

    2014-01-01

    Recently, the droplet microfluidic system attracts interests due to its high throughput and low cost to detect and screen. The picoliter micro-droplets from droplet microfluidics are uniform with respect to the size and shape, and could be used as monodispensed micro-reactors for encapsulation and detection of single cell or its metabolites. Therefore, it is indispensable to characterize micro-droplet and its application from droplet microfluidic system. We first constructed the custom-designed droplet microfluidic system for generating micro-droplets, and then used the micro-droplets to encapsulate important amino acids such as glutamic acid, phenylalanine, tryptophan or tyrosine to test the droplets' properties, including the stability, diffusivity and bio-compatibility for investigating its application for amino acid detection and sorting. The custom-designed droplet microfluidic system could generate the uniformed micro-droplets with a controllable size between 20 to 50 microm. The micro-droplets could be stable for more than 20 h without cross-contamination or fusion each other. The throughput of detection and sorting of the system is about 600 micro-droplets per minute. This study provides a high-throughput platform for the analysis and screening of amino acid-producing microorganisms.

  20. Sensitive Thin-Layer Chromatography Detection of Boronic Acids Using Alizarin

    NARCIS (Netherlands)

    Duval, F.L.; Beek, van T.A.; Zuilhof, H.

    2012-01-01

    A new method for the selective and sensitive detection of boronic acids on thin-layer chromatography plates is described. The plate is briefly dipped in an alizarin solution, allowed to dry in ambient air, and observed under 366 nm light. Alizarin emits a bright yellow fluorescence only in the prese

  1. Nucleic acid sequence-based amplification with oligochromatography for detection of Trypanosoma brucei in clinical samples

    NARCIS (Netherlands)

    C.M. Mugasa; T. Laurent; G.J. Schoone; P.A. Kager; G.W. Lubega; H.D.F.H. Schallig

    2009-01-01

    Molecular tools, such as real-time nucleic acid sequence-based amplification (NASBA) and PCR, have been developed to detect Trypanosoma brucei parasites in blood for the diagnosis of human African trypanosomiasis (HAT). Despite good sensitivity, these techniques are not implemented in HAT control pr

  2. Detection of p-coumaric acid from cell supernatant using surfaceenhanced Raman spectroscopy

    DEFF Research Database (Denmark)

    Morelli, Lidia; Jendresen, Christian Bille; Zor, Kinga

    2016-01-01

    A standard protocol for analysis of microbial factories requires the screening of several populations in order to find the bestperforming ones. Standard analytical methods usually include high performance liquid chromatography (HPLC), thin layerchromatography (TLC) or spectrophotometry, which...... on detection ofp-coumaric acid (pHCA) in cell supernatant.SERS active substrates, based on leaning gold-capped silicon nanopillars, were used for detection. They were successfullyused to detect culture medium spiked with pHCA, and the effect of medium dilution was studied. For analysis of biologicalproduction...

  3. Optical biosensor based on liquid crystal droplets for detection of cholic acid

    Science.gov (United States)

    Niu, Xiaofang; Luo, Dan; Chen, Rui; Wang, Fei; Sun, Xiaowei; Dai, Haitao

    2016-12-01

    A highly sensitive cholic acid biosensor based on 4-cyano-4‧-penthlbiphenyl (5CB) Liquid crystal droplets in phosphate buffer saline solution was reported. A radial-to-bipolar transition of 5CB droplet would be triggered during competitive reaction of CA at the sodium dodecyl sulfate surfactant-laden 5CB droplet surface. Our liquid crystal droplet sensor is a low-cost, simple and fast method for CA detection. The detection limit (5 μM) of our method is 2.4 times lower than previously report by using liquid crystal film to detection of CA.

  4. Cluster Formation of Sulfuric Acid with Dimethylamine or Diamines and Detection with Chemical Ionization

    Science.gov (United States)

    Jen, C. N.; McMurry, P. H.; Hanson, D. R.

    2015-12-01

    Chemical ionization (CI) mass spectrometers are used to study atmospheric nucleation by detecting clusters produced by reactions of sulfuric acid and various basic gases. These instruments typically use nitrate to chemically ionize clusters for detection. In this study, we compare measured cluster concentrations formed by reacting sulfuric acid vapor with dimethylamine, ethylene diamine, tetramethylethylene diamine, or butanediamine (also known as putrescine) using nitrate and acetate ions. We show from flow reactor measurements that nitrate is unable to chemically ionize clusters with weak acidities. In addition, we vary the ion-molecule reaction time to probe the chemical ionization processes and lifetimes of ions composed of sulfuric acid and base molecules. We then model the neutral and ion cluster formation pathways, including chemical ionization, ion-induced clustering, and ion decomposition, to better identify which cluster types cannot be chemically ionized by nitrate. Our results show that sulfuric acid dimer with two diamines and sulfuric acid trimer with 2 or more base molecules cannot be chemical ionized by nitrate. We conclude that cluster concentrations measured with acetate CI gives a better representation of both cluster abundancies and their base content than nitrate CI.

  5. TRACE ANALYSIS OF FLUORESCEIN-DERIVATIZED PHENOXY ACID HERBICIDES BY MICELLAR ELECTROKINETIC CHROMATOGRAPHY WITH LASER-INDUCTED FLUORESCENCE DETECTION

    Science.gov (United States)

    Micellar electrokinetic chromatography (MEKC) with laser-induced fluorescence (LIF) detection was used for the trace analysis of phenoxy acid herbicides. Capillary electrophoresis (CE) with LIF detection, which has not previously been used for pesticide analysis, overcomes the po...

  6. Haustral fold segmentation with curvature-guided level set evolution.

    Science.gov (United States)

    Zhu, Hongbin; Barish, Matthew; Pickhardt, Perry; Liang, Zhengrong

    2013-02-01

    Human colon has complex structures mostly because of the haustral folds. The folds are thin flat protrusions on the colon wall, which complicate the shape analysis for computer-aided detection (CAD) of colonic polyps. Fold segmentation may help reduce the structural complexity, and the folds can serve as an anatomic reference for computed tomographic colonography (CTC). Therefore, in this study, based on a model of the haustral fold boundaries, we developed a level-set approach to automatically segment the fold surfaces. To evaluate the developed fold segmentation algorithm, we first established the ground truth of haustral fold boundaries by experts' drawing on 15 patient CTC datasets without severe under/over colon distention from two medical centers. The segmentation algorithm successfully detected 92.7% of the folds in the ground truth. In addition to the sensitivity measure, we further developed a merit of segmented-area ratio (SAR), i.e., the ratio between the area of the intersection and union of the expert-drawn folds and the area of the automatically segmented folds, to measure the segmentation accuracy. The segmentation algorithm reached an average value of SAR = 86.2%, showing a good match with the ground truth on the fold surfaces. We believe the automatically segmented fold surfaces have the potential to benefit many postprocedures in CTC, such as CAD, taenia coli extraction, supine-prone registration, etc.

  7. Analysis of Glutamic Acid in Cerebrospinal Fluid by Capillary Electrophoresis with High Frequency Conductivity Detection

    Institute of Scientific and Technical Information of China (English)

    Hai Yun ZHAI; Jun Mei WANG; Xiao Li YAO; Xue Cai TAN; Pei Xiang CAI; Zuan Guang CHEN

    2005-01-01

    A rapid method to determine glutamic acid (Glu) in cerebrospinal fluid (CSF) by capillary electrophoresis with high frequency conductivity detection (contactless conductivity detection) was described. The CSF sample was pretreated with silver cation resin to remove high concentration of Cl- ions in CSF. The separation was achieved in the buffer solution of 10 mmol/L Tris and 8 mmol/L boric acid at the separation voltage of 20.0 kV. Glu showed linear response in the range of 5.0×10-6 to 6.0×10-3 mol/L, the limit of detection was 1.0×10-6 mol/L. The method was used for analysis Glu in CSF satisfactorily with a recovery of 97.8-98.8%.

  8. A micro E-DNA sensor for selective detection of dopamine in presence of ascorbic acid

    Institute of Scientific and Technical Information of China (English)

    朱丹; 李敏; 王丽华; 左小磊

    2015-01-01

    In this paper, a novel method for selectively detection of dopamine (DA) in the interference of ascorbic acid (AA) is described. A nanometer-sized gold flower microelectrode (NGFME) is prepared by flame-etching and electrochemical deposition. The electrode tip was characterized by scanning electron microscope (SEM). The NGFME is sized at about 100 µm and dimensions of thorns of the electrode were in nanometers. By modifying with DA aptamer on the surface, the prepared aptasensor can selectively detect DA even in the presence of high concentration AA. Experimental results show that this NGFME has no response to AA. As a comparison, the carbon fiber electrode without DA aptamer modification is unable to effectively detect DA in the presence of AA. The NGFME is easy-to-prepare, selective and sensitive for DA detection down to 25 µM. The electrode can be expected to detect DA in vivo and in real biological samples.

  9. Unifying model for two-state and downhill protein folding

    Science.gov (United States)

    Mi, D.; Meng, W. Q.; Sun, Y. Q.

    2011-04-01

    A protein-folding model is proposed at the amino acid level, in which the folding process is divided into two successive stages: the rate-determining step, dominated by the “stochastic interactions”of solvent molecules, and the rapid phase, dominated by the “order interactions”among atoms in polypeptide. The master equation approach is used to investigate the folding kinetics, and an analytical treatment of the master equation yields a simple three-parameter expression for folding time. It is found that both two-state and downhill protein-folding kinetics can be described by a unifying model.

  10. Quantification of underivatized fatty acids from vegetable oils by HPLC with UV detection.

    Science.gov (United States)

    Guarrasi, V; Mangione, M R; Sanfratello, V; Martorana, V; Bulone, D

    2010-09-01

    We propose a chromatographic method for the separation of saturated and unsaturated fatty acids by a high-performance liquid chromatography system, equipped with a photo diode array detector. Central to the method is the use of an appropriate mobile phase composed of acetonitrile, methanol, and n-hexane in ratio 90:8:2 acidified with 0.2% acetic acid, which allows the detection of fatty acids without a preliminary derivatization with chromophores or fluorescent dyes. Calibration on solutions of standards mixtures gives a quantification limit (at a wavelength of 208 nm) of 0.232, 0.093, 0.039, 0.056, 0.068, 0.004, 0.0005, 0.067 mg/mL for the myristic, palmitic, palmitoleic, stearic, oleic, linoleic, linolenic, and erucic acids, respectively. The method, applied to different vegetable oils (olive, sunflower, soybean, and palm) was able to distinguish the main fatty acids and quantify their amount. Data reliability was tested by comparing our results (on the relative percentages of some fatty acids in the olive oil) with those obtained by gas chromatographic analysis. Differences of the order of 0.3%, 0.6%, 2%, and 6% were observed for the oleic, linoleic, palmitic, and linolenic acids. Although less accurate, our method proved to be a simple alternative to standard gas chromatographic technique, as it can be applied even using a simple UV detector.

  11. Nucleic Acid Extraction from Synthetic Mars Analog Soils for in situ Life Detection

    Science.gov (United States)

    Mojarro, Angel; Ruvkun, Gary; Zuber, Maria T.; Carr, Christopher E.

    2017-08-01

    Biological informational polymers such as nucleic acids have the potential to provide unambiguous evidence of life beyond Earth. To this end, we are developing an automated in situ life-detection instrument that integrates nucleic acid extraction and nanopore sequencing: the Search for Extra-Terrestrial Genomes (SETG) instrument. Our goal is to isolate and determine the sequence of nucleic acids from extant or preserved life on Mars, if, for example, there is common ancestry to life on Mars and Earth. As is true of metagenomic analysis of terrestrial environmental samples, the SETG instrument must isolate nucleic acids from crude samples and then determine the DNA sequence of the unknown nucleic acids. Our initial DNA extraction experiments resulted in low to undetectable amounts of DNA due to soil chemistry-dependent soil-DNA interactions, namely adsorption to mineral surfaces, binding to divalent/trivalent cations, destruction by iron redox cycling, and acidic conditions. Subsequently, we developed soil-specific extraction protocols that increase DNA yields through a combination of desalting, utilization of competitive binders, and promotion of anaerobic conditions. Our results suggest that a combination of desalting and utilizing competitive binders may establish a "universal" nucleic acid extraction protocol suitable for analyzing samples from diverse soils on Mars.

  12. Prostate-specific RNA aptamer: promising nucleic acid antibody-like cancer detection.

    Science.gov (United States)

    Marangoni, Karina; Neves, Adriana F; Rocha, Rafael M; Faria, Paulo R; Alves, Patrícia T; Souza, Aline G; Fujimura, Patrícia T; Santos, Fabiana A A; Araújo, Thaise G; Ward, Laura S; Goulart, Luiz R

    2015-07-15

    We described the selection of a novel nucleic acid antibody-like prostate cancer (PCa) that specifically binds to the single-stranded DNA molecule from a 277-nt fragment that may have been partially paired and bound to the PCA3 RNA conformational structure. PCA3-277 aptamer ligands were obtained, and the best binding molecule, named CG3, was synthesized for validation. Aiming to prove its diagnostic utility, we used an apta-qPCR assay with CG3-aptamer conjugated to magnetic beads to capture PCA3 transcripts, which were amplified 97-fold and 7-fold higher than conventional qPCR in blood and tissue, respectively. Histopathologic analysis of 161 prostate biopsies arranged in a TMA and marked with biotin-labeled CG3-aptamer showed moderate staining in both cytoplasm and nucleus of PCa samples; in contrast, benign prostatic hyperplasia (BPH) samples presented strong nuclear staining (78% of the cases). No staining was observed in stromal cells. In addition, using an apta-qPCR, we demonstrated that CG3-aptamer specifically recognizes the conformational PCA3-277 molecule and at least three other transcript variants, indicating that long non-coding RNA (lncRNA) is processed after transcription. We suggest that CG3-aptamer may be a useful PCa diagnostic tool. In addition, this molecule may be used in drug design and drug delivery for PCa therapy.

  13. Understanding the role of the topology in protein folding by computational inverse folding experiments.

    Science.gov (United States)

    Mucherino, Antonio; Costantini, Susan; di Serafino, Daniela; D'Apuzzo, Marco; Facchiano, Angelo; Colonna, Giovanni

    2008-08-01

    Recent studies suggest that protein folding should be revisited as the emergent property of a complex system and that the nature allows only a very limited number of folds that seem to be strongly influenced by geometrical properties. In this work we explore the principles underlying this new view and show how helical protein conformations can be obtained starting from simple geometric considerations. We generated a large data set of C-alpha traces made of 65 points, by computationally solving a backbone model that takes into account only topological features of the all-alpha proteins; then, we built corresponding tertiary structures, by using the sequences associated to the crystallographic structures of four small globular all-alpha proteins from PDB, and analysed them in terms of structural and energetic properties. In this way we obtained four poorly populated sets of structures that are reasonably similar to the conformational states typical of the experimental PDB structures. These results show that our computational approach can capture the native topology of all-alpha proteins; furthermore, it generates backbone folds without the influence of the side chains and uses the protein sequence to select a specific fold among the generated folds. This agrees with the recent view that the backbone plays an important role in the protein folding process and that the amino acid sequence chooses its own fold within a limited total number of folds.

  14. Deletion of mitochondrial associated ubiquitin fold modifier protein Ufm1 in Leishmania donovani results in loss of β-oxidation of fatty acids and blocks cell division in the amastigote stage.

    Science.gov (United States)

    Gannavaram, Sreenivas; Connelly, Patricia S; Daniels, Mathew P; Duncan, Robert; Salotra, Poonam; Nakhasi, Hira L

    2012-10-01

    Recently, we described the existence of the ubiquitin fold modifier 1 (Ufm1) and its conjugation pathway in Leishmania donovani. We demonstrated the conjugation of Ufm1 to proteins such as mitochondrial trifunctional protein (MTP) that catalyses β-oxidation of fatty acids in L. donovani. To elucidate the biological roles of the Ufm1-mediated modifications, we made an L. donovani Ufm1 null mutant (Ufm1(-/-)). Loss of Ufm1 and consequently absence of Ufm1 conjugation with MTP resulted in diminished acetyl-CoA, the end-product of the β-oxidation in the Ufm1(-/-) amastigote stage. The Ufm1(-/-) mutants showed reduced survival in the amastigote stage in vitro and ex vivo in human macrophages. This survival was restored by re-expression of wild-type Ufm1 with concomitant induction of acetyl-CoA but not by re-expressing the non-conjugatable Ufm1, indicating the essential nature of Ufm1 conjugation and β-oxidation. Both cell cycle analysis and ultrastructural studies of Ufm1(-/-) parasites confirmed the role of Ufm1 in amastigote growth. The defect in vitro growth of amastigotes in human macrophages was further substantiated by reduced survival. Therefore, these studies suggest the importance of Ufm1 in Leishmania pathogenesis with larger impact on other organisms and further provide an opportunity to test Ufm1(-/-) parasites as drug and vaccine targets.

  15. Desiccation and zinc binding induce transition of tomato abscisic acid stress ripening 1, a water stress- and salt stress-regulated plant-specific protein, from unfolded to folded state.

    Science.gov (United States)

    Goldgur, Yehuda; Rom, Slava; Ghirlando, Rodolfo; Shkolnik, Doron; Shadrin, Natalia; Konrad, Zvia; Bar-Zvi, Dudy

    2007-02-01

    Abscisic acid stress ripening 1 (ASR1) is a low molecular weight plant-specific protein encoded by an abiotic stress-regulated gene. Overexpression of ASR1 in transgenic plants increases their salt tolerance. The ASR1 protein possesses a zinc-dependent DNA-binding activity. The DNA-binding site was mapped to the central part of the polypeptide using truncated forms of the protein. Two additional zinc-binding sites were shown to be localized at the amino terminus of the polypeptide. ASR1 protein is presumed to be an intrinsically unstructured protein using a number of prediction algorithms. The degree of order of ASR1 was determined experimentally using nontagged recombinant protein expressed in Escherichia coli and purified to homogeneity. Purified ASR1 was shown to be unfolded using dynamic light scattering, gel filtration, microcalorimetry, circular dichroism, and Fourier transform infrared spectrometry. The protein was shown to be monomeric by analytical ultracentrifugation. Addition of zinc ions resulted in a global change in ASR1 structure from monomer to homodimer. Upon binding of zinc ions, the protein becomes ordered as shown by Fourier transform infrared spectrometry and microcalorimetry, concomitant with dimerization. Tomato (Solanum lycopersicum) leaf soluble ASR1 is unstructured in the absence of added zinc and gains structure upon binding of the metal ion. The effect of zinc binding on ASR1 folding and dimerization is discussed.

  16. Isothermal Amplification Methods for the Detection of Nucleic Acids in Microfluidic Devices

    Directory of Open Access Journals (Sweden)

    Giuseppe Spoto

    2012-12-01

    Full Text Available Diagnostic tools for biomolecular detection need to fulfill specific requirements in terms of sensitivity, selectivity and high-throughput in order to widen their applicability and to minimize the cost of the assay. The nucleic acid amplification is a key step in DNA detection assays. It contributes to improving the assay sensitivity by enabling the detection of a limited number of target molecules. The use of microfluidic devices to miniaturize amplification protocols reduces the required sample volume and the analysis times and offers new possibilities for the process automation and integration in one single device. The vast majority of miniaturized systems for nucleic acid analysis exploit the polymerase chain reaction (PCR amplification method, which requires repeated cycles of three or two temperature-dependent steps during the amplification of the nucleic acid target sequence. In contrast, low temperature isothermal amplification methods have no need for thermal cycling thus requiring simplified microfluidic device features. Here, the use of miniaturized analysis systems using isothermal amplification reactions for the nucleic acid amplification will be discussed.

  17. Direct determination of amino acids and carbohydrates by high-performance capillary electrophoresis with refractometric detection.

    Science.gov (United States)

    Ivano, A R; Nazimov, I V; Lobazov, A P; Popkovich, G B

    2000-10-13

    This is an initial report to propose a novel approach in high-performance capillary electrophoresis (HPCE) for the direct detection of compounds without natural absorbance in the UV and visible spectral range, such as amino acids and carbohydrates. A refractometry detector with the 2 nl cell (Applied Systems, Minsk, Belarus) was employed to identify amino acids and carbohydrates without derivatization. The first results are provided on separation of seven free amino acids in the phosphate running buffer and three free carbohydrates in the borate-sodium dodecyl sulfate running buffer and detection by refractometer. Fused capillaries of 50 or 75 microm internal diameter and separation voltage (10-23 kV) were applied. Detection limits ranged typically from 10 to 100 fmol and the response was linear over two orders of magnitude for most of the amino acids and carbohydrates. The HPCE system demonstrated good long-term stability and reproducibility with a relative standard deviation, less than 5% for the migration time (n=10).

  18. Strong emissive nanofibers of organogels for the detection of volatile acid vapors.

    Science.gov (United States)

    Xue, Pengchong; Sun, Jiabao; Yao, Boqi; Gong, Peng; Zhang, Zhenqi; Qian, Chong; Zhang, Yuan; Lu, Ran

    2015-03-16

    Two L-phenylalanine derivatives with 5,8-bis(2-(carbazol-3-yl)vinyl)quinoxaline (PCQ) and 5,8-bis[2-(carbazol-3-yl)]-2,3-dimethylquinoxaline (DCQ) as fluorophores were synthesized, and their photophysical properties were measured and compared. The two compounds were found to gelate some organic solvents and self-assemble into 1D nanofibers in gels. The wet gel of PCQ emitted a weak orange fluorescence, but the DCQ gel had a strong green one. This result can be due to the presence of two methyl groups and the nonplanar conformation of fluorophore in DCQ. The gel film of DCQ also showed significantly stronger fluorescence than that of PCQ. Thus, the wet gel and xerogel film of DCQ were selected to study their sensing properties to acids. The yellow wet gel of DCQ transformed into a brown sol upon the addition of 0.2 equiv trifluoroacetic acid (TFA), accompanied by emission quenching. The xerogel film of DCQ rapidly responded to volatile acids, such as TFA, HCl, and HOAc. The fluorescence of the xerogel film was gradually quenched with increased concentration of volatile acid vapors. The fibrous film exhibited low detection limits for volatile acid. The detection limits of the thin films for TFA, HCl, and HOAc reached 43, 122, and 950 ppb, respectively.

  19. A Novel Fiber Optic Surface Plasmon Resonance Biosensors with Special Boronic Acid Derivative to Detect Glycoprotein

    Directory of Open Access Journals (Sweden)

    Yang Zhang

    2017-10-01

    Full Text Available We proposed and demonstrated a novel tilted fiber Bragg grating (TFBG-based surface plasmon resonance (SPR label-free biosensor via a special boronic acid derivative to detect glycoprotein with high sensitivity and selectivity. TFBG, as an effective sensing element for optical sensing in near-infrared wavelengths, possess the unique capability of easily exciting the SPR effect on fiber surface which coated with a nano-scale metal layer. SPR properties can be accurately detected by measuring the variation of transmitted spectra at optical communication wavelengths. In our experiment, a 10° TFBG coated with a 50 nm gold film was manufactured to stimulate SPR on a sensor surface. To detect glycoprotein selectively, the sensor was immobilized using designed phenylboronic acid as the recognition molecule, which can covalently bond with 1,2- or 1,3-diols to form five- or six-membered cyclic complexes for attaching diol-containing biomolecules and proteins. The phenylboronic acid was synthetized with long alkyl groups offering more flexible space, which was able to improve the capability of binding glycoprotein. The proposed TFBG-SPR sensors exhibit good selectivity and repeatability with a protein concentration sensitivity up to 2.867 dB/ (mg/mL and a limit of detection (LOD of 15.56 nM.

  20. Highly sensitive detection of cancer cells with an electrochemical cytosensor based on boronic acid functional polythiophene.

    Science.gov (United States)

    Dervisevic, Muamer; Senel, Mehmet; Sagir, Tugba; Isik, Sevim

    2017-04-15

    The detection of cancer cells through important molecular recognition target such as sialic acid is significant for the clinical diagnosis and treatment. There are many electrochemical cytosensors developed for cancer cells detection but most of them have complicated fabrication processes which results in poor reproducibility and reliability. In this study, a simple, low-cost, and highly sensitive electrochemical cytosensor was designed based on boronic acid-functionalized polythiophene. In cytosensors fabrication simple single-step procedure was used which includes coating pencil graphite electrode (PGE) by means of electro-polymerization of 3-Thienyl boronic acid and Thiophen. Electrochemical impedance spectroscopy and cyclic voltammetry were used as an analytical methods to optimize and measure analytical performances of PGE/P(TBA0.5Th0.5) based electrode. Cytosensor showed extremely good analytical performances in detection of cancer cells with linear rage of 1×10(1) to 1×10(6) cellsmL(-1) exhibiting low detection limit of 10 cellsmL(-1) and incubation time of 10min. Next to excellent analytical performances, it showed high selectivity towards AGS cancer cells when compared to HEK 293 normal cells and bone marrow mesenchymal stem cells (BM-hMSCs). This method is promising for future applications in early stage cancer diagnosis.

  1. Barcode DNA length polymorphisms vs fatty acid profiling for adulteration detection in olive oil.

    Science.gov (United States)

    Uncu, Ali Tevfik; Uncu, Ayse Ozgur; Frary, Anne; Doganlar, Sami

    2017-04-15

    The aim of this study was to compare the performance of a DNA-barcode assay with fatty acid profile analysis to authenticate the botanical origin of olive oil. To achieve this aim, we performed a PCR-capillary electrophoresis (PCR-CE) approach on olive oil: seed oil blends using the plastid trnL (UAA) intron barcode. In parallel to genomic analysis, we subjected the samples to gas chromatography analysis of fatty acid composition. While the PCR-CE assay proved equally efficient as gas chromatography analysis in detecting adulteration with soybean, palm, rapeseed, sunflower, sesame, cottonseed and peanut oils, it was superior to the widely utilized analytical chemistry approach in revealing the adulterant species and detecting small quantities of corn and safflower oils in olive oil. Moreover, the DNA-based test correctly identified all tested olive oil: hazelnut oil blends whereas it was not feasible to detect hazelnut oil adulteration through fatty acid profile analysis. Thus, the present research has shown the feasibility of a PCR-CE barcode assay to detect adulteration in olive oil.

  2. Fluorescent probes for detection of picric acid explosive: A greener approach

    Energy Technology Data Exchange (ETDEWEB)

    Chakravarty, Sudesna; Gogoi, Bedanta; Sen Sarma, Neelotpal, E-mail: neelot@iasst.gov.in

    2015-09-15

    Green materials with advantages of low cost and high sensitivity are important from the perspective of human health, environment and homeland security. Herein, we have reported two cost effective modified biomaterials as fluorophores for detection of Picric acid in aqueous state. The biomaterials Scutellarin–Hispiduloside and Curcumin have been modified with green solvent glycerol for Picric acid detection in aqueous solution. The limit of detection for Picric acid by Scutellarin–Hispiduloside–glycerol and Curcumin–glycerol are 9.1×10{sup −8} M and 6.03×10{sup −8} M respectively. These luminescence based sensors have also been able to detect Picric acid in real samples with high efficiency. The fluorescence quenching efficiency of Scutellarin–Hispiduloside–glycerol has been found to be 99% while that for Curcumin–glycerol, it is 88.9% for 0.5 µM Picric acid in aqueous state. In both the cases, the quenching is governed by FRET between the fluorophore and the quencher and the FRET efficiency has been found to be 0.968 and 0.792 respectively. In addition, both the systems show excellent selectivity towards PA in presence of other nitroaromatic compounds and are also statistically accessible. The utilization of readily available cheap biomaterials without using multistep protocol for synthesis and devoid of any kind of sophisticated equipments for the processs further enhances the utility of the method. - Highlights: • Environmentally benign systems – Scutellarin, Hispiduloside and curcumin with green solvent glycerol – have been used for Picric acid sensing. • The method is simple and cost effective with a detection limit for CIG and CG found to be 9.1×10−8 M and 6.03×10−8 M of PA respectively. • Both the sensing systems were found to be highly selective for Picric acid in the presence of structurally similar compounds. • The quenching occurs by FRET between the fluorophore and the quencher and the FRET efficiency is determined

  3. How the genome folds

    Science.gov (United States)

    Lieberman Aiden, Erez

    2012-02-01

    I describe Hi-C, a novel technology for probing the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. Working with collaborators at the Broad Institute and UMass Medical School, we used Hi-C to construct spatial proximity maps of the human genome at a resolution of 1Mb. These maps confirm the presence of chromosome territories and the spatial proximity of small, gene-rich chromosomes. We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. The fractal globule is distinct from the more commonly used globular equilibrium model. Our results demonstrate the power of Hi-C to map the dynamic conformations of whole genomes.

  4. Surface-structured molecular sensor for the optical detection of acidity.

    Science.gov (United States)

    Martínez-Otero, Alberto; Evangelio, Emilia; Alibés, Ramon; Bourdelande, José Luis; Ruiz-Molina, Daniel; Busqué, Félix; Hernando, Jordi

    2008-04-01

    In this letter, we report on the development of a surface molecular sensor for the detection of acidity. Lithographically controlled wetting deposition has been applied to form the nanostructure of a new fluorescent compound with three protonation states featuring different optical properties on a glass substrate. Atomic force microscopy demonstrates the functionalization of the surface with ordered arrays of the sensor molecules. The fluorescence properties of the resulting nanopattern at different pH values have been investigated by confocal fluorescene microsopy, thus revealing the fast, sensitive, reversible response of the prepared nanosensor to gas flows of varying acidity.

  5. Determination of ascorbic acid and carotenoids in food commodities by liquid chromatography with mass spectrometry detection.

    Science.gov (United States)

    Frenich, A Garrido; Torres, M E Hernández; Vega, A Belmonte; Vidal, J L Martínez; Bolaños, P Plaza

    2005-09-21

    Two methods, one to determine ascorbic acid and one to determine lycopene and beta-carotene, in vegetables and fruits by liquid chromatography coupled with mass spectrometry (LC-MS) have been established. The chromatographic separation of the studied compounds and their MS parameters were optimized to improve selectivity and sensitivity. In both methods, separation was carried out with two coupled columns, first a C(18) and then a dC(18), using as mobile phase 70% methanol (0.005% acetic acid) and 30% acetic acid 0.05% for ascorbic acid determination and a mixture of methanol, tetrahydrofuran, and acetonitrile (60:30:10 v/v/v) for carotenoid analysis in isocratic mode. The molecular ion was selected for the quantification in selective ion monitoring (SIM) mode. Ascorbic acid was detected with electrospray ionization probe (ESI) in negative mode, while chemical ionization atmospheric pressure (APCI) in positive mode was used for the target carotenoids. The methodology for ascorbic acid analysis is based on an extraction with polytron using methanol and a mixture of methaphosphoric acid and acetic acid. Extraction of the carotenoids was carried out with tetrahydrofuran/methanol (1:1) (v/v). The proposed methods were applied, after their corresponding validations, to the analysis of four varieties of tomatoes, tomato in tin enriched and dried tomato, and to the analysis of mango and kiwi fruits, to compare the content in these compounds. Moreover, the influence of the process of freezing and the effect that the manipulation/preservation has in the content of ascorbic acid in tomato have also been studied.

  6. Selective extraction by dissolvable (nitriloacetic acid-nickel)-layered double hydroxide coupled with reaction with potassium thiocyanate for sensitive detection of iron(III).

    Science.gov (United States)

    Tang, Sheng; Chang, Yuepeng; Shen, Wei; Lee, Hian Kee

    2016-07-01

    A highly selective method has been proposed for the determination of iron cation (Fe(3+)). (Nitriloacetic acid-nickel)-layered double hydroxide ((NTA-Ni)-LDH) was successfully synthesized and used as dissolvable sorbent in dispersive solid-phase extraction to pre-concentrate and separate Fe(3+) from aqueous phase. Since Fe(3+) has a larger formation constant with NTA compared to Ni(2+), subsequently ion exchange occurred when (NTA-Ni)-LDH was added to the sample solution. The resultant (NTA-Fe)-LDH sol was isolated and transferred in an acidic medium containing potassium thiocyanate (KSCN). Since (NTA-Fe)-LDH could be dissolved in acidic conditions, Fe(3+)was released and reacted with SCN(-) to form an Fe-SCN complex. The resulting product was measured by ultraviolet-visible spectrometry for quantitative detection of Fe(3+). Extraction factors, including sample pH, reaction pH, extraction temperature, extraction time, reaction time and concentration of KSCN were optimized. This method achieved a low limit of detection of 15.2nM and a good linear range from 0.05 to 50μM (r(2)=0.9937). A nearly 18-fold enhancement of signal intensity was achieved after selective extraction. The optimized conditions were validated by applying the method to determine Fe(3+) in seawater samples.

  7. Relative analytical sensitivity of donor nucleic acid amplification technology screening and diagnostic real-time polymerase chain reaction assays for detection of Zika virus RNA.

    Science.gov (United States)

    Stone, Mars; Lanteri, Marion C; Bakkour, Sonia; Deng, Xutao; Galel, Susan A; Linnen, Jeffrey M; Muñoz-Jordán, Jorge L; Lanciotti, Robert S; Rios, Maria; Gallian, Pierre; Musso, Didier; Levi, José E; Sabino, Ester C; Coffey, Lark L; Busch, Michael P

    2017-03-01

    Zika virus (ZIKV) has spread rapidly in the Pacific and throughout the Americas and is associated with severe congenital and adult neurologic outcomes. Nucleic acid amplification technology (NAT) assays were developed for diagnostic applications and for blood donor screening on high-throughput NAT systems. We distributed blinded panels to compare the analytical performance of blood screening relative to diagnostic NAT assays. A 25-member, coded panel (11 half-log dilutions of a 2013 French Polynesia ZIKV isolate and 2015 Brazilian donor plasma implicated in transfusion transmission, and 3 negative controls) was sent to 11 laboratories that performed 17 assays with 2 to 12 replicates per panel member. Results were analyzed for the percentage reactivity at each dilution and by probit analysis to estimate the 50% and 95% limits of detection (LOD50 and LOD95 , respectively). Donor-screening NAT assays that process approximately 500 µL of plasma into amplification reactions were comparable in sensitivity (LOD50 and LOD95 , 2.5 and 15-18 copies/mL) and were approximately 10-fold to 100-fold more sensitive than research laboratory-developed and diagnostic reverse transcriptase-polymerase chain reaction tests that process from 10 to 30 µL of plasma per amplification. Increasing sample input volume assayed with the Centers for Disease Control and Prevention reverse transcriptase-polymerase chain reaction assays increased the LODs by 10-fold to 30-fold. Blood donor-screening ZIKV NAT assays demonstrate similar excellent sensitivities to assays currently used for screening for transfusion-transmitted viruses and are substantially more sensitive than most other laboratory-developed and diagnostic ZIKV reverse transcriptase-polymerase chain reaction assays. Enhancing sensitivities of laboratory-developed and diagnostic assays may be achievable by increasing sample input. © 2017 AABB.

  8. Application of carbon and hydrogen stable isotope analyses to detect exogenous citric acid in Japanese apricot liqueur.

    Science.gov (United States)

    Akamatsu, Fumikazu; Oe, Takaaki; Hashiguchi, Tomokazu; Hisatsune, Yuri; Kawao, Takafumi; Fujii, Tsutomu

    2017-08-01

    Japanese apricot liqueur manufacturers are required to control the quality and authenticity of their liqueur products. Citric acid made from corn is the main acidulant used in commercial liqueurs. In this study, we conducted spiking experiments and carbon and hydrogen stable isotope analyses to detect exogenous citric acid used as an acidulant in Japanese apricot liqueurs. Our results showed that the δ(13)C values detected exogenous citric acid originating from C4 plants but not from C3 plants. The δ(2)H values of citric acid decreased as the amount of citric acid added increased, whether the citric acid originated from C3 or C4 plants. Commercial liqueurs with declared added acidulant provided higher δ(13)C values and lower δ(2)H values than did authentic liqueurs and commercial liqueurs with no declared added acidulant. Carbon and hydrogen stable isotope analyses are suitable as routine methods for detecting exogenous citric acid in Japanese apricot liqueur.

  9. Determination of some aliphatic carboxylic acids in anaerobic digestion process waters by ion-exclusion chromatography with conductimetric detection on a weakly acidic cation-exchange resin column.

    Science.gov (United States)

    Ito, Kazuaki; Takayama, Yohichi; Ikedo, Mikaru; Mori, Masanobu; Taoda, Hiroshi; Xu, Qun; Hu, Wenzhi; Sunahara, Hiroshi; Hayashi, Tsuneo; Sato, Shinji; Hirokawa, Takeshi; Tanaka, Kazuhiko

    2004-06-11

    The determination of seven aliphatic carboxylic acids, formic, acetic, propionic, isobutyric, n-butyric, isovaleric and n-valeric acids in anaerobic digestion process waters was examined using ion-exclusion chromatography with conductimetric detection. The analysis of these biologically important carboxylic acids is necessary as a measure for evaluating and controlling the process. The ion-exclusion chromatography system employed consisted of polymethacrylate-based weakly acidic cation-exchange resin columns (TSKgel OApak-A or TSKgel Super IC-A/C). weakly acidic eluent (benzoic acid), and conductimetric detection. Particle size and cation-exchange capacity were 5 microm and 0.1 meq./ml for TSKgel OApak-A and 3 microm and 0.2 meq./ml for TSKgel Super IC-A/C, respectively. A dilute eluent (1.0-2.0 mM) of benzoic acid was effective for the high resolution and highly conductimetric detection of the carboxylic acids. The good separation of isobutyric and n-butyric acids was performed using the TSKgel Super IC-A/C column (150 mm x 6.0 mm i.d. x 2). The simple and good chromatograms were obtained by the optimized ion-exclusion chromatography conditions for real samples from mesophilic anaerobic digestors, thus the aliphatic carboxylic acids were successfully determined without any interferences.

  10. Paper-based fluorescence resonance energy transfer assay for directly detecting nucleic acids and proteins.

    Science.gov (United States)

    Li, Hua; Fang, Xueen; Cao, Hongmei; Kong, Jilie

    2016-06-15

    Paper-based fluorescence resonance energy transfer assay (FRET) is gaining great interest in detecting macro-biological molecule. It is difficult to achieve conveniently and fast detection for macro-biological molecule. Herein, a graphene oxide (GO)-based paper chip (glass fiber) integrated with fluorescence labeled single-stranded DNA (ssDNA) for fast, inexpensive and direct detection of biological macromolecules (proteins and nucleic acids) has been developed. In this paper, we employed the Cy3/FAM-labeled ssDNA as the reporter and the GO as quencher and the original glass fiber paper as data acquisition substrates. The chip which was designed and fabricated by a cutting machine is a miniature biosensor that monitors fluorescence recovery from resonance energy transfer. The hybridization assays and fluorescence detection were all simplified, and the surface of the chip did not require immobilization or washing. A Nikon Eclipse was employed as excited resource and a commercial digital camera was employed for capturing digital images. This paper-based microfluidics chip has been applied in the detection of proteins and nucleic acids. The biosensing capability meets many potential requirements for disease diagnosis and biological analysis.

  11. Synthetic oligonucleotide antigens modified with locked nucleic acids detect disease specific antibodies

    Science.gov (United States)

    Samuelsen, Simone V.; Solov'Yov, Ilia A.; Balboni, Imelda M.; Mellins, Elizabeth; Nielsen, Christoffer Tandrup; Heegaard, Niels H. H.; Astakhova, Kira

    2016-10-01

    New techniques to detect and quantify antibodies to nucleic acids would provide a significant advance over current methods, which often lack specificity. We investigate the potential of novel antigens containing locked nucleic acids (LNAs) as targets for antibodies. Particularly, employing molecular dynamics we predict optimal nucleotide composition for targeting DNA-binding antibodies. As a proof of concept, we address a problem of detecting anti-DNA antibodies that are characteristic of systemic lupus erythematosus, a chronic autoimmune disease with multiple manifestations. We test the best oligonucleotide binders in surface plasmon resonance studies to analyze binding and kinetic aspects of interactions between antigens and target DNA. These DNA and LNA/DNA sequences showed improved binding in enzyme-linked immunosorbent assay using human samples of pediatric lupus patients. Our results suggest that the novel method is a promising tool to create antigens for research and point-of-care monitoring of anti-DNA antibodies.

  12. Synthetic oligonucleotide antigens modified with locked nucleic acids detect disease specific antibodies

    Science.gov (United States)

    Samuelsen, Simone V.; Solov’yov, Ilia A.; Balboni, Imelda M.; Mellins, Elizabeth; Nielsen, Christoffer Tandrup; Heegaard, Niels H. H.; Astakhova, Kira

    2016-01-01

    New techniques to detect and quantify antibodies to nucleic acids would provide a significant advance over current methods, which often lack specificity. We investigate the potential of novel antigens containing locked nucleic acids (LNAs) as targets for antibodies. Particularly, employing molecular dynamics we predict optimal nucleotide composition for targeting DNA-binding antibodies. As a proof of concept, we address a problem of detecting anti-DNA antibodies that are characteristic of systemic lupus erythematosus, a chronic autoimmune disease with multiple manifestations. We test the best oligonucleotide binders in surface plasmon resonance studies to analyze binding and kinetic aspects of interactions between antigens and target DNA. These DNA and LNA/DNA sequences showed improved binding in enzyme-linked immunosorbent assay using human samples of pediatric lupus patients. Our results suggest that the novel method is a promising tool to create antigens for research and point-of-care monitoring of anti-DNA antibodies. PMID:27775006

  13. Mechanism of intracellular detection of glucose through nonenzymatic and boronic acid functionalized carbon dots.

    Science.gov (United States)

    Kiran, S; Misra, R D K

    2015-09-01

    The objective of the research described here is to elucidate the fundamental mechanism by which the new class of "inert" non-enzymatic and boronic acid functionalized carbon dots-based sensors facilitate intracellular detection of glucose. The study suggests that the mechanism of detection of glucose involved selective assembly and fluorescence quenching of the carbon dots with excellent dynamic response to varying concentration of glucose within the biological range (1-100 mM). The strong dynamic response was related to high selectivity to biomolecules and inertness of carbon dots. Furthermore, the functionalization of carbon dots with boronic acid was the governing factor response for the passive character of the carbon dots. The study lays the foundation for the new field of carbon-based nanochemosensors.

  14. [Advancement in the research of early detection of bacterial nucleic acid in molecular diagnosis of sepsis].

    Science.gov (United States)

    Liu, Xiao; Ren, Hui; Peng, Dai-zhi

    2013-04-01

    Early diagnosis of sepsis helps make effective clinical decisions and improve the survival rate of patients with severe infection. However, the timely and accurate diagnosis of sepsis is still a great challenge in clinic. In order to settle the very problem, the scientists in the world have made a lot of exploration and research in the field of rapid molecular identification of pathogens. Nowadays, the nucleic acid detection of sepsis is mainly composed of 3 types of methodological strategies, either based on positive blood culture, single colonies, or directly on blood specimens. This paper presents a comprehensive overview of advances in the research of early detection of bacterial nucleic acid as molecular diagnosis of sepsis.

  15. High-Resolution Electrospray Ionization/Ion Mobility Spectrometer for Detection of Abiotic Amino Acids

    Science.gov (United States)

    Beegle, L. W.; Terrell, C. A.; Kim, H.; Kanik, I.

    2003-01-01

    One of the primary goals of the current NASA thrust in Astrobiology is the detection and identification of organic molecules as part of an in-situ lander platform on the surface of Mars or Europa. The identification of these molecules should help determine whether indigenous organisms exist on the surface of Mars or in an undersea environment on Europa. In addition, a detailed organic chemical inventory of surface and near surface molecules will help elucidate the possibilities of life elsewhere in the Universe. Terrestrial life has, as its backbone, the family of molecules known as the amino acids (AA), and while AA can be found in the terrestrial environments as part of more complex molecules, such as peptides, and proteins, they also exist as individual molecules due to of the hydrolyses of biopolymers. In terrestrial biochemistry, there are 20 principal amino acids which are necessary for life. However, some forms of these molecules can be found in nature synthesized via abiotic process. For example, they are known to exist extraterrestrially as a component of carbonaceous meteorites. The idea that amino acids are readily created by abiotic means has been demonstrated by their positive identification in the Murchison CM2 meteorite, which fell in 1969. This meteorite was analyzed before contamination by terrestrial microbes could result. Three laboratories individually tested parts of the meteorite and concluded that the amino acids present in them were indigenous to the meteorite because, among other reasons, they had equal L- and D- enantiomers. Final identification of the constituents of the Murchison included 33 amino acids which have no known biotic source, 11 amino acids which have limited distribution and 8 (Glycine, Alanine, Valine, Proline, Leucine, Isoleucine, Aspartic Acid, and Glutamic Acid), which readily occur in terrestrial proteins.

  16. Luciferin Amides Enable in Vivo Bioluminescence Detection of Endogenous Fatty Acid Amide Hydrolase Activity.

    Science.gov (United States)

    Mofford, David M; Adams, Spencer T; Reddy, G S Kiran Kumar; Reddy, Gadarla Randheer; Miller, Stephen C

    2015-07-15

    Firefly luciferase is homologous to fatty acyl-CoA synthetases. We hypothesized that the firefly luciferase substrate d-luciferin and its analogs are fatty acid mimics that are ideally suited to probe the chemistry of enzymes that release fatty acid products. Here, we synthesized luciferin amides and found that these molecules are hydrolyzed to substrates for firefly luciferase by the enzyme fatty acid amide hydrolase (FAAH). In the presence of luciferase, these molecules enable highly sensitive and selective bioluminescent detection of FAAH activity in vitro, in live cells, and in vivo. The potency and tissue distribution of FAAH inhibitors can be imaged in live mice, and luciferin amides serve as exemplary reagents for greatly improved bioluminescence imaging in FAAH-expressing tissues such as the brain.

  17. Dynamics of protein folding: probing the kinetic network of folding-unfolding transitions with experiment and theory.

    Science.gov (United States)

    Buchner, Ginka S; Murphy, Ronan D; Buchete, Nicolae-Viorel; Kubelka, Jan

    2011-08-01

    The problem of spontaneous folding of amino acid chains into highly organized, biologically functional three-dimensional protein structures continues to challenge the modern science. Understanding how proteins fold requires characterization of the underlying energy landscapes as well as the dynamics of the polypeptide chains in all stages of the folding process. In recent years, important advances toward these goals have been achieved owing to the rapidly growing interdisciplinary interest and significant progress in both experimental techniques and theoretical methods. Improvements in the experimental time resolution led to determination of the timescales of the important elementary events in folding, such as formation of secondary structure and tertiary contacts. Sensitive single molecule methods made possible probing the distributions of the unfolded and folded states and following the folding reaction of individual protein molecules. Discovery of proteins that fold in microseconds opened the possibility of atomic-level theoretical simulations of folding and their direct comparisons with experimental data, as well as of direct experimental observation of the barrier-less folding transition. The ultra-fast folding also brought new questions, concerning the intrinsic limits of the folding rates and experimental signatures of barrier-less "downhill" folding. These problems will require novel approaches for even more detailed experimental investigations of the folding dynamics as well as for the analysis of the folding kinetic data. For theoretical simulations of folding, a main challenge is how to extract the relevant information from overwhelmingly detailed atomistic trajectories. New theoretical methods have been devised to allow a systematic approach towards a quantitative analysis of the kinetic network of folding-unfolding transitions between various configuration states of a protein, revealing the transition states and the associated folding pathways at

  18. RNA folding: structure prediction, folding kinetics and ion electrostatics.

    Science.gov (United States)

    Tan, Zhijie; Zhang, Wenbing; Shi, Yazhou; Wang, Fenghua

    2015-01-01

    Beyond the "traditional" functions such as gene storage, transport and protein synthesis, recent discoveries reveal that RNAs have important "new" biological functions including the RNA silence and gene regulation of riboswitch. Such functions of noncoding RNAs are strongly coupled to the RNA structures and proper structure change, which naturally leads to the RNA folding problem including structure prediction and folding kinetics. Due to the polyanionic nature of RNAs, RNA folding structure, stability and kinetics are strongly coupled to the ion condition of solution. The main focus of this chapter is to review the recent progress in the three major aspects in RNA folding problem: structure prediction, folding kinetics and ion electrostatics. This chapter will introduce both the recent experimental and theoretical progress, while emphasize the theoretical modelling on the three aspects in RNA folding.

  19. Autoinducer-2 detection among commensal oral streptococci is dependent on pH and boric acid.

    Science.gov (United States)

    Cuadra, Giancarlo A; Frantellizzi, Ashley J; Gaesser, Kimberly M; Tammariello, Steven P; Ahmed, Anika

    2016-07-01

    Autoinducer-2, considered a universal signaling molecule, is produced by many species of bacteria; including oral strains. Structurally, autoinducer-2 can exist bound to boron (borated autoinducer-2). Functionally, autoinducer-2 has been linked to important bacterial processes such as virulence and biofilm formation. In order to test production of autoinducer-2 by a given bacterial strain, a bioassay using marine bioluminescent bacteria Vibrio harveyi as a reporter for autoinducer-2 has been designed. We hypothesize that pH adjustment and addition of boron are required for optimal bioluminescence and accurate autoinducer-2 detection. Using this reporter strain we tested autoinducer-2 activity from two oral commensal species, Streptococcus gordonii DL1 and Streptococcus oralis 34. Spent broth was collected and adjusted to pH 7.5 and supplemented with boric acid prior to measuring autoinducer- 2 activity. Results show that low pH inhibits bioluminescence of the reporter strain, but pH 7.5 allows for bioluminescence induction and proper readings of autoinducer-2 activity. Addition of boric acid also has a positive effect on bioluminescence allowing for a more sensitive detection of autoinducer-2 activity. Our data suggests that although autoinducer-2 is present in spent broth, low pH and/or low levels of boric acid become an obstacle for proper autoinducer-2 detection. For proper autoinducer-2 detection, we propose a protocol using this bioassay to include pH adjustment and boric acid addition to spent broth. Studies on autoinducer-2 activity in several bacteria species represent an important area of study as this universal signaling molecule is involved in critical bacterial phenotypes such as virulence and biofilm formation.

  20. Phenylboronic acid functionalized gold nanoparticles for highly sensitive detection of Staphylococcus aureus

    Science.gov (United States)

    Wang, Jine; Gao, Jingqing; Liu, Dianjun; Han, Dongxue; Wang, Zhenxin

    2012-01-01

    Herein, we report a phenylboronic acid functionalized gold nanoparticle (GNP)-based colorimetric assay for rapid detection of Staphylococcus aureus (S. aureus) with high sensitivity. In this approach, GNPs can bind to S. aureus by the reaction of phenylboronic acid with the cis-diol configuration in glycans on the bacterial surface, providing a colorimetric readout of the binding event. Using this strategy, we have been able to quantify S. aureus at a concentration of 50 cells per mL (three times the standard deviation divided by the slope of the working curve) in aqueous solution.Herein, we report a phenylboronic acid functionalized gold nanoparticle (GNP)-based colorimetric assay for rapid detection of Staphylococcus aureus (S. aureus) with high sensitivity. In this approach, GNPs can bind to S. aureus by the reaction of phenylboronic acid with the cis-diol configuration in glycans on the bacterial surface, providing a colorimetric readout of the binding event. Using this strategy, we have been able to quantify S. aureus at a concentration of 50 cells per mL (three times the standard deviation divided by the slope of the working curve) in aqueous solution. Electronic supplementary information (ESI) available: Details of experimental method and additional figures are available. See DOI: 10.1039/c2nr11657j

  1. Designing pH induced fold switch in proteins

    Science.gov (United States)

    Baruah, Anupaul; Biswas, Parbati

    2015-05-01

    This work investigates the computational design of a pH induced protein fold switch based on a self-consistent mean-field approach by identifying the ensemble averaged characteristics of sequences that encode a fold switch. The primary challenge to balance the alternative sets of interactions present in both target structures is overcome by simultaneously optimizing two foldability criteria corresponding to two target structures. The change in pH is modeled by altering the residual charge on the amino acids. The energy landscape of the fold switch protein is found to be double funneled. The fold switch sequences stabilize the interactions of the sites with similar relative surface accessibility in both target structures. Fold switch sequences have low sequence complexity and hence lower sequence entropy. The pH induced fold switch is mediated by attractive electrostatic interactions rather than hydrophobic-hydrophobic contacts. This study may provide valuable insights to the design of fold switch proteins.

  2. Highly-sensitive Detection of Salvianolic Acid B using Alumina Microfibers-modified Electrode

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Dong; Zheng, Xiaoyong; Xie, Xiafeng; Yang, Xiaofeng; Zhang, Huajie [Wenzhou Medical Univ., Wenzhou (China)

    2013-11-15

    Alumina microfibers with porous structures were prepared through hydrothermal reaction, and then used to modify the surface of carbon paste electrode (CPE). After modification with alumina microfibers, the electrochemical activity of CPE was found to be greatly improved. On the surface of alumina microfibers-modified CPE, the oxidation peak current of salvianolic acid B, a main bioactive compound in Danshen with anti-oxidative and anti-inflammatory effects, was remarkably increased compared with that on the bare CPE surface. The influences of pH value, amount of alumina microfibers and accumulation time were studied. Based on the strong signal amplification effects of alumina microfibers, a novel electrochemical method was developed for the detection of salvianolic acid B. The linear range was from 5 μg L{sup -1} to 0.3 mg L{sup -1}, and the detection limit was 2 μg L{sup -1} (2.78 nM) after 1-min accumulation. The new method was successfully used to detect salvianolic acid B in ShuangDan oral liquid samples, and the recovery was over the range from 97.4% to 102.9%.

  3. Simultaneous electrochemical detection of ascorbic acid, dopamine and uric acid based on graphene anchored with Pd-Pt nanoparticles.

    Science.gov (United States)

    Yan, Jun; Liu, Shi; Zhang, Zhenqin; He, Guangwu; Zhou, Ping; Liang, Haiying; Tian, Lulu; Zhou, Xuemin; Jiang, Huijun

    2013-11-01

    Pd-Pt bimetallic nanoparticles anchored on functionalized reduced graphene oxide (RGO) nanomaterials were synthesized via a one-step in situ reduction process, in which Pt and Pd ions were first attached to poly(diallyldimethylammonium chloride) (PDDA) functionalized graphene oxide (GO) sheets, and then the encased metal ions and GO were subjected to simultaneous reduction by ethylene glycol. The as-prepared Pd3Pt1/PDDA-RGO nanocomposites were characterized by transmission electron microscopy (TEM), X-ray photoelectron spectroscopy (XPS), Raman spectroscopy and electrochemical methods. In addition, an electrochemical sensor based on the graphene nanocomposites was fabricated for the simultaneous detection of ascorbic acid (AA), dopamine (DA) and uric acid (UA) in their ternary mixture. Three well-separated voltammetric peaks along with remarkable increasing electro-oxidation currents were obtained in differential pulse voltammetry (DPV) measurements. Under the optimized conditions, there were linear relationships between the peak currents and the concentrations in the range of 40-1200 μM for AA, 4-200 μM for DA and 4-400 μM for UA, with the limit of detection (LOD) (based on S/N=3) of 0.61, 0.04 and 0.10 μM for AA, DA and UA, respectively. This improved electrochemical performance can be attributed to the synergistic effect of metallic nanoparticles and RGO and the combination of the bimetallic nanoparticles. Furthermore, the practical electroanalytical utility of the sensor was demonstrated by the determination of AA, DA and together with UA in human urine and blood serum samples with satisfactory results. Copyright © 2013 Elsevier B.V. All rights reserved.

  4. Surfing the free energy landscape of flavodoxin folding

    NARCIS (Netherlands)

    Bollen, Y.J.M.

    2004-01-01

    The research described in this thesis has been carried out to obtain a better understanding of the fundamental rules describing protein folding. Protein folding is the process in which a linear chain of amino acids contracts to a compact state in which it is active. Flavodoxin from Azotobacter vinel

  5. Sensitive detection of dopamine via leucodopaminechrome on polyacrylic acid-coated ceria nanorods

    Science.gov (United States)

    Sheng, Weiqin; Zheng, Liang; Liu, Yan; Zhao, Xueqin; Weng, Jian; Zhang, Yang

    2017-09-01

    The major hurdle in detection of dopamine (DA) by electro-analysis is the presence of physiological interferents with a similar oxidation potential of DA. The conventional method is to enlarge the difference of their oxidation potentials. Here, we report an unconventional method to detect DA via leucodopaminechrome on CeO2 nanorods. Leucodopaminechrome is produced from the cyclization of dopamine-quinone, a product of two-electron oxidation of DA. Thus, its concentration is proportional to the DA concentration. Determining DA is demonstrated by measuring the reduction current of leucodopaminechrome on CeO2 nanorods. CeO2 nanorods demonstrate high electrocatalytic activity for reduction of leucodopaminechrome with a low potential at -0.27 V. The low detection potential of leucodopaminechrome can avoid the interference from ascorbic acid (AA) and uric acid (UA). Therefore, detecting DA via leucodopaminechrome is an effective method to avoid interference from AA and UA, and the suggested biosensor also displays good reproducibility and stability.

  6. Detection of glycoprotein using fiber optic surface plasmon resonance sensors with boronic acid

    Science.gov (United States)

    Wang, Fang; Zhang, Yang; Liu, Zigeng; Qian, Siyu; Gu, Yiying; Jing, Zhenguo; Sun, Changsen; Peng, Wei

    2017-04-01

    In this paper, we present a tilted fiber Bragg gratings (TFBG) based surface Plasmon resonance (SPR) label-free sensors with boronic acid derivative (ABA-PBA) as receptor molecule to detect glycoprotein with high sensitivity and selectivity. Tilted fiber Bragg gratings (TFBG) as a near infrared wavelengths detecting element can be able to excite a number of cladding modes whose properties can be detected accurately by measuring the variation of transmitted spectra. A 10° TFBG coated by 50nm gold film was manufactured to stimulate surface plasmon resonance on the surface of the sensor. The sensor was loaded with boronic acid derivative as the recognition molecule which has been widely used in various areas for the recognition matrix of diol-containing biomolecules. The proposed TFBG-SPR sensors exhibit good selectivity and repeatability with the protein concentration sensitivity up to 2.867dB/ (mg/ml) and the limit of detection was 2*10-5g/ml.

  7. Detection of amino acid neurotransmitters by surface enhanced Raman scattering and hollow core photonic crystal fiber

    Science.gov (United States)

    Tiwari, Vidhu S.; Khetani, Altaf; Monfared, Ali Momenpour T.; Smith, Brett; Anis, Hanan; Trudeau, Vance L.

    2012-03-01

    The present work explores the feasibility of using surface enhanced Raman scattering (SERS) for detecting the neurotransmitters such as glutamate (GLU) and gamma-amino butyric acid (GABA). These amino acid neurotransmitters that respectively mediate fast excitatory and inhibitory neurotransmission in the brain, are important for neuroendocrine control, and upsets in their synthesis are also linked to epilepsy. Our SERS-based detection scheme enabled the detection of low amounts of GLU (10-7 M) and GABA (10-4 M). It may complement existing techniques for characterizing such kinds of neurotransmitters that include high-performance liquid chromatography (HPLC) or mass spectrography (MS). This is mainly because SERS has other advantages such as ease of sample preparation, molecular specificity and sensitivity, thus making it potentially applicable to characterization of experimental brain extracts or clinical diagnostic samples of cerebrospinal fluid and saliva. Using hollow core photonic crystal fiber (HC-PCF) further enhanced the Raman signal relative to that in a standard cuvette providing sensitive detection of GLU and GABA in micro-litre volume of aqueous solutions.

  8. Transversal Clifford gates on folded surface codes

    Science.gov (United States)

    Moussa, Jonathan E.

    2016-10-01

    Surface and color codes are two forms of topological quantum error correction in two spatial dimensions with complementary properties. Surface codes have lower-depth error detection circuits and well-developed decoders to interpret and correct errors, while color codes have transversal Clifford gates and better code efficiency in the number of physical qubits needed to achieve a given code distance. A formal equivalence exists between color codes and folded surface codes, but it does not guarantee the transferability of any of these favorable properties. However, the equivalence does imply the existence of constant-depth circuit implementations of logical Clifford gates on folded surface codes. We achieve and improve this result by constructing two families of folded surface codes with transversal Clifford gates. This construction is presented generally for qudits of any dimension. The specific application of these codes to universal quantum computation based on qubit fusion is also discussed.

  9. Improvement of a Vocal Fold Imaging System

    Energy Technology Data Exchange (ETDEWEB)

    Krauter, K. G. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2017-02-01

    Medical professionals can better serve their patients through continual update of their imaging tools. A wide range of pathologies and disease may afflict human vocal cords or, as they’re also known, vocal folds. These diseases can affect human speech hampering the ability of the patient to communicate. Vocal folds must be opened for breathing and the closed to produce speech. Currently methodologies to image markers of potential pathologies are difficult to use and often fail to detect early signs of disease. These current methodologies rely on a strobe light and slower frame rate camera in an attempt to obtain images as the vocal folds travel over the full extent of their motion.

  10. Graphene folding on flat substrates

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Xiaoming; Zhao, Yadong; Ke, Changhong, E-mail: cke@binghamton.edu [Department of Mechanical Engineering, State University of New York at Binghamton, Binghamton, New York 13902 (United States); Zhang, Liuyang; Wang, Xianqiao [College of Engineering, University of Georgia, Athens, Georgia 30602 (United States)

    2014-10-28

    We present a combined experimental-theoretical study of graphene folding on flat substrates. The structure and deformation of the folded graphene sheet are experimentally characterized by atomic force microscopy. The local graphene folding behaviors are interpreted based on nonlinear continuum mechanics modeling and molecular dynamics simulations. Our study on self-folding of a trilayer graphene sheet reports a bending stiffness of about 6.57 eV, which is about four times the reported values for monolayer graphene. Our results reveal that an intriguing free sliding phenomenon occurs at the interlayer van der Waals interfaces during the graphene folding process. This work demonstrates that it is a plausible venue to quantify the bending stiffness of graphene based on its self-folding conformation on flat substrates. The findings reported in this work are useful to a better understanding of the mechanical properties of graphene and in the pursuit of its applications.

  11. Total Acid Value Titration of Hydrotreated Biomass Fast Pyrolysis Oil: Determination of Carboxylic Acids and Phenolics with Multiple End-Point Detection

    Energy Technology Data Exchange (ETDEWEB)

    Christensen, E.; Alleman, T. L.; McCormick, R. L.

    2013-01-01

    Total acid value titration has long been used to estimate corrosive potential of petroleum crude oil and fuel oil products. The method commonly used for this measurement, ASTM D664, utilizes KOH in isopropanol as the titrant with potentiometric end point determination by pH sensing electrode and Ag/AgCl reference electrode with LiCl electrolyte. A natural application of the D664 method is titration of pyrolysis-derived bio-oil, which is a candidate for refinery upgrading to produce drop in fuels. Determining the total acid value of pyrolysis derived bio-oil has proven challenging and not necessarily amenable to the methodology employed for petroleum products due to the different nature of acids present. We presented an acid value titration for bio-oil products in our previous publication which also utilizes potentiometry using tetrabutylammonium hydroxide in place of KOH as the titrant and tetraethylammonium bromide in place of LiCl as the reference electrolyte to improve the detection of these types of acids. This method was shown to detect numerous end points in samples of bio-oil that were not detected by D664. These end points were attributed to carboxylic acids and phenolics based on the results of HPLC and GC-MS studies. Additional work has led to refinement of the method and it has been established that both carboxylic acids and phenolics can be determined accurately. Use of pH buffer calibration to determine half-neutralization potentials of acids in conjunction with the analysis of model compounds has allowed us to conclude that this titration method is suitable for the determination of total acid value of pyrolysis oil and can be used to differentiate and quantify weak acid species. The measurement of phenolics in bio-oil is subject to a relatively high limit of detection, which may limit the utility of titrimetric methodology for characterizing the acidic potential of pyrolysis oil and products.

  12. Molecular detection of harmful algal blooms (HABs) using locked nucleic acids and bead array technology.

    Science.gov (United States)

    Diaz, Mara R; Jacobson, James W; Goodwin, Kelly D; Dunbar, Sherry A; Fell, Jack W

    2010-06-01

    Harmful algal blooms (HABs) are a serious public health risk in coastal waters. As the intensity and frequency of HABs continue to rise, new methods of detection are needed for reliable identification. Herein, we developed a high-throughput, multiplex, bead array technique for the detection of the dinoflagellates Karenia brevis and Karenia mikimotoi. The method combined the Luminex detection system with two novel technologies: locked nucleic acid-modified oligonucleotides (LNA) and Mirus Label IT(®) nucleic acid technology. To study the feasibility of the method, we evaluated the performance of modified and unmodified LNA probes with amplicon targets that were biotin labeled with two different strategies: direct chemical labeling (Mirus Label IT) versus enzymatic end-labeling (single biotinylated primer). The results illustrated that LNA probes hybridized to complementary single-stranded DNA with better affinity and displayed higher fluorescence intensities than unmodified oligonucleotide DNA probes. The latter effect was more pronounced when the assay was carried out at temperatures above 53°C degree. As opposed to the enzymatic 5' terminal labeling technique, the chemical-labeling method enhanced the level of fluorescence by as much as ~83%. The detection limits of the assay, which were established with LNA probes and Mirus Label IT system, ranged from 0.05 to 46 copies of rRNA. This high-throughput method, which represents the first molecular detection strategy to integrate Luminex technology with LNA probes and Mirus Label IT, can be adapted for the detection of other HABs and is well suited for the monitoring of red tides at pre-blooming and blooming conditions.

  13. Folding superfunnel to describe cooperative folding of interacting proteins.

    Science.gov (United States)

    Smeller, László

    2016-07-01

    This paper proposes a generalization of the well-known folding funnel concept of proteins. In the funnel model the polypeptide chain is treated as an individual object not interacting with other proteins. Since biological systems are considerably crowded, protein-protein interaction is a fundamental feature during the life cycle of proteins. The folding superfunnel proposed here describes the folding process of interacting proteins in various situations. The first example discussed is the folding of the freshly synthesized protein with the aid of chaperones. Another important aspect of protein-protein interactions is the folding of the recently characterized intrinsically disordered proteins, where binding to target proteins plays a crucial role in the completion of the folding process. The third scenario where the folding superfunnel is used is the formation of aggregates from destabilized proteins, which is an important factor in case of several conformational diseases. The folding superfunnel constructed here with the minimal assumption about the interaction potential explains all three cases mentioned above. Proteins 2016; 84:1009-1016. © 2016 Wiley Periodicals, Inc.

  14. Unambiguous detection of astaxanthin and astaxanthin fatty acid esters in krill (Euphausia superba Dana).

    Science.gov (United States)

    Grynbaum, Marc David; Hentschel, Petra; Putzbach, Karsten; Rehbein, Jens; Krucker, Manfred; Nicholson, Graeme; Albert, Klaus

    2005-09-01

    HPLC atmospheric pressure chemical ionization (APCI)/MS, GC MS, HPLC diode array detection (DAD), and NMR were used for the identification of astaxanthin and astaxanthin fatty acid esters in krill (Euphausia superba Dana). Matrix solid phase dispersion was applied for the extraction of the carotenoids. This gentle and expeditious extraction technique for solid and viscous samples leads to distinct higher enrichment rates than the conventional liquid-liquid extraction. The chromatographic separation was achieved employing a C30 RP column that allows the separation of shape-constrained geometrical isomers. A methanol/tert-butylmethyl ether/water gradient was applied. (all-E) Astaxanthin and the geometrical isomers were identified by HPLC APCI/MS, by coelution with isomerized authentical standard, by UV spectroscopy (DAD), and three isomers were unambiguously assigned by microcoil NMR spectroscopy. In this method, microcoils are transversally aligned to the magnetic field and have an increased sensitivity compared to the conventional double-saddle Helmholtz coils, thus enabling the measurement on small samples. The carotenol fatty acid esters were saponified enzymatically with Lipase type VII from Candida rugosa. The fatty acids were detected by GC MS after transesterification, but also without previous derivatization by HPLC APCI/MS. C14:0, C16:0, C16:1, C18:1, C20:0, C20:5, and C22:6 were found in astaxanthin monoesters and in astaxanthin diesters. (all-E) Astaxanthin was identified as the main isomer in six fatty acid ester fractions by NMR. Quantitation was carried out by the method of internal standard. (13-cis) Astaxanthin (70 microg/g), 542 microg/g (all-E) astaxanthin, 36 microg/g unidentified astaxanthin isomer, 62 microg/g (9-cis) astaxanthin, and 7842 microg/g astaxanthin fatty acid esters were found.

  15. Detection and formation scenario of citric acid, pyruvic acid, and other possible metabolism precursors in carbonaceous meteorites.

    Science.gov (United States)

    Cooper, George; Reed, Chris; Nguyen, Dang; Carter, Malika; Wang, Yi

    2011-08-23

    Carbonaceous meteorites deliver a variety of organic compounds to Earth that may have played a role in the origin and/or evolution of biochemical pathways. Some apparently ancient and critical metabolic processes require several compounds, some of which are relatively labile such as keto acids. Therefore, a prebiotic setting for any such individual process would have required either a continuous distant source for the entire suite of intact precursor molecules and/or an energetic and compact local synthesis, particularly of the more fragile members. To date, compounds such as pyruvic acid, oxaloacetic acid, citric acid, isocitric acid, and α-ketoglutaric acid (all members of the citric acid cycle) have not been identified in extraterrestrial sources or, as a group, as part of a "one pot" suite of compounds synthesized under plausibly prebiotic conditions. We have identified these compounds and others in carbonaceous meteorites and/or as low temperature (laboratory) reaction products of pyruvic acid. In meteorites, we observe many as part of three newly reported classes of compounds: keto acids (pyruvic acid and homologs), hydroxy tricarboxylic acids (citric acid and homologs), and tricarboxylic acids. Laboratory syntheses using (13)C-labeled reactants demonstrate that one compound alone, pyruvic acid, can produce several (nonenzymatic) members of the citric acid cycle including oxaloacetic acid. The isotopic composition of some of the meteoritic keto acids points to interstellar or presolar origins, indicating that such compounds might also exist in other planetary systems.

  16. Novel bioluminescent quantitative detection of nucleic acid amplification in real-time.

    Directory of Open Access Journals (Sweden)

    Olga A Gandelman

    Full Text Available BACKGROUND: The real-time monitoring of polynucleotide amplification is at the core of most molecular assays. This conventionally relies on fluorescent detection of the amplicon produced, requiring complex and costly hardware, often restricting it to specialised laboratories. PRINCIPAL FINDINGS: Here we report the first real-time, closed-tube luminescent reporter system for nucleic acid amplification technologies (NAATs enabling the progress of amplification to be continuously monitored using simple light measuring equipment. The Bioluminescent Assay in Real-Time (BART continuously reports through bioluminescent output the exponential increase of inorganic pyrophosphate (PPi produced during the isothermal amplification of a specific nucleic acid target. BART relies on the coupled conversion of inorganic pyrophosphate (PPi produced stoichiometrically during nucleic acid synthesis to ATP by the enzyme ATP sulfurylase, and can therefore be coupled to a wide range of isothermal NAATs. During nucleic acid amplification, enzymatic conversion of PPi released during DNA synthesis into ATP is continuously monitored through the bioluminescence generated by thermostable firefly luciferase. The assay shows a unique kinetic signature for nucleic acid amplifications with a readily identifiable light output peak, whose timing is proportional to the concentration of original target nucleic acid. This allows qualitative and quantitative analysis of specific targets, and readily differentiates between negative and positive samples. Since quantitation in BART is based on determination of time-to-peak rather than absolute intensity of light emission, complex or highly sensitive light detectors are not required. CONCLUSIONS: The combined chemistries of the BART reporter and amplification require only a constant temperature maintained by a heating block and are shown to be robust in the analysis of clinical samples. Since monitoring the BART reaction requires only a

  17. Fast preconcentration of trace rare earth elements from environmental samples by di(2-ethylhexyl)phosphoric acid grafted magnetic nanoparticles followed by inductively coupled plasma mass spectrometry detection

    Science.gov (United States)

    Yan, Ping; He, Man; Chen, Beibei; Hu, Bin

    2017-10-01

    In this work, di(2-ethylhexyl)phosphoric acid (P204) grafted magnetic nanoparticles were synthesized by fabricating P204 onto Fe3O4@TiO2 nanoparticles based on Lewis acid-base interaction between Ti and phosphate group under weakly acidic condition. The prepared Fe3O4@TiO2@P204 nanoparticles exhibited excellent selectivity for rare earth elements, and good anti-interference ability. Based on it, a method of magnetic solid phase extraction (MSPE) combined with inductively coupled plasma mass spectrometry (ICP-MS) was developed for fast preconcentration and determination of trace rare earth elements in environmental samples. Under the optimal conditions, the detection limits of rare earth elements were in the range of 0.01 (Tm)-0.12 (Nd) ng L- 1 with an enrichment factor of 100-fold, and the relative standard deviations ranged from 4.9 (Pr) to 10.7% (Er). The proposed method was successfully applied to the determination of rare earth elements in environmental samples, including river water, lake water, seawater and sediment.

  18. Early detection of Mycobacterium tuberculosis complex in BACTEC MGIT cultures using nucleic acid amplification.

    Science.gov (United States)

    Lin, S Y; Hwang, S C; Yang, Y C; Wang, C F; Chen, Y H; Chen, T C; Lu, P L

    2016-06-01

    We evaluated the application of nucleic acid amplification (NAA) in liquid cultures for the early detection of Mycobacterium tuberculosis. The Cobas TaqMan MTB test, IS6110 real-time PCR, and hsp65 PCR-restriction fragment length polymorphism (RFLP) analysis were used to detect BACTEC MGIT 960 (MGIT) cultures on days 3, 5, 7, and 14. The procedure was initially tested with a reference strain, H37Rv (ATCC 27294). Subsequently, 200 clinical specimens, including 150 Acid Fast bacillus (AFB) smear-positive and 50 AFB smear-negative samples, were examined. The Cobas TaqMan MTB test and IS6110-based PCR analysis were able to detect M. tuberculosis after 1 day when the inoculum of H37Rv was >3 x 10(-2) CFU/ml. After a 5-day incubation in the MGIT system, all three NAA assays had a positive detection regardless of the inoculum size. After a 1-day incubation of the clinical specimens in the MGIT system, the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) for the Cobas TaqMan MTB assay were 70.2%, 100%, 100%, and 82.3% respectively. For IS6110-based PCR analysis, these values were 63.1%, 100%, 100%, and 78.9%, and were 88.1%, 100%, 100%, and 92.1% respectively for hsp65 PCR-RFLP analysis. After a 3-day incubation, the specificity and PPV were 100% for all three NAA tests; the Cobas TaqMan MTB assay had the best sensitivity (97.6%) and NPV (98.3%). The sensitivity, specificity, PPV, and NPV for conventional culture analysis were 98.8%, 100%, 100%, and 99.1%. Thus, NAA may be useful for the early detection of M. tuberculosis after 3 days in MGIT.

  19. Teaching computers to fold proteins

    DEFF Research Database (Denmark)

    Winther, Ole; Krogh, Anders Stærmose

    2004-01-01

    A new general algorithm for optimization of potential functions for protein folding is introduced. It is based upon gradient optimization of the thermodynamic stability of native folds of a training set of proteins with known structure. The iterative update rule contains two thermodynamic averages...

  20. Novel sequences propel familiar folds.

    Science.gov (United States)

    Jawad, Zahra; Paoli, Massimo

    2002-04-01

    Recent structure determinations have made new additions to a set of strikingly different sequences that give rise to the same topology. Proteins with a beta propeller fold are characterized by extreme sequence diversity despite the similarity in their three-dimensional structures. Several fold predictions, based in part on sequence repeats thought to match modular beta sheets, have been proved correct.

  1. A novel silicon based mags-biosensor for nucleic acid detection by magnetoelectronic transduction

    Directory of Open Access Journals (Sweden)

    Maria Eloisa Castagna

    2015-12-01

    Full Text Available We developed a novel silicon biosensor based on magnetoelectronic transduction (MAGS for nucleic acid detection. The mags-biosensor is a planar device composed by a primary micro-coil, and two secondary coils which produce a differential voltage due to the induced magnetic field. The presence of magnetic material over one of the secondary coils causes variations of induced magnetic field density that in turn results in a total output voltage different from zero. The voltage variation, therefore, is a measure of the amount of magnetic material present in the active zone. A device sensitivity of 5.1 mV/ng and a resolution of 0.008 ng have been observed. The biosensor also presents a micro-heater and a thermal sensor respectively to set and read-out the chip temperature: this aspect enables the device to be used for several biochemical applications that need temperature control and activation such for example nucleic acid amplification (real-time PCR, antigen- antibody detection (immune-assay and SNP detection.

  2. Entropy Beacon: A Hairpin-Free DNA Amplification Strategy for Efficient Detection of Nucleic Acids.

    Science.gov (United States)

    Lv, Yifan; Cui, Liang; Peng, Ruizi; Zhao, Zilong; Qiu, Liping; Chen, Huapei; Jin, Cheng; Zhang, Xiao-Bing; Tan, Weihong

    2015-12-01

    Here, we propose an efficient strategy for enzyme- and hairpin-free nucleic acid detection called an entropy beacon (abbreviated as Ebeacon). Different from previously reported DNA hybridization/displacement-based strategies, Ebeacon is driven forward by increases in the entropy of the system, instead of free energy released from new base-pair formation. Ebeacon shows high sensitivity, with a detection limit of 5 pM target DNA in buffer and 50 pM in cellular homogenate. Ebeacon also benefits from the hairpin-free amplification strategy and zero-background, excellent thermostability from 20 °C to 50 °C, as well as good resistance to complex environments. In particular, based on the huge difference between the breathing rate of a single base pair and two adjacent base pairs, Ebeacon also shows high selectivity toward base mutations, such as substitution, insertion, and deletion and, therefore, is an efficient nucleic acid detection method, comparable to most reported enzyme-free strategies.

  3. Protein Folding:. Physics on Products of Evolution

    Science.gov (United States)

    Go, Nobuhiro

    2001-09-01

    Proteins are self-assembling molecular systems. A polypeptide chain of a protein molecule folds into a globular three-dimensional structure, which is specific to the amino acid sequence of the chain. A protein molecule is in the "native state" when folded into its specific three-dimensional structure. Only in the native state, a protein molecule carries out its biological function. This extraordinary self-assembly ability of proteins can be explained based on the three generally accepted empirical observations in proteins: (1) Two-state character; Folding and unfolding transitions in small globular proteins are generally of the two-state character. (2) Consistency principle; Various components of intra-molecular interactions responsible for stabilizing the native state of globular proteins are consistent to each other in their native state. (3) Principle of marginal stability; The native folded states of globular proteins are generally only marginally stable against their unfolded states. Deduction of the self-assembly ability from the three observations is a problem of physical nature. Very sophisticated theories have been developed recently as to this point. I shall give a very simple and intuitive discussion on this point. Asking why protein molecules show the three observations is another problem. Observation (1) can be derived from the globularity of native states. Observations (2) and (3) can be understood only by considering the evolutionary history of protein molecules, i.e., only polypeptide chains with very specific amino acid sequences selected during the history of evolution show properties of observations (2) and (3). Here we see a case where the mechanism of an extraordinary ability of biopolymers is elucidated in terms of physics, and physics expects that only a very small fraction of amino acid sequences have such an ability. Nature has left the job of finding able sequences to the history of evolution.

  4. Detection and characterization of p-coumaric acid hydroxylase in mung bean, Vigna mungo, seedlings.

    Science.gov (United States)

    Kojima, M; Takeuchi, W

    1989-02-01

    A new p-coumaric acid (4-hydroxycinnamic acid) hydroxylase was detected in mung bean seedlings treated with tentoxin, a fungal toxin, in which polyphenol oxidase that hydroxylates a wide variety of monophenols in vitro was completely eliminated. The enzyme required molecular oxygen and showed a pH optimum of 5.0. The enzyme acted only on p-coumaric acid (Km, 3.0 X 10(-5) M), while its specificity for the electron donor was rather broad. The Km value for NADPH (1.5 X 10(-4) M) was much lower than that for L-ascorbic acid (1.0 X 10(-2) M), although the Vmax value was almost the same with both electron donors. The enzyme was potently inhibited by beta-mercaptoethanol (Ki, 3.5 X 10(-6) M) and diethyldithiocarbamate (Ki, 2.3 X 10(-4) M), but was insensitive to p-chloromercuribenzoate. The enzyme was localized in the cell organelles which sedimented between mitochondria and endplasmic reticulum on sucrose density gradient centrifugation. The enzyme activity in the seedling was changed in response to induction by light in a manner suggesting its involvement in biosynthesis of phenolic compounds in mung bean seedlings.

  5. Detection of iso-α-acids to confirm beer consumption in postmortem specimens.

    Science.gov (United States)

    Rodda, Luke N; Gerostamoulos, Dimitri; Drummer, Olaf H

    2015-01-01

    Iso-α-acids (IAAs) can be used as markers for the consumption of beer. Postmortem specimens from a range of coronial cases were analyzed for IAAs in order to determine the prevalence of beer consumption and any correlation to blood alcohol concentrations (BAC). A total of 130 cases were included in this study including those where beer was mentioned in the case circumstances, cases where beer was not mentioned specifically but alcohol was detected, and cases where neither beer was mentioned nor a positive BAC was present. Available blood, serum, vitreous humour and urine specimens were analyzed. Of the 50 cases where beer was mentioned, 86% had one or more IAAs detected. In cases that only had a positive BAC (n = 60), 57% of these cases also showed the presence of these beer markers. IAAs were detected in specimens obtained from traumatized, burnt, and decomposed cases with a mention of beer consumption or where BAC was positive in blood. No IAAs were detected in cases where BAC was negative. There was little or no correlation between blood IAA concentrations and BAC. This study demonstrates the possible detection of IAAs as a marker for beer consumption.

  6. Equi-Gaussian Curvature Folding

    Indian Academy of Sciences (India)

    E M El-Kholy; El-Said R Lashin; Salama N Daoud

    2007-08-01

    In this paper we introduce a new type of folding called equi-Gaussian curvature folding of connected Riemannian 2-manifolds. We prove that the composition and the cartesian product of such foldings is again an equi-Gaussian curvature folding. In case of equi-Gaussian curvature foldings, $f:M→ P_n$, of an orientable surface onto a polygon $P_n$ we prove that (i) $f\\in\\mathcal{F}_{EG}(S^2)\\Leftrightarrow n=3$ (ii) $f\\in\\mathcal{F}_{EG}(T^2)\\Rightarrow n=4$ (iii) $f\\in\\mathcal{F}_{EG}(\\# 2T^2)\\Rightarrow n=5, 6$ and we generalize (iii) for $\\# nT^2$.

  7. Determination of CYP4A11-catalyzed lauric acid 12-hydroxylation by high-performance liquid chromatography with radiometric detection.

    Science.gov (United States)

    Crespi, Charles L; Chang, Thomas K H; Waxman, David J

    2006-01-01

    Lauric acid serves as an endogenous substrate for the cytochrome P450 enzyme CYP4A11. A reverse-phase, high-performance liquid chromatography method is described for the quantification of 12-hydroxylauric acid formed enzymatically by incubation of 14C-labeled lauric acid with cDNA-expressed CYP4A11 or human liver microsomes. Analytical separation is achieved using a C18 column and a gradient of 30% acetonitrile and 2 mM perchloric acid to 100% methanol, using a detection scintillation counter. This method is applicable to enzymatic studies for determination of lauric acid 12-hydroxylation activity.

  8. [Detection of erucic acid and glucosinolate in intact rapeseed by near-infrared diffuse reflectance spectroscopy].

    Science.gov (United States)

    Riu, Yu-kui; Huang, Kun-lun; Wang, Wei-min; Guo, Jing; Jin, Yin-hua; Luo, Yun-bo

    2006-12-01

    With the rapid development of transgenic food, more and more transgenic food has been pouring into the market, raising great concern about transgenic food' s edible safety. To analyze the content of erucic acid and glucosinolate in transgenic rapeseed and its parents, all the seeds were scanned intact by continuous wave of near infrared diffuse reflectance spectrometry ranging from 12 000 to 4 000 cm(-1) with a resolution of 4 cm(-1) and 64 times of scanning. Bruker OPUS software package was applied for quantification, while the results were compared with the standard methods. The results showed that the method of NIRS was very precise, which proved that infrared diffuse reflectance spectroscopy can be applied to detect the toxins in transgenic food. On the other hand, the results also showed that the content of erucic acid in transgenic rapeseeds is 0. 5-1. 0 times

  9. Detection of trace amino acid biomarkers in ice from extreme environments with the Mars Organic Analyzer

    Science.gov (United States)

    Jayarajah, Christine; Jayarajah, Christine; Botta, Oliver; Aubrey, Andrew; Parker, Eric; Bada, Jeffrey; Mathies, Richard

    A portable microfabricated capillary electrophoresis (CE) system named the Mars Organic Analyzer (MOA) has been developed to analyze fluorescently-labeled biomarkers including amino acids, amines, nucleobases, and amino sugars with the goal of life detection on Mars (1,2). This system consists of a multilayer microfabricated glass wafer containing electrophoresis channels as well as microfluidic valves and pumps for sample manipulation, a confocal laser excitation and fluorescence detection system, and integrated CE power supplies. The MOA has been successfully field tested in the Panoche Valley, CA and in the Atacama Desert, Chile, detecting amino acids at the ppb levels (3). In addition, this technology has been shown to be effective in screening the formation of biogenic amines during fermentation (4). The MOA is a part of the Urey instrument package that has been selected for the 2013 European ExoMars mission by ESA. The identification of recent gully erosion sites, observations of ice on and beneath the surface of Mars, and the discovery of large reservoirs of sub-surface ice on Mars point to water-ice as an important target for astrobiological analyses (5). In addition, the ice moons Europa and Enceladus are of astrobiological interest due to the possibility that they may contain liquid water under their ice crusts. Consequently, we explore here the use of the MOA instrument for the analysis of amino acids in polar ice samples. Soil extracts as well as concentrated icecore samples tend to be highly saline and inhomogeneous. Furthermore, brine pockets in ice form potential refugia for extant extra-terrestrial life, rendering near surface ice a key target for the search for a record of past life on the planet (6). Therefore, we have determined the effect of salinity on sample injection parameters in ice-core samples retrieved from Greenland. The amino acids valine, alanine/serine, glycine, glutamic acid, and aspartic acid were found in the parts

  10. Simultaneous separation and quantitative determination of monosaccharides, uronic acids, and aldonic acids by high performance anion-exchange chromatography coupled with pulsed amperometric detection in corn stover prehydrolysates

    Directory of Open Access Journals (Sweden)

    Xing Wang

    2012-11-01

    Full Text Available A method for simultaneous separation and quantitative determination of arabinose, galactose, glucose, xylose, xylonic acid, gluconic acid, galacturonic acid, and glucuronic acid was developed by using high performance anion-exchange chromatography coupled with pulsed amperometric detection (HPAEC-PAD. The separation was performed on a CarboPacTM PA-10 column (250 mm × 2 mm with a various gradient elution of NaOH-NaOAc solution as the mobile phase. The calibration curves showed good linearity (R2 ≥ 0.9993 for the monosaccharides, uronic acids, and aldonic acids in the range of 0.1 to 12.5 mg/L. The detection limits (LODs and the quantification limits (LOQs were 4.91 to 18.75 μg/L and 16.36 to 62.50 μg/L, respectively. Relative standard deviations (RSDs of the retention times and peak areas for the seven consecutive determinations of an unknown amount of mixture were 0.15% to 0.44% and 0.22% to 2.31%, respectively. The established method was used to separate and determine four monosaccharides, two uronic acids, and two aldonic acids in the prehydrolysate from dilute acid steam-exploded corn stover within 21 min. The spiked recoveries of monosaccharides, uronic acids, and aldonic acids ranged from 91.25% to 108.81%, with RSDs (n=3 of 0.04% ~ 6.07%. This method was applied to evaluate the quantitative variation of sugar and sugar acid content in biomass prehydrolysates.

  11. Comparison of the boronic acid disk potentiation test and cefepime-clavulanic acid method for the detection of ESBL among AmpC-producing Enterobacteriaceae

    Directory of Open Access Journals (Sweden)

    R M Shoorashetty

    2011-01-01

    Full Text Available Purpose: Extended spectrum β-lactamase (ESBL and AmpC β-lactamase are important mechanisms of betalactam resistance among Enterobacteriaceae . The ESBL confirmation test described by Clinical Laboratory Standards Institute (CLSI is in routine use. This method fails to detect ESBL in the presence of AmpC. Therefore, we compared two different ESBL detection methods against the CLSI confirmatory test. Materials and Methods: A total 200 consecutive clinical isolates of Enterobacteriaceae from various clinical samples were tested for ESBL production using (i CLSI described phenotypic confirmatory test (PCT, (ii boronic acid disk potentiation test and (iii cefepime-CA disk potentiation method. AmpC confirmation was done by a modified three-dimensional test. Results: Among total 200 Enterobacteriaceae isolates, 82 were only ESBL producers, 12 were only AmpC producers, 55 were combined ESBL and AmpC producers, 14 were inducible AmpC producers and 37 isolates did not harboured any enzymes. The CLSI described PCT detected ESBL-producing organisms correctly but failed to detect 36.3% of ESBLs among combined enzyme producers. The boronic acid disk potentiation test reliably detected all ESBL, AmpC, and combined enzyme producers correctly. The cefepime-CA method detected all ESBLs correctly but another method of AmpC detection has to be adopted. Conclusion: The use of boronic acid in disk diffusion testing along with the CLSI described PCT enhances ESBL detection in the presence of AmpC betalactamases.

  12. Stability studies of some glycolamide ester prodrugs of niflumic acid in aqueous buffers and human plasma by HPLC with UV detection.

    Science.gov (United States)

    Talath, Sirajunisa; Shirote, Pramod J; Lough, W John; Gadad, Andanappa K

    2006-01-01

    Glycolamide esters (compounds 1-17) of 2-(3-trifluoromethyl-phenylamino)nicotinic acid (niflumic acid, CAS 4394-00-7) have been synthesized and evaluated as possible prodrugs. In-vitro hydrolysis studies were conducted at selected pH values (1.2, 3.5, 4.8, 7.4 and 7.8) and in human plasma at 37 +/- 0.5 degree C using HPLC with UV detection. The aqueous (pH 7.4 and 7.8) and enzymatic rates of hydrolysis were substantially affected by the nature of promoieties in this series. The compounds showed good chemical stability in the buffers of low pH values (1.2, 3.5 and 4.8) and appreciable hydrolysis under alkaline conditions and in human plasma. They exhibited long hydrolytic half-lives of 7-46 h in aqueous buffer solutions (pH 7.4 and 7.8) and 14-21 min in human plasma, respectively. It was observed that N,N-disubstituted and cyclic glycolamide derivatives showed 2 fold more hydrolysis in the alkaline pH than monosubstituted derivatives, whereas the piperidino and thiomorpholino derivatives did not undergo chemical hydrolysis. The compounds contain two possible sites for hydrolysis with an increased hydrolytic susceptibility at the terminal aliphatic carbonyl site in aqueous buffers and human plasma solutions. They were found to be cleaved at two hydrolytic carbonyls, namely the nicotinyl (2-5 % in enzymatic hydrolysis) and the aliphatic site (7-55 % and 70-85 % in buffer and plasma hydrolysis, respectively) as revealed by HPLC analysis. The glycolamide ester prodrugs of niflumic acid underwent chemical and enzymatic hydrolysis to release mainly the metabolite 2-(3-trifluoromethyl-phenylamino) nicotinic acid carboxymethyl ester (III) and not the parent drug 2-(3-trifluoromethyl-phenylamino)nicotinic acid. The structure of the metabolite was confirmed by liquid chromatography-mass spectroscopy (LCMS).

  13. Effects of knots on protein folding properties.

    Directory of Open Access Journals (Sweden)

    Miguel A Soler

    Full Text Available This work explores the impact of knots, knot depth and motif of the threading terminus in protein folding properties (kinetics, thermodynamics and mechanism via extensive Monte Carlo simulations of lattice models. A knotted backbone has no effect on protein thermodynamic stability but it may affect key aspects of folding kinetics. In this regard, we found clear evidence for a functional advantage of knots: knots enhance kinetic stability because a knotted protein unfolds at a distinctively slower rate than its unknotted counterpart. However, an increase in knot deepness does not necessarily lead to more effective changes in folding properties. In this regard, a terminus with a non-trivial conformation (e.g. hairpin can have a more dramatic effect in enhancing kinetic stability than knot depth. Nevertheless, our results suggest that the probability of the denatured ensemble to keep knotted is higher for proteins with deeper knots, indicating that knot depth plays a role in determining the topology of the denatured state. Refolding simulations starting from denatured knotted conformations show that not every knot is able to nucleate folding and further indicate that the formation of the knotting loop is a key event in the folding of knotted trefoils. They also show that there are specific native contacts within the knotted core that are crucial to keep a native knotting loop in denatured conformations which otherwise have no detectable structure. The study of the knotting mechanism reveals that the threading of the knotting loop generally occurs towards late folding in conformations that exhibit a significant degree of structural consolidation.

  14. Development of Peptide Nucleic Acid Probes for Detection of the HER2 Oncogene

    Science.gov (United States)

    Song, Young K.; Evangelista, Jennifer; Aschenbach, Konrad; Johansson, Peter; Wen, Xinyu; Chen, Qingrong; Lee, Albert; Hempel, Heidi; Gheeya, Jinesh S.; Getty, Stephanie; Gomez, Romel; Khan, Javed

    2013-01-01

    Peptide nucleic acids (PNAs) have gained much interest as molecular recognition tools in biology, medicine and chemistry. This is due to high hybridization efficiency to complimentary oligonucleotides and stability of the duplexes with RNA or DNA. We have synthesized 15/16-mer PNA probes to detect the HER2 mRNA. The performance of these probes to detect the HER2 target was evaluated by fluorescence imaging and fluorescence bead assays. The PNA probes have sufficiently discriminated between the wild type HER2 target and the mutant target with single base mismatches. Furthermore, the probes exhibited excellent linear concentration dependence between 0.4 to 400 fmol for the target gene. The results demonstrate potential application of PNAs as diagnostic probes with high specificity for quantitative measurements of amplifications or over-expressions of oncogenes. PMID:23593123

  15. Development of peptide nucleic acid probes for detection of the HER2 oncogene.

    Directory of Open Access Journals (Sweden)

    Belhu Metaferia

    Full Text Available Peptide nucleic acids (PNAs have gained much interest as molecular recognition tools in biology, medicine and chemistry. This is due to high hybridization efficiency to complimentary oligonucleotides and stability of the duplexes with RNA or DNA. We have synthesized 15/16-mer PNA probes to detect the HER2 mRNA. The performance of these probes to detect the HER2 target was evaluated by fluorescence imaging and fluorescence bead assays. The PNA probes have sufficiently discriminated between the wild type HER2 target and the mutant target with single base mismatches. Furthermore, the probes exhibited excellent linear concentration dependence between 0.4 to 400 fmol for the target gene. The results demonstrate potential application of PNAs as diagnostic probes with high specificity for quantitative measurements of amplifications or over-expressions of oncogenes.

  16. Detection of anhydrous hydrochloric acid, HCl, in IRC+10216 with the Herschel SPIRE and PACS spectrometers

    CERN Document Server

    Cernicharo, J; Barlow, M J; Agundez, M; Royer, P; Vandenbussche, B; Wesson, R; Polehampton, E T; De Beck, E; Blommaert, J A D L; Daniel, F; De Meester, W; Exter, K M; Feuchtgruber, H; Gear, W K; Goicoechea, J R; Gomez, H L; Groenewegen, M A T; Hargrave, P C; Huygen, R; Imhof, P; Ivison, R J; Jean, C; Kerschbaum, F; Leeks, S J; Lim, T L; Matsuura, M; Olofsson, G; Posch, T; Regibo, S; Savini, G; Sibthorpe, B; Swinyard, B M; Vandenbussche, B; Waelkens, C

    2010-01-01

    We report on the detection of anhydrous hydrochloric acid (hydrogen chlorine, HCl) in the carbon-rich star IRC+10216 using the spectroscopic facilities onboard the Herschel satellite. Lines from J=1-0 up to J=7-6 have been detected. From the observed intensities, we conclude that HCl is produced in the innermost layers of the circumstellar envelope with an abundance relative to H2 of 5x10^-8 and extends until the molecules reach its photodissociation zone. Upper limits to the column densities of AlH, MgH, CaH, CuH, KH, NaH, FeH, and other diatomic hydrides have also been obtained.

  17. Simultaneous determination of tricarboxylic acid cycle metabolites by high-performance liquid chromatography with ultraviolet detection.

    Science.gov (United States)

    Shurubor, Yevgeniya I; Cooper, Arthur J L; Isakova, Elena P; Deryabina, Yulia I; Beal, M Flint; Krasnikov, Boris F

    2016-06-15

    Here we describe a simple high-performance liquid chromatography (HPLC) procedure for the simultaneous detection and quantitation in standard solutions of 13 important metabolites of cellular energy metabolism, including 9 tricarboxylic acid (TCA) cycle components and 4 additional metabolites. The metabolites are detected by their absorbance at 210 nm. The procedure does not require prior derivatization, and an analysis can be carried out at ambient temperature within 15 min. The significance of the current work is that the current HPLC procedure should motivate the development of simplified TCA cycle enzyme assays, isotopomer analysis, and determination of selected TCA metabolite levels in plasma/tissues. Copyright © 2016 Elsevier Inc. All rights reserved.

  18. New Fluorescent Nanoparticles for Ultrasensitive Detection of Nucleic Acids by Optical Methods

    DEFF Research Database (Denmark)

    Westergaard Mulberg, Mads; Taskova, Maria; Thomsen, Rasmus P.

    2017-01-01

    in the synthesis of new fluorescent nanoparticles. Here, the fluorescent nanoparticles were made by simple and inexpensive radical emulsion polymerization of butyl acrylate in the presence of fluorescent dyes and additional functionalization reagents. This provided ultra-bright macrofluorophores of 9-84nm mean...... diameter, modified with additional alkyne and amino groups for bioconjugation. By using click and NHS chemistries, the new nanoparticles were attached to target-specific DNA probes that were used in fluorimetry and fluorescence microscopy. Overall, these fluorescent nanoparticles and their oligonucleotide...... derivatives have higher photostability, brighter fluorescence and hence dramatically lower limits of target detection than the individual organic dyes. These properties make them useful in approaches directed towards ultrasensitive detection of nucleic acids, in particular for imaging and in vitro diagnostics...

  19. Diagnostic efficacy of Ziehl-Neelsen method against fluorescent microscopy in detection of acid fast bacilli

    Institute of Scientific and Technical Information of China (English)

    Soham Gupta; Vishnu Prasad Shenoy; Indira Bairy; MuralidharanS

    2010-01-01

    Objective:To investigate the application of Ziehl-Neelsen (Z-N) and fluorescent microscopy in detection of acid fast bacilli (AFB).Methods: Duplicate smears were prepared from 260 sputum samples and stained with Z-N and fluorescent staining (FS) methods. The efficiency of both methods in primary diagnosis of tuberculosis were evaluated.Results:The smears were positive for AFB in 15 (5.77%) samples by Z-N staining method and in 16 (6.15%) samples by FS method. The sensitivity and specificity of Z-N staining method against FS method were 93.75% and 100% respectively.Conclusions: Though lesser cost-effective than Z-N, FS method is a more sensitive and better case finding tool in detection of AFB.

  20. Detection of Glutamate and γ-aminobutyric Acid in Vitreous of Patients with Proliferative Diabetic Retinopathy

    Institute of Scientific and Technical Information of China (English)

    Juan Deng; De-Zheng Wu; Rulong Gao

    2000-01-01

    Purpose: To study the levels of glutamate and γ-aminobutyric acid (GABA) in vitreous of patients with proliferative diabetic retinopathy(PDR) and to investigate their roles in retinal ischemia.Method: Vitreous samples were collected from 25 patients (27 eyes) with PDR and 14patients ( 14 eyes) with idiopathic macular hole. Glutamate and GABA detection were performed by high-performance liquid chromatography (HPLC).Results: Patients with PDR had significantly higher concentrations of glutamate and GABA than the control group. The glutamate level has a significantly positive correlation with GABA level.Conclusion: Detection of glutamate and GABA in vitreous provides biochemical support for the mechanism and treatment of ischemic retinal damage in patients with PDR.

  1. DNA detection using water-soluble conjugated polymers and peptide nucleic acid probes

    Science.gov (United States)

    Gaylord, Brent S.; Heeger, Alan J.; Bazan, Guillermo C.

    2002-08-01

    The light-harvesting properties of cationic conjugated polymers are used to sensitize the emission of a dye on a specific peptide nucleic acid (PNA) sequence for the purpose of homogeneous, "real-time" DNA detection. Signal transduction is controlled by hybridization of the neutral PNA probe and the negative DNA target. Electrostatic interactions bring the hybrid complex and cationic polymer within distances required for Förster energy transfer. Conjugated polymer excitation provides fluorescein emission >25 times higher than that obtained by exciting the dye, allowing detection of target DNA at concentrations of 10 pM with a standard fluorometer. A simple and highly sensitive assay with optical amplification that uses the improved hybridization behavior of PNA/DNA complexes is thus demonstrated.

  2. [THE DETECTION OF CONTENT OF DIAGNOSTICALLY SIGNIFICANT FATTY ACIDS AND INDIVIDUAL TRIGLYCERIDES IN BIOLOGICAL MEDIUMS BASED ON INFRARED SPECTROMETRY].

    Science.gov (United States)

    Kalinin, A V; Krasheninnikov, V N; Sviridov, A P; Titov, V N

    2015-11-01

    The content of clinically important fatty acids and individual triglycerides in food and biological mediums are traditionally detected by gas and fluid chromatography in various methodical modifications. The techniques are hard-to-get in laboratories of clinical biochemistry. The study was carried out to develop procedures and equipment for operative quantitative detection of concentration of fatty acids, primarily palmitic saturated fatty acid and oleic mono unsaturated fatty acid. Also detection was applied to sums ofpolyenoic (eicosapentaenoic and docosahexaenoic acid) fatty acids in biological mediums (cod-liver oil, tissues, blood plasma) using spectrometers of short-range infrared band of different types: with Fourier transform, diffraction and combined scattering. The evidences of reliable and reproducible quantitative detection offatty acids were received on the basis of technique of calibration (regression) by projection on latent structures using standard samples of mixtures of oils and fats. The evaluation is implemented concerning possibility of separate detection of content of palmitic and oleic triglycerides in mediums with presence of water The choice of technical conditions and mode of application of certain types of infrared spectrometers and techniques of their calibration is substantiated

  3. Determination of Amino Acids in Single Human Lymphocytes after On-capillary Derivatization by Capillary Zone Electrophoresis with Electrochemical Detection

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Amino acids in individual human lymphocytes were determined by capillary zone electrophoresis with electrochemical detection after on-capillary derivatization. In order to inject cells easily, a cell injector was designed. Four amino acids (serine, alanine, taurine, and glycine) in single human lymphocytes have been identified. Quantitation has been accomplished through the use of calibration curves.

  4. Simple high-performance liquid chromatographic method for the concurrent determination of the amine metabolites vanillylmandelic acid, 3-methoxy-4-hydroxyphenylglycol, 5-hydroxyindoleacetic acid, dihydroxyphenylacetic acid and homovanillic acid in urine using electrochemical detection.

    Science.gov (United States)

    Joseph, M H; Kadam, B V; Risby, D

    1981-12-11

    A simple method for the concurrent analysis of the noradrenaline metabolites vanillylmandelic acid and 3-methoxy-4-hydroxyphenylglycol, the dopamine metabolites dihydroxyphenylacetic acid and homovanillic acid, and the serotonin metabolite 5-hydroxyindoleacetic acid in human urine is described. Following organic extraction of the metabolites from acidified urine, they are separated by single-step gradient elution high-performance liquid chromatography on a reversed-phase column. Detection and quantification are achieved with an electrochemical detector using a carbon-paste electrode; samples can be injected at 40-min intervals. Optimisation of analytical parameters is described, and examples of the application of the method in the fields of clinical chemistry and clinical neuroscience are given. This provides a convenient method for the concurrent study of the metabolism of three major biogenic amines, and is readily adaptable for studies on cerebrospinal fluid and brain tissue.

  5. Aluminium bismuthate nanorods and the electrochemical performance for detection of tartaric acid

    Energy Technology Data Exchange (ETDEWEB)

    Pei, L.Z., E-mail: lzpei@ahut.edu.cn [Key Lab of Materials Science and Processing of Anhui Province, School of Materials Science and Engineering, Anhui University of Technology, Ma' anshan, Anhui 243002 (China); Wei, T.; Lin, N.; Fan, C.G. [Key Lab of Materials Science and Processing of Anhui Province, School of Materials Science and Engineering, Anhui University of Technology, Ma' anshan, Anhui 243002 (China); Yang, Zao, E-mail: yangzao888@tom.com [National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, Sichuan 610064 (China)

    2016-09-15

    Aluminium bismuthate nanorods had been synthesized by a facile hydrothemral method. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) observations showed that the lengh and diameter were 2–10 μm and 50–200 nm, respectively. X-ray diffraction (XRD) and high-resolution TEM (HRTEM) showed that the nanorods were composed of single crystalline orthorhombic Al{sub 4}Bi{sub 2}O{sub 9} phase. The aluminium bismuthate nanorods could be explained by the nucleation and crystalline growth process based on the products obtained from different hydrothermal conditions. Aluminium bismuthate nanorods modified glassy carbon electrode (GCE) was fabricated for the electrochemical detection of tartaric acid (TA) in neutral solution. A pair of semi-reversible redox peaks located at −0.08 V and −0.53 V, respectively were observed. The current intensity of the cyclic voltammogram (CV) peak increased linearly obviously with increasing the scan rate and TA concentration. The detection limit and linear range were 0.64 μM and 0.001–2 mM, respectively with the correlation coefficient of 0.995. The aluminium bismuthate nanorods modified GCE had good reproducibility and stability for the detection of TA. - Highlights: • Aluminium bismuthate nanorods were synthesized by a facile hydrothermal process. • The size of aluminium bismuthate nanorods could be controlled by growth conditions. • Aluminium bismuthate nanorods showed good electrochemical performance for the detection of tartaric acid. • Aluminium bismuthate nanorods modified GCE had good reproducibility and stability.

  6. Electrochemical paper-based peptide nucleic acid biosensor for detecting human papillomavirus.

    Science.gov (United States)

    Teengam, Prinjaporn; Siangproh, Weena; Tuantranont, Adisorn; Henry, Charles S; Vilaivan, Tirayut; Chailapakul, Orawon

    2017-02-01

    A novel paper-based electrochemical biosensor was developed using an anthraquinone-labeled pyrrolidinyl peptide nucleic acid (acpcPNA) probe (AQ-PNA) and graphene-polyaniline (G-PANI) modified electrode to detect human papillomavirus (HPV). An inkjet printing technique was employed to prepare the paper-based G-PANI-modified working electrode. The AQ-PNA probe baring a negatively charged amino acid at the N-terminus was immobilized onto the electrode surface through electrostatic attraction. Electrochemical impedance spectroscopy (EIS) was used to verify the AQ-PNA immobilization. The paper-based electrochemical DNA biosensor was used to detect a synthetic 14-base oligonucleotide target with a sequence corresponding to human papillomavirus (HPV) type 16 DNA by measuring the electrochemical signal response of the AQ label using square-wave voltammetry before and after hybridization. It was determined that the current signal significantly decreased after the addition of target DNA. This phenomenon is explained by the rigidity of PNA-DNA duplexes, which obstructs the accessibility of electron transfer from the AQ label to the electrode surface. Under optimal conditions, the detection limit of HPV type 16 DNA was found to be 2.3 nM with a linear range of 10-200 nM. The performance of this biosensor on real DNA samples was tested with the detection of PCR-amplified DNA samples from the SiHa cell line. The new method employs an inexpensive and disposable device, which easily incinerated after use and is promising for the screening and monitoring of the amount of HPV-DNA type 16 to identify the primary stages of cervical cancer.

  7. A FRET-enabled molecular peptide beacon with a significant red shift for the ratiometric detection of nucleic acids.

    Science.gov (United States)

    Maity, Debabrata; Jiang, Juanjuan; Ehlers, Martin; Wu, Junchen; Schmuck, Carsten

    2016-05-01

    A cationic molecular peptide beacon NAP1 functionalized with a fluorescence resonance energy transfer-pair at its ends allows the ratiometric detection of ds-DNA with a preference for AT rich sequences. NAP1 most likely binds in a folded form into the minor groove of ds-DNA, which results in a remarkable change in its fluorescence properties. As NAP1 exhibits quite low cytotoxicity, it can also be used for imaging of nuclear DNA in cells.

  8. Emerging Loop-Mediated Isothermal Amplification-Based Microchip and Microdevice Technologies for Nucleic Acid Detection.

    Science.gov (United States)

    Safavieh, Mohammadali; Kanakasabapathy, Manoj K; Tarlan, Farhang; Ahmed, Minhaz U; Zourob, Mohammed; Asghar, Waseem; Shafiee, Hadi

    2016-03-14

    Rapid, sensitive, and selective pathogen detection is of paramount importance in infectious disease diagnosis and treatment monitoring. Currently available diagnostic assays based on polymerase chain reaction (PCR) and enzyme-linked immunosorbent assay (ELISA) are time-consuming, complex, and relatively expensive, thus limiting their utility in resource-limited settings. Loop-mediated isothermal amplification (LAMP) technique has been used extensively in the development of rapid and sensitive diagnostic assays for pathogen detection and nucleic acid analysis and hold great promise for revolutionizing point-of-care molecular diagnostics. Here, we review novel LAMP-based lab-on-a-chip (LOC) diagnostic assays developed for pathogen detection over the past several years. We review various LOC platforms based on their design strategies for pathogen detection and discuss LAMP-based platforms still in development and already in the commercial pipeline. This review is intended as a guide to the use of LAMP techniques in LOC platforms for molecular diagnostics and genomic amplifications.

  9. Immobilization-free electrochemical DNA detection with anthraquinone-labeled pyrrolidinyl peptide nucleic acid probe.

    Science.gov (United States)

    Kongpeth, Jutatip; Jampasa, Sakda; Chaumpluk, Piyasak; Chailapakul, Orawon; Vilaivan, Tirayut

    2016-01-01

    Electrochemical detection provides a simple, rapid, sensitive and inexpensive method for DNA detection. In traditional electrochemical DNA biosensors, the probe is immobilized onto the electrode. Hybridization with the DNA target causes a change in electrochemical signal, either from the intrinsic signal of the probe/target or through a label or a redox indicator. The major drawback of this approach is the requirement for probe immobilization in a controlled fashion. In this research, we take the advantage of different electrostatic properties between PNA and DNA to develop an immobilization-free approach for highly sequence-specific electrochemical DNA sensing on a screen-printed carbon electrode (SPCE) using a square-wave voltammetric (SWV) technique. Anthraquinone-labeled pyrrolidinyl peptide nucleic acid (AQ-PNA) was employed as a probe together with an SPCE that was modified with a positively-charged polymer (poly quaternized-(dimethylamino-ethyl)methacrylate, PQDMAEMA). The electrostatic attraction between the negatively-charged PNA-DNA duplex and the positively-charged modified SPCE attributes to the higher signal of PNA-DNA duplex than that of the electrostatically neutral PNA probe, resulting in a signal change. The calibration curve of this proposed method exhibited a linear range between 0.35 and 50 nM of DNA target with a limit of detection of 0.13 nM (3SD(blank)/Slope). The sub-nanomolar detection limit together with a small sample volume required (20 μL) allowed detection of DNA. With the high specificity of the pyrrolidinyl PNA probe used, excellent discrimination between complementary and various single-mismatched DNA targets was obtained. An application of this new platform for a sensitive and specific detection of isothermally-amplified shrimp's white spot syndrome virus (WSSV) DNA was successfully demonstrated.

  10. Determination of aristolochic acids by high-performance liquid chromatography with fluorescence detection.

    Science.gov (United States)

    Wang, Yinan; Chan, Wan

    2014-06-25

    Nephrotoxic and carcinogenic aristolochic acids (AAs) are naturally occurring nitrophenanthrene carboxylic acids in the herbal genus Aristolochia. The misuse of AA-containing herbs in preparing slimming drugs has caused hundred of cases of kidney disease in Belgium women in a slimming regime in the early 1990s. Accumulating evidence also suggested that prolong dietary intake of AA-contaminated food is one of the major causes to the Balkan endemic nephropathy that was first observed in the late 1950s. Therefore, analytical methods of high sensitivity are extremely important for safeguarding human exposure to AA-containing herbal medicines, herbal remedies, and food composites. In this paper, we describe the development of a new high-performance liquid chromatography coupled fluorescence detector (HPLC-FLD) method for the sensitive determination of AAs. The method makes use of a novel cysteine-induced denitration reaction that "turns on" the fluorescence of AAs for fluorometric detections. Our results showed that the combination of cysteine-induced denitration and HPLC-FLD analysis allows for sensitive quantification of AA-I and AA-II at detection limits of 27.1 and 25.4 ng/g, respectively. The method was validated and has been successfully applied in quantifying AAs in Chinese herbal medicines.

  11. Label-Free Potentiometry for Detecting DNA Hybridization Using Peptide Nucleic Acid and DNA Probes

    Directory of Open Access Journals (Sweden)

    Yuji Miyahara

    2013-02-01

    Full Text Available Peptide nucleic acid (PNA has outstanding affinity over DNA for complementary nucleic acid sequences by forming a PNA-DNA heterodimer upon hybridization via Watson-Crick base-pairing. To verify whether PNA probes on an electrode surface enhance sensitivity for potentiometric DNA detection or not, we conducted a comparative study on the hybridization of PNA and DNA probes on the surface of a 10-channel gold electrodes microarray. Changes in the charge density as a result of hybridization at the solution/electrode interface on the self-assembled monolayer (SAM-formed microelectrodes were directly transformed into potentiometric signals using a high input impedance electrometer. The charge readout allows label-free, reagent-less, and multi-parallel detection of target oligonucleotides without any optical assistance. The differences in the probe lengths between 15- to 22-mer dramatically influenced on the sensitivity of the PNA and DNA sensors. Molecular type of the capturing probe did not affect the degree of potential shift. Theoretical model for charged rod-like duplex using the Gouy-Chapman equation indicates the dominant effect of electrostatic attractive forces between anionic DNA and underlying electrode at the electrolyte/electrode interface in the potentiometry.

  12. Label-free potentiometry for detecting DNA hybridization using peptide nucleic acid and DNA probes.

    Science.gov (United States)

    Goda, Tatsuro; Singi, Ankit Balram; Maeda, Yasuhiro; Matsumoto, Akira; Torimura, Masaki; Aoki, Hiroshi; Miyahara, Yuji

    2013-02-07

    Peptide nucleic acid (PNA) has outstanding affinity over DNA for complementary nucleic acid sequences by forming a PNA-DNA heterodimer upon hybridization via Watson-Crick base-pairing. To verify whether PNA probes on an electrode surface enhance sensitivity for potentiometric DNA detection or not, we conducted a comparative study on the hybridization of PNA and DNA probes on the surface of a 10-channel gold electrodes microarray. Changes in the charge density as a result of hybridization at the solution/electrode interface on the self-assembled monolayer (SAM)-formed microelectrodes were directly transformed into potentiometric signals using a high input impedance electrometer. The charge readout allows label-free, reagent-less, and multi-parallel detection of target oligonucleotides without any optical assistance. The differences in the probe lengths between 15- to 22-mer dramatically influenced on the sensitivity of the PNA and DNA sensors. Molecular type of the capturing probe did not affect the degree of potential shift. Theoretical model for charged rod-like duplex using the Gouy-Chapman equation indicates the dominant effect of electrostatic attractive forces between anionic DNA and underlying electrode at the electrolyte/electrode interface in the potentiometry.

  13. Reduced graphene oxide/molecular imprinted polymer-organic thin film transistor for amino acid detection

    Science.gov (United States)

    Halim, Nurul Farhanah AB.; Musa, Nur Hazwani; Zakaria, Zulkhairi; Von Schleusingen, Mubaraq; Ahmad, Mohd Noor; Derman, Nazree; Shakaff, Ali Yeon Md.

    2017-03-01

    This works reports the electrical performance of reduced graphene oxide (RGO)/Molecular imprinted polymer (MIP)- organic thin film transistor (OTFT) for amino-acid detection, serine. These biomimetic sensors consider MIP as man-tailored biomimetic recognition sites that play an important role in signal transduction. MIP provides recognition sites compatible with serine molecules was developed by dispersing serine with methylacrylate acid (MAA) as functional monomer and Ethylene glycol dimethylacrylate (EGDMA) as cross-linker. The imprinted polymeric were mixed with reduced graphene oxide to produced sensing layer for the sensor. RGO-MIP layer was introduced between source and drain of OTFT via spin coating as a detecting layer for serine molecules. RGO was introduced into MIP, to allow a highly conductive sensing material thus enhanced selectivity and sensitivity of the sensor. By analyzing the electrical performance of the sensors, the performances of OTFT sensor enhanced with RGO/MIP interlayer and OTFT sensor with MIP interlayer when exposed to serine analyte were obtained. The results showed that there were remarkable shifts of drain current (ID) obtained from OTFT sensor with RGO/MIP interlayer after exposed to serine analyte. Moreover, the sensitivity of OTFT sensor with RGO/MIP interlayer was nearly higher than the OTFT sensor with MIP interlayer. Hence, it proved that RGO successfully enhanced the sensing performance of OTFT sensor.

  14. Study on the spectrophotometric detection of free fatty acids in palm oil utilizing enzymatic reactions.

    Science.gov (United States)

    Azeman, Nur Hidayah; Yusof, Nor Azah; Abdullah, Jaafar; Yunus, Robiah; Hamidon, Mohd Nizar; Hajian, Reza

    2015-07-07

    In this paper, a comprehensive study has been made on the detection of free fatty acids (FFAs) in palm oil via an optical technique based on enzymatic aminolysis reactions. FFAs in crude palm oil (CPO) were converted into fatty hydroxamic acids (FHAs) in a biphasic lipid/aqueous medium in the presence of immobilized lipase. The colored compound formed after complexation between FHA and vanadium (V) ion solution was proportional to the FFA content in the CPO samples and was analyzed using a spectrophotometric method. In order to develop a rapid detection system, the parameters involved in the aminolysis process were studied. The utilization of immobilized lipase as catalyst during the aminolysis process offers simplicity in the product isolation and the possibility of conducting the process under extreme reaction conditions. A good agreement was found between the developed method using immobilized Thermomyces lanuginose lipase as catalyst for the aminolysis process and the Malaysian Palm Oil Board (MPOB) standard titration method (R2 = 0.9453).

  15. Novel microbial screen for detection of 1,4-butanediol, ethylene glycol, and adipic acid.

    Science.gov (United States)

    Stieglitz, B; Weimer, P J

    1985-03-01

    A novel microbial-screening procedure was developed for separate detection of 1,4-butanediol, ethylene glycol, and adipic acid, three commercially important oxychemicals potentially derivable from bacterial omega-oxidation of n-butanol, ethanol, and hexanoic acid, respectively. The screening method involved postproduction addition of one of several specific Pseudomonas strains which produce a soluble fluorescent pigment during growth on the product of interest. A mutation and selection procedure was developed for isolation of specific strains with phenotypes for growth and pigment production on the desired product (e.g., 1,4-butanediol), but not on its bioconversion substrate (e.g., n-butanol), common by-products (e.g., n-butyrate), or product isomers. Pigment production was growth associated and required cultivation of the screening strains under limiting Fe3+ concentrations. The pigments resembled well-characterized, iron-chelating siderophores produced by other fluorescent pseudomonads. The sensitivity of the assay for product accumulation was enhanced by (i) conducting the screening in microtiter dishes to permit examination of individual isolates of putative producers and to control product diffusion, (ii) using a wavelength cutoff filter to reduce background source light, and (iii) using adapted screening strains which grew at lower (0.3 mM) concentrations of test compounds. The potential utility of the method for detecting a variety of oxidative catabolic products is discussed.

  16. Immobilization of Tyrosinase from Avocado Crude Extract in Polypyrrole Films for Inhibitive Detection of Benzoic Acid

    Directory of Open Access Journals (Sweden)

    André Brisolari

    2014-07-01

    Full Text Available Inhibition-based biosensors were developed by immobilizing tyrosinase (Tyr, polyphenol oxidase from the crude extract of avocado fruit on electrochemically prepared polypyrrole (PPy films. The biosensors were prepared during the electropolymerization of pyrrole in a solution containing a fixed volume of the crude extract of avocado. The dependence of the biosensor responses on the volume used from the crude extract, values of pH and temperature was studied, and a substrate, catechol, at different concentrations, was amperometrically detected by these biosensors. Benzoic acid, a competitive inhibitor of Try, was added to the catechol solutions at specific concentrations aimed at obtaining the inhibition constant, K’m, which ranged from 1.7 to 4.6 mmol∙L−1 for 0.0 and 60 µmol∙L−1 of benzoic acid, respectively. Studies on the inhibition caused by benzoic acid by using PPy/Try films, and catechol as a substrate, allowed us propose how to develop, under optimized conditions, simple and low-cost biosensors based on the use of avocado fruit.

  17. Focal liver lesions detection and characterization: The advantages of gadoxetic acid-enhanced liver MRI

    Institute of Scientific and Technical Information of China (English)

    Stefano; Palmucci

    2014-01-01

    Since its clinical introduction, several studies in literature have investigated gadolinium ethoxybenzhyl diethylenetriaminepentaacetic acid or gadoxetic acid(Gd-EOB-DTPA) properties. Following contrast injection, it provides dynamic vascular phases(arterial, portal and equilibrium phases) and hepatobiliary phase, the latter due to its uptake by functional hepatocytes. The main advantages of Gd-EOB-DTPA of focal liver lesion detection and characterization are discussed in this paper. Namely, we focus on the possibility of distinguishing focal nodular hyperplasia(FNH) from hepatic adenoma(HA), the identification of early hepatocellular carcinoma(HCC) and the pre-operative assessment of metastasis in liver parenchyma. Regarding the differentiation between FNH and HA, adenoma typically appears hypointense in hepatobiliary phase, whereas FNH is isointense or hyperintense to the surrounding hepatic parenchyma. As for the identification of early HCCs, many papers recently published in literature have emphasized the contribution of hepatobiliary phase in the characterization of nodules without a typical hallmark of HCC. Atypical nodules(no hypervascularizaton observed on arterial phase and/or no hypovascular appearance on portal phase) with low signal intensity in the hepatobiliary phase, have a high probability of malignancy. Finally, regarding the evaluation of focal hepatic metastases, magnetic resonance pre-operative assessment using gadoxetic acid allows for more accurate diagnosis.

  18. Electrochemical detection of interaction between capsaicin and nucleic acids in comparison to agarose gel electrophoresis.

    Science.gov (United States)

    Yilmaz, Nilay; Eksin, Ece; Karacicek, Bilge; Eraç, Yasemin; Erdem, Arzum

    2017-10-15

    In this study, the biomolecular interaction occurred between nucleic acids and Capsaicin (CPS), the active compound in chilli peppers, which has been reported to have anti-carcinogenic properties, was investigated for the first time herein using disposable electrochemical biosensor. It is aimed to perform the surface-confined interaction between CPS and different types of nucleic acids and under this aim, the experimental conditions were optimized; such as, the concentration of CPS and DNA, DNA immobilization time and interaction time etc. The detection limit of DNA was estimated based on guanine oxidation signal in the linear concentration range of DNA from 1 to 5 μg/mL, and it was found to be 0.62 μg/mL. The effect of time-dependent manner from 1 min to 30 min on the interaction of CPS with nucleic acids was explored upon to the changes at guanine signal coming from double stranded DNA and cDNA as well as PCR samples. The interaction of CPS with double stranded DNA was also determined by agarose gel electrophoresis. Copyright © 2017 Elsevier Inc. All rights reserved.

  19. Folding gravitational-wave interferometers

    Science.gov (United States)

    Sanders, J. R.; Ballmer, Stefan W.

    2017-01-01

    The sensitivity of kilometer-scale terrestrial gravitational wave interferometers is limited by mirror coating thermal noise. Alternative interferometer topologies can mitigate the impact of thermal noise on interferometer noise curves. In this work, we explore the impact of introducing a single folding mirror into the arm cavities of dual-recycled Fabry–Perot interferometers. While simple folding alone does not reduce the mirror coating thermal noise, it makes the folding mirror the critical mirror, opening up a variety of design and upgrade options. Improvements to the folding mirror thermal noise through crystalline coatings or cryogenic cooling can increase interferometer range by as much as a factor of two over the Advanced LIGO reference design.

  20. Colorimetric detection of Cr{sup 3+} using gold nanoparticles functionalized with 4-amino hippuric acid

    Energy Technology Data Exchange (ETDEWEB)

    Jin, Weiwei; Huang, Pengcheng; Chen, Yueji; Wu, Fangying, E-mail: fywu@ncu.edu.cn; Wan, Yiqun [Nanchang University, College of Chemistry (China)

    2015-09-15

    A facile and effective technique for monitoring Cr{sup 3+} concentration based on 4-amino hippuric acid (PAH) decorated Au nanoparticles (PAH-AuNPs) is introduced. The modified AuNPs were easily aggregated in the presence of Cr{sup 3+}, resulting in the color change from red to violet or blue, which is in response to the surface plasmon absorption of dispersed or aggregated nanoparticles. Under the optimized conditions, a good linear relationship (correlation coefficient r = 0.998) was obtained between the ratio of the absorbance at 635 nm to that at 520 nm (A{sub 635 nm}/A{sub 520 nm}), and the concentration of Cr{sup 3+} was over the range of 5.0–120 µM with detection limit of 1.17 µM. This method exhibited excellent selectivity for Cr{sup 3+} over other tested heavy metal ions. Furthermore, there was no significant difference for the parameters of calibration equation between the presence and absence of ethylenediamine tetraacetic acid (EDTA), which suggests that the method can be applied in various real samples owing to the strong masking ability of EDTA. The assay was used to detect the concentrations of Cr{sup 3+} in liquid milk, milk power, and lake water samples with recoveries ranging from 93.5 to 114 %, indicating that the method could be used for extensive practical application. Graphical Abstract: A facile and effective technique for monitoring Cr{sup 3+} based on 4-amino hippuric acid decorated Au nanoparticles is introduced. The modified AuNPs were aggregated in the presence of Cr{sup 3+} resulting in the color change from red to violet or blue, which is in response to the surface plasmon absorption of dispersed or aggregated nanoparticles.

  1. Teaching computers to fold proteins

    OpenAIRE

    Winther, Ole; Krogh, Anders Stærmose

    2004-01-01

    A new general algorithm for optimization of potential functions for protein folding is introduced. It is based upon gradient optimization of the thermodynamic stability of native folds of a training set of proteins with known structure. The iterative update rule contains two thermodynamic averages which are estimated by (generalized ensemble) Monte Carlo. We test the learning algorithm on a Lennard-Jones (LJ) force field with a torsional angle degrees-of-freedom and a single-atom side-chain. ...

  2. Protein folding by motion planning

    Science.gov (United States)

    Thomas, Shawna; Song, Guang; Amato, Nancy M.

    2005-12-01

    We investigate a novel approach for studying protein folding that has evolved from robotics motion planning techniques called probabilistic roadmap methods (PRMs). Our focus is to study issues related to the folding process, such as the formation of secondary and tertiary structures, assuming we know the native fold. A feature of our PRM-based framework is that the large sets of folding pathways in the roadmaps it produces, in just a few hours on a desktop PC, provide global information about the protein's energy landscape. This is an advantage over other simulation methods such as molecular dynamics or Monte Carlo methods which require more computation and produce only a single trajectory in each run. In our initial studies, we obtained encouraging results for several small proteins. In this paper, we investigate more sophisticated techniques for analyzing the folding pathways in our roadmaps. In addition to more formally revalidating our previous results, we present a case study showing that our technique captures known folding differences between the structurally similar proteins G and L. This research was supported in part by NSF CAREER Award CCR-9624315, NSF Grants ACI-9872126, EIA-9975018, EIA-0103742, EIA-9805823, ACR-0113971, CCR-0113974, EIA-9810937, EIA-0079874 and the Texas Higher Education Coordinating Board grant ATP-000512-0261-2001. ST was supported in part by an NSF Graduate Research Fellowship. GS was supported in part by an IBM PhD Fellowship.

  3. Protein folding and protein metallocluster studies using synchrotron small angler X-ray scattering

    Energy Technology Data Exchange (ETDEWEB)

    Eliezer, D.

    1994-06-01

    Proteins, biological macromolecules composed of amino-acid building blocks, possess unique three dimensional shapes or conformations which are intimately related to their biological function. All of the information necessary to determine this conformation is stored in a protein`s amino acid sequence. The problem of understanding the process by which nature maps protein amino-acid sequences to three-dimensional conformations is known as the protein folding problem, and is one of the central unsolved problems in biophysics today. The possible applications of a solution are broad, ranging from the elucidation of thousands of protein structures to the rational modification and design of protein-based drugs. The scattering of X-rays by matter has long been useful as a tool for the characterization of physical properties of materials, including biological samples. The high photon flux available at synchrotron X-ray sources allows for the measurement of scattering cross-sections of dilute and/or disordered samples. Such measurements do not yield the detailed geometrical information available from crystalline samples, but do allow for lower resolution studies of dynamical processes not observable in the crystalline state. The main focus of the work described here has been the study of the protein folding process using time-resolved small-angle x-ray scattering measurements. The original intention was to observe the decrease in overall size which must accompany the folding of a protein from an extended conformation to its compact native state. Although this process proved too fast for the current time-resolution of the technique, upper bounds were set on the probable compaction times of several small proteins. In addition, an interesting and unexpected process was detected, in which the folding protein passes through an intermediate state which shows a tendency to associate. This state is proposed to be a kinetic molten globule folding intermediate.

  4. Classification scheme for acid rock drainage detection - the Hamersley Basin, Western Australia

    Science.gov (United States)

    Skrzypek, Grzegorz; Dogramaci, Shawan; McLean, Laura

    2017-04-01

    levels of the aqueous system. This classification scheme enables a more direct monitoring regime for early detection of acid rock drainage processes and better groundwater quality management. References Dogramaci S., McLean L., Skrzypek G., 2017. Hydrochemical and stable isotope indicators of pyrite oxidation in carbonate-rich environment; the Hamersley Basin, Western Australia. Journal of Hydrology 545, 288-298.

  5. Copper- or manganese-doped ZnS quantum dots as fluorescent probes for detecting folic acid in aqueous media

    Energy Technology Data Exchange (ETDEWEB)

    Geszke-Moritz, Malgorzata [Laboratoire Reactions et Genie des Procedes (LRGP), Nancy-University, CNRS, 1 rue Grandville, 54001 Nancy Cedex (France); Department of Pharmaceutical Technology, Poznan University of Medical Sciences, Grunwaldzka 6, 60-780 Poznan (Poland); Clavier, Gilles [PPSM, ENS Cachan, CNRS, UniverSud, 61 avenue President Wilson, 94230 Cachan (France); Lulek, Janina [Department of Pharmaceutical Technology, Poznan University of Medical Sciences, Grunwaldzka 6, 60-780 Poznan (Poland); Schneider, Raphaeel, E-mail: raphael.schneider@ensic.inpl-nancy.fr [Laboratoire Reactions et Genie des Procedes (LRGP), Nancy-University, CNRS, 1 rue Grandville, 54001 Nancy Cedex (France)

    2012-04-15

    3-Mercaptopropionic acid-capped core/shell ZnS:Cu/ZnS and ZnS:Mn/ZnS doped quantum dots (QDs) prepared through hydrothermal methods exhibit high photoluminescence intensity as well as good photostability. These water-dispersible nanoparticles exhibit high fluorescence sensitivity to folic acid due to the high affinity of the carboxylate groups and nitrogen atoms of folic acid towards the Zn surface atoms of the doped dots. Quenching of the fluorescence intensity of the QDs allows the detection of folic acid concentrations as low as 11 {mu}M, thus affording a very sensitive system for the sensing of this biologically active molecule in aqueous solution. The possible quenching mechanism is discussed. - Graphical abstract: A sensitive method for the detection of folic acid based on the fluorescence quenching of Mn- or Cu-doped ZnS quantum dots was developed. Highlights: Black-Right-Pointing-Pointer Quenching of the fluorescence intensity of doped ZnS QDs in the presence of folic acid. Black-Right-Pointing-Pointer New fluorescent sensors for folic acid. Black-Right-Pointing-Pointer Detection of folic acid concentrations as low as 11 {mu}M in aqueous solution. Black-Right-Pointing-Pointer The Perrin model and fluorescence lifetimes of ZnS:Mn QDs demonstrate a static quenching mechanism. Black-Right-Pointing-Pointer Quenching efficiency of ZnS:Cu QDs correlates with the Stern-Volmer model.

  6. Human immunodeficiency virus trans-activator of transcription peptide detection via ribonucleic acid aptamer on aminated diamond biosensor

    Science.gov (United States)

    Rahim Ruslinda, A.; Wang, Xianfen; Ishii, Yoko; Ishiyama, Yuichiro; Tanabe, Kyosuke; Kawarada, Hiroshi

    2011-09-01

    The potential of ribonucleic acid (RNA) as both informational and ligand binding molecule have opened a scenario in the development of biosensors. An aminated diamond-based RNA aptasensor is presented for human immunodeficiency virus (HIV) trans-activator of transcription (Tat) peptide protein detection that not only gives a labeled or label-free detection method but also provides a reusable platform for a simple, sensitive, and selective detection of proteins. The immobilized procedure was based on the binding interaction between positively charged amine terminated diamond and the RNA aptamer probe molecules with the negatively charged surface carboxylic compound linker molecule such as terephthalic acid.

  7. Separation and Detection of Lanthanide Ions with Nitrilotri (methylenephosphonic) Acid as Complexing Agent and Eluent by IPC

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    A mixture containing eleven lanthanide ions was separated and detected on an anion-exchange co-lumn by ion chromatography with indirect photometry detection (IPC).An aqueous solution of 1.5×10-2mol/L nitrilotri(methylenephosphonic) acid and 2.5×10-3mol/L tiron was used as the eluent in which the former served as complexing agent and eluent,the latter played as color reagent and eluent.The effects of acidity,concentration and composition of eluent on the retention behavior of the analytes and detection sensitivity are discussed.

  8. On-line concentration of trace genistein by acid barrage stacking in capillary electrophoresis with UV detection

    Institute of Scientific and Technical Information of China (English)

    Hai Yan Feng; Xiang Jun Li; Shu Rong Hou; Na Zheng; Zhong Bo Hu; Zhuo Bin Yuan

    2008-01-01

    A capillary electrophoresis method with UV detection was developed for high sensitively determining genistein. In this method, the online acid barrage stacking was applied. Four key factors influencing the stacking efficiency were systematically optimized. Genistein can be detected within 5 rain at the concentration of 10 nmol/L, which was 300 times lower than that from conventional hydrodynamic injection. The repeatability, linear range, and limit of detection of the method were investigated with satisfactory result.

  9. Synthesis of Au/Graphene Oxide Composites for Selective and Sensitive Electrochemical Detection of Ascorbic Acid

    Science.gov (United States)

    Song, Jian; Xu, Lin; Xing, Ruiqing; Li, Qingling; Zhou, Chunyang; Liu, Dali; Song, Hongwei

    2014-12-01

    In this work, we present a novel ascorbic acid (AA) sensor applied to the detection of AA in human sera and pharmaceuticals. A series of Au nanoparticles (NPs) and graphene oxide sheets (Au NP/GO) composites were successfully synthesized by reduction of gold (III) using sodium citrate. Then the Au NP/GO composites were used to construct nonenzymatic electrodes in practical AA measurement. The electrode that has the best performance presents attractive analytical features, such as a low working potential of +0.15 V, a high sensitivity of 101.86 μA mM-1 cm-2 to AA, a low detection limit of 100 nM, good reproducibility and excellent selectivity. And more,it was also employed to accurately and practically detect AA in human serum and clinical vitamin C tablet with the existence of some food additive. The enhanced AA electrochemical properties of the Au NP/GO modified electrode in our work can be attributed to the improvement of electroactive surface area of Au NPs and the synergistic effect from the combination of Au NPs and GO sheets. This work shows that the Au NP/GO/GCEs hold the prospect for sensitive and selective determination of AA in practical clinical application.

  10. Excretion and detection of SARS coronavirus and its nucleic acid from digestive system

    Institute of Scientific and Technical Information of China (English)

    Xin-Wei Wang; Xiao-Ming Wu; Wen-Jun Xiao; Xiu-Mei Zhu; Chang-Qing Gu; Jing Yin; Wei Wei; Wei Yao; Chao Liu; Jian-Feng Li; Guo-Rong Ou; Jin-Song Li; Min-Nian Wang; Tong-Yu Fang; Gui-Jie Wang; Yao-Hui Qiu; Huai-Huan Wu; Fu-Huan Chao; Jun-Wen Li; Ting-Kai Guo; Bei Zhen; Qing-Xin Kong; Bin Yi; Zhong Li; Nong Song; Min Jin

    2005-01-01

    AIM: To study whether severe acute respiratory syndrome coronavirus (SARS-CoV) could be excreted from digestive system.METHODS: Cell culture and semi-nested RT-PCR were used to detect SARS-CoV and its RNA from 21 stool and urine samples, and a kind of electropositive filter media particles was used to concentrate the virus in 10 sewage samples from two hospitals receiving SAPS patients in Beijing in China.RESULTS: It was demonstrated that there was no live SARS-CoV in all samples collected, but the RNA of SARS-CoV could be detected in seven stool samples from SARS patients with any one of the symptoms of fever, malaise,cough, or dyspnea, in 10 sewage samples before disinfection and 3 samples after disinfection from the two hospitals.The RNA could not be detected in urine and stool samples from patients recovered from SARS.CONCLUSION: Nucleic acid of SARS-CoV can be excreted through the stool of patients into sewage system, and the possibility of SARS-CoV transmitting through digestive system cannot be excluded.

  11. Ultrasensitive Detection of Ferulic Acid Using Poly(diallyldimethylammonium chloride Functionalized Graphene-Based Electrochemical Sensor

    Directory of Open Access Journals (Sweden)

    Lin-jie Liu

    2014-01-01

    Full Text Available The electrochemical redox of ferulic acid (FA was investigated systematically by cyclic voltammetry (CV with a poly(diallyldimethylammonium chloride functionalized graphene-modified glassy carbon electrode (PDDA-G/GCE as a working electrode. A simple and sensitive differential pulse voltammetry (DPV technique was proposed for the direct quantitative determination of FA in Angelica sinensis and spiked human urine samples for the first time. The dependence of the intensities of currents and potentials on nature of the supporting electrolyte, pH, scan rate, and concentration was investigated. Under optimal conditions, the proposed sensor exhibited excellent electrochemical sensitivity to FA, and the oxidation peak current was proportional to FA concentration in the range of 8.95×10-8 M ~5.29×10-5 M, with a relatively low detection limit of 4.42×10-8 M. This fabricated sensor also displayed acceptable reproducibility, long-term stability, and high selectivity with negligible interferences from common interfering species. Besides, it was applied to detect FA in Angelica sinensis and biological samples with satisfactory results, making it a potential alternative tool for the quantitative detection of FA in pharmaceutical analysis.

  12. Cell-Free Nucleic Acids As Noninvasive Biomarkers For Colorectal Cancer Detection

    Directory of Open Access Journals (Sweden)

    Hicham eMansour

    2014-08-01

    Full Text Available Cell-free nucleic acids (CFNA have been reported by several authors in blood, stool and urine of patients with colorectal cancer (CRC. These genetic biomarkers can be an indication of neoplastic colorectal epithelial cells, so they can potentially be used as noninvasive tests for the detection of the disease in CRC patients and monitor their staging, without the need to use heavier and invasive tools. In a number of test-trials, these genetic tests have shown the advantage of non-invasiveness, making them well accepted by most of the patients, without major side effects. They have also shown a promising sensitivity and specificity in the detection of malignant and premalignant neoplasms. Moreover, costs for performing such tests can be very low. Several studies reported and confirmed the proof of the principle for these genetic tests for screening, diagnosis and prognosis; the main challenge of translating this approach from research to clinical laboratory is the validation in large and long-term randomized trials to prove sustainable high sensitivity and specificity. In this paper, we present a review on the noninvasive genetics biomarkers for CRC detection described in the literature and the challenges that can be encountered for validation processes.

  13. Field Effect Sensors for Nucleic Acid Detection: Recent Advances and Future Perspectives

    Directory of Open Access Journals (Sweden)

    Bruno Veigas

    2015-05-01

    Full Text Available In the last decade the use of field-effect-based devices has become a basic structural element in a new generation of biosensors that allow label-free DNA analysis. In particular, ion sensitive field effect transistors (FET are the basis for the development of radical new approaches for the specific detection and characterization of DNA due to FETs’ greater signal-to-noise ratio, fast measurement capabilities, and possibility to be included in portable instrumentation. Reliable molecular characterization of DNA and/or RNA is vital for disease diagnostics and to follow up alterations in gene expression profiles. FET biosensors may become a relevant tool for molecular diagnostics and at point-of-care. The development of these devices and strategies should be carefully designed, as biomolecular recognition and detection events must occur within the Debye length. This limitation is sometimes considered to be fundamental for FET devices and considerable efforts have been made to develop better architectures. Herein we review the use of field effect sensors for nucleic acid detection strategies—from production and functionalization to integration in molecular diagnostics platforms, with special focus on those that have made their way into the diagnostics lab.

  14. Ternary surface monolayers for ultrasensitive (zeptomole) amperometric detection of nucleic acid hybridization without signal amplification.

    Science.gov (United States)

    Wu, Jie; Campuzano, Susana; Halford, Colin; Haake, David A; Wang, Joseph

    2010-11-01

    A ternary surface monolayer, consisting of coassembled thiolated capture probe, mercaptohexanol and dithiothreitol, is shown to offer dramatic improvements in the signal-to-noise characteristics of electrochemical DNA hybridization biosensors based on common self-assembled monolayers. Remarkably low detection limits down to 40 zmol (in 4 μL samples) as well as only 1 CFU Escherichia coli per sensor are thus obtained without any additional amplification step in connection to the commonly used horseradish peroxidase/3,3',5,5'-tetramethylbenzidine system. Such dramatic improvements in the detection limits (compared to those of common binary alkanethiol interfaces and to those of most electrochemical DNA sensing strategies without target or signal amplification) are attributed primarily to the remarkably higher resistance to nonspecific adsorption. This reflects the highly compact layer (with lower pinhole density) produced by the coupling of the cyclic- and linear-configuration "backfillers" that leads to a remarkably low background noise even in the presence of complex sample matrixes. A wide range of surface compositions have been investigated, and the ternary mixed monolayer has been systematically optimized. Detailed impedance spectroscopy and cyclic voltammetric studies shed useful insights into the surface coverage. The impressive sensitivity and high specificity of the simple developed methodology indicate great promise for a wide range of nucleic acid testing, including clinical diagnostics, biothreat detection, food safety, and forensic analysis.

  15. Determination of catecholamines by ion chromatography coupled to acidic potassium permanganate chemiluminescence detection

    Institute of Scientific and Technical Information of China (English)

    Hong Wei Wu; Mei Lan Chen; Dan Shou; Yan Zhu

    2012-01-01

    A simple,fast,sensitive,highly selective and eco-friendly analytical method for the determination of catecholamines in human urine by ion chromatography (IC) with chemiluminescence (CL) detection was described in this paper.Using 12 mmoi/L H2SO4 without any organic additive as eluent,three catecholamines including epinephrine (EP),norepinephrine (NE) and dopamine (DA)were well separated on a cation-exchange column.The CL detection was based on the reaction of analytes with acidic potassium permanganate in the presence of formaldehyde as an enhancer.The absence of methanol and acetonitrile in eluent made the proposed method more sensitive and eco-friendly.Under the optimal conditions,the linear range of the proposed method was in the range of 0.02-0.5 μg/mL.The limit of detection (LOD) was in the range of 0.6 and 5.1 μg/L.The relative standard deviations (RSD) for 0.1 μg/mL mixed standard solution were in the range of 0.8-1.9% (n =11).The method has been applied to the determination of catecholamines in human urine successfully.Excellent spiked recoveries were achieved for catecholamines ranged from 91.2% to 112.7%.

  16. Cell-free nucleic acids as noninvasive biomarkers for colorectal cancer detection

    KAUST Repository

    Mansour, Hicham

    2014-08-27

    Cell-free nucleic acids (CFNA) have been reported by several authors in blood, stool, and urine of patients with colorectal cancer (CRC). These genetic biomarkers can be an indication of neoplastic colorectal epithelial cells, and can thus potentially be used as noninvasive tests for the detection of the disease in CRC patients and monitor their staging, without the need to use heavier and invasive tools. In a number of test-trials, these genetic tests have shown the advantage of non-invasiveness, making them well accepted by most of the patients, without major side effects. They have also shown a promising sensitivity and specificity in the detection of malignant and premalignant neoplasms. Moreover, costs for performing such tests are very low. Several studies reported and confirmed the proof of the principle for these genetic tests for screening, diagnosis, and prognosis; the main challenge of translating this approach from research to clinical laboratory is the validation from large and long-term randomized trials to prove sustainable high sensitivity and specificity. In this paper, we present a review on the noninvasive genetics biomarkers for CRC detection described in the literature and the challenges that can be encountered for validation processes.

  17. Improved focal liver lesion detection by increasing flip angle during gadoxetic acid-enhancement in MRI

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Se Jy [Dept. of Medical science Graduate school, Chonnam National University, Kwangju (Korea, Republic of); Kim, Young Keun [Dept. of Radiotechnology, Gwang-ju Health university, Gwangju (Korea, Republic of)

    2015-06-15

    To study the differences of focal liver lesion image detection at 3 minute, 10 minute and 15 minute time points on gadoxetic acid (GA)’s enhanced MR imaging with a flip angle (FA) of 30° compared with a 11°. The subjects were 69 patients evaluated with GA enhanced MR imaging with 3.0T MR scanner. The patients are total 35(23 men and 7 women at the mean age of 60.4 years), hepatocellular carcinoma(23) and metastsis(12) except for normal, cyst and hemangioma. After GA was injected, FA 11° and 30° images were obtained at 3 minute, 10 minute and 15 minute time points respectively. After quantitative and qualitative assessment of each image was done, statistical analysis was performed by using the independent sample T-test. From both quantitative and qualitative assessment of 3 minute and 10 minute MR images after the injection of GA, FA 30° images was found to be superior than FA 11°, but there were no statistical significance. However, at 15 minute time point, Statistically significant FA 30° image(p<0.05) was better than FA 11° therefore, the FA 30° improves the focal liver lesion detection. FA 30° of MR image can detect liver lesion more sensitively than the existing FA11° image after GA contrast enhancement at 15 minute time point.

  18. High-speed separation and detection of amino acids in laver using a short capillary electrophoresis system.

    Science.gov (United States)

    Wang, Wei; Ma, Lihong; Yao, Fenzeng; Lin, Xiuli; Xu, Kaixuan

    2015-01-01

    A high-speed separation method of capillary MEKC with LIF detection had been developed for separation and determination of amino acids in laver. The CE system comprised a manual slotted-vial array (SVA) for sample introduction that could improve the separation efficiency by reducing injection volume. Using a capillary with 80 mm effective separation length, the separation conditions for amino acids were optimized. Applied with the separation electric field strength of 300 V/cm, the ten amino acids could be completely separated within 2.5 min with 10 mol/L Na2HPO4-NaOH buffer (pH = 11.5) including 30 mmol/L SDS. Theoretical plates for amino acids ranged from 72,000 to 40,000 (corresponding to 1.1-2.0 μm plate heights) and the detection limits were between 25 and 80 nmol/L. Finally, this method was applied to analyze the composition of amino acids in laver and eight known amino acids could be found in the sample. The contents of five amino acids, tyrosine, glutamic acid, glycine, lysine, and aspartic acid that could be completely separated in real sample were determined. The recoveries ranged from 82.3% to 123% that indicated the good reliability for this method in laver sample analysis.

  19. The construction of a novel nucleic acids detection microplatform based on the NSET for one-step detecting TK1-DNA and microRNA-21.

    Science.gov (United States)

    Zhang, Jian; Zhao, Qian; Wu, Yudong; Zhang, Bo; Peng, Weipan; Piao, Jiafang; Zhou, Yurui; Gao, Weichen; Gong, Xiaoqun; Chang, Jin

    2017-11-15

    Microbeads-based microchip technology has become the potential for a new generation of nucleic acids detection in a high-throughput and sensitive manner. However the specificity and operational complexity limit the microchip applied in nucleic acids detection. Herein, in this work, we designed a kind of gold-nanoparticles coated polystyrene microbeads as microplatform conjugating with the molecular beacons as probes. Due to the nanoparticle surface energy transfer of gold-nanoparticles, the fluorescence of dye on one end of molecular beacons was effectively quenched. When the target nucleic acids existed, the fluorescence of dye was quickly "turn-on" with high sensitivity. Due to the nanoparticle surface energy transfer effect of gold-nanoparticles, the designed platform performed better sensitivity than traditional microbead-based detection methods and realized quickly detection within 10min without purification steps. In addition, compared with the linear chain probes, the molecular beacons probes enabled higher specificity and wash-free operation. Through different dyes encoded, TK1-DNA and microRNA-21 were simultaneously detected in one step and finally quantified by flow cytometry. The proposed detection method was also capable of monitoring TK1-DNA and microRNA-21 levels in human serum. Our study provides the potential multidetection of DNA and RNA. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. 核酸检测与抗体检测在HIV感染中的应用%Application of nucleic acid detection and antibody detection in HIV infection

    Institute of Scientific and Technical Information of China (English)

    侯海燕; 燕清丽; 刘靓; 刘纯成

    2015-01-01

    Objective To compare the accuracy of nucleic acid detection and antibody detection for diagnosing human immunode‐ficiency virus(HIV) infection .Methods Retrospectively analysed data of nucleic acid detection and antibody detection from 124 ca‐ses of patients diagnosed with HIV infection from 2005 to 2014 .The positive rates of the two methods were compared respectively in patients with early‐stage of HIV infection(76 cases) and patients with intermediate and advanced stage of HIV infection (48 ca‐ses) .Results In patients with early‐stage of HIV infectionn ,the positive rate of nucleic acid detection (94 .74% ) was higher than that of antibody detection (84 .21% );while in patients with intermediate and advanced stage of HIV infection ,the positive rate of antibody detection(97 .92% ) was higher than that of nucleic acid detection (81 .25% );both had statistically significant difference (P<0 .05) .Conclusion On the early stage of HIV infection ,the accuracy of nucleic acid detection is higher than that of antibody detection ;while on the intermediate and advanced stage of HIV infection ,antibody detection shows better accuracy .%目的:比较核酸检测与抗体检测在人类免疫缺陷病毒(HIV )感染诊断中的准确性。方法回顾性分析2005~2014年124例确诊H IV感染者的抗体检测与核酸检测资料,并分别比较两种方法在早期感染者(76例)与中晚期感染者(48例)中的检出阳性率。结果早期感染者核酸检测阳性率(94.74%)高于抗体检测(84.21%),中晚期感染者抗体检测阳性率(97.92%)高于核酸检测(81.25%),差异均有统计学意义( P<0.05)。结论核酸检测在H IV感染早期准确性高于抗体检测,而在H IV感染中晚期,抗体检测准确性较高。

  1. Separation and conductimetric detection of C1-C7 aliphatic monocarboxylic acids and C1-C7 aliphatic monoamines on unfunctionized polymethacrylate resin columns.

    Science.gov (United States)

    Ohta, Kazutoku; Towata, Atsuya; Ohashi, Masayoshi; Takeuchi, Toyohide

    2004-06-11

    The application of unfunctionized polymethacrylate resin (TSKgel G3000PWXL) as a stationary phase in liquid chromatography with conductimetric detection for C1-C7 aliphatic monocarboxylic acids (formic acid, acetic acid, propionic acid, butyric acid, isovaleric acid, valeric acid, 3,3-dimethylbutyric acid, 4-methylvaleric acid, hexanoic acid, 2-methylhexanoic acid, 5-methylhexanoic acid and heptanoic acid) and C1-C7 aliphatic monoamines (methylamine, ethylamine, propylamine, isobutylamine, butylamine, isoamylamine, amylamine, 1,3-dimethylbutylamine, hexylamine, 2-heptylamine and heptylamine) was attempted with C8 aliphatic monocarboxylic acids (2-propylvaleric acid, 2-ethylhexanoic acid, 2-methylheptanoic acid and octanoic acid) and C8 aliphatic monoamines (1,5-dimethylhexylamine, 2-ethylhexylamine, 1-methylheptylamine and octylamine) as eluents, respectively. Using 1 mM 2-methylheptanoic acid at pH 4.0 as the eluent, excellent separation and relatively high sensitive detection for these C1-C7 carboxylic acids were achieved on a TSKgel G3000PWXL column (150 mm x 6 mm i.d.) in 60 min. Using 2 mM octylamine at pH 11.0 as the eluent, excellent separation and relatively high sensitive detection for these C1-C7 amines were also achieved on the TSKgel G3000PWXL column in 60 min.

  2. Detection of pantothenic acid-immunoreactive neurons in the rat lateral septal nucleus by a newly developed antibody.

    Science.gov (United States)

    Mangas, Arturo; Yajeya, Javier; Gonzalez, Noelia; Husson, Marianne; Geffard, Michel; Coveñas, Rafael

    2016-01-01

    The available immunohistochemical techniques have documented restricted distribution of vitamins in the mammalian brain. The aim of the study was to develop a highly specific antiserum directed against pantothenic acid to explore the presence of this vitamin in the mammalian brain. According to ELISA tests, the anti-pantothenic acid antiserum used showed a good affinity (10-8 M) and specificity. The antiserum was raised in rabbits. Using an indirect immunoperoxidase technique, the mapping of pantothenic acid-immunoreactive structures was carried out in the rat brain. Pantothenic acid-immunoreactive perikarya were exclusively found in the intermediate part of the lateral septal nucleus. These cells were generally small, round, fusiform or pyramidal and showed 2-3 long (50-100 μm) immunoreactive dendrites. Any immunoreactive axons containing pantothenic acid were detected. The very restricted anatomical distribution of the pantothenic acid suggests that this vitamin could be involved in some specific neurophysiological mechanisms.

  3. Locked Nucleic Acid Probes (LNA) for Enhanced Detection of Low-Level, Clinically Significant Mutations.

    Science.gov (United States)

    Nafa, Khedoudja; Hameed, Meera; Arcila, Marie E

    2016-01-01

    The detection of clinically significant somatic mutations present at low level in a tissue sample represents a challenge in any laboratory. While several high sensitivity methods are described, the incorporation of these new techniques in a clinical lab may be difficult if the technology is not readily available or requires major changes in the workflow of the laboratory. Techniques that are robust and easily adapted to existing laboratory protocols are highly advantageous. In this chapter we describe the use of locked nucleic acid (LNA) probes to modify existing polymerase chain reaction (PCR)-based protocols which can then be sequenced by Sanger sequencing. LNA probes are used to enhance the sensitivity of Sanger sequencing to mutation frequencies below 1 %. The method is robust and is easily incorporated for assessment of any sample with low tumor content or low mutant allele burden.

  4. A STUDY ON DETECTION OF SERUMFASTING TOTAL BILE ACID AND CHOLOYGLYCIN IN NEONATE FOR CHOLESTASIS

    Institute of Scientific and Technical Information of China (English)

    郭文; 吴明昌; 裴学义; 关德华; 徐洛

    1996-01-01

    Enzyme-linked colorimetric analysis and radioimmunossay were employed to detect serum fasting total bile acids(FBA) and choloyglyein (CG) respectively in eases of 32 neonatal hepatitis, 33 cases of neona-tal uneonjugated hyperbilirubinemia and 34 cases of breast milk jaundice(BMJ). FBA and CG in acute period of neonatal hepatitis were obviously elevated and decreased gradually in convalescent and recovered period. The difference was significant for each stage as compared with controls. Acute FBA correlated strongly with the course. Both neonatal unconjugated hyperbilirubinemia and BMJ differed significantlyfrom controls in FBA and CG. The results suggested that serum FBA and CGr were helpful in judging the course and state of neonatal hepatitis, and eholestasls might existed in neonatal unconjngated hyperbilirubinemia.

  5. Cascade enzymatic catalysis in poly(acrylic acid) brushes-nanospherical silica for glucose detection.

    Science.gov (United States)

    Zhao, Yan; Wang, Ying; Zhang, Xiaobin; Kong, Rongmei; Xia, Lian; Qu, Fengli

    2016-08-01

    The ultrasensitive monitoring of glucose with a fast and accurate method is significant in potential therapeutics and optimizes protein biosynthesis. Incorporation of enzyme into matrix is considered as promising candidates for constructing highly sensitive glucose-responsive systems. In this study, three-dimensional poly(acrylic acid) brushes-nanospherical silica (PAA-nano silica) with high amplification capability and stability were used to covalently immobilize bienzymes for cascade enzymatic catalysis. The major advantages of PAA-nano silica-bienzyme co-incorporation is that the enzymes are proximity distribution, and such close confinement both minimized the diffusion of intermediates among the enzymes in the consecutive reaction and improve the utilization efficiency of enzymes, thereby enhancing the overall reaction efficiency and specificity. Thus, this present bienzymatic biosensor shows robust signal amplification and ultrasensitivity of glucose-responsive properties with a detection limit of 0.04μM.

  6. Terahertz microfluidic chips for detection of amino acids in aqueous solutions

    Science.gov (United States)

    Su, Bo; Zhang, Cong; Fan, Ning; Zhang, Cunlin

    2016-11-01

    Microfluidic technology can control the fluidic thickness accurately in less than 100 micrometers. So the combination of terahertz (THz) and microfluidic technology becomes one of the most interesting directions towards biological detection. We designed microfluidic chips for terahertz spectroscopy of biological samples in aqueous solutions. Using the terahertz time-domain spectroscopy (THz-TDS) system, we experimentally measured the transmittance of the chips and the THz absorption spectra of L-threonine and L-arginine, respectively. The results indicated the feasibility of performing high sensitivity THz spectroscopy of amino acids solutions. Therefore, the microfluidic chips can realize real-time and label-free measurement for biochemistry samples in THz-TDS system.

  7. Peroxidase-like activity of nanocrystalline cobalt selenide and its application for uric acid detection.

    Science.gov (United States)

    Zhuang, Quan-Quan; Lin, Zhi-Hang; Jiang, Yan-Cheng; Deng, Hao-Hua; He, Shao-Bin; Su, Li-Ting; Shi, Xiao-Qiong; Chen, Wei

    2017-01-01

    Dendrite-like cobalt selenide nanostructures were synthesized from cobalt and selenium powder precursors by a solvothermal method in anhydrous ethylenediamine. The as-prepared nanocrystalline cobalt selenide was found to possess peroxidase-like activity that could catalyze the reaction of peroxidase substrates in the presence of H2O2. A spectrophotometric method for uric acid (UA) determination was developed based on the nanocrystalline cobalt selenide-catalyzed coupling reaction between N-ethyl-N-(3-sulfopropyl)-3-methylaniline sodium salt and 4-aminoantipyrine (4-AAP) in the presence of H2O2. Under optimum conditions, the absorbance was proportional to the concentration of UA over the range of 2.0-40 μM with a detection limit of 0.5 μM. The applicability of the proposed method has been validated by determination of UA in human serum samples with satisfactory results.

  8. Detection of Gold Nanoparticles Aggregation Growth Induced by Nucleic Acid through Laser Scanning Confocal Microscopy

    Science.gov (United States)

    Gary, Ramla; Carbone, Giovani; Petriashvili, Gia; De Santo, Maria Penelope; Barberi, Riccardo

    2016-01-01

    The gold nanoparticle (GNP) aggregation growth induced by deoxyribonucleic acid (DNA) is studied by laser scanning confocal and environmental scanning electron microscopies. As in the investigated case the direct light scattering analysis is not suitable, we observe the behavior of the fluorescence produced by a dye and we detect the aggregation by the shift and the broadening of the fluorescence peak. Results of laser scanning confocal microscopy images and the fluorescence emission spectra from lambda scan mode suggest, in fact, that the intruding of the hydrophobic moiety of the probe within the cationic surfactants bilayer film coating GNPs results in a Förster resonance energy transfer. The environmental scanning electron microscopy images show that DNA molecules act as template to assemble GNPs into three-dimensional structures which are reminiscent of the DNA helix. This study is useful to design better nanobiotechnological devices using GNPs and DNA. PMID:26907286

  9. Detection of Gold Nanoparticles Aggregation Growth Induced by Nucleic Acid through Laser Scanning Confocal Microscopy

    Directory of Open Access Journals (Sweden)

    Ramla Gary

    2016-02-01

    Full Text Available The gold nanoparticle (GNP aggregation growth induced by deoxyribonucleic acid (DNA is studied by laser scanning confocal and environmental scanning electron microscopies. As in the investigated case the direct light scattering analysis is not suitable, we observe the behavior of the fluorescence produced by a dye and we detect the aggregation by the shift and the broadening of the fluorescence peak. Results of laser scanning confocal microscopy images and the fluorescence emission spectra from lambda scan mode suggest, in fact, that the intruding of the hydrophobic moiety of the probe within the cationic surfactants bilayer film coating GNPs results in a Förster resonance energy transfer. The environmental scanning electron microscopy images show that DNA molecules act as template to assemble GNPs into three-dimensional structures which are reminiscent of the DNA helix. This study is useful to design better nanobiotechnological devices using GNPs and DNA.

  10. Simultaneous determination of acetylsalicylic acid and salicylic acid in human plasma by isocratic high-pressure liquid chromatography with post-column hydrolysis and fluorescence detection.

    Science.gov (United States)

    Hobl, Eva-Luise; Jilma, Bernd; Ebner, Josef; Schmid, Rainer W

    2013-06-01

    A selective, sensitive and rapid high-performance liquid chromatography method with post-column hydrolysis and fluorescence detection was developed for the simultaneous quantification of acetylsalicylic acid and its metabolite salicylic acid in human plasma. Following the addition of 2-hydroxy-3-methoxybenzoic acid as internal standard and simple protein precipitation with acetonitrile, the analytes were separated on a ProntoSIL 120 C18 ace-EPS column (150 × 2 mm, 3 µm) protected by a C8 guard column (5 µm). The mobile phase, 10 mm formic acid in water (pH 2.9) and acetonitrile (70:30, v/v), was used at a flow rate of 0.35 mL/min. After on-line post-column hydrolysis of acetylsalicylic acid (ASA) to salicylic acid (SA) by addition of alkaline solution, the analytes were measured at 290 nm (λex ) and 400 nm (λem ). The method was linear in the concentration ranges between 0.05 and 20 ng/μL for both ASA and SA with a lower limit of quantification of 25 pg/μL for SA and 50 pg/μL for ASA. The limit of detection was 15 pg/μL for SA and 32.5 pg/μL for ASA. The analysis of ASA and SA can be carried out within 8 min; therefore this method is suitable for measuring plasma concentrations of salicylates in clinical routine.

  11. Determination of vanillylmandelic acid, vanillactic acid, and homovanillic acid in dried urine on filter-paper discs by high-performance liquid chromatography with coulometric electrochemical detection for neuroblastoma screening.

    Science.gov (United States)

    Kinoshita, Y; Yamada, S; Haraguchi, K; Takayanagi, T; Mori, Y; Takahashi, T; Haruki, E

    1988-11-01

    We report a method for determination of vanillylmandelic acid, vanillactic acid, and homovanillic acid by high-performance liquid chromatography (HPLC), with coulometric electrochemical detection, for mass screening of neuroblastoma. Urine samples were collected on filter paper, dried, and then pretreated. The chromatographic procedure is reliable and fast, allowing for a large sample throughput for routine screening. Intricate extraction procedures and centrifugal separation are unnecessary. Screening for neuroblastoma by HPLC is rapidly gaining acceptance in Japan, and our method is being used at many screening centers. Of 26,571 infants screened in one year in Yokohama City, our method detected five with neuroblastoma.

  12. Differential equations and folding of $n$-mani-folds

    Directory of Open Access Journals (Sweden)

    I. Mousa

    2005-09-01

    Full Text Available In this paper we will describe some topological and geometric characters of $n$-manifold by using the properties of differential equations. The folding and unfolding of $n$-manifold into itself will be deduced from viewpoint of the differential equations.

  13. Simultaneous analysis of six aristolochic acids and five aristolactams in herbal plants and their preparations by high-performance liquid chromatography-diode array detection-fluorescence detection.

    Science.gov (United States)

    Yuan, Jinbin; Liu, Qian; Zhu, Weifeng; Ding, Li; Tang, Fei; Yao, Shouzhuo

    2008-02-22

    Aristolochic acid analogues, including aristolochic acids (AAs) and aristolactams (ALs), are known to be nephrotoxic, carcinogenic and mutagenic. In this paper, a high-performance liquid chromatography-diode array detection-fluorescence detection (HPLC-DAD-FLD) method was developed for the simultaneous determination of six AAs together with five ALs. Baseline separation was obtained on an ODS C18 analytical column with 0.2% HAc/methanol gradient elution. The hyphenation of DAD and FLD allows the method to directly meet the analysis requirements of most herbal plants with high sensitivity and selectivity. For trace analysis, aristolochic acids were reduced to their corresponding aritstolactams in acidic solution containing iron powder, and then high sensitive detection and quantification were carried out. The method was successfully validated in the matrices of various Aristolochiaceae plants and their preparations. Linearities of around 3-4 orders of magnitude were obtained with correlation coefficients exceeding 0.9970. The detection limits were decreased to 0.2ng/ml. Satisfactory intra-day and inter-day precisions were achieved with RSDs less than 5.74%, and the average recovery factors were in the range of 94.5-99.2%.

  14. Detection of polyglutamine expansion in a new acidic protein: a candidate for childhood onset schizophrenia?

    Science.gov (United States)

    Moriniere, S; Saada, C; Holbert, S; Sidransky, E; Galat, A; Ginns, E; Rapoport, J L; Neri, C

    1999-01-01

    Polyglutamine expansion (PGE) encoded by a CAG repeat underlies eight inherited neurodegenerative diseases, among which is Huntington's disease. CAG expansion has also been reported in schizophrenia, suggesting a role for PGE. To investigate the potential role of PGE as a candidate for schizophrenia, we searched for PGE in nuclear families comprising a patient affected by childhood onset schizophrenia (COS, a rare and severe form of the disease) as a variation of the candidate gene approach for identifying susceptibility genes. We tested lymphoblastoid cell lines from COS patients (n = 32) by Western blot analysis with 1C2, a monoclonal antibody that specifically recognizes long polyglutamines. Eight of 11 unrelated black American COS patients showed a 60-kDa (approximately) band indicative of PGE. A strong 60-kDa band (suggestive of a large PGE) was detected in two of the eight positive patients. A weaker 60-kDa band (suggestive of a smaller and non pathogenic PGE) was detected in some unaffected parents or sibs of these two COS patients, and in six other black American COS patients. The strong and weak PGE signals were found to correspond to two different proteins. Unrelated black Americans unaffected by COS (n = 38) were negative for the strong 60-kDa PGE signal. Healthy white Americans (n = 53) were negative for both the strong and weak 60-kDa PGE signals. Two-dimensional gel analysis suggested that the strong PGE signal corresponds to an acidic (pI 4 approximately) protein and resulted in a more precise estimation (52-57 kDa) of its relative mass. This protein appeared to be not represented in Genbank, as suggested by the exclusion of several candidate CAG repeats. Our data suggest that this acidic protein might be a candidate for COS.

  15. Biocompatible 3D SERS substrate for trace detection of amino acids and melamine.

    Science.gov (United States)

    Satheeshkumar, Elumalai; Karuppaiya, Palaniyandi; Sivashanmugan, Kundan; Chao, Wei-Ting; Tsay, Hsin-Sheng; Yoshimura, Masahiro

    2017-03-21

    A novel, low-cost and biocompatible three-dimensional (3D) substrate for surface-enhanced Raman spectroscopy (SERS) is fabricated using gold nanoparticles (AuNPs) loaded on cellulose paper for detection of amino acids and melamine. Dysosma pleiantha rhizome (Dp-Rhi) capped AuNPs (Dp-Rhi_AuNPs) were prepared by in situ using aqueous extract of Dp-Rhi and in situ functionalized Dp-Rhi on AuNPs surface was verified by Fourier transform infrared spectroscopy and zeta potentials analysis shows a negative (-18.4mV) surface charges, which confirm that presence of Dp-Rhi on AuNPs. The biocompatibility of Dp-Rhi_AuNPs is also examined by cell viability of FaDu cells using MTS assay and compared to control group. In conclusion, the SERS performance of AuNPs@cellulose paper substrates were systematically demonstrated and examined with different excitation wavelengths (i.e. 532, 632.8 and 785nm lasers) and the as-prepared 3D substrates provided an enhancement factor approaching 7 orders of magnitude compared with conventional Raman intensity using para-nitrothiophenol (p-NTP), para-aminothiophenol (p-ATP) and para-mercaptobenzoic acid (p-MBA) as probe molecules. The strong electromagnetic effect was generated at the interface of AuNPs and pre-treated roughened cellulose paper is also investigated by simulation in which the formation of possible Raman hot-spot zone in fiber-like microstructure of cellulose paper decorated with AuNPs. Notably, with optimized condition of as-prepared 3D AuNPs@cellulose paper is highly sensitive in the SERS detection of aqueous tyrosine (10(-10)M) and melamine (10(-9)M).

  16. Colorimetric detection of melamine based on p-chlorobenzenesulfonic acid-modified AuNPs

    Science.gov (United States)

    Li, Jianfang; Huang, Pengcheng; Wu, Fangying

    2016-06-01

    A highly selective and sensitive method is developed for colorimetric detection of melamine using gold nanoparticles (AuNPs) functionalized with p-chlorobenzenesulfonic acid. The addition of melamine induced the aggregation of AuNPs, as evidenced from the morphological characterizations and the color changed from red wine to blue, which could also be monitored by the UV-visible spectrometer and even naked eyes. This process caused a significant increase in the absorbance ratio (A650nm/A520nm) of p-chlorobenzenesulfonic acid-AuNPs. Under optimized conditions, the system exhibited a linear response to melamine in the range of 6.0 × 10-7-1.5 × 10-6 mol L-1 with a correlation coefficient of 0.997, and the limit of detection can even be 2.3 nM, which was much lower than some other methods and the safe limits (20 μM in both the USA and EU, 8.0 μM for infant formula in China, 1.2 μM in the CAC (Codex Alimentarius Commission) review for melamine in liquid infant formula). More importantly, the developed method presented excellent tolerance to coexisting common metal ions such as Ca2+, Zn2+, whose concentration is 1000 times of melamine, so that it had been applied to the analysis of melamine in liquid milk and milk powder with the recovery of 97.0-101 % and 100-103 %, respectively, indicating that the proposed method is quite a highly effective means to determine melamine in milk products.

  17. Role of Visual Inspection of Cervix with Acetic Acid (VIA in Detecting Precancerous Lesions of Cervix

    Directory of Open Access Journals (Sweden)

    Kamrun Nessa

    2014-01-01

    Full Text Available Background: Carcinoma of cervix is the most common malignancy in female and a major public health problem worldwide. It is the leading cause of death from cancer among women in low resource settings. In Bangladesh, mortality rate is high as most of the cases with cervical cancer are diagnosed in advanced stage. World Health Organization considers cervical cancer as a preventable disease as it can be identified in preinvasive stage. Considerable efforts have been given in detection and treatment of the condition all over the world. A number of cervical cancer screening tests are available. Among them, visual inspection of cervix with acetic acid is rational and can be competently performed by physicians with proper training. Objective: To find out the feasibility of the visual inspection of cervix with acetic acid for the detection of the precancerous lesions of the cervix in our country. Materials and Methods: This cross sectional, analytical study was carried out among the patients attending the outpatient department of Bangabandhu Sheikh Mujib Medical University (BSMMU who were VIA positive and sent for colposcopy in the colposcopy clinic in the department of Obstetrics and Gynecology in BSMMU from June to December 2004. Two hundred samples were considered for this study. Results: Out of 200 cases, colposcopically 85% had CIN and invasive lesions, 4% had inflammatory lesions while 11% had normal findings. Colposcopy directed punch biopsy revealed positive lesions in 81%, 4% had inflammatory lesions while 15% had normal findings. Conclusion: The study concluded that VIA and colposcopy are the important methods in the evaluation of cervical premalignancy. VIA may be an important tool for screening of cervical cancer in low resource settings as it is simple, easy to perform and cost-effective. After screening, VIA positive cases must be referred for colposcopic evaluation. We can screen cervical cancer by VIA all over the country and thus reduce

  18. A combinatorial approach to detect coevolved amino acid networks in protein families of variable divergence.

    Directory of Open Access Journals (Sweden)

    Julie Baussand

    2009-09-01

    Full Text Available Communication between distant sites often defines the biological role of a protein: amino acid long-range interactions are as important in binding specificity, allosteric regulation and conformational change as residues directly contacting the substrate. The maintaining of functional and structural coupling of long-range interacting residues requires coevolution of these residues. Networks of interaction between coevolved residues can be reconstructed, and from the networks, one can possibly derive insights into functional mechanisms for the protein family. We propose a combinatorial method for mapping conserved networks of amino acid interactions in a protein which is based on the analysis of a set of aligned sequences, the associated distance tree and the combinatorics of its subtrees. The degree of coevolution of all pairs of coevolved residues is identified numerically, and networks are reconstructed with a dedicated clustering algorithm. The method drops the constraints on high sequence divergence limiting the range of applicability of the statistical approaches previously proposed. We apply the method to four protein families where we show an accurate detection of functional networks and the possibility to treat sets of protein sequences of variable divergence.

  19. NoFold: RNA structure clustering without folding or alignment.

    Science.gov (United States)

    Middleton, Sarah A; Kim, Junhyong

    2014-11-01

    Structures that recur across multiple different transcripts, called structure motifs, often perform a similar function-for example, recruiting a specific RNA-binding protein that then regulates translation, splicing, or subcellular localization. Identifying common motifs between coregulated transcripts may therefore yield significant insight into their binding partners and mechanism of regulation. However, as most methods for clustering structures are based on folding individual sequences or doing many pairwise alignments, this results in a tradeoff between speed and accuracy that can be problematic for large-scale data sets. Here we describe a novel method for comparing and characterizing RNA secondary structures that does not require folding or pairwise alignment of the input sequences. Our method uses the idea of constructing a distance function between two objects by their respective distances to a collection of empirical examples or models, which in our case consists of 1973 Rfam family covariance models. Using this as a basis for measuring structural similarity, we developed a clustering pipeline called NoFold to automatically identify and annotate structure motifs within large sequence data sets. We demonstrate that NoFold can simultaneously identify multiple structure motifs with an average sensitivity of 0.80 and precision of 0.98 and generally exceeds the performance of existing methods. We also perform a cross-validation analysis of the entire set of Rfam families, achieving an average sensitivity of 0.57. We apply NoFold to identify motifs enriched in dendritically localized transcripts and report 213 enriched motifs, including both known and novel structures.

  20. Co-transcriptional folding is encoded within RNA genes

    Directory of Open Access Journals (Sweden)

    Miklós István

    2004-08-01

    Full Text Available Abstract Background Most of the existing RNA structure prediction programs fold a completely synthesized RNA molecule. However, within the cell, RNA molecules emerge sequentially during the directed process of transcription. Dedicated experiments with individual RNA molecules have shown that RNA folds while it is being transcribed and that its correct folding can also depend on the proper speed of transcription. Methods The main aim of this work is to study if and how co-transcriptional folding is encoded within the primary and secondary structure of RNA genes. In order to achieve this, we study the known primary and secondary structures of a comprehensive data set of 361 RNA genes as well as a set of 48 RNA sequences that are known to differ from the originally transcribed sequence units. We detect co-transcriptional folding by defining two measures of directedness which quantify the extend of asymmetry between alternative helices that lie 5' and those that lie 3' of the known helices with which they compete. Results We show with statistical significance that co-transcriptional folding strongly influences RNA sequences in two ways: (1 alternative helices that would compete with the formation of the functional structure during co-transcriptional folding are suppressed and (2 the formation of transient structures which may serve as guidelines for the co-transcriptional folding pathway is encouraged. Conclusions These findings have a number of implications for RNA secondary structure prediction methods and the detection of RNA genes.

  1. pH jump induced α-helix folding.

    Directory of Open Access Journals (Sweden)

    Donten M. L.

    2013-03-01

    Full Text Available pH can be used to impact the folding equilibrium of peptides and proteins. This fact is utilized, similarly to temperature jumps, in pH jump experiments employing laser time-resolved spectroscopy to study the function and structural dynamics of these molecules. Here the application of pH jumps in folding experiments was investigated. Experiments with poly-L-glutamic acid alpha-helix formation shown the critical aspects of pH jump experiments and yielded direct information about the folding kinetics monitored with the amide I IR band.

  2. Analysis of protein folds using protein contact networks

    Indian Academy of Sciences (India)

    Pankaj Barah; Somdatta Sinha

    2008-08-01

    Proteins are important biomolecules, which perform diverse structural and functional roles in living systems. Starting from a linear chain of amino acids, proteins fold to different secondary structures, which then fold through short- and long-range interactions to give rise to the final three-dimensional shapes useful to carry out the biophysical and biochemical functions. Proteins are defined as having a common `fold' if they have major secondary structural elements with same topological connections. It is known that folding mechanisms are largely determined by a protein's topology rather than its interatomic interactions. The native state protein structures can, thus, be modelled, using a graph-theoretical approach, as coarse-grained networks of amino acid residues as `nodes' and the inter-residue interactions/contacts as `links'. Using the network representation of protein structures and their 2D contact maps, we have identified the conserved contact patterns (groups of contacts) representing two typical folds – the EF-hand and the ubiquitin-like folds. Our results suggest that this direct and computationally simple methodology can be used to infer about the presence of specific folds from the protein's contact map alone.

  3. Determination of iodide using flow injection with acidic potassium permanganate chemiluminescence detection.

    Science.gov (United States)

    Yaqoob, Mohammad; Atiq-ur-Rehman; Waseem, Amir; Nabi, Abdul

    2006-01-01

    A simple and rapid flow-injection method is described for the determination of iodide, based on potassium permanganate chemiluminescence detection via oxidation of formaldehyde in aqueous hydrochloric acid. The calibration graph was linear over the range 1.0-12 x 10(-6) mol/L (r2 = 0.9955) with relative standard deviations (n = 4) in the range 1.0-3.5%. The detection limit (3sigma) was 1.0 x 10(-7) mol/L, with sample throughput of 120/h. The effect of interfering cations [Ca(II), Mg(II), Ni(II), Fe(II), Fe(III) and Pb(II)] and anions (Cl-, SO4(2-), PO4(3-), NO3-, NO2-, F- and SO3(2-)) were studied. The method was applied to iodized salt samples and the results obtained in the range 0.03 +/- 0.005 - 0.10 +/- 0.006 mg I/g were in reasonable agreement with the amount labelled. The method was statistically compared with the results obtained by titration; no significant disagreement at 95% confidence was observed.

  4. Improved microscopical detection of acid-fast bacilli by the modified bleach method in lymphnode aspirates

    Directory of Open Access Journals (Sweden)

    Annam Vamseedhar

    2009-07-01

    Full Text Available Objectives: To improve the smear microscopy for detection of acid-fast bacilli (AFB in fine needle aspiration cytology (FNAC of lymph node using the bleach method and also to compare this with cytological diagnosis and the conventional Ziehl-Neelsen (ZN method. Study Design: In 99 consecutive patients with clinical suspicion of tuberculosis (TB presenting with lymphadenopathy, FNACs were performed. Smears from the aspirates were processed for routine cytology and the conventional ZN method. The remaining material in the needle hub and/or the syringe was used for the bleach method. The significance of the bleach method over the conventional ZN method and cytology was analyzed using the χ2 test. Results: Of 99 aspirates, 93 were studied and the remaining six were excluded from the study due to diagnosis of malignancy in 4.04% (4/6 and inadequate aspiration in 2.02% (2/6. Among the 93 aspirates, 33.33% (31/93 were positive for AFB on conventional ZN method, 41.94% (39/93 were indicative of TB on cytology and the smear positivity increased to 63.44% (59/93 on bleach method. Conclusion: The bleach method is simple, inexpensive and potent disinfectant, also limiting the risk of laboratory-acquired infections. The implementation of the bleach method clearly improves microscopic detection and can be a useful contribution to routine cytology.

  5. Multicolor instrumentation for direct fluorescent detection of nucleic acids in a microchip format

    Science.gov (United States)

    Bogdanov, Valery L.; Rogers, Yu-Hui; Lan, Guang; Boyce-Jacino, Michael

    1998-04-01

    Deposition of nucleic acids on solid support in the form of high density arrays (a DNA microarray) creates a powerful nonelectrophoretic technology for highly parallel genetic analysis. Microarrays have applications in the areas of DNA sequencing, genetic mutation detection and gene expression monitoring. We report here the design and utility of an experimental instrument for microchip parallel hyperspectral fluorescent imaging. The instrument integrates in-line laser excitation of microarray, parallel fluorescent spectrometry with cooled CCD and dye-base spectral classification software. Instrument has been applied for imaging detection, spectral analysis and base classification of Genetic Bit Analysis (GBA) reactions in a microchip format on a glass support. GBA is a solid phase DNA sequence analysis method that provides single nucleotide resolution by specific extension of dye-labeled dideoxynucleotidetriphosphates (ddNTPs). GBA testing yields one or two different ddNTPs on any given microarray spot, so analysis must resolve any pair wise combination of all possible ddNTPs labeled with distinct fluorescent dyes.

  6. Assessment of Urinary-5-Hydroxyindolacetic Acid as A Diagnostic Parameter in Early Detection of Acute Appendicitis

    Directory of Open Access Journals (Sweden)

    Zuhair B Kamal

    2017-04-01

    Full Text Available Background: Acute appendicitis is the most common abdominal surgical emergency especially in children and young adults. The diagnosis of appendicitis is difficult because half the cases are incorrectly identified. Serotonin was defined as a good diagnostic marker for many inflammations including appendicitis and it is metabolite into 5-hydroxyindolacetic acid (5-HIAA to be excreted in urine. 5-HIAA is suggested to be of diagnostic importance in the detection of this disease. The aim of this study was to evaluate the diagnostic importance of urinary-5-HIAA as an added parameter to Alvarado score. Methods: Seventy patients (35 females and 35 males with acute appendicitis (35 were mild and 35 severe-perforated and gangrenous were included in this study and 70 healthy individuals were taken as a control group. Urinary-5-HIAA was estimated in all patients and control group using ELISA method. Results: Sensitivity for the mild group is 94.2%, specificity 100% and diagnostic accuracy is 97.4%, while the sensitivity for the severe group is 37%. It was found that there is a highly significant difference between mild and control groups (P<0.05. The diagnostic accuracy for the mild group is 97.4% and for the severe is 68.5%. Conclusion: We conclude that urinary-5-HIAA is a high sensitive test for early detection of acute appendicitis.

  7. Colorimetric detection of Cd2+ using 1-amino-2-naphthol-4-sulfonic acid functionalized silver nanoparticles

    Science.gov (United States)

    Huang, Pengcheng; Liu, Bowen; Jin, Weiwei; Wu, Fangying; Wan, Yiqun

    2016-11-01

    A colorimetric assay has been developed for facile, rapid, and sensitive detection of Cd2+ using 1-amino-2-naphthol-4-sulfonic acid functionalized silver nanoparticles (ANS-AgNPs). The presence of Cd2+ induces the aggregation of ANS-AgNPs through cooperative metal-ligand interaction. As a result, the characteristic surface plasmon resonance (SPR) peak of ANS-AgNPs at 390 nm was red-shifted to 580 nm, yielding a color change from bright yellow to reddish-brown. The color change is monitored by UV-Vis spectrometer and can be directly read out by the naked eye. Under the optimized conditions, a good linear relationship (correlation coefficient R = 0.997) was obtained between the ratio of the absorbance at 580 nm to that at 390 nm (A580nm/A390nm) and the concentration of Cd2+ over the range of 1.0-10 μM with detection limit of 87 nM. The proposed method is simple and efficient, which has been applied for determining Cd2+ in milk powder, serum, and lake water with satisfactory results.

  8. Glyphosate detection with ammonium nitrate and humic acids as potential interfering substances by pulsed voltammetry technique.

    Science.gov (United States)

    Martínez Gil, Pablo; Laguarda-Miro, Nicolas; Camino, Juan Soto; Peris, Rafael Masot

    2013-10-15

    Pulsed voltammetry has been used to detect and quantify glyphosate on buffered water in presence of ammonium nitrate and humic substances. Glyphosate is the most widely used herbicide active ingredient in the world. It is a non-selective broad spectrum herbicide but some of its health and environmental effects are still being discussed. Nowadays, glyphosate pollution in water is being monitored but quantification techniques are slow and expensive. Glyphosate wastes are often detected in countryside water bodies where organic substances and fertilizers (commonly based on ammonium nitrate) may also be present. Glyphosate also forms complexes with humic acids so these compounds have also been taken into consideration. The objective of this research is to study the interference of these common pollutants in glyphosate measurements by pulsed voltammetry. The statistical treatment of the voltammetric data obtained lets us discriminate glyphosate from the other studied compounds and a mathematical model has been built to quantify glyphosate concentrations in a buffer despite the presence of humic substances and ammonium nitrate. In this model, the coefficient of determination (R(2)) is 0.977 and the RMSEP value is 2.96 × 10(-5) so the model is considered statistically valid.

  9. Polyoxometalate-Graphene Nanocomposite Modified Electrode for Electrocatalytic Detection of Ascorbic Acid

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Weiying; Du, Dan; Gunaratne, Don; Colby, Robert; Lin, Yuehe; Laskin, Julia

    2013-11-15

    Phosphomolybdate functionalized graphene nanocomposite (PMo12-GS) has been successfully formed on a glassy carbon electrode (GCE) for the detection of ascorbic acid (AA). The obtained PMo12-GS modified GCE, was characterized by cyclic voltammetry, electrochemical impedance spectroscopy, scanning electron microscopy (SEM) and Fourier transform infrared (FT-IR) spectroscopy and compared with GCE, GS modified GCE, and PMo12 modified GCE. It shows an increased current and a decrease in over-potential of ~210 mV. The amperometric signals are linearly proportional to the AA concentration in a wide concentration range from 1×10-6 M to 8×10-3 M, with a detection limit of 0.5×10-6 M. Finally, the PMo12-GS modified electrode was employed for the determination of the AA level in vitamin C tablets, with recoveries between 96.3 and 100.8 %.

  10. Highly sensitive SERS detection and quantification of sialic acid on single cell using photonic-crystal fiber with gold nanoparticles.

    Science.gov (United States)

    Gong, Tianxun; Cui, Ying; Goh, Douglas; Voon, Kong Kien; Shum, Perry Ping; Humbert, Georges; Auguste, Jean-Louis; Dinh, Xuan-Quyen; Yong, Ken-Tye; Olivo, Malini

    2015-02-15

    An ultrasensitive surface enhanced Raman spectroscopy (SERS) based sensing platform was developed to detect the mean sialic acid level on the surface of single cell with sensitivity as low as 2 fmol. This platform adopted the use of an interference-free Raman tag, 4-(dihydroxyborophenyl) acetylene (DBA), which selectively binds to sialic acid on the cell membrane. By loading the side channel of a photonic crystal fiber with a mixture of gold nanoparticles and DBA-tagged HeLa cell, and subsequently propagating laser light through the central solid core, strong SERS signal was obtained. This SERS technique achieved accurate detection and quantification of concentration of sialic acid on a single cell, surpassing previously reported methods that required more than 10(5) cells. Moreover, this platform can be developed into a clinical diagnostic tool to potentially analyze sialic acid-related diseases such as tumor malignancy and metastasis in real-time.

  11. Detection of Acid Rain Stress Effect on Plant Using Hyperspectral Data in Three Gorges Region,China

    Institute of Scientific and Technical Information of China (English)

    SONG Xiaodong; JIANG Hong; YU Shuquan; ZHOU Guomo

    2008-01-01

    This paper aims to use hyperspectral data to detect the spectral change caused by acid stress to a native forest type in the Three Gorges region of China.For this purpose,a ground-based hyperspectral experiment was conducted at the Three Gorges region to detect acid deposition that caused Masson pine (Pinus massoniana) forest degradation.Continuum removal method was used to isolate wavebands more responsive to stress in wavelengths 450-750nm.The differences in chlorophyll concentrations and needle thickness caused by acidic stress are found to be explicable to the different spectral reflectance patterns in the visible and near-infrared wavelengths.Two new chlorotic indices were utilized to explain the stress-caused leaf chiorosis.The comparison of simulated vegetation indices and principal component analysis (PCA) results suggests that it would be possible to monitor acid rain stress effect on forest ecosystem from some wider spectral regions.

  12. CERVICAL ACID PHOSPHATASE: EVALUATION AS AN ADJUVANT TO PAPANICOLAOU SMEAR SCREENING IN CERVICAL CANCER DETECTION

    Directory of Open Access Journals (Sweden)

    Niranjan

    2015-02-01

    Full Text Available INTRODUCTION: Carcinoma of cervix accounts for 15% of all cancers diagnosed worldwide and is the second most common cancer in women. In the year 2000 there were over 4,71,000 new cases diagnosed and 2,88,000 deaths from cervical cancer. (1 Approximately 79% of these deaths occurred in developing countries. (2 Cervical cancer is preventable, but most women in poorer countries do not have access to effective screening programs. In India it is estimated that approximately 100,000 women develop cervical cancer each year. (3 Cancer cervix occupies either the top r ank or second among cancers in women in developing countries, whereas, in the developed countries cancer cervix does not find a place even in top five leading cancers in women. This is due to routine screening by cervical smear. Cervical smear cytology scr eening by Papanicolaou (Pap stained smears is the most efficacious and cost - effective method of cancer screening, decreasing the incidence and mortality from cervical cancer. (4 However, cervical smear screening has significant rates of false - positive and false - negative results, ranging from 10.3% for false positive cases to 5.6% for false negative cases. (5,6 To improve the detection and screening of cancerous and precancerous lesions of the cervix a number of sophisticated tests are available which are e xpensive and can be done only in a tertiary laboratory. To over - come this problems a cost effective cytochemical stain was introduced to measure the acid phosphatase activity in the cervical epithelium. (7 Since the description of the new Cervical Acid Phosphatase Test (CAP Test for visualization of cervical acid phosphatase activity (CAP inside abnormal cervical cells on smears, it has become possible to explore this enzyme as a biomarker for cervical dys plasia, and as a possible surrogate for PAP smear in detection of cervical intraepithelial neoplasia (CIN. AIMS AND OBJECTIVES: To assess the utility of Cervical Acid

  13. Rapid detection of equine influenza virus H3N8 subtype by insulated isothermal RT-PCR (iiRT-PCR) assay using the POCKIT™ Nucleic Acid Analyzer.

    Science.gov (United States)

    Balasuriya, Udeni B R; Lee, Pei-Yu Alison; Tiwari, Ashish; Skillman, Ashley; Nam, Bora; Chambers, Thomas M; Tsai, Yun-Long; Ma, Li-Juan; Yang, Pai-Chun; Chang, Hsiao-Fen Grace; Wang, Hwa-Tang Thomas

    2014-10-01

    Equine influenza (EI) is an acute, highly contagious viral respiratory disease of equids. Currently, equine influenza virus (EIV) subtype H3N8 continues to be the most important respiratory pathogen of horses in many countries around the world. The need to achieve a rapid diagnosis and to implement effective quarantine and movement restrictions is critical in controlling the spread of EIV. In this study, a novel, inexpensive and user-friendly assay based on an insulated isothermal RT-PCR (iiRT-PCR) method on the POCKIT™, a field-deployable device, was described and validated for point-of-need detection of EIV-H3N8 in clinical samples. The newly established iiRT-PCR assay targeting the EIV HA3 gene was evaluated for its sensitivity using in vitro transcribed (IVT) RNA, as well as ten-fold serial dilutions of RNA extracted from the prototype H3N8 strain A/equine/Miami/1/63. Inclusivity and exclusivity panels were tested for specificity evaluation. Published real-time RT-PCR (rRT-PCR) assays targeting the NP and HA3 genes were used as the reference standards for comparison of RNA extracted from field strains and from nasal swab samples collected from experimentally infected horses, respectively. Limit of detection with a 95% probability (LoD95%) was estimated to be 11copies of IVT RNA. Clinical sensitivity analysis using RNA prepared from serial dilutions of a prototype EIV (Miami 1/63/H3N8) showed that the iiRT-PCR assay was about 100-fold more sensitive than the rRT-PCR assay targeting the NP gene of EIV subtype H3N8. The iiRT-PCR assay identified accurately fifteen EIV H3N8 strains and two canine influenza virus (CIV) H3N8 strains, and did not cross-react with H6N2, H7N7, H1N1 subtypes or any other equine respiratory viral pathogens. Finally, 100% agreement was found between the iiRT-PCR assay and the universal influenza virus type A rRT-PCR assay in detecting the EIV A/equine/Kentucky/7/07 strain in 56 nasal swab samples collected from experimentally inoculated

  14. Quantification of fold growth of frontal antiforms in the Zagros fold and thrust belt (Kurdistan, NE Iraq)

    Science.gov (United States)

    Bretis, Bernhard; Bartl, Nikolaus; Graseman, Bernhard; Lockhart, Duncan

    2010-05-01

    The Zagros fold and thrust belt is a seismically active orogen, where actual kinematic models based on GPS networks suggest a north-south shortening between Arabian and Eurasian in the order of 1.5-2.5 cm/yr. Most of this deformation is partitioned in south-southwest oriented folding and thrusting with northwest-southeast to north-south trending dextral strike slip faults. The Zagros fold and thrust belt is of great economic interest because it has been estimated that this area contains about 15% of the global recoverable hydrocarbons. Whereas the SE parts of the Zagros have been investigated by detailed geological studies, the NW extent being part of the Republic of Iraq have experienced considerably less attention. In this study we combine field work and remote sensing techniques in order to investigate the interaction of erosion and fold growth in the area NE of Erbil (Kurdistan, Iraq). In particular we focus on the interaction of the transient development of drainage patterns along growing antiforms, which directly reflects the kinematics of progressive fold growth. Detailed geomorphological studies of the Bana Bawi-, Permam- and Safeen fold trains show that these anticlines have not developed from subcylindrical embryonic folds but they have merged from different fold segments that joined laterally during fold amplification. This fold segments with length between 5 and 25 km have been detected by mapping ancient and modern river courses that initially cut the nose of growing folds and eventually got defeated leaving behind a wind gap. Fold segments, propagating in different directions force rivers to join resulting in steep gorges, which dissect the merging fold noses. Along rapidly lateral growing folds (e.g. at the SE end of the Bana Bawi Anticline) we observed "curved wind gaps", a new type of abandoned river course, where form of the wind gap mimics a formed nose of a growing antiform. The inherited curved segments of uplifted curved river courses strongly

  15. Bodies Folded in Migrant Crypts

    DEFF Research Database (Denmark)

    Galis, Vasilis; Tzokas, Spyros; Tympas, Aristotle

    2016-01-01

    and human migrants generates a dis/abled subject. In this context, dis/ability may be a cause or consequence of migration, both in physical/material (the folding of bodies in the crypt) and cultural/semiotic terms, and may become a barrier to accessing protection, to entering and/or crossing a country...

  16. Gothic Elements in Folding Beijing

    Institute of Scientific and Technical Information of China (English)

    Hua Yan

    2016-01-01

    The study claims that Folding Beijing can not only be read as science fiction but also as Gothic literature,in which perspective,Gothic Elements such as Gothic Setting, Gothic Wanderer and Transgressions,and Gothic Terror are discussed respectively.

  17. Simultaneous electrochemical detection of dopamine and uric acid over ceria supported three dimensional gold nanoclusters

    Science.gov (United States)

    Palanisamy, Sivakumar

    2014-12-01

    CeO2 is well known for being an active material to support the growth of Au nanoclusters (Au NCs). In this work, three dimensional (3D) Au NCs were deposited on three different shaped CeO2 nanostructures such as nanoparticles (NPs), nanorod arrays (NRAs) and nanoflowers (NFs) modified Ti substrate for electrochemical simultaneous detection of dopamine (DA) and uric acid (UA). The electrodeposition of 3D Au NCs were carried out via cyclic voltammetric (CV) method at over-potential, while CeO2 nanostructures were deposited by galvanostatic constant current method under the optimized conditions. The morphology and elemental composition analysis of 3D Au NCs with CeO2 nanostructures were characterized by SEM, XRD, XPS and EDAX measurements. The electrocatalytic activity of 3D Au NCs on different CeO2 supports were thoroughly investigated by using voltammetric and amperometric techniques. According to the obtained results, CeO2 NPs supported 3D Au NCs (3D Au NCs@CeO2 NPs) displayed strong signal for DA as compared to that of CeO2 NRAs (3D Au NCs@CeO2 NRAs) and CeO2 NFs supported 3D Au NCs (3D Au NCs@CeO2 NFs). In addition, the 3D Au NCs@CeO2 NPs electrode resulted in more sensitive and simultaneous detection of DA in the presence of excess UA. Thus, the 3D Au NCs@CeO2 NPs electrode can practically be applied for the detection of DA using biological samples.

  18. Microfluidic mixers for studying protein folding.

    Science.gov (United States)

    Waldauer, Steven A; Wu, Ling; Yao, Shuhuai; Bakajin, Olgica; Lapidus, Lisa J

    2012-04-10

    The process by which a protein folds into its native conformation is highly relevant to biology and human health yet still poorly understood. One reason for this is that folding takes place over a wide range of timescales, from nanoseconds to seconds or longer, depending on the protein. Conventional stopped-flow mixers have allowed measurement of folding kinetics starting at about 1 ms. We have recently developed a microfluidic mixer that dilutes denaturant ~100-fold in ~8 μs. Unlike a stopped-flow mixer, this mixer operates in the laminar flow regime in which turbulence does not occur. The absence of turbulence allows precise numeric simulation of all flows within the mixer with excellent agreement to experiment. Laminar flow is achieved for Reynolds numbers Re ≤100. For aqueous solutions, this requires micron scale geometries. We use a hard substrate, such as silicon or fused silica, to make channels 5-10 μm wide and 10 μm deep (See Figure 1). The smallest dimensions, at the entrance to the mixing region, are on the order of 1 μm in size. The chip is sealed with a thin glass or fused silica coverslip for optical access. Typical total linear flow rates are ~1 m/s, yielding Re~10, but the protein consumption is only ~0.5 nL/s or 1.8 μL/hr. Protein concentration depends on the detection method: For tryptophan fluorescence the typical concentration is 100 μM (for 1 Trp/protein) and for FRET the typical concentration is ~100 nM. The folding process is initiated by rapid dilution of denaturant from 6 M to 0.06 M guanidine hydrochloride. The protein in high denaturant flows down a central channel and is met on either side at the mixing region by buffer without denaturant moving ~100 times faster (see Figure 2). This geometry causes rapid constriction of the protein flow into a narrow jet ~100 nm wide. Diffusion of the light denaturant molecules is very rapid, while diffusion of the heavy protein molecules is much slower, diffusing less than 1 μm in 1 ms. The

  19. Position-specific incorporation of fluorescent non-natural amino acids into maltose-binding protein for detection of ligand binding by FRET and fluorescence quenching.

    Science.gov (United States)

    Iijima, Issei; Hohsaka, Takahiro

    2009-04-17

    Position-specific incorporation of fluorescent groups is a useful method for analysis of the functions and structures of proteins. We have developed a method for the incorporation of visible-wavelength-fluorescent non-natural amino acids into proteins in a cell-free translation system. Using this technique, we introduced one or two BODIPY-linked amino acids into maltose-binding protein (MBP) to obtain MBP derivatives showing ligand-dependent changes in fluorescence intensity or intensity ratio. BODIPY-FL-aminophenylalanine was incorporated in place of 15 tyrosines, as well as the N-terminal Lys1, and the C-terminal Lys370 of MBP. Fluorescence measurements revealed that MBP containing a BODIPY-FL moiety in place of Tyr210 showed a 13-fold increase in fluorescence upon binding of maltose. Tryptophan-to-phenylalanine substitutions suggest that the increase in fluorescence was the result of a decrease in the quenching of BODIPY-FL by tryptophan located around the binding site. MBP containing a BODIPY-558 moiety also showed a maltose-dependent increase in fluorescence. BODIPY-FL was then additionally incorporated in place of Lys1 of the BODIPY-558-containing MBP as a response to the amber codon. Fluorescence measurements with excitation of BODIPY-FL showed a large change in fluorescence intensity ratio (0.13 to 1.25) upon binding of maltose; this change can be attributed to fluorescence resonance energy transfer (FRET) and maltose-dependent quenching of BODIPY-558. These results demonstrate the usefulness of the position-specific incorporation of fluorescent amino acids in the fluorescence-based detection of protein functions.

  20. Development of a Generic Microfluidic Device for Simultaneous Detection of Antibodies and Nucleic Acids in Oral Fluids

    Directory of Open Access Journals (Sweden)

    Zongyuan Chen

    2013-01-01

    Full Text Available A prototype dual-path microfluidic device (Rheonix CARD capable of performing simultaneously screening (antigen or antibody and confirmatory (nucleic acid detection of pathogens is described. The device fully integrates sample processing, antigen or antibody detection, and nucleic acid amplification and detection, demonstrating rapid and inexpensive “sample-to-result” diagnosis with performance comparable to benchtop analysis. For the chip design, a modular approach was followed allowing the optimization of individual steps in the sample processing process. This modular design provides great versatility accommodating different disease targets independently of the production method. In the detection module, a lateral flow (LF protocol utilizing upconverting phosphor (UCP reporters was employed. The nucleic acid (NA module incorporates a generic microtube containing dry reagents. Lateral flow strips and PCR primers determine the target or disease that is diagnosed. Diagnosis of HIV infection was used as a model to investigate the simultaneous detection of both human antibodies against the virus and viral RNA. The serological result is available in less than 30 min, and the confirmation by RNA amplification takes another 60 min. This approach combines a core serological portable diagnostic with a nucleic acid-based confirmatory test.

  1. Indirect UV detection-ion-exclusion/cation-exchange chromatography of common inorganic ions with sulfosalicylic acid eluent.

    Science.gov (United States)

    Kozaki, Daisuke; Mori, Masanobu; Nakatani, Nobutake; Arai, Kaori; Masuno, Tomoe; Koseki, Masakazu; Itabashi, Hideyuki; Tanaka, Kazuhiko

    2013-01-01

    Herein, we describe indirect UV detection-ion-exclusion/cation-exchange chromatography (IEC/CEC) on a weakly acidic cation-exchange resin in the H(+)-form (TSKgel Super IC-A/C) using sulfosalicylic acid as the eluent. The goal of the study was to characterize the peaks detected by UV detector. The peak directions of analyte ions in UV at 315 nm were negative because the molar absorbance coefficients of analyte anions and cations were lower than that of the sulfosalicylic acid eluent. Good chromatographic resolution and high signal-to-noise ratios of analyte ions were obtained for the separations performed using 1.1 mM sulfosalicylic acid and 1.5 mM 18-crown-6 as the eluent. The relative standard deviations (RSDs) of the peak areas ranged from 0.6 to 4.9%. Lower detection limits of the analytes were achieved using indirect UV detection at 315 nm (0.23 - 0.98 μM) than those obtained with conductometric detection (CD) (0.61 - 2.1 μM) under the optimized elution conditions. The calibration curves were linear in the range from 0.01 to 1.0 mM except for Cl(-), which was from 0.02 to 2.0 mM. The present method was successfully applied to determine common inorganic ions in a pond water sample.

  2. Conformation and sequence evidence for two-fold symmetry in left-handed beta-helix fold.

    Science.gov (United States)

    Shen, Xiaojuan

    2011-09-21

    The left-handed beta-helix (LβH) has received interest recently as it folds as a possible solution for the structure of misfolded proteins associated with prion and Huntington's diseases. Through a combination of sequence and structure analysis, we uncover a novel feature that is common to this unique fold: a two-fold symmetry in both sequence and structure, and this feature always coupled with extended loops in the middle of the helix. Since the results reveal a two-fold symmetric pattern both in the sequence and structure, it may indicate that the symmetry in tertiary structure is coded by the symmetry in primary sequence, which agrees with Anfisen's proposal that a protein's amino-acid sequence specify its three-dimensional structure. It may also indicate that LβH adopts a two-fold repeat pattern during the evolution process and symmetry helps maintaining the stability of the helix structure. The two-fold symmetric pattern and extended loops might be important in maintaining stability of helix proteins. This discovery can be useful in understanding the folding mechanisms of this protein fold and provide insights in the relation between sequences and structures.

  3. A novel l-leucine modified Sol-Gel-Carbon electrode for simultaneous electrochemical detection of homovanillic acid, dopamine and uric acid in neuroblastoma diagnosis.

    Science.gov (United States)

    Khamlichi, Redouan El; Bouchta, Dounia; Anouar, El Hassane; Atia, Mounia Ben; Attar, Aisha; Choukairi, Mohamed; Tazi, Saloua; Ihssane, Raissouni; Faiza, Chaoukat; Khalid, Draoui; Khalid, Riffi Temsamani

    2017-02-01

    Neuroblastoma is a pediatric neuroblastic tumor arising in the sympathetic nervous crest cells. A high grade of Neuroblastoma is characterized by a high urinary excretion of homovanillic acid and dopamine. In this work l-leucine modified Sol-Gel-Carbon electrode was used for a sensitive voltammetric determination of homovanillic acid and dopamine in urine. The electrochemical response characteristics were investigated by cyclic and differential pulse voltammetry; the modified electrode has shown an increase in the effective area of up to 40%, a well-separated oxidation peaks and an excellent electrocatalytic activity. High sensitivity and selectivity in the linear range of 0,4-100μML(-1) of homovanillic acid and 10-120μML(-1) of dopamine were also obtained. Moreover, a sub-micromolar limit of detection of 0.1μM for homovanillic acid and 1.0μM for the dopamine was achieved. Indeed, high reproducibility with simple preparation and regeneration of the electrode surface made this electrode very suitable for the determination of homovanillic acid and dopamine in pharmaceutical and clinical preparations. The mechanism of homovanillic acid and the electrochemical oxidation at l-leucine modified Sol-Gel-Carbon electrode is described out the B3P86/6-31+G(d,p) level of theory as implemented in Gaussian software. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. Protein Folding Pathways Revealed by Essential Dynamics Sampling.

    Science.gov (United States)

    Narzi, Daniele; Daidone, Isabella; Amadei, Andrea; Di Nola, Alfredo

    2008-11-11

    The characterization of the protein folding process represents one of the major challenges in molecular biology. Here, a method to simulate the folding process of a protein to its native state is reported, the essential dynamics sampling (EDS) method, and is successfully applied to detecting the correct folding pathways of two small proteins, the all-β SH3 domain of Src tyrosine kinase transforming protein (SH3) and the α/β B1 domain of streptococcal protein G (GB1). The main idea of the method is that a subset of the natural modes of fluctuation in the native state is key in directing the folding process. A biased molecular dynamics simulation is performed, in which the restrained degrees of freedom are chosen among those obtained by a principal component, or essential dynamics, analysis of the positional fluctuations of the Cα atoms in the native state. Successful folding is obtained if the restraints are applied only to the eigenvectors with lowest eigenvalues, representing the most rigid quasi-constraint motions. If the essential eigenvectors, the ones accounting for most of the variance, are used, folding is not successful. These results clearly show that the eigenvectors with lowest eigenvalues contain the main mechanical information necessary to drive the folding process, while the essential eigenvectors represent the large concerted motions which can occur without folding/unfolding the protein.

  5. Hybridization-Based Detection of Helicobacter pylori at Human Body Temperature Using Advanced Locked Nucleic Acid (LNA) Probes

    DEFF Research Database (Denmark)

    Fontenete, Sílvia; Guimarães, Nuno; Leite, Marina

    2013-01-01

    the possibility of developing a variant of fluorescence in situ hybridization (FISH), named fluorescence in vivo hybridization (FIVH), for the detection of Helicobacter pylori. Using oligonucleotide variations comprising locked nucleic acids (LNA) and 2'-O-methyl RNAs (2'OMe) with two types of backbone linkages...

  6. Development of a nucleic acid lateral flow immunoassay for simultaneous detection of Listeria spp. and Listeriamonocytogenes in food

    NARCIS (Netherlands)

    Blazkova, M.; Koets, M.; Rauch, P.; Amerongen, van A.

    2009-01-01

    We present a new nucleic acid lateral flow immunoassay (NALFIA) for the assessment of listeria contamination. The detection procedure starts with enrichment of sample in Half Fraser broth (24 h). Following isolation of DNA, a duplex PCR is performed with two labelled primer sets, one generic and dir

  7. Phylogenetic group- and species-specific oligonucleotide probes for single-cell detection of lactic acid bacteria in oral biofilms

    NARCIS (Netherlands)

    Quevedo, Beatrice; Giertsen, Elin; Zijnge, Vincent; Luethi-Schaller, Helga; Guggenheim, Bernhard; Thurnheer, Thomas; Gmuer, Rudolf

    2011-01-01

    Background: The purpose of this study was to design and evaluate fluorescent in situ hybridization (FISH) probes for the single-cell detection and enumeration of lactic acid bacteria, in particular organisms belonging to the major phylogenetic groups and species of oral lactobacilli and to Abiotroph

  8. Direct detection of potato leafroll virus in potato tubers by immunocapture and the isothermal nucleic acid amplification method NASBA

    NARCIS (Netherlands)

    Leone, G.; Schijndel, van H.B.; Gemen, van B.; Schoen, C.D.

    1997-01-01

    NASBA, an isothermal amplification method for nucleic acids, was applied to the detection of RNA of potato leafroll virus (PLRV) in a single enzymatic reaction at 41 °C. A set of primers was selected from the coat protein open reading frame sequence of PLRV to allow amplification of viral RNA. The

  9. Phylogenetic group- and species-specific oligonucleotide probes for single-cell detection of lactic acid bacteria in oral biofilms

    NARCIS (Netherlands)

    Quevedo, Beatrice; Giertsen, Elin; Zijnge, Vincent; Luethi-Schaller, Helga; Guggenheim, Bernhard; Thurnheer, Thomas; Gmuer, Rudolf

    2011-01-01

    Background: The purpose of this study was to design and evaluate fluorescent in situ hybridization (FISH) probes for the single-cell detection and enumeration of lactic acid bacteria, in particular organisms belonging to the major phylogenetic groups and species of oral lactobacilli and to Abiotroph

  10. Probing folding free energy landscape of small proteins through minimalistic models: Folding of HP-36 and -amyloid

    Indian Academy of Sciences (India)

    Arnab Mukherjee; Biman Bagchi

    2003-10-01

    Folding dynamics and energy landscape picture of protein conformations of HP-36 and -amyloid (A) are investigated by extensive Brownian dynamics simulations, where the inter amino acid interactions are given by a minimalistic model (MM) we recently introduced [J. Chem. Phys. 118 4733 (2003)]. In this model, a protein is constructed by taking two atoms for each amino acid. One atom represents the backbone C atom, while the other mimics the whole side chain residue. Sizes and interactions of the side residues are all different and specific to a particular amino acid. The effect of water-mediated folding is mapped into the MM by suitable choice of interaction parameters of the side residues obtained from the amino acid hydropathy scale. A new non-local helix potential is incorporated to generate helices at the appropriate positions in a protein. Simulations have been done by equilibrating the protein at high temperature followed by a sudden quench. The subsequent folding is monitored to observe the dynamics of topological contacts (topo), relative contact order parameter (RCO), and the root mean square deviation (RMSD) from the realprotein native structure. The folded structures of different model proteins (HP-36 and ) resemble their respective real native state rather well. The dynamics of folding shows multistage decay, with an initial hydrophobic collapse followed by a long plateau. Analysis of topo and RCO correlates the late stage folding with rearrangement of the side chain residues, particularly those far apart in the sequence. The long plateau also signifies large entropic free energy barrier near the native state, as predicted from theories of protein folding.

  11. Simultaneous detection of ascorbic acid, dopamine, uric acid and tryptophan with Azure A-interlinked multi-walled carbon nanotube/gold nanoparticles composite modified electrode

    Directory of Open Access Journals (Sweden)

    Hayati Filik

    2016-05-01

    Full Text Available In this paper, multi-walled carbon nanotube/Azure A/gold nanoparticle composites (Nafion/AuNPs/AzA/MWCNTs were prepared by binding gold nanoparticles to the surfaces of Azure A-coated carbon nanotubes. Nafion/AuNPs/AzA/MWCNTs based electrochemical sensor was fabricated for the simultaneous determination of ascorbic acid, dopamine, uric acid, and tryptophan. Cyclic voltammetry and electrochemical impedance spectroscopy were used to characterize the electrochemical properties of the modified electrodes. The modified electrode showed excellent electrocatalytic activity toward ascorbic acid, dopamine, uric acid, and tryptophan (pH 7.0. The experiment results showed that the linear response range for simultaneous detection of AA, DA, UA and Trp were 300–10,000 μM, 0.5–50 μM, 0.5–50 μM and 1.0–100 μM, respectively, and the detection limits were 16 μM, 0.014 μM, 0.028 μM and 0.56 μM (S/N = 3. The proposed method offers promise for simple, rapid, selective and cost-effective analysis of small biomolecules. The procedure was also applied to the determination of tryptophan in spiked milk samples.

  12. First improvements in the detection and quantification of label-free nucleic acids by laser-induced breakdown spectroscopy: Application to the deoxyribonucleic acid micro-array technology

    Energy Technology Data Exchange (ETDEWEB)

    Le Meur, Julien [Laboratoire de Cancerologie Experimentale, Commissariat a l' Energie Atomique de Fontenay-aux-Roses, Direction des Sciences du Vivant, Departement de Radiobiologie et Radiopathologie, Fontenay-aux-Roses (France); Menut, Denis [Laboratoire de Reactivite des Surfaces et des Interfaces, Commissariat a l' Energie Atomique de Saclay, Direction de l' Energie Nucleaire, Departement de Physico-Chimie, Gif sur Yvette (France); Wodling, Pascal [Laboratoire d' Interaction Laser-Matiere, Commissariat a l' Energie Atomique de Saclay, Direction de l' Energie Nucleaire, Departement de Physico-Chimie, Gif sur Yvette (France); Salmon, Laurent [Laboratoire de Reactivite des Surfaces et des Interfaces, Commissariat a l' Energie Atomique de Saclay, Direction de l' Energie Nucleaire, Departement de Physico-Chimie, Gif sur Yvette (France); Thro, Pierre-Yves [Laboratoire d' Interaction Laser-Matiere, Commissariat a l' Energie Atomique de Saclay, Direction de l' Energie Nucleaire, Departement de Physico-Chimie, Gif sur Yvette (France); Chevillard, Sylvie [Laboratoire de Cancerologie Experimentale, Commissariat a l' Energie Atomique de Fontenay-aux-Roses, Direction des Sciences du Vivant, Departement de Radiobiologie et Radiopathologie, Fontenay-aux-Roses (France); Ugolin, Nicolas [Laboratoire de Cancerologie Experimentale, Commissariat a l' Energie Atomique de Fontenay-aux-Roses, Direction des Sciences du Vivant, Departement de Radiobiologie et Radiopathologie, Fontenay-aux-Roses (France)], E-mail: nugolin@cea.fr

    2008-04-15

    The accurate quantification of nucleic acids is essential in many fields of modern biology and industry, and in some cases requires the use of fluorescence labeling. Yet, in addition to standardization problems and quantification reproducibility, labeling can modify the physicochemical properties of molecules or affect their stability. To address these limitations, we have developed a novel method to detect and quantify label-free nucleic acids. This method is based on stoichiometric proportioning of phosphorus in the nucleic acid skeleton, using laser-induced breakdown spectroscopy, and a specific statistical analysis, which indicates the error probability for each measurement. The results obtained appear to be quantitative, with a limit of detection of 10{sup 5} nucleotides/{mu}m{sup 2} (i.e. 2 x 10{sup 13} phosphorus atoms/cm{sup 2}). Initial micro-array analysis has given very encouraging results, which point to new ways of quantifying hybridized nucleic acids. This is essential when comparing molecules of different sequences, which is presently very difficult with fluorescence labeling.

  13. 6LiF oleic acid capped nanoparticles entrapment in siloxanes for thermal neutron detection

    Science.gov (United States)

    Carturan, S.; Maggioni, G.; Marchi, T.; Gramegna, F.; Cinausero, M.; Quaranta, A.; Palma, M. Dalla

    2016-07-01

    The good light output of siloxane based scintillators as displayed under γ-rays and α particles has been exploited here to obtain clear and reliable response toward thermal neutrons. Sensitization towards thermal neutrons has been pursued by adding 6LiF, in form of nanoparticles. Aiming at the enhancement of compatibility between the inorganic nanoparticles and the low polarity, siloxane based surrounding medium, oleic acid-capped 6LiF nanoparticles have been synthesized by thermal decomposition of Li trifluoroacetate. Thin pellets siloxane scintillator maintained their optical transmittance up to weight load of 2% of 6Li. Thin samples with increasing 6Li concentration and thicker ones with fixed 6Li amount have been prepared and tested with several sources (α, γ-rays, moderated neutrons). Light output as high as 80% of EJ212 under α irradiation was measured with thin samples, and negligible changes have been observed as a result of 6LiF addition. In case of thick samples, severe light loss has been observed, as induced by opacity. Nevertheless, thermal neutrons detection has been assessed and the data have been compared with GS20, based on Li glass, taken as a reference material.

  14. Reverse lectin ELISA for detecting fucosylated forms of α1-acid glycoprotein associated with hepatocellular carcinoma

    Science.gov (United States)

    Stål, Per; Zenlander, Robin; Edenvik, Pia; Alexandersson, Catharina; Haglund, Mats; Rydén, Ingvar; Påhlsson, Peter

    2017-01-01

    Altered fucosylation of glycoproteins is associated with development of hepatocellular carcinoma (HCC). Lectins have been commonly used to assay changes in fucosylation of plasma glycoproteins. In the present study a recombinantly engineered form of the fucose binding lectin Aleuria aurantia (AAL) consisting of a single binding site for fucose (S2), was used to construct a reverse lectin ELISA method. Microtiter plates coated with the S2 lectin were used to capture glycoproteins from plasma samples followed by antibody detection of S2-bound fucosylated α1-acid glycoprotein (S2-bound AGP). The method was used to compare the level of S2-bound AGP in serum samples from a small cohort of patients with hepatitis, cirrhosis or HCC. Using the reverse S2 lectin ELISA it was shown that the levels of S2-bound AGP was significantly higher in HCC patients compared to non-cancer patients and that there was also a significant elevation of S2-bound AGP in HCC patients compared to cirrhosis patients. There was no correlation between the level of S2-bound AGP and total AGP concentration. The performance of S2-bound AGP in differentiating HCC from cirrhosis samples or hepatitis samples were compared to other markers. A combination of S2-bound AGP, α-fetoprotein and AGP concentration showed performances giving area under receiver operating curves of 0.87 and 0.95 respectively. PMID:28296934

  15. Detection of Serum Hyaluronic Acid and Laminin in Patients with Bladder Tumors

    Institute of Scientific and Technical Information of China (English)

    李令勋; 丁国富

    2003-01-01

    In order to investigate the changes of serum hyaluronic acid (HA) and laminin (LN) levels and their clinical implication in the patients with bladder tumors, the serum HA and LN levels in 34 patients with bladder tumor and 30 cases of control group were detected by radioimmunoassay before and after operation. The results showed that the serum HA and LN levels in the patients with bladder tumors were significantly higher than those in control group (P<0. 01) before operation, and decreased significantly after operation (P<0. 05). The serum levels of HA and LN in infiltration tumors were higher than those in superficial tumors (P<0.05). The serum HA and LN levels in patients with lymph node metastasis were higher than those without lymph node metastasis (P<0.01 ). The investigation revealed that HA and LN might be involved in the malignant biology behavior of bladder tumors and could be used as important markers of assistant diagnosis and condition monitoring.

  16. Significance of the detection of esters of p-hydroxybenzoic acid (parabens) in human breast tumours.

    Science.gov (United States)

    Harvey, Philip W; Everett, David J

    2004-01-01

    This issue of Journal of Applied Toxicology publishes the paper Concentrations of Parabens in Human Breast Tumours by Darbre et al. (2004), which reports that esters of p-hydroxybenzoic acid (parabens) can be detected in samples of tissue from human breast tumours. Breast tumour samples were supplied from 20 patients, in collaboration with the Edinburgh Breast Unit Research Group, and analysed by high-pressure liquid chromatography and tandem mass spectrometry. The parabens are used as antimicrobial preservatives in underarm deodorants and antiperspirants and in a wide range of other consumer products. The parabens also have inherent oestrogenic and other hormone related activity (increased progesterone receptor gene expression). As oestrogen is a major aetiological factor in the growth and development of the majority of human breast cancers, it has been previously suggested by Darbre that parabens and other chemicals in underarm cosmetics may contribute to the rising incidence of breast cancer. The significance of the finding of parabens in tumour samples is discussed here in terms of 1). Darbre et al's study design, 2). what can be inferred from this type of data (and what can not, such as the cause of these tumours), 3). the toxicology of these compounds and 4). the limitations of the existing toxicology database and the need to consider data that is appropriate to human exposures. Copyright 2004 John Wiley & Sons, Ltd.

  17. 3D graphene foams decorated by CuO nanoflowers for ultrasensitive ascorbic acid detection.

    Science.gov (United States)

    Ma, Ye; Zhao, Minggang; Cai, Bin; Wang, Wei; Ye, Zhizhen; Huang, Jingyun

    2014-09-15

    When the in vitro research works of biosensing begin to mimic in vivo conditions, some certain three-dimensional (3D) structures of biosensors are needed to accommodate biomolecules, bacteria or even cells to resemble the in vivo 3D environment. To meet this end, a novel method of synthesizing CuO nanoflowers on the 3D graphene foam (GF) was first demonstrated. The 3DGF/CuO nanoflowers composite was used as a monolithic free-standing 3D biosensor for electrochemical detection of ascorbic acid (AA). The 3D conductive structure of the GF is favorable for current collection, mass transport and loading bioactive chemicals. And CuO nanoflowers further increase the active surface area and catalyze the redox of AA. Thus, all these features endows 3DGF/CuO composite with outstanding biosensing properties such as an ultrahigh sensitivity of 2.06 mA mM(-1) cm(-2) to AA at 3 s response time.

  18. Capillary electrophoresis with laser-induced fluorescence detection for studying amino acid uptake by yeast during beer fermentation.

    Science.gov (United States)

    Turkia, Heidi; Sirén, Heli; Penttilä, Merja; Pitkänen, Juha-Pekka

    2015-01-01

    The amino acid composition of cultivation broth is known to affect the biomass accumulation, productivity, and vitality of yeast during cultivation. A separation method based on capillary electrophoresis with laser-induced fluorescence (LIF) detection was developed for the determination of amino acid consumption by Saccharomyces cerevisiae during beer fermentation. Intraday relative standard deviations were less than 2.1% for migration times and between 2.9% and 9.9% for peak areas. Interday relative standard deviations were less than 2.5% for migration times and between 4.4% and 18.9% for peak areas. The quantification limit was even as low as 62.5 pM which equals to below attomole level detection. The method was applied to study the rate of amino acid utilization during beer fermentation.

  19. Cytotoxicity detection of poly(lactic-co-glycolic acid/tricalcium phosphate

    Directory of Open Access Journals (Sweden)

    Meng SUN

    2011-12-01

    Full Text Available Objective To detecte the cytotoxicity of the PLGA/TCP(poly(lactic-co-glycolic acid/Tricalcium phosphate composite that based on the precedent experiments conducted in Tsinghua University.Methods Compared with the PLGA scaffold material,observated the surface and interior structure of the PLGA/TCP scaffold material by SEM(scanning electron microscope,the surface and interior of PLGA/TCP scaffold material appeared to be homogeneous porous under SEM,with fairly even porosity distribution.The pore diameter was approximately 400μm.The interpenetrative micro-pores were scattered over bigger pores’ periphery with approximately circular contour and 3~5 μm in diameter.These pores were interpenetrative,the average factor of porosity was 89.6%.And which selected rat L929 cell strain,and detected the cytotoxicity of the PLGA/TCP composite in vitro by MTT method.Results The surface and interior of PLGA/TCP scaffold material appeared to be homogeneous porous under SEM,with fairly even porosity distribution.The pore diameter was approximately 400μm.The interpenetrative micro-pores were scattered over bigger pores’ periphery with approximately circular contour and 3~5 μm in diameter.These pores were interpenetrative,the average factor of porosity was 89.6%.On rat L929 cell strain,used MTT Method to detect the cytotoxicity of the composite PLGA/ TCP in vitro,the result showed that the cytotoxicity of the PLGA/TCP composite was level I,according to the criterion,it can be considered as non cytotoxic.Conclusion This research has proved that the PLGA/TCP compound scaffold material has a more homogeneous structure,with the vesicular interior and the structure of PLGA/TCP composite is similar to natural bone trabecula,PLGA/TCP is non cytotoxicity,which satisfy the basic requirement of biological material application and provides a good experimental foundation for repairing autologous bone defect in the near future.

  20. Statistical Analysis of Native Contact Formation in the Folding of Designed Model Proteins

    OpenAIRE

    Tiana, G.; R. A. Broglia(University of Milano, INFN Milano and University of Copenhagen)

    2000-01-01

    The time evolution of the formation probability of native bonds has been studied for designed sequences which fold fast into the native conformation. From this analysis a clear hierarchy of bonds emerge a) local, fast forming highly stable native bonds built by some of the most strongly interacting amino acids of the protein, b) non-local bonds formed late in the folding process, in coincidence with the folding nucleus, and involving essentially the same strongly interacting amino acids alrea...

  1. THE APPLICATION OF PEPTIDE NUCLEIC ACID PROBES FOR RAPID DETECTION AND ENUMERATION OF EUBACTERIA, STAPHYLOCOCCUS AUREUS AND PSEUDOMONAS AERUGINOSA IN RECREATIONAL BEACHES OF S. FLORIDA. (R828830)

    Science.gov (United States)

    A novel chemiluminescent in situ hybridization technique using peptide nucleic acids (PNA) was adapted for the detection of bacteria in beach sand and recreational waters in South Florida. The simultaneous detection and enumeration of eubacteria and the novel indicators, S...

  2. High-volume extraction of nucleic acids by magnetic bead technology for ultrasensitive detection of bacteria in blood components.

    Science.gov (United States)

    Störmer, Melanie; Kleesiek, Knut; Dreier, Jens

    2007-01-01

    Nucleic acid isolation, the most technically demanding and laborious procedure performed in molecular diagnostics, harbors the potential for improvements in automation. A recent development is the use of magnetic beads covered with nucleic acid-binding matrices. We adapted this technology with a broad-range 23S rRNA real-time reverse transcription (RT)-PCR assay for fast and sensitive detection of bacterial contamination of blood products. We investigated different protocols for an automated high-volume extraction method based on magnetic-separation technology for the extraction of bacterial nucleic acids from platelet concentrates (PCs). We added 2 model bacteria, Staphylococcus epidermidis and Escherichia coli, to a single pool of apheresis-derived, single-donor platelets and assayed the PCs by real-time RT-PCR analysis with an improved primer-probe system and locked nucleic acid technology. Co-amplification of human beta(2)-microglobulin mRNA served as an internal control (IC). We used probit analysis to calculate the minimum concentration of bacteria that would be detected with 95% confidence. For automated magnetic bead-based extraction technology with the real-time RT-PCR, the 95% detection limit was 29 x 10(3) colony-forming units (CFU)/L for S. epidermidis and 22 x 10(3) CFU/L for E. coli. No false-positive results occurred, either due to nucleic acid contamination of reagents or externally during testing of 1030 PCs. High-volume nucleic acid extraction improved the detection limit of the assay. The improvement of the primer-probe system and the integration of an IC make the RT-PCR assay appropriate for bacteria screening of platelets.

  3. The combined-disk boronic acid test as an accurate strategy for the detection of KPC carbapenemase in Central America.

    Science.gov (United States)

    Zúñiga, Julio; Cruz, Gerardo; Pérez, Carlos; Tarajia, Musharaf

    2016-03-31

    Carbapenemase-producing Klebsiella pneumoniae (KPC) outbreaks may cause a huge economical burden on developing countries. Furthermore, KPC can be challenging to detect. We describe the laboratory strategy for the detection of KPC from 2011 to 2013 in a tertiary care hospital in Central America with approximately 1,000 beds. A retrospective analysis of a clinical laboratory database was done to determine the pragmatic application of the combined-disk boronic acid test during a KPC outbreak in Panama. A total of 1,026 Klebsiella pneumoniae isolates were found, of which 133 were positive for KPC. The strategy during two phases was described according to the test employed as a confirmatory test for KPC. After the K. pneumoniae isolates were detected by the VITEK 2 system, blaKPC polymerase chain reaction (PCR) and the combined-disk boronic acid test were employed as a confirmatory test during phase one. The combined-disk boronic acid test was employed as a confirmatory test for KPC during phase two. The sensitivity, specificity, positive predictive value, and negative predictive value of the boronic acid test were 100%, 97%, 91%, and 100%, respectively, when blaKPC PCR was employed as a confirmatory test during the start of the outbreak. Afterwards, modified VITEK 2 system parameters resulted in 116 suspicious KPC samples and the boronic acid test confirmed 102 isolates. The use of an automated bacterial identification system and the boronic acid test for the detection of KPC was an effective and low-cost strategy for a clinical laboratory in Panama during an outbreak.

  4. SDR-ELISA: Ultrasensitive and high-throughput nucleic acid detection based on antibody-like DNA nanostructure.

    Science.gov (United States)

    Wen, Junlin; Chen, Junhua; Zhuang, Li; Zhou, Shungui

    2017-04-15

    An ultrasensitive and high-throughput nucleic acid detection system, termed as strand displacement reaction-enzyme linked immunosorbent assay (SDR-ELISA), has been developed on the basis of antibody-like DNA nanostructures. Three digoxigenin or biotin modified hairpin probes are utilized to construct antibody-like DNA nanostructures that feature affinity toward streptavidin and anti-digoxigenin antibody via isothermal target-triggered SDR amplification. These antibody-like nanostructures have been employed to conjugate horseradish-peroxidase-labeled anti-digoxigenin antibody with streptavidin that is immobilized on microliter plate wells for enzyme-linked colorimetric assay. The resulting SDR-ELISA system is ultrasensitive for target DNA with a low detection limit of 5 fM. Moreover, the SDR-ELISA system is capable of discriminating DNA sequences with single base mutations, and do so in a high-throughput manner by detection and quantification of up to 96 or 384 DNA samples in a single shot. This detection system is further applied to detect other DNA targets such as Shewanella oneidensis specific DNA sequence, which indicates the generality of proposed SDR-ELISA system. The integration of SDR amplification and convenient ELISA technique advances an intelligent strategy for ultrasensitive and high-throughput nucleic acid detection, which may be amenable for direct visual detection and quantification using an accompanying quantitative color chart.

  5. An optical sensor based on H-acid/layered double hydroxide composite film for the selective detection of mercury ion.

    Science.gov (United States)

    Sun, Zhiyong; Jin, Lan; Zhang, Shitong; Shi, Wenying; Pu, Min; Wei, Min; Evans, David G; Duan, Xue

    2011-09-19

    A novel optical chemosensor was fabricated based on 1-amino-8-naphthol-3,6-disulfonic acid sodium (H-acid) intercalated layered double hydroxide (LDH) film via the electrophoretic deposition (EPD) method. The film of H-acid/LDH with the thickness of 1 μm possesses a well c-orientation of the LDH microcrystals confirmed by X-ray diffraction (XRD) and scanning electron microscopy (SEM). The fluorescence detection for Hg(II) in aqueous solution was performed by using the H-acid/LDH film sensor at pH 7.0, with a linear response range in 1.0 × 10(-7) to 1.0 × 10(-5) mol L(-1) and a detection limit of 6.3 × 10(-8) mol L(-1). Furthermore, it exhibits excellent selectivity for Hg(II) over a large number of competitive cations including alkali, alkaline earth, heavy metal and transitional metals. The specific fluorescence response of the optical sensor is attributed to the coordination between Hg(II) and sulfonic group in the H-acid immobilized in the LDH matrix, which was verified by NMR spectroscopy and UV-vis spectra. In addition, density functional theory (DFT) calculation further confirms that the coordination occurs between one Hg(2+) and two O atoms in the sulfonic group, which is responsible for the significant fluorescence quenching of the H-acid/LDH film. The results indicate that the H-acid/LDH composite film can be potentially used as a chemosensor for the detection of Hg(2+) in the environmental and biomedical field.

  6. Focused upon hybridization: rapid and high sensitivity detection of DNA using isotachophoresis and peptide nucleic acid probes.

    Science.gov (United States)

    Ostromohov, Nadya; Schwartz, Ortal; Bercovici, Moran

    2015-09-15

    We present a novel assay for rapid and high sensitivity detection of nucleic acids without amplification. Utilizing the neutral backbone of peptide nucleic acids (PNA), our method is based on the design of low electrophoretic mobility PNA probes, which do not focus under isotachophoresis (ITP) unless bound to their target sequence. Thus, background noise associated with free probes is entirely eliminated, significantly improving the signal-to-noise ratio while maintaining a simple single-step assay requiring no amplification steps. We provide a detailed analytical model and experimentally demonstrate the ability to detect targets as short as 17 nucleotides (nt) and a limit of detection of 100 fM with a dynamic range of 5 decades. We also demonstrate that the assay can be successfully implemented for detection of DNA in human serum without loss of signal. The assay requires 15 min to complete, and it could potentially be used in applications where rapid and highly sensitive amplification-free detection of nucleic acids is desired.

  7. A carbon dot-based "off-on" fluorescent probe for highly selective and sensitive detection of phytic acid.

    Science.gov (United States)

    Gao, Zhao; Wang, Libing; Su, Rongxin; Huang, Renliang; Qi, Wei; He, Zhimin

    2015-08-15

    We herein report a facile, one-step pyrolysis synthesis of photoluminescent carbon dots (CDs) using citric acid as the carbon source and lysine as the surface passivation reagent. The as-prepared CDs show narrow size distribution, excellent blue fluorescence and good photo-stability and water dispersivity. The fluorescence of the CDs was found to be effectively quenched by ferric (Fe(III)) ions with high selectivity via a photo-induced electron transfer (PET) process. Upon addition of phytic acid (PA) to the CDs/Fe(III) complex dispersion, the fluorescence of the CDs was significantly recovered, arising from the release of Fe(III) ions from the CDs/Fe(III) complex because PA has a higher affinity for Fe(III) ions compared to CDs. Furthermore, we developed an "off-on" fluorescence assay method for the detection of phytic acid using CDs/Fe(III) as a fluorescent probe. This probe enables the selective detection of PA with a linear range of 0.68-18.69 μM and a limit of detection (signal-to-noise ratio is 3) of 0.36 μM. The assay method demonstrates high selectivity, repeatability, stability and recovery ratio in the detection of the standard and real PA samples. We believe that the facile operation, low-cost, high sensitivity and selectivity render this CD-based "off-on" fluorescent probe an ideal sensing platform for the detection of PA.

  8. A new instrument for intraoperative assessment of individual vocal folds.

    Science.gov (United States)

    Heaton, James T; Kobler, James B; Hillman, Robert E; Zeitels, Steven M

    2005-07-01

    Intraoperative assessment of vocal fold vibration during phonomicrosurgery performed under general anesthesia may enhance surgical decision-making. We therefore developed and bench-tested a new device we refer to as the aerodynamic vocal fold driver (AVFD). The AVFD comprises a hand-held probe that uses airflow to drive individual vocal folds into phonatory-like vibration. This permits stroboscopic visualization of mucosal waves with simultaneous control of subglottal air pressure. In initial experiments to validate the technique, AVFD driven phonation and conventional whole-larynx phonation were compared using excised canine larynges (n = 14). Single vocal fold phonation using the AVFD and whole larynx phonation yielded similar, positive correlations between subglottal pressure and both amplitude and frequency of vibration. Experiments simulating vocal fold scar-related mucosal stiffening by subepithelial injection of fixative showed the expected elevation of phonation threshold pressures as measured with the AVFD. Likewise, unilateral tissue compression injury disrupted vocal fold vibration, and the AVFD was useful for quantifying improvement in the damaged vocal fold after repair with injection of cross-linked hyaluronic acid gel. These results show that this new instrument has the potential to provide novel and useful information for laryngeal experimentation and to improve phonosurgery.

  9. ANALYSIS OF PERFLUORINATED CARBOXYLIC ACIDS IN SOILS: DETECTION AND QUANTITATION ISSUES AT LOW CONCENTRATIONS

    Science.gov (United States)

    Methods were developed for the extraction from soil, identification, confirmation and quantitation by LC/MS/MS of trace levels of perfluorinated octanoic acid (PFOA), perfluorinated nonanoic acid (PFNA) and perfluorinated decanoic acid (PFDA). Whereas PFOA, PFNA and PFDA all can...

  10. ANALYSIS OF PERFLUORINATED CARBOXYLIC ACIDS IN SOILS: DETECTION AND QUANTITATION ISSUES AT LOW CONCENTRATIONS

    Science.gov (United States)

    Methods were developed for the extraction from soil, identification, confirmation and quantitation by LC/MS/MS of trace levels of perfluorinated octanoic acid (PFOA), perfluorinated nonanoic acid (PFNA) and perfluorinated decanoic acid (PFDA). Whereas PFOA, PFNA and PFDA all can...

  11. Ventricular-Fold Dynamics in Human Phonation

    Science.gov (United States)

    Bailly, Lucie; Bernardoni, Nathalie Henrich; Müller, Frank; Rohlfs, Anna-Katharina; Hess, Markus

    2014-01-01

    Purpose: In this study, the authors aimed (a) to provide a classification of the ventricular-fold dynamics during voicing, (b) to study the aerodynamic impact of these motions on vocal-fold vibrations, and (c) to assess whether ventricular-fold oscillations could be sustained by aerodynamic coupling with the vocal folds. Method: A 72-sample…

  12. Synovial folds in equine articular process joints

    DEFF Research Database (Denmark)

    Thomsen, Line Nymann; Berg, Lise Charlotte; Markussen, Bo;

    2013-01-01

    Cervical synovial folds have been suggested as a potential cause of neck pain in humans. Little is known about the extent and characteristics of cervical synovial folds in horses.......Cervical synovial folds have been suggested as a potential cause of neck pain in humans. Little is known about the extent and characteristics of cervical synovial folds in horses....

  13. Combined measurement of thyroid and plasma homocysteic acid for detecting the severity of vascular dementia

    Institute of Scientific and Technical Information of China (English)

    Bin Zhao; Junjian Zhang; Shifeng Wang; Guanghui Chen; Fayun Hu

    2006-01-01

    and content of homocysteic acid was measured with high performance liquid chromatogram (HPLC) electrochemical detection.MAIN OUTCOME MEASURES: Levels of homocysteic acid and thyroxine among patients with vascular dementia and non-dementia cerebral infarction.RESULTS: A total of 38 patients with vascular dementia and 40 patients with non-dementia cerebral infarction were involved in the final analysis. ① Levels of triiodothyronine (T3), thyroxine (T4) and free T3 (FT3) were (0.9±0.4) μg/L, (92.9±26.4) μg/L and (3.9±1.8) pmol/L in vascular dementia group respectively, which were higher than those in control group [(1.3±0.3) μg/L, (110.2±28.7) μg/L, (7.2±2.1) pmol/L, t=2.766 6-7.433 6, P<0.01]; while, level of homocysteic acid was (29.57±7.12) μmol/L in vascular dementia group, which was higher than that in control group [(24.53±4.98) μmol/L, t =3.637 7, P < 0.01]. There were no significant differences of free T4 (FT4) and thyrotropic-stimulating hormone (TSH) between the two groups (P> 0.05). ② Levels of FT3of patients with mild, moderate and severe vascular dementia were (1.0±0.2), (0.9±0.1) and (0.8±0.1) μg/L,respectively; levels of homocysteic acid were (26.52±4.84), (29.59±5.56) and (32.71±6.17) μmol/L,respectively. There were significant differences among patients at the three degrees of vascular dementia (F=3.59-32.4, P < 0.01). However, there were no significant differences of T4, FT4 and TSH among the three kinds of patients (P> 0.05).CONCLUSION: Levels of thyroxine of patients with vascular dementia decrease; however, levels of homocysteic acid increase. Therefore, the results can indirectly reflect severities of vascular dementia.

  14. Automated high multiplex qPCR platform for simultaneous detection and quantification of multiple nucleic acid targets.

    Science.gov (United States)

    Hlousek, Louis; Voronov, Sergey; Diankov, Vesselin; Leblang, Amy B; Wells, Patrick J; Ford, Donna M; Nolling, Jork; Hart, Kyle W; Espinoza, Patricio A; Bristol, Michael R; Tsongalis, Gregory J; Yen-Lieberman, Belinda; Slepnev, Vladimir I; Kong, Lilly I; Lee, Ming-Chou

    2012-05-01

    Quantitative PCR (qPCR) using real-time detection of amplification is limited to a small number of targets within a single reaction. The ICEPlex system, using our scalable target analysis routine (STAR) technology, was developed to provide an automated, high multiplexing PCR solution. ICEPlex combines PCR thermal cycling with dynamic, sequential amplicon separation by capillary electrophoresis and two-color quantitative detection in a single integrated system. In contrast to probe-based qPCR, ICEPlex directly measures amplicon accumulation through incorporation of labeled primers. Three orders of magnitude of optical detection range and at least 7 logs of detectable target concentration range are demonstrated. The system can separate more than 50 amplicons per color channel, ranging from 100 to 500 bases, providing broad multiplexing capabilities for a wide spectrum of nucleic acid amplification applications. ICEPlex can be used for analysis of viral DNA or RNA targets, detection of genetic variants, and for reverse-transcriptase PCR gene expression panels.

  15. Simultaneous determination of 4-hydroxyphenyl lactic acid, 4-hydroxyphenyl acetic acid, and 3-4-hydroxyphenyl propionic acid in human urine by Ultra high performance liquid chromatography with fluorescence detection.

    Science.gov (United States)

    Yang, Yongli; Liu, Fan; Wan, Yiqun

    2017-03-27

    A simple and reliable method was established for simultaneous determination of 4-hydroxyphenyl acetic acid, 4-hydroxyphenyl lactic acid, and 3-4-hydroxyphenyl propionic acid in human urine by high-performance liquid chromatography with fluorescence detection. Solid-phase extraction was used to eliminate the interferences in urine. The separation of three analytes was achieved using a C18 column and a mobile phase formed by a 95:5 v/v mixture of 50 mmol/L ammonium acetate buffer at pH 6.8 that contained 5 mmol/L tetrabutyl ammonium bromide and acetonitrile. Under the optimized conditions, the detection limits of 4-hydroxyphenyl acetic acid, 4-hydroxyphenyl lactic acid, and 3-4-hydroxyphenyl propionic acid were 4.8 × 10(-3) , 8.80 × 10(-3) , and 9.00 × 10(-3) mg/L, respectively, and the recoveries were in the range of 85.0-120.0% with relative standard deviations of 1.5-3.1%. This method was used to analyze urine samples from breast cancer patients, healthy people and postsurgery breast cancer patients. Significant differences of urinary levels of 4-hydroxyphenyl acetic acid and 4-hydroxyphenyl lactic acid could be found between the breast cancer patients group and other two groups. No effect of age and sex was observed on the urinary levels of 4-hydroxyphenyl acetic acid and 4-hydroxyphenyl lactic acid. This method might be helpful for cancer biomarkers discovery in urine. This article is protected by copyright. All rights reserved.

  16. Detection and formation scenario of citric acid, pyruvic acid, and other possible metabolism precursors in carbonaceous meteorites

    OpenAIRE

    Cooper, George; Reed, Chris; Nguyen, Dang Van; Carter, Malika; Wang, Yi

    2011-01-01

    Carbonaceous meteorites deliver a variety of organic compounds to Earth that may have played a role in the origin and/or evolution of biochemical pathways. Some apparently ancient and critical metabolic processes require several compounds, some of which are relatively labile such as keto acids. Therefore, a prebiotic setting for any such individual process would have required either a continuous distant source for the entire suite of intact precursor molecules and/or an energetic and compact ...

  17. Solitons and protein folding: An In Silico experiment

    Energy Technology Data Exchange (ETDEWEB)

    Ilieva, N., E-mail: nevena.ilieva@parallel.bas.bg [Institute of Information and Communication Technologies, Bulgarian Aacademy of Sciences, Sofia (Bulgaria); Dai, J., E-mail: daijing491@gmail.com [School of Physics, Beijing Institute of Technology, Beijing (China); Sieradzan, A., E-mail: adams86@wp.pl [Faculty of Chemistry, University of Gdańsk, Gdańsk (Poland); Niemi, A., E-mail: Antti.Niemi@physics.uu.se [Department of Physics and Astronomy, Uppsala University, Uppsala (Sweden); LMPT–CNRS, Université de Tours, Tours (France)

    2015-10-28

    Protein folding [1] is the process of formation of a functional 3D structure from a random coil — the shape in which amino-acid chains leave the ribosome. Anfinsen’s dogma states that the native 3D shape of a protein is completely determined by protein’s amino acid sequence. Despite the progress in understanding the process rate and the success in folding prediction for some small proteins, with presently available physics-based methods it is not yet possible to reliably deduce the shape of a biologically active protein from its amino acid sequence. The protein-folding problem endures as one of the most important unresolved problems in science; it addresses the origin of life itself. Furthermore, a wrong fold is a common cause for a protein to lose its function or even endanger the living organism. Soliton solutions of a generalized discrete non-linear Schrödinger equation (GDNLSE) obtained from the energy function in terms of bond and torsion angles κ and τ provide a constructive theoretical framework for describing protein folds and folding patterns [2]. Here we study the dynamics of this process by means of molecular-dynamics simulations. The soliton manifestation is the pattern helix–loop–helix in the secondary structure of the protein, which explains the importance of understanding loop formation in helical proteins. We performed in silico experiments for unfolding one subunit of the core structure of gp41 from the HIV envelope glycoprotein (PDB ID: 1AIK [3]) by molecular-dynamics simulations with the MD package GROMACS. We analyzed 80 ns trajectories, obtained with one united-atom and two different all-atom force fields, to justify the side-chain orientation quantification scheme adopted in the studies and to eliminate force-field based artifacts. Our results are compatible with the soliton model of protein folding and provide first insight into soliton-formation dynamics.

  18. Solitons and protein folding: An In Silico experiment

    Science.gov (United States)

    Ilieva, N.; Dai, J.; Sieradzan, A.; Niemi, A.

    2015-10-01

    Protein folding [1] is the process of formation of a functional 3D structure from a random coil — the shape in which amino-acid chains leave the ribosome. Anfinsen's dogma states that the native 3D shape of a protein is completely determined by protein's amino acid sequence. Despite the progress in understanding the process rate and the success in folding prediction for some small proteins, with presently available physics-based methods it is not yet possible to reliably deduce the shape of a biologically active protein from its amino acid sequence. The protein-folding problem endures as one of the most important unresolved problems in science; it addresses the origin of life itself. Furthermore, a wrong fold is a common cause for a protein to lose its function or even endanger the living organism. Soliton solutions of a generalized discrete non-linear Schrödinger equation (GDNLSE) obtained from the energy function in terms of bond and torsion angles κ and τ provide a constructive theoretical framework for describing protein folds and folding patterns [2]. Here we study the dynamics of this process by means of molecular-dynamics simulations. The soliton manifestation is the pattern helix-loop-helix in the secondary structure of the protein, which explains the importance of understanding loop formation in helical proteins. We performed in silico experiments for unfolding one subunit of the core structure of gp41 from the HIV envelope glycoprotein (PDB ID: 1AIK [3]) by molecular-dynamics simulations with the MD package GROMACS. We analyzed 80 ns trajectories, obtained with one united-atom and two different all-atom force fields, to justify the side-chain orientation quantification scheme adopted in the studies and to eliminate force-field based artifacts. Our results are compatible with the soliton model of protein folding and provide first insight into soliton-formation dynamics.

  19. Carbon-Pt nanoparticles modified TiO2 nanotubes for simultaneous detection of dopamine and uric acid.

    Science.gov (United States)

    Mahshid, Sara; Luo, Shenglian; Yang, Lixia; Mahshid, Sahar Sadat; Askari, Masoud; Dolati, Abolghasem; Cai, Qingyun

    2011-08-01

    The present work describes sensing application of modified TiO2 nanotubes having carbon-Pt nanoparticles for simultaneous detection of dopamine and uric acid. The TiO2 nanotubes electrode was prepared using anodizing method, followed by electrodeposition of Pt nanoparticles onto the tubes. Carbon was deposited by decomposition of polyethylene glycol in a tube furnace to improve the conductivity. The C-Pt-TiO2 nanotubes modified electrode was characterized by cyclic voltammetry and differential pulse voltammetry methods. The modified electrode displayed high sensitivity towards the oxidation of dopamine and uric acid in a phosphate buffer solution (pH 7.00). The electro-oxidation currents of dopamine and uric acid were linearly related to the concentration over a wide range of 3.5 x 10(-8) M to 1 x 10(-5) M and 1 x 10(-7) M to 3 x 10(-5) M respectively. The limit of detection was determined as 2 x 10(-10) M for dopamine at signal-to-noise ratio of 3. The interference of uric acid was also investigated. Electro-oxidation currents of dopamine in the presence of fix amount of uric acid represented a linear behaviour towards successive addition of dopamine in range of 1 x 10(-7) M to 1 x 10(-5) M. Furthermore, in a solution containing dopamine, uric acid and ascorbic acid the overlapped oxidation peaks of dopamine and ascorbic acid could be easily separated by using C-Pt-TiO2 nanotubes modified electrode.

  20. Detection of atypical bile acids in disease states and their identification by gas chromatography-mass spectrometry-computer techniques

    Energy Technology Data Exchange (ETDEWEB)

    Szczepanik-Van Leeuwen, P. A.; Stellaard, F.

    1978-01-01

    The study of the bile acid constituents of serum, bile, urine, and stool of patients exhibiting liver disease has increased in importance with the availability of newer methods for their detection and identification. A cogent question for study has been whether specific bile acids are toxic and thus are the cause of liver disease, or whether they accumulate as a result of disease-induced alteration in metabolism. Examining a wide variety of clinical samples, we have observed that many patients with diagnosed cholestasis show the presence of atypical bile acids due to metabolic aberrations in either the side chain or in the steroid ring. Because cholestasis represents a spectrum of diseases with differing metabolic and/or anatomic defects and because our studies cover a variety of cholestatic states, we have sought to establish a correlation between the presence of these atypical bile acids and the disease state. The complexity of the bile acid mixtures to be examined requires that gas chromatographic-mass spectrometric-computer techniques be used to provide a reliable analysis. It is believed that atypical bile acids can be readily identified by GC/CI mass spectrometry with great sensitivity. It is also believed that such bile acid analysis may prove useful to the study and diagnosis of liver disease. Present data suggest that the identification of atypical bile acids in biological samples may enable differentiation between different types of intrahepatic cholestasis. Such analyses may prove useful to distinguish specific diseases, such as Byler's disease (and Byler's-like cholestasis) from other types of cholestasis and may distinguish diseases involving mitochondrial defects. Finally, the presence of atypical bile acids may indicate, by the particular compounds formed, where and what kind of damage occurs in a disease and may ultimately establish if these atypical bile acids are a cause or effect of the liver damage.

  1. Folded MEMS approach to NMRG

    Science.gov (United States)

    Gundeti, Venu Madhav

    Atomic gyroscopes have a potential for good performance advantages and several attempts are being made to miniaturize them. This thesis describes the efforts made in implementing a Folded MEMS based NMRG. The micro implementations of all the essential components for NMRG (Nuclear Magnetic Resonance Gyroscope) are described in detail in regards to their design, fabrication, and characterization. A set of micro-scale Helmholtz coils are described and the homogeneity of the generated magnetic field is analyzed for different designs of heaters. The dielectric mirrors and metallic mirrors are compared in terms of reflectivity and polarization change up on reflection. A pyramid shaped folded backbone structure is designed, fabricated, and assembled along with all the required components. A novel double-folded structure 1/4th the size of original version is fabricated and assembled. Design and modeling details of a 5 layered shield with shielding factor > 106 and total volume of around 90 cc are also presented. A table top setup for characterization of atomic vapor cell is described in detail. A micro vapor cell based Rb magnetometer with a sensitivity of 108 pT/√Hz is demonstrated. The challenges due to DC heating are addressed and mitigated using an AC heater. Several experiments related to measuring the relaxation time of Xe are provided along with results. For Xe131, relaxation times of T1 = 23.78 sec, T2 = 18.06 sec and for Xe129, T1 = 21.65 sec and T2 = 20.45 sec are reported.

  2. Low Power Folded Cascode OTA

    Directory of Open Access Journals (Sweden)

    Swati Kundra

    2012-03-01

    Full Text Available Low power is one of the key research area in today’s electronic industry. Need of low power has created a major pattern shift in the field of electronics where power dissipation is equally important as area, performance etc. Several low power portable electronic equipments, low voltage design techniques havebeen developed and have driven analog designers to create techniques eg. Self cascode mosfet and stacking technique. For this aim in mind we designed a Folded Cascode using low power techniques and analyzed its various properties through the Spice simulations for 0.13 micron CMOS technology from TSMC and thesupply voltage 1.8V.

  3. Low Power Folded Cascode OTA

    Directory of Open Access Journals (Sweden)

    Swati Kundra

    2012-02-01

    Full Text Available Low power is one of the key research area in today’s electronic industry. Need of low power has created a major pattern shift in the field of electronics where power dissipation is equally important as area, performance etc. Several low power portable electronic equipments, low voltage design techniques have been developed and have driven analog designers to create techniques eg. Self cascode mosfet and stacking technique. For this aim in mind we designed a Folded Cascode using low power techniques and analyzed its various properties through the Spice simulations for 0.13 micron CMOS technology from TSMC and the supply voltage 1.8V.

  4. Metabotropic glutamate receptors are involved in the detection of IMP and L-amino acids by mouse taste sensory cells.

    Science.gov (United States)

    Pal Choudhuri, S; Delay, R J; Delay, E R

    2016-03-01

    G-protein-coupled receptors are thought to be involved in the detection of umami and L-amino acid taste. These include the heterodimer taste receptor type 1 member 1 (T1r1)+taste receptor type 1 member 3 (T1r3), taste and brain variants of mGluR4 and mGluR1, and calcium sensors. While several studies suggest T1r1+T1r3 is a broadly tuned lLamino acid receptor, little is known about the function of metabotropic glutamate receptors (mGluRs) in L-amino acid taste transduction. Calcium imaging of isolated taste sensory cells (TSCs) of T1r3-GFP and T1r3 knock-out (T1r3 KO) mice was performed using the ratiometric dye Fura 2 AM to investigate the role of different mGluRs in detecting various L-amino acids and inosine 5' monophosphate (IMP). Using agonists selective for various mGluRs such as (RS)-3,5-dihydroxyphenylglycine (DHPG) (an mGluR1 agonist) and L-(+)-2-amino-4-phosphonobutyric acid (l-AP4) (an mGluR4 agonist), we evaluated TSCs to determine if they might respond to these agonists, IMP, and three L-amino acids (monopotassium L-glutamate, L-serine and L-arginine). Additionally, we used selective antagonists against different mGluRs such as (RS)-L-aminoindan-1,5-dicarboxylic acid (AIDA) (an mGluR1 antagonist), and (RS)-α-methylserine-O-phosphate (MSOP) (an mGluR4 antagonist) to determine if they can block responses elicited by these L-amino acids and IMP. We found that L-amino acid- and IMP-responsive cells also responded to each agonist. Antagonists for mGluR4 and mGluR1 significantly blocked the responses elicited by IMP and each of the L-amino acids. Collectively, these data provide evidence for the involvement of taste and brain variants of mGluR1 and mGluR4 in L-amino acid and IMP taste responses in mice, and support the concept that multiple receptors contribute to IMP and L-amino acid taste.

  5. RNAiFOLD: a constraint programming algorithm for RNA inverse folding and molecular design.

    Science.gov (United States)

    Garcia-Martin, Juan Antonio; Clote, Peter; Dotu, Ivan

    2013-04-01

    Synthetic biology is a rapidly emerging discipline with long-term ramifications that range from single-molecule detection within cells to the creation of synthetic genomes and novel life forms. Truly phenomenal results have been obtained by pioneering groups--for instance, the combinatorial synthesis of genetic networks, genome synthesis using BioBricks, and hybridization chain reaction (HCR), in which stable DNA monomers assemble only upon exposure to a target DNA fragment, biomolecular self-assembly pathways, etc. Such work strongly suggests that nanotechnology and synthetic biology together seem poised to constitute the most transformative development of the 21st century. In this paper, we present a Constraint Programming (CP) approach to solve the RNA inverse folding problem. Given a target RNA secondary structure, we determine an RNA sequence which folds into the target structure; i.e. whose minimum free energy structure is the target structure. Our approach represents a step forward in RNA design--we produce the first complete RNA inverse folding approach which allows for the specification of a wide range of design constraints. We also introduce a Large Neighborhood Search approach which allows us to tackle larger instances at the cost of losing completeness, while retaining the advantages of meeting design constraints (motif, GC-content, etc.). Results demonstrate that our software, RNAiFold, performs as well or better than all state-of-the-art approaches; nevertheless, our approach is unique in terms of completeness, flexibility, and the support of various design constraints. The algorithms presented in this paper are publicly available via the interactive webserver http://bioinformatics.bc.edu/clotelab/RNAiFold; additionally, the source code can be downloaded from that site.

  6. An ion-exchange nanomembrane sensor for detection of nucleic acids using a surface charge inversion phenomenon.

    Science.gov (United States)

    Senapati, Satyajyoti; Slouka, Zdenek; Shah, Sunny S; Behura, Susanta K; Shi, Zonggao; Stack, M Sharon; Severson, David W; Chang, Hsueh-Chia

    2014-10-15

    We present a novel low-cost biosensor for rapid, sensitive and selective detection of nucleic acids based on an ionic diode feature of an anion exchange nanoporous membrane under DC bias. The ionic diode feature is associated with external surface charge inversion on the positively charged anion exchange nanomembrane upon hybridization of negatively charged nucleic acid molecules to single-stranded oligoprobes functionalized on the membrane surface resulting in the formation of a cation selective monolayer. The resulting bipolar membrane causes a transition from electroconvection-controlled to water-splitting controlled ion conductance, with a large ion current signature that can be used to accurately quantify the hybridized nucleic acids. The platform is capable of distinguishing two base-pair mismatches in a 22-base pairing segment of microRNAs associated with oral cancer, as well as serotype-specific detection of dengue virus. We also show the sensor' capability to selectively capture target nucleic acids from a heterogeneous mixture. The limit of detection is 1 pM for short 27 base target molecules in a 15-min assay. Similar hybridization results are shown for short DNA molecules as well as RNAs from Brucella and Escherichia coli. The versatility and simplicity of this low-cost biosensor should enable point-of-care diagnostics in food, medical and environmental safety markets.

  7. Direct Detection of Nucleic Acid with Minimizing Background and Improving Sensitivity Based on a Conformation-Discriminating Indicator.

    Science.gov (United States)

    Zhu, Lixuan; Qing, Zhihe; Hou, Lina; Yang, Sheng; Zou, Zhen; Cao, Zhong; Yang, Ronghua

    2017-08-25

    As is well-known, the nucleic acid indicator-based strategy is one of the major approaches to monitor the nucleic acid hybridization-mediated recognition events in biochemical analysis, displaying obvious advantages including simplicity, low cost, convenience, and generality. However, conventional indicators either hold strong self-fluorescence or can be lighted by both ssDNA and dsDNA, lacking absolute selectivity for a certain conformation, always with high background interference and low sensitivity in sensing; and additional processing (e.g., nanomaterial-mediated background suppression, and enzyme-catalyzed signal amplification) is generally required to improve the detection performance. In this work, a carbazole derivative, EBCB, has been synthesized and screened as a dsDNA-specific fluorescent indicator. Compared with conventional indicators under the same conditions, EBCB displayed a much higher selective coefficient for dsDNA, with little self-fluorescence and negligible effect from ssDNA. Based on its superior capability in DNA conformation-discrimination, high sensitivity with minimizing background interference was demonstrated for direct detection of nucleic acid, and monitoring nucleic acid-based circuitry with good reversibity, resulting in low detection limit and high capability for discriminating base-mismatching. Thus, we expect that this highly specific DNA conformation-discriminating indicator will hold good potential for application in biochemical sensing and molecular logic switching.

  8. Direct Determination of a Small-Molecule Drug, Valproic Acid, by an Electrically-Detected Microcantilever Biosensor for Personalized Diagnostics

    Directory of Open Access Journals (Sweden)

    Long-Sun Huang

    2015-01-01

    Full Text Available Direct, small-molecule determination of the antiepileptic drug, valproic acid, was investigated by a label-free, nanomechanical biosensor. Valproic acid has long been used as an antiepileptic medication, which is administered through therapeutic drug monitoring and has a narrow therapeutic dosage range of 50–100 μg·mL−1 in blood or serum. Unlike labeled and clinically-used measurement techniques, the label-free, electrical detection microcantilever biosensor can be miniaturized and simplified for use in portable or hand-held point-of-care platforms or personal diagnostic tools. A micromachined microcantilever sensor was packaged into the micro-channel of a fluidic system. The measurement of the antiepileptic drug, valproic acid, in phosphate-buffered saline and serum used a single free-standing, piezoresistive microcantilever biosensor in a thermally-controlled system. The measured surface stresses showed a profile over a concentration range of 50–500 μg·mL−1, which covered the clinically therapeutic range of 50–100 μg·mL−1. The estimated limit of detection (LOD was calculated to be 45 μg·mL−1, and the binding affinity between the drug and the antibody was measured at around 90 ± 21 μg·mL−1. Lastly, the results of the proposed device showed a similar profile in valproic acid drug detection with those of the clinically-used fluorescence polarization immunoassay.

  9. Simultaneous Detection of Dopamine and Uric Acid Using a Poly(l-lysine/Graphene Oxide Modified Electrode

    Directory of Open Access Journals (Sweden)

    Yuehua Zhang

    2016-09-01

    Full Text Available A novel, simple and selective electrochemical method was investigated for the simultaneous detection of dopamine (DA and uric acid (UA on a poly(l-lysine/graphene oxide (GO modified glassy carbon electrode (PLL/GO/GCE by differential pulse voltammetry (DPV. The electrochemically prepared PLL/GO sensory platform toward the oxidation of UA and DA exhibited several advantages, including high effective surface area, more active sites and enhanced electrochemical activity. Compared to the PLL-modified GCE (PLL/GCE, GO-modified GCE and bare GCE, the PLL/GO/GCE exhibited an increase in the anodic potential difference and a remarkable enhancement in the current responses for both UA and DA. For the simultaneous detection of DA and UA, the detection limits of 0.021 and 0.074 μM were obtained, while 0.031 and 0.018 μM were obtained as the detection limits for the selective detection of UA and DA, using DPV in the linear concentration ranges of 0.5 to 20.0 and 0.5 to 35 μM, respectively. In addition, the PLL/GO/GCE demonstrated good reproducibility, long-term stability, excellent selectivity and negligible interference of ascorbic acid (AA. The proposed modified electrode was successfully implemented in the simultaneous detection of DA and UA in human blood serum, urine and dopamine hydrochloride injection with satisfactory results.

  10. SeqX: a tool to detect, analyze and visualize residue co-locations in protein and nucleic acid structures

    Directory of Open Access Journals (Sweden)

    Fördös Gergely

    2005-07-01

    Full Text Available Abstract Background The interacting residues of protein and nucleic acid sequences are close to each other – they are co-located. Structure databases (like Protein Data Bank, PDB and Nucleic Acid Data Bank, NDB contain all information about these co-locations; however it is not an easy task to penetrate this complex information. We developed a JAVA tool, called SeqX for this purpose. Results SeqX tool is useful to detect, analyze and visualize residue co-locations in protein and nucleic acid structures. The user a. selects a structure from PDB; b. chooses an atom that is commonly present in every residues of the nucleic acid and/or protein structure(s c. defines a distance from these atoms (3–15 Å. The SeqX tool detects every residue that is located within the defined distances from the defined "backbone" atom(s; provides a DotPlot-like visualization (Residues Contact Map, and calculates the frequency of every possible residue pairs (Residue Contact Table in the observed structure. It is possible to exclude +/- 1 to 10 neighbor residues in the same polymeric chain from detection, which greatly improves the specificity of detections (up to 60% when tested on dsDNA. Results obtained on protein structures showed highly significant correlations with results obtained from literature (p Conclusion The tool is simple and easy to use and provides a quick and reliable visualization and analyses of residue co-locations in protein and nucleic acid structures. Availability and requirements http://janbiro.com/Downloads.html SeqX, Java J2SE Runtime Environment 5.0 (available from [see Additional file 1] http://www.sun.com and at least a 1 GHz processor and with a minimum 256 Mb RAM. Source codes are available from the authors. Additional File 1 SeqX_1.041_05601.jar. see this article Click here for file

  11. Nucleic Acid-Based Detection and Identification of Bacterial and Fungal Plant Pathogens - Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Kingsley, Mark T.

    2001-03-13

    The threat to American interests from terrorists is not limited to attacks against humans. Terrorists might seek to inflict damage to the U.S. economy by attacking our agricultural sector. Infection of commodity crops by bacterial or fungal crop pathogens could adversely impact U.S. agriculture, either directly from damage to crops or indirectly from damage to our ability to export crops suspected of contamination. Recognizing a terrorist attack against U.S. agriculture, to be able to prosecute the terrorists, is among the responsibilities of the members of Hazardous Material Response Unit (HMRU) of the Federal Bureau of Investigation (FBI). Nucleic acid analysis of plant pathogen strains by the use of polymerase chain reaction (PCR) amplification techniques is a powerful method for determining the exact identity of pathogens, as well as their possible region of origin. This type of analysis, however, requires that PCR assays be developed specific to each particular pathogen strain, and analysis protocols developed that are specific to the particular instrument used for detection. The objectives of the work described here were threefold: 1) to assess the potential terrorist threat to U.S. agricultural crops, 2) to determine whether suitable assays exist to monitor that threat, and 3) where assays are needed for priority plant pathogen threats, to modify or develop those assays for use by specialists at the HMRU. The assessment of potential threat to U.S. commodity crops and the availability of assays for those threats were described in detail in the Technical Requirements Document (9) and will be summarized in this report. This report addresses development of specific assays identified in the Technical Requirements Document, and offers recommendations for future development to ensure that HMRU specialists will be prepared with the PCR assays they need to protect against the threat of economic terrorism.

  12. Clinical validation of integrated nucleic acid and protein detection on an electrochemical biosensor array for urinary tract infection diagnosis.

    Directory of Open Access Journals (Sweden)

    Ruchika Mohan

    Full Text Available BACKGROUND: Urinary tract infection (UTI is a common infection that poses a substantial healthcare burden, yet its definitive diagnosis can be challenging. There is a need for a rapid, sensitive and reliable analytical method that could allow early detection of UTI and reduce unnecessary antibiotics. Pathogen identification along with quantitative detection of lactoferrin, a measure of pyuria, may provide useful information towards the overall diagnosis of UTI. Here, we report an integrated biosensor platform capable of simultaneous pathogen identification and detection of urinary biomarker that could aid the effectiveness of the treatment and clinical management. METHODOLOGY/PRINCIPAL FINDINGS: The integrated pathogen 16S rRNA and host lactoferrin detection using the biosensor array was performed on 113 clinical urine samples collected from patients at risk for complicated UTI. For pathogen detection, the biosensor used sandwich hybridization of capture and detector oligonucleotides to the target analyte, bacterial 16S rRNA. For detection of the protein biomarker, the biosensor used an analogous electrochemical sandwich assay based on capture and detector antibodies. For this assay, a set of oligonucleotide probes optimized for hybridization at 37°C to facilitate integration with the immunoassay was developed. This probe set targeted common uropathogens including E. coli, P. mirabilis, P. aeruginosa and Enterococcus spp. as well as less common uropathogens including Serratia, Providencia, Morganella and Staphylococcus spp. The biosensor assay for pathogen detection had a specificity of 97% and a sensitivity of 89%. A significant correlation was found between LTF concentration measured by the biosensor and WBC and leukocyte esterase (p<0.001 for both. CONCLUSION/SIGNIFICANCE: We successfully demonstrate simultaneous detection of nucleic acid and host immune marker on a single biosensor array in clinical samples. This platform can be used for

  13. [Studies on rapid detection of food-borne pathogenic bacteria by nucleic acid testing and related technology].

    Science.gov (United States)

    Cao, Wei; Wang, Mingzhong; Wang, Xiaoying; Liu, Xiumei

    2008-03-01

    The traditional methods of bacteria isolation, cultivation and identification are time-consuming, which can't meet the needs of the control and prevention of food-borne diseases. Recently, various kinds of rapid methods for food-borne pathogenic bacteria detection have emerged with the prompt development of nucleic acid testing technology. The application studies on polymerase chain reaction and the techniques derived from it, nucleic acid isothermal amplification, oligonucleotide microarray, immunomagnetic separation and DNA biosensing on food-borne pathogenic bacteria including Salmonella, Staphylococcus aureus and Enterohemorrhagic Escherchia coli, etc. were reviewed.

  14. Determination of Amino Acids in Panax notoginseng by Microwave Hydrolysis and Derivatization Coupled with Capillary Zone Electrophoresis Detection

    Institute of Scientific and Technical Information of China (English)

    LI Xiao-tian; ZHAO Ya-jing; JIANG Cheng-fei; ZHANG Han-qi; YU Ai-min

    2013-01-01

    The microwave hydrolysis and derivatization coupled with capillary electrophoresis detection were developed for the separation and determination of the amino acids in Panax notoginseng.The experimental conditions for the microwave hydrolysis and derivatization were examined and optimized.Several parameters of capillary electrophoresis,such as pH value of background electrolyte,borate concentration and applied voltage were optimized.Under the selected conditions,11 amino acids were completely separated.The real sample was analyzed and the results were satisfactory.Compared with that of conventional heat hydrolysis and derivatization,the analytical time of this method was significantly shortened.

  15. New light on protein folding: Unraveling folding and unfolding mechanisms using time-resolved and two-dimensional vibrational spectroscopy

    NARCIS (Netherlands)

    H. Meuzelaar

    2015-01-01

    How a protein folds from its one-dimensional sequence of amino acids into its three-dimensional, functional structure on biologically relevant time scales (typically on the micro- to millisecond time scale) is one of the most challenging questions currently investigated in several scientific discipl

  16. New light on protein folding: Unraveling folding and unfolding mechanisms using time-resolved and two-dimensional vibrational spectroscopy

    NARCIS (Netherlands)

    Meuzelaar, H.

    2015-01-01

    How a protein folds from its one-dimensional sequence of amino acids into its three-dimensional, functional structure on biologically relevant time scales (typically on the micro- to millisecond time scale) is one of the most challenging questions currently investigated in several scientific

  17. [Use of column and thin layer chromatography for detection of vanillyl mandelic acid in urine].

    Science.gov (United States)

    Riabichenko, V V; Barchukov, V G; Chernyĭ, A V; Salenko, Iu A

    2002-03-01

    The excretion of vanillylmandelic acid was measured by column chromatography of urinary samples on aluminum oxide with subsequent thin-layer chromatography on silica gel. Use of aluminum oxide allowed application of greater urine samples (up to 0.1% of 24-h diuresis) onto chromatographic plates and essentially improved the quality of separation of vanillylmandelic acid from other phenylcarbonic acids by thin-layer chromatography, as well as the specificity and reproducibility of measurements.

  18. Early aggregated States in the folding of interleukin-1β.

    Science.gov (United States)

    Finke, J M; Jennings, P A

    2001-06-01

    Kinetic data measured from folding of the protein interleukin-1β fits best to three exponential phases when studied with tryptophan fluorescence but only two exponential phases when measured using other methods. The technique of ANS fluorescence was used to determine whether the additional phase observed in tryptophan fluorescence was also detected with ANS dye binding. Unlike trytophan fluorescence, the ANS fluorescence was highly dependent on the concentration of protein present during the folding experiment. Experimental controls provide evidence that ANS binds to protein aggregates, present at higher concentrations and absent at lower concentrations. Protein concentration-dependent folding studies demonstrate that, at lower interleukin-1β concentrations, tryptophan fluorescence kinetics can be fit adequately with a two exponential fit. This study indicates that (1) measured interleukin-1β folding kinetics fit to a 2 phase model and (2) at higher protein concentrations, transient association of IL-1β may result in a kinetic fit of 3 phases.

  19. A HMM-Based Method for Vocal Fold Pathology Diagnosis

    Directory of Open Access Journals (Sweden)

    Vahid Majidnezhad

    2012-11-01

    Full Text Available Acoustic analysis is a proper method in vocal fold pathology diagnosis so that it can complement and in some cases replace the other invasive, based on direct vocal fold observations methods. There are different approaches for vocal fold pathology diagnosis. This paper presents a method based on hidden markov model which classifies speeches into two classes: the normal and the pathological. Two hidden markov models are trained based on these two classes of speech and then the trained models are used to classify the dataset. The proposed method is able to classify the speeches with an accuracy of 93.75%. The results of this algorithm provide insights that can help biologists and computer scientists design high-performance system for detection of vocal fold pathology diagnosis.

  20. Ultra-sensitive detection of zinc oxide nanowires using a quartz crystal microbalance and phosphoric acid DNA

    Science.gov (United States)

    Jang, Kuewhan; You, Juneseok; Park, Chanhoo; Park, Hyunjun; Choi, Jaeyeong; Choi, Chang-Hwan; Park, Jinsung; Lee, Howon; Na, Sungsoo

    2016-09-01

    Recent advancements of nanomaterials have inspired numerous scientific and industrial applications. Zinc oxide nanowires (ZnO NWs) is one of the most important nanomaterials due to their extraordinary properties. However, studies performed over the past decade have reported toxicity of ZnO NWs. Therefore, there has been increasing demand for effective detection of ZnO NWs. In this study, we propose a method for the detection of ZnO NW using a quartz crystal microbalance (QCM) and DNA probes. The detection method is based on the covalent interaction between ZnO NWs and the phosphoric acid group of single-stranded DNA (i.e., linker DNA), and DNA hybridization between the linker DNA and the probe DNA strand on the QCM electrode. Rapid, high sensitivity, in situ detection of ZnO NWs was demonstrated for the first time. The limit of detection was 10-4 μg ml-1 in deionized water, which represents a sensitivity that is 100000 times higher than the toxic ZnO NW concentration level. Moreover, the selectivity of the ZnO NW detection method was demonstrated by comparison with other types of nanowires and the method was able to detect ZnO NWs in tap water sensitively even after stored for 14 d in a refrigerator. The performance of our proposed method was sufficient to achieve detection of ZnO NW in the ‘real-world’ environment.

  1. Detection of Salmonella invA by isothermal and chimeric primer-initiated amplification of nucleic acids (ICAN) in Zambia.

    Science.gov (United States)

    Isogai, Emiko; Makungu, Chitwambi; Yabe, John; Sinkala, Patson; Nambota, Andrew; Isogai, Hiroshi; Fukushi, Hideto; Silungwe, Manda; Mubita, Charles; Syakalima, Michelo; Hang'ombe, Bernard Mudenda; Kozaki, Shunji; Yasuda, Jun

    2005-01-01

    The isothermal and chimeric primer-initiated amplification of nucleic acids (ICAN) is a new isothermal DNA amplification method composed of exo Bca DNA polymerase, RNaseH and DNA-RNA chimeric primers. We detected invA of Salmonella from chicken carcasses, egg yolk and cattle fecal samples. Fifty-three of 59 isolates were invA-positive in ICAN-chromatostrip detection. The result was consistent with those obtained by standard PCR. Salmonella invA was detected in 12 of 14 carcass rinses by ICAN, while in 7 of 14 rinses by standard PCR. These results indicate that ICAN is an efficient, sensitive and simple system to detect invA of Salmonella species in developing countries such as Zambia.

  2. Microfluidic Chip-based Nucleic Acid Testing using Gingival Crevicular Fluid as a New Technique for Detecting HIV-1 Infection

    Directory of Open Access Journals (Sweden)

    Alex Willyandre

    2013-05-01

    Full Text Available Transmission of HIV-1 infection by individuals in window period who are tested negative in conventional HIV-1 detection would pose the community with serious problems. Several diagnostic tools require specific labora-tory equipment, perfect timing of diagnosis, antibody to HIV-1, and invasive technique to get sample for examination, until high amount of time to process the sample as well as accessibility of remote areas. Many attempts have been made to solve those problems to come to a new detection technique. This review aims to give information about the current development technique for detection of HIV infection. Microfluidic Chip-based Nucleic Acid Testing is currently introduced for detection of HIV-1 infection. This review also cover the possible usage of gingival crevicular fluid as sample specimen that could be taken noninvasively from the individual.DOI: 10.14693/jdi.v18i2.63

  3. Stretching Folding Instability and Nanoemulsions

    CERN Document Server

    Chan, Chon U

    2009-01-01

    Here we show a folding-stretching instability in a microfluidic flow focusing device using silicon oil (100cSt) and water. The fluid dynamics video demonstrates an oscillating thread of oil focused by two co-flowing streams of water. We show several high-speed sequences of these oscillations with 30,000 frames/s. Once the thread is decelerated in a slower moving pool downstream an instability sets in and water-in-oil droplets are formed. We reveal the details of the pinch-off with 500,000 frames/s. The pinch-off is so repeatable that complex droplet patterns emerge. Some of droplets are below the resolution limit, thus smaller than 1 micrometer in diameter.

  4. Topological Solitons and Folded Proteins

    CERN Document Server

    Chernodub, M N; Niemi, Antti J

    2010-01-01

    We propose that protein loops can be interpreted as topological domain-wall solitons. They interpolate between ground states that are the secondary structures like alpha-helices and beta-strands. Entire proteins can then be folded simply by assembling the solitons together, one after another. We present a simple theoretical model that realizes our proposal and apply it to a number of biologically active proteins including 1VII, 2RB8, 3EBX (Protein Data Bank codes). In all the examples that we have considered we are able to construct solitons that reproduce secondary structural motifs such as alpha-helix-loop-alpha-helix and beta-sheet-loop-beta-sheet with an overall root-mean-square-distance accuracy of around 0.7 Angstrom or less for the central alpha-carbons, i.e. within the limits of current experimental accuracy.

  5. Protein folding and wring resonances

    DEFF Research Database (Denmark)

    Bohr, Jakob; Bohr, Henrik; Brunak, Søren

    1997-01-01

    The polypeptide chain of a protein is shown to obey topological contraints which enable long range excitations in the form of wring modes of the protein backbone. Wring modes of proteins of specific lengths can therefore resonate with molecular modes present in the cell. It is suggested that prot......The polypeptide chain of a protein is shown to obey topological contraints which enable long range excitations in the form of wring modes of the protein backbone. Wring modes of proteins of specific lengths can therefore resonate with molecular modes present in the cell. It is suggested...... that protein folding takes place when the amplitude of a wring excitation becomes so large that it is energetically favorable to bend the protein backbone. The condition under which such structural transformations can occur is found, and it is shown that both cold and hot denaturation (the unfolding...

  6. Analysis and detection of the herbicides dimethenamid and flufenacet and their sulfonic and oxanilic acid degradates in natural water

    Science.gov (United States)

    Zimmerman, L.R.; Schneider, R.J.; Thurman, E.M.

    2002-01-01

    Dimethenamid [2-chloro-N-(2,4-dimethyl-3-thienyl)-N-(2-methoxy-1-methylethyl)acetamide] and flufenacet [N-(4-fluorophenyl)-N-(1-methylethyl)-2-(5-(trifluoromethyl)-1,3,4- thiadiazol-2-yl)oxy] were isolated by C-18 solid-phase extraction and separated from their ethanesulfonic acid (ESA) and oxanilic acid (OXA) degradates during their elution using ethyl acetate for the parent compound, followed by methanol for the polar degradates. The parent compounds were detected using gas chromatography-mass spectrometry in selected-ion mode. The ESA and OXA degradates were detected using high-performance liquid chromatography-electrospray mass spectrometry (HPLC-ESPMS) in negative-ion mode. The method detection limits for a 123-mL sample ranged from 0.01 to 0.07 μg/L. These methods are compatible with existing methods and thus allow for analysis of 17 commonly used herbicides and 18 of their degradation compounds with one extraction. In a study of herbicide transport near the mouth of the Mississippi River during 1999 and 2000, dimethenamid and its ESA and OXA degradates were detected in surface water samples during the annual spring flushes. For flufenacet, the only detections at the study site were for the ESA degradates in samples collected at the peak of the herbicide spring flush in 2000. The low frequency of detections in surface water likely is due to dimethenamid and flufenacet being relatively new herbicides. In addition, detectable amounts of the stable degradates have not been detected in ground water.

  7. Technetium-99m diethylene triamine penta-acetic acid and dimercaptosuccinic acid in the detection of a segmental branch stenosis of the renal artery by captopril renography

    Energy Technology Data Exchange (ETDEWEB)

    Bajnok, L.; Varga, J. (University Medical School, Debrecen (Hungary). Central Nuclear Medicine Lab.); Kurta, G. (University Medical School, Debrecen (Hungary). 1. Dept. of Medicine)

    1992-01-01

    We present a case in which a 39-year-old woman with correctable bilateral renovascular hypertension did not show abnormality during post-captopril technetium-99m dimercaptosuccinic acid (DMSA) study. Post-captopril {sup 99m}Tc-diethylene triamine pentaacetic acid (DTPA) scintigraphy revealed the adverse effect of a stenosis of the artery supplying the upper part of her left kidney but failed to uncover the existence of severe multiple narrowings of the right renal artery. After bilateral renovascular reconstructive surgery, the hypertension completely disappeared. This case illustrates that DTPA may be more efficacious than DMSA in the detection of segmental loss of renal function induced by angiotensin converting enzyme inhibition. (orig.).

  8. Simultaneous characterization of bile acid, sterols, and determination of acylglycerides in feces from soluble cellulose-fed hamsters using HPLC with evaporative light-scattering detection and APCI-MS.

    Science.gov (United States)

    Hong, Yun-Jeong; Turowski, Maciej; Lin, Jiann-Tsyh; Yokoyama, Wallace H

    2007-11-28

    The rapid rise in obesity-related diseases has increased interest in oral and dietary agents that disrupt fat metabolism, resulting in the excretion of dietary lipids in the feces. In this study, a rapid and convenient liquid chromatography method to comprehensively analyze fecal lipids in a single injection was developed. An evaporative light-scattering detector (ELSD) for routine analysis or atmosphere pressure chemical ionization tandem mass spectrometry [(+)APCI-MS/MS] for structural confirmation and peak purity was used. The method was applied to characterize lipid components of feces from hamsters fed high-fat diets with either 5% microcrystalline cellulose or 5% hydroxypropyl methylcellulose (HPMC) fibers, to test the effect of HPMC on lipid metabolism. HPMC is a nonfermentable, soluble cellulose fiber. The fecal lipid components identified using this method includes two secondary bile acids, deoxycholic acid, lithocholic acid, and neutral sterols including cholesterol, coprostanol, stigmastanol, and sitosterol. The profile of fecal lipid components was compared between two groups. It was found that the bile acid excretion was increased 2-fold in HPMC-fed hamsters. More interestingly, diacylglycerides and triacylglycerides were detected in feces from hamsters on HPMC-included high-fat diets. We believe that this is the first report of excretion of acylglycerides following neutral soluble fiber feeding.

  9. 13C-detected NMR experiments for measuring chemical shifts and coupling constants in nucleic acid bases.

    Science.gov (United States)

    Fiala, Radovan; Sklenár, Vladimír

    2007-10-01

    The paper presents a set of two-dimensional experiments that utilize direct (13)C detection to provide proton-carbon, carbon-carbon and carbon-nitrogen correlations in the bases of nucleic acids. The set includes a (13)C-detected proton-carbon correlation experiment for the measurement of (13)C-(13)C couplings, the CaCb experiment for correlating two quaternary carbons, the HCaCb experiment for the (13)C-(13)C correlations in cases where one of the carbons has a proton attached, the HCC-TOCSY experiment for correlating a proton with a network of coupled carbons, and a (13)C-detected (13)C-(15)N correlation experiment for detecting the nitrogen nuclei that cannot be detected via protons. The IPAP procedure is used for extracting the carbon-carbon couplings and/or carbon decoupling in the direct dimension, while the S(3)E procedure is preferred in the indirect dimension of the carbon-nitrogen experiment to obtain the value of the coupling constant. The experiments supply accurate values of (13)C and (15)N chemical shifts and carbon-carbon and carbon-nitrogen coupling constants. These values can help to reveal structural features of nucleic acids either directly or via induced changes when the sample is dissolved in oriented media.

  10. Colorimetric method for the detection of melamine using in-situ formed silver nanoparticles via tannic acid

    Science.gov (United States)

    Alam, Md. Fazle; Laskar, Amaj Ahmed; Ahmed, Shahbaz; Shaida, Mohd. Azfar; Younus, Hina

    2017-08-01

    Melamine toxicity has recently attracted worldwide attention as it causes renal failure and the death of humans and animals. Therefore, developing a simple, fast and sensitive method for the routine detection of melamine is the need of the hour. Herein, we have developed a selective colorimetric method for the detection of melamine in milk samples based upon in-situ formation of silver nanoparticles (AgNPs) via tannic acid. The AgNPs thus formed were characterized by UV-Visible spectrophotometer, transmission electron microscope (TEM), zetasizer and dynamic light scattering (DLS). The AgNPs were used to detect melamine under in vitro condition and in raw milk spiked with melamine. Under optimal conditions, melamine could be selectively detected in vitro within the concentration range of 0.05-1.4 μM with a limit of detection (LOD) of 0.01 μM, which is lower than the strictest melamine safety requirement of 1 ppm. In spiked raw milk, the recovery percentage range was 99.5-106.5% for liquid milk and 98.5-105.5% for powdered milk. The present method shows extreme selectivity with no significant interference with other substances like urea, glucose, glycine, ascorbic acid etc. This assay method does not utilize organic cosolvents, enzymatic reactions, light sensitive dye molecules and sophisticated instrumentation, thereby overcoming some of the limitations of the other conventional methods.

  11. A fully integrated paperfluidic molecular diagnostic chip for the extraction, amplification, and detection of nucleic acids from clinical samples.

    Science.gov (United States)

    Rodriguez, Natalia M; Wong, Winnie S; Liu, Lena; Dewar, Rajan; Klapperich, Catherine M

    2016-02-21

    Paper diagnostics have successfully been employed to detect the presence of antigens or small molecules in clinical samples through immunoassays; however, the detection of many disease targets relies on the much higher sensitivity and specificity achieved via nucleic acid amplification tests (NAAT). The steps involved in NAAT have recently begun to be explored in paper matrices, and our group, among others, has reported on paper-based extraction, amplification, and detection of DNA and RNA targets. Here, we integrate these paper-based NAAT steps into a single paperfluidic chip in a modular, foldable system that allows for fully integrated fluidic handling from sample to result. We showcase the functionality of the chip by combining nucleic acid isolation, isothermal amplification, and lateral flow detection of human papillomavirus (HPV) 16 DNA directly from crude cervical specimens in less than 1 hour for rapid, early detection of cervical cancer. The chip is made entirely of paper and adhesive sheets, making it low-cost, portable, and disposable, and offering the potential for a point-of-care molecular diagnostic platform even in remote and resource-limited settings.

  12. Amino acid detection using fluoroquinolone–Cu{sup 2+} complex as a switch-on fluorescent probe by competitive complexation without derivatization

    Energy Technology Data Exchange (ETDEWEB)

    Farokhcheh, Alireza; Alizadeh, Naader, E-mail: alizaden@modares.ac.ir

    2014-01-15

    In this work, we describe the use of fluoroquinolone–Cu{sup 2+} complex as a competitive switch-on fluorescence probe for amino acid determination without derivatization. The fluorescence intensity of this probe, which has been reduced due to effective quenching by Cu{sup 2+} ion, increases drastically by an addition of amino acid (glycine, phenylalanine, sarcosine, aspargine, alanine, proline, arginine, aspartic acid, glutamic acid, lysine, leucine and isoleucine). The overall stability constants of Cu{sup 2+} ion complexes with amino acids were determined by fluorometric titration of fluoroquinolone-Cu{sup 2+} complex with the amino acid solution. Furthermore, the probe shows high calibration sensitivity toward aspartic acid. The fluorescence signal depends linearly on the amino acid concentration within the range of concentration from 1.2×10{sup −7} to 1.1×10{sup −5} mol L{sup −1} for aspartic acid. The detection limit was found 2.7×10{sup −8} mol L{sup −1} with the relative standard deviation (RSD%) about 2.1% (five replicate). -- Highlights: • Amino acids are detected by using fluoroquinolone–Cu{sup 2+} complex as fluorescent probe. • Amino acids were detected based on a competitive complexation reaction. • Probe has been able to recognize amino acids through switch-on fluorescence behavior. • Ultra-trace level of aspartic and glutamic acid is determined without derivatization.

  13. Detection of acid and hop shock induced responses in beer spoiling Lactobacillus brevis by MALDI-TOF MS.

    Science.gov (United States)

    Schurr, Benjamin C; Behr, Jürgen; Vogel, Rudi F

    2015-04-01

    Due to the harsh environment, microorganisms encounter in beer, spoilage bacteria must be able to customise their metabolism and physiology in an order to master various kinds of perturbations. Proteomic approaches have been used to examine differences between various beer spoilage bacteria and between different stress conditions, such as acid and hop (Humulus lupulus) stress. However, these investigations cannot detect changes in low molecular weight (lmw) proteins (beer spoiling L. brevis. It is demonstrated that MALDI-TOF MS is a fast tool to detect and characterise stress situations in beer spoiling bacteria along the lmw sub-proteome.

  14. Determination of oxolinic acid, danofloxacin, ciprofloxacin, and enrofloxacin in porcine and bovine meat by micellar liquid chromatography with fluorescence detection.

    Science.gov (United States)

    Terrado-Campos, David; Tayeb-Cherif, Khaled; Peris-Vicente, Juan; Carda-Broch, Samuel; Esteve-Romero, Josep

    2017-04-15

    A method was developed for the determination of oxolinic acid, danofloxacin, ciprofloxacin and enrofloxacin by micellar liquid chromatography - fluorescence detection in commercial porcine and bovine meat. The samples were ultrasonicated in a micellar solution, free of organic solvent, to extract the analytes, and the supernatant was directly injected. The quinolones were resolved in 0.9998), trueness (89.3-105.1%), precision (<8.3%), decision limit (<12% over the maximum residue limit), detection capability (<21% over the maximum residue limit), ruggedness (<5.6%) and stability. The procedure was rapid, eco-friendly, safe and easy-to-handle.

  15. A review of enzymatic uric acid biosensors based on amperometric detection.

    Science.gov (United States)

    Erden, Pınar Esra; Kılıç, Esma

    2013-03-30

    This review summarizes the studies carried on the development of amperometric uric acid biosensors over the past twenty years. Sensing principles, enzyme immobilization techniques, the electrode types, different approaches and various matrices used for biosensor fabrication are presented along with their benefits and limitations. Uric acid biosensors based on different modes of transducing devices such as optical, potentiometric, conductometric are also referred.

  16. Detection and Quantification of Valerenic Acid in Commercially Available Valerian Products

    Science.gov (United States)

    Douglas, Ruth H.; Muldowney, Ciaran A.; Mohamed, Rabab; Keohane, Fiona; Shanahan, Catherine; Walsh, John J.; Kavanagh, Pierce V.

    2007-01-01

    Several valerian-containing products sold in pharmacies were evaluated to verify the presence of Valeriana officinalis by identifying the presence of valerenic acid found only in species of Valeriana. The content of valerenic acid was found to vary considerably in the products analyzed, thus emphasizing the importance of standardizing herbal…

  17. Neuropsychological Outcomes in Fatty Acid Oxidation Disorders: 85 Cases Detected by Newborn Screening

    Science.gov (United States)

    Waisbren, Susan E.; Landau, Yuval; Wilson, Jenna; Vockley, Jerry

    2013-01-01

    Mitochondrial fatty acid oxidation disorders include conditions in which the transport of activated acyl-Coenzyme A (CoA) into the mitochondria or utilization of these substrates is disrupted or blocked. This results in a deficit in the conversion of fat into energy. Most patients with fatty acid oxidation defects are now identified through…

  18. A new dual-channel optical signal probe for Cu2+ detection based on morin and boric acid.

    Science.gov (United States)

    Wang, Peng; Yuan, Bin Fang; Li, Nian Bing; Luo, Hong Qun

    2014-01-01

    In this work we utilized the common analytical reagent morin to develop a new a dual-channel, cost-effective, and sensitive method for determination of Cu(2+). It is found that morin is only weakly fluorescent by itself, but forms highly fluorescent complexes with boric acid. Moreover, the fluorescence of complexes of morin with boric acid is quenched linearly by Cu(2+) in a certain concentration range. Under optimum conditions, the fluorescence quenching efficiency was linearly proportional to the concentration of cupric ions in the range of 0.5-25 μM with high sensitivity, and the detection limit for Cu(2+) was 0.38 μM. The linear range was 1-25 μM determined by spectrophotometry, and the detection limit for cupric ions was 0.8 μM. Furthermore, the mechanism of sensitive fluorescence quenching response of morin to Cu(2+) is discussed.

  19. Adulteration of Argentinean milk fats with animal fats: Detection by fatty acids analysis and multivariate regression techniques.

    Science.gov (United States)

    Rebechi, S R; Vélez, M A; Vaira, S; Perotti, M C

    2016-02-01

    The aims of the present study were to test the accuracy of the fatty acid ratios established by the Argentinean Legislation to detect adulterations of milk fat with animal fats and to propose a regression model suitable to evaluate these adulterations. For this purpose, 70 milk fat, 10 tallow and 7 lard fat samples were collected and analyzed by gas chromatography. Data was utilized to simulate arithmetically adulterated milk fat samples at 0%, 2%, 5%, 10% and 15%, for both animal fats. The fatty acids ratios failed to distinguish adulterated milk fats containing less than 15% of tallow or lard. For each adulterant, Multiple Linear Regression (MLR) was applied, and a model was chosen and validated. For that, calibration and validation matrices were constructed employing genuine and adulterated milk fat samples. The models were able to detect adulterations of milk fat at levels greater than 10% for tallow and 5% for lard. Copyright © 2015 Elsevier Ltd. All rights reserved.

  20. Derivatization and fluorescence detection of amino acids and peptides with 9-fluorenylmethyl chloroformate on the surface of a solid adsorbent.

    Science.gov (United States)

    Shangguan, D; Zhao, Y; Han, H; Zhao, R; Liu, G

    2001-05-01

    An approach that exploits the surface of a solid adsorbent is proposed for precolumn FMOC derivatization of amino acids and peptides. Amino acids (Ser, Glu, GABA, Val, Phe, Lys) and two neuropeptides (substance P and Leuenkephalin) were adsorbed on alkaline silica gel cartridges. After drying, they were reacted with 9-fluorenyl-methyl chloroformate (FMOC-Cl) in toluene. After washing off the excess FMOC-Cl with ethyl acetate, the derivatives were eluted with aqueous eluant. The eluates were separated and detected by means of HPLC with fluorescence detection. Compared with the traditional derivatization in the liquid phase, the extent of formation of byproducts of FMOC-Cl with water was greatly decreased, and the excess FMOC-Cl was eliminated completely.

  1. An optimized analytical method for the simultaneous detection of iodoform, iodoacetic acid, and other trihalomethanes and haloacetic acids in drinking water.

    Directory of Open Access Journals (Sweden)

    Xiaolin Liu

    Full Text Available An optimized method is presented using liquid-liquid extraction and derivatization for the extraction of iodoacetic acid (IAA and other haloacetic acids (HAA9 and direct extraction of iodoform (IF and other trihalomethanes (THM4 from drinking water, followed by detection by gas chromatography with electron capture detection (GC-ECD. A Doehlert experimental design was performed to determine the optimum conditions for the five most significant factors in the derivatization step: namely, the volume and concentration of acidic methanol (optimized values  = 15%, 1 mL, the volume and concentration of Na2SO4 solution (129 g/L, 8.5 mL, and the volume of saturated NaHCO3 solution (1 mL. Also, derivatization time and temperature were optimized by a two-variable Doehlert design, resulting in the following optimized parameters: an extraction time of 11 minutes for IF and THM4 and 14 minutes for IAA and HAA9; mass of anhydrous Na2SO4 of 4 g for IF and THM4 and 16 g for IAA and HAA9; derivatization time of 160 min and temperature at 40°C. Under optimal conditions, the optimized procedure achieves excellent linearity (R(2 ranges 0.9990-0.9998, low detection limits (0.0008-0.2 µg/L, low quantification limits (0.008-0.4 µg/L, and good recovery (86.6%-106.3%. Intra- and inter-day precision were less than 8.9% and 8.8%, respectively. The method was validated by applying it to the analysis of raw, flocculated, settled, and finished waters collected from a water treatment plant in China.

  2. An optimized analytical method for the simultaneous detection of iodoform, iodoacetic acid, and other trihalomethanes and haloacetic acids in drinking water.

    Science.gov (United States)

    Liu, Xiaolin; Wei, Xiao; Zheng, Weiwei; Jiang, Songhui; Templeton, Michael R; He, Gengsheng; Qu, Weidong

    2013-01-01

    An optimized method is presented using liquid-liquid extraction and derivatization for the extraction of iodoacetic acid (IAA) and other haloacetic acids (HAA9) and direct extraction of iodoform (IF) and other trihalomethanes (THM4) from drinking water, followed by detection by gas chromatography with electron capture detection (GC-ECD). A Doehlert experimental design was performed to determine the optimum conditions for the five most significant factors in the derivatization step: namely, the volume and concentration of acidic methanol (optimized values  = 15%, 1 mL), the volume and concentration of Na2SO4 solution (129 g/L, 8.5 mL), and the volume of saturated NaHCO3 solution (1 mL). Also, derivatization time and temperature were optimized by a two-variable Doehlert design, resulting in the following optimized parameters: an extraction time of 11 minutes for IF and THM4 and 14 minutes for IAA and HAA9; mass of anhydrous Na2SO4 of 4 g for IF and THM4 and 16 g for IAA and HAA9; derivatization time of 160 min and temperature at 40°C. Under optimal conditions, the optimized procedure achieves excellent linearity (R(2) ranges 0.9990-0.9998), low detection limits (0.0008-0.2 µg/L), low quantification limits (0.008-0.4 µg/L), and good recovery (86.6%-106.3%). Intra- and inter-day precision were less than 8.9% and 8.8%, respectively. The method was validated by applying it to the analysis of raw, flocculated, settled, and finished waters collected from a water treatment plant in China.

  3. RIG-I detects infection with live Listeria by sensing secreted bacterial nucleic acids

    Science.gov (United States)

    Abdullah, Zeinab; Schlee, Martin; Roth, Susanne; Mraheil, Mobarak Abu; Barchet, Winfried; Böttcher, Jan; Hain, Torsten; Geiger, Sergej; Hayakawa, Yoshihiro; Fritz, Jörg H; Civril, Filiz; Hopfner, Karl-Peter; Kurts, Christian; Ruland, Jürgen; Hartmann, Gunther; Chakraborty, Trinad; Knolle, Percy A

    2012-01-01

    Immunity against infection with Listeria monocytogenes is not achieved from innate immune stimulation by contact with killed but requires viable Listeria gaining access to the cytosol of infected cells. It has remained ill-defined how such immune sensing of live Listeria occurs. Here, we report that efficient cytosolic immune sensing requires access of nucleic acids derived from live Listeria to the cytoplasm of infected cells. We found that Listeria released nucleic acids and that such secreted bacterial RNA/DNA was recognized by the cytosolic sensors RIG-I, MDA5 and STING thereby triggering interferon β production. Secreted Listeria nucleic acids also caused RIG-I-dependent IL-1β-production and inflammasome activation. The signalling molecule CARD9 contributed to IL-1β production in response to secreted nucleic acids. In conclusion, cytosolic recognition of secreted bacterial nucleic acids by RIG-I provides a mechanistic explanation for efficient induction of immunity by live bacteria. PMID:23064150

  4. Optimization of the treatment of wheat samples for the determination of phytic acid by HPLC with refractive index detection.

    Science.gov (United States)

    Amaro, Rosa; Murillo, Miguel; González, Zurima; Escalona, Andrés; Hernández, Luís

    2009-01-01

    The treatment of wheat samples was optimized before the determination of phytic acid by high-performance liquid chromatography with refractive index detection. Drying by lyophilization and oven drying were studied; drying by lyophilization gave better results, confirming that this step is critical in preventing significant loss of analyte. In the extraction step, washing of the residue and collection of this water before retention of the phytates in the NH2 Sep-Pak cartridge were important. The retention of phytates in the NH2 Sep-Pak cartridge and elimination of the HCI did not produce significant loss (P = 0.05) in the phytic acid content of the sample. Recoveries of phytic acid averaged 91%, which is a substantial improvement with respect to values reported by others using this methodology.

  5. A Study on Tannic Acid-doped Polypyrrole Films on Gold Electrodes for Selective Electrochemical Detection of Dopamine

    OpenAIRE

    Shouzhuo Yao; Yunlong Li; Zhili Li; Qingji Xie; Ling Jiang

    2005-01-01

    Tannic acid-doped polypyrrole (PPY/TA) films have been grown on gold electrodes for selective electrochemical detection of dopamine (DA). Electrochemical quartz crystal microbalance (EQCM) studies revealed that, in vivid contrast to perchlorate-doped polypyrrole films (PPY/ClO4 -), the redox switching of PPY/TA films in aqueous solutions involved only cation transport if the solution pH was greater than 3∼4. The PPY/TA Au electrodes also exhibited attractive permselectivity for electroactive ...

  6. Simultaneous determination of furfural, acetic acid, and 5-hydroxymethylfurfural in corncob hydrolysates using liquid chromatography with ultraviolet detection.

    Science.gov (United States)

    Dong, Bo-Yu; Chen, Ye-Fu; Zhao, Chang-Chun; Zhang, Shi-Jie; Guo, Xue-Wu; Xiao, Dong-Guang

    2013-01-01

    A single-laboratory validation study was conducted using HPLC for detecting and quantifying acetic acid, furfural, and 5-hydroxymethylfurfural (HMF) in corncob hydrolysates. A pretreatment procedure using dilute sulfuric acid was optimized for corncob hydrolysis. The final hydrolysates were analyzed by HPLC using a C18 RP column with aqueous 0.01% (v/v) H2SO4-CH3OH (95 + 5) as the mobile phase at a flow rate of 1 mL/min. The wavelengths for detecting the three compounds were changed to their optimal UV detection wavelengths at the time of elution. The wavelength detection adjustments were as follow: 205 nm (0 to 4 min); 284 nm (4 to 7 min); and 276 nm (7 to 10 min). Separation was achieved with a chromatographic run time of 10 min. The calibration curves for the three compounds had correlation coefficients (r2) > or = 99.8%. The analytical range, as defined by the calibration curves, was 0.5-10 mg/L for acetic acid, 0.4-22 mg/L for furfural, and 0.1-18 mg/L for HMF. The LODs for acetic acid, furfural, and HMF were estimated to be 0.05, 0.03, and 0.02 mg/L, respectively; the LOQs were 0.196, 0.135, and 0.074 mg/L, respectively. The RSD values for the intraday precision study ranged from 0.31 to 2.22%, and from 0.57 to 2.43% for the interday study. The mean recovery rates in all compounds were between 100.08 and 101.49%.

  7. Detection of capripoxvirus DNA using a field-ready nucleic acid extraction and real-time PCR platform

    OpenAIRE

    Armson, B; Fowler, V. L.; Tuppurainen, E.S.M.; Howson, E. L. A.; Madi, M.; Sallu, R.; Kasanga, C. J.; Pearson, C; Wood, J.; Martin, P.; Mioulet, V; King, D. P.

    2015-01-01

    Summary Capripoxviruses, comprising sheep pox virus, goat pox virus and lumpy skin disease virus cause serious diseases of domesticated ruminants, notifiable to The World Organization for Animal Health. This report describes the evaluation of a mobile diagnostic system (Enigma Field Laboratory) that performs automated sequential steps for nucleic acid extraction and real?time PCR to detect capripoxvirus DNA within laboratory and endemic field settings. To prepare stable reagents that could be...

  8. Graphene nanoplatelets based matrix solid-phase dispersion microextraction for phenolic acids by ultrahigh performance liquid chromatography with electrochemical detection.

    Science.gov (United States)

    Peng, Li-Qing; Yi, Ling; Yang, Qiu-Cheng; Cao, Jun; Du, Li-Jing; Zhang, Qi-Dong

    2017-08-08

    A simple, rapid and eco-friendly approach based on matrix solid-phase dispersion microextraction (MSPDM) followed by ultrahigh performance liquid chromatography coupled with electrochemical detection (UHPLC-ECD) was presented for the microextraction and determination of six phenolic acids in a plant preparation (Danshen tablets). The parameters that influenced the extraction performance of phenolic acids were investigated and optimized. The optimal MSPDM conditions were determined as follows: sorbent, using graphene nanoplatelets with sample/sorbent ratio of 1:1, grinding time set at 60 s, and 0.2 mL of water as elution solvent. Under the optimum conditions, the validation experiments indicated that the proposed method exhibited good linearity (r(2) ≥ 0.9991), excellent precision (RSD ≤ 4.57%), and satisfactory recoveries (82.34-98.34%). The limits of detection were from 1.19 to 4.62 ng/mL for six phenolic acids. Compared with other reported methods, this proposal required less sample, solvent and extraction time. Consequently, the proposed method was successfully used to the extraction and determination of phenolic acids in Danshen tablets.

  9. Gadoxetic acid-enhanced MRI and diffusion-weighted imaging for the detection of colorectal liver metastases after neoadjuvant chemotherapy

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Mi Hye [Konkuk University Medical Center, Department of Radiology, Seoul (Korea, Republic of); Lee, Jeong Min; Han, Joon Koo; Choi, Byung-Ihn [Seoul National University Hospital, Department of Radiology, Seoul (Korea, Republic of); Hur, Bo Yun [Boramae Medical Center, Department of Radiology, Seoul (Korea, Republic of); Kim, Tae-You [Seoul National University Hospital, Department of Internal Medicine, Seoul (Korea, Republic of); Jeong, Seung-Yong; Yi, Nam-Joon; Suh, Kyung-Suk [Seoul National University Hospital, Department of Surgery, Seoul (Korea, Republic of)

    2015-08-15

    To investigate the diagnostic performance of gadoxetic acid-enhanced MRI including diffusion-weighted imaging (DWI) for the detection of colorectal liver metastases (CRLMs) after neoadjuvant chemotherapy (NAC). Our study population comprised 77 patients with 140 CRLMs who underwent gadoxetic acid-enhanced MRI within 1 month prior to surgery: group A (without NAC, n = 38) and group B (with NAC, n = 39). Two radiologists independently assessed all MR images and graded their diagnostic confidence for CRLM on a 5-point scale. Diagnostic accuracy, sensitivity and positive predictive values (PPV) were calculated and compared between the two groups. Diagnostic accuracy of gadoxetic acid-enhanced MRI in group B was slightly lower than in group A, but a statistically significant difference was not observed (observer 1: A{sub z}, 0.926 in group A, 0.905 in group B; observer 2: A{sub z}, 0.944 in group A, 0.885 in group B; p > 0.05). Sensitivity and PPV of group B were comparable to those of group A (observer 1: sensitivity = 93.5 % vs. 93.6 %, PPV = 95.1 % vs. 86.9 %; observer 2: sensitivity = 96.8 % vs. 91.0 %; PPV = 90.0 % vs. 89.7 %; all p > 0.05). Gadoxetic acid-enhanced MRI including DWI provided good diagnostic performance with high sensitivity (>90 %) for the detection of CRLMs, regardless of the influence of NAC. (orig.)

  10. Simultaneous Analysis of Oil-Soluble, Basic, and Acidic Illegal Dyes in Foods Using Liquid Chromatography-Diode-Array Detection.

    Science.gov (United States)

    Uematsu, Yoko; Mizumachi, Toshiko; Monma, Kimio

    2017-07-01

    A method for simutaneously detecting 8 oil-soluble and 10 water-soluble (3 basic and 7 acidic) illegal dyes in foods was developed. The sample was mixed with water, followed by methanol and tetrahydrofuran. Transesterification with sodium methoxide was applied to the mixture, which allowed the triglycerides in the sample to be converted to fatty acid methyl esters. This treatment resulted in a biphasic mixture. Oil-soluble dyes and fatty acid methyl esters were deposited in the upper organic phase, which was cleaned using a silica-gel solid-phase extraction (SPE) column to remove the fatty acid methyl esters from the solution. The water-soluble dyes were deposited in the aqueous phase, and an Oasis hydrophilic-lipophilic-balanced SPE column was used to remove polar matrix components from the solution. The resulting dyes were subsequently analyzed via LC-diode-array detection using a single method. The practical LODs of the samples were defined as the lowest spiked dye concentrations at which the similarity coefficient for the spectra of the LC test solution and the corresponding reference standard solution were greater than 0.99, thus affording LODs of 0.5-1.0 µg/g. Recoveries of the dyes at a spiking level of 5.0 µg/g from soft drink, chili sauce, and mustard were generally greater than 70%. Recoveries from paprika powder were between 33 and 103%.

  11. Detection of Vibrio cholerae by isothermal cross-priming amplification combined with nucleic acid detection strip analysis.

    Science.gov (United States)

    Zhang, Xia; Du, Xin-Jun; Guan, Chun; Li, Ping; Zheng, Wen-Jie; Wang, Shuo

    2015-08-01

    Vibrio cholerae is a water- and food-borne human pathogen, and V. cholerae serotypes O1 and O139 have attracted attention because of their severe pathogenesis. However, non-O1, non-O139 cholera vibrios (NCVs) were also recently recognized as having virulence properties. In this study, we developed a cross-priming amplification (CPA) method for the detection of all serotypes of V. cholerae. The specificity of the CPA method was tested using a panel of 60 different bacterial strains. All of the V. cholerae strains showed positive results, and 41 other types of bacteria gave negative results. The limit of detection of the CPA method was 79.28 fg of genomic DNA, 4.2 × 10(2) CFU/ml for bacteria in pure culture, and 5.6 CFU per 25 g of sample with pre-enrichment. This method showed a higher sensitivity than the loop-mediated isothermal amplification (LAMP) method did and was more convenient to perform. These results indicate that the CPA method can be used for the rapid preliminary screening of V. cholerae. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. A novel, sensitive and label-free loop-mediated isothermal amplification detection method for nucleic acids using luminophore dyes.

    Science.gov (United States)

    Roy, Sharmili; Wei, Sim Xiao; Ying, Jean Liew Zhi; Safavieh, Mohammadali; Ahmed, Minhaz Uddin

    2016-12-15

    Electrochemiluminescence (ECL) has been widely rendered for nucleic acid testing. Here, we integrate loop-mediated isothermal amplification (LAMP) with ECL technique for DNA detection and quantification. The target LAMP DNA bound electrostatically with [Ru(bpy)3](+2) on the carbon electrode surface, and an ECL reaction was triggered by tripropylamine (TPrA) to yield luminescence. We illustrated this method as a new and highly sensitive strategy for the detection of sequence-specific DNA from different meat species at picogram levels. The proposed strategy renders the signal amplification capacities of TPrA and combines LAMP with inherently high sensitivity of the ECL technique, to facilitate the detection of low quantities of DNA. By leveraging this technique, target DNA of Sus scrofa (pork) meat was detected as low as 1pg/µL (3.43×10(-1)copies/µL). In addition, the proposed technique was applied for detection of Bacillus subtilis DNA samples and detection limit of 10pg/µL (2.2×10(3)copies/µL) was achieved. The advantages of being isothermal, sensitive and robust with ability for multiplex detection of bio-analytes makes this method a facile and appealing sensing modality in hand-held devices to be used at the point-of-care (POC).

  13. Topology, Geometry, and Stability: Protein Folding and Evolution

    CERN Document Server

    Simmons, Walter

    2015-01-01

    The protein folding problem must ultimately be solved on all length scales from the atomic up through a hierarchy of complicated structures. By analyzing the stability of the folding process using physics and mathematics, this paper shows that features without length scales, i.e. topological features, are potentially of central importance. Topology is a natural mathematical tool for the study of shape and we avail ourselves of that tool to examine the relationship between the amino acid sequence and the shapes of protein molecules. We apply what we learn to conjectures about their biological evolution.

  14. The parallel universe of RNA folding.

    Science.gov (United States)

    Batey, R T; Doudna, J A

    1998-05-01

    How do large RNA molecules find their active conformations among a universe of possible structures? Two recent studies reveal that RNA folding is a rapid and ordered process, with surprising similarities to protein folding mechanisms.

  15. Simple determination of L-ascorbic acid on TLC by visual detection using autocatalytic reaction.

    Science.gov (United States)

    Akasaka, Kazuaki

    2013-01-01

    The L-ascorbic acid concentration in beverages was measured after separation by silica gel thin layer chromatography (TLC) by visually determining the time in autocatalytic reaction for the L-ascorbic acid spot to turn the same yellow color of the background and disappear (the end time of the induction period) after spraying the slide with a 3,6-dihydroxyxanthane solution. There was a good linear relationship between the end time of the induction period and the concentration of L-ascorbic acid for concentrations in the range of 5.0 - 20 mM (r(2) = 0.9944). In addition, there was a good relationship expressed by a quadratic equation in the concentration range of 0.1 - 5.0 mM (r(2) = 0.9975). The relative standard deviations of the L-ascorbic acid values for 3 beverages (2.2 - 8.6 mM) were less than 5% (n = 5), and the recovery of 5.0 mM L-ascorbic acid from 4 beverages (0.7 - 7 mM) was 97 - 110%. A good correlation was also observed between the L-ascorbic acid values of 23 beverages (0 - 86 mM) determined by the proposed TLC method and the colorimetric method contained in a commercially available kit for L-ascorbic acid (r(2) = 0.9945).

  16. Amplified voltammetric detection of glycoproteins using 4-mercaptophenylboronic acid/biotin-modified multifunctional gold nanoparticles as labels

    Directory of Open Access Journals (Sweden)

    Liu L

    2014-05-01

    Full Text Available Lin Liu,1,2 Yun Xing,1 Hui Zhang,1 Ruili Liu,1 Huijing Liu,1 Ning Xia1,21College of Chemistry and Chemical Engineering, Anyang Normal University, Anyang, Henan, People’s Republic of China; 2College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan, People’s Republic of ChinaAbstract: Ultrasensitive detection of protein biomarkers is essential for early diagnosis and therapy of many diseases. Glycoproteins, differing from other types of proteins, contain carbohydrate moieties in the oligosaccharide chains. Boronic acid can form boronate ester covalent bonds with diol-containing species. Herein, we present a sensitive and cost-effective electrochemical method for glycoprotein detection using 4-mercaptophenylboronic acid (MBA/biotin-modified gold nanoparticles (AuNPs (MBA-biotin-AuNPs as labels. To demonstrate the feasibility and sensitivity of this method, recombinant human erythropoietin (rHuEPO was tested as a model analyte. Specifically, rHuEPO was captured by the anti-rHuEPO aptamer-covered electrode and then derivatized with MBA-biotin-AuNPs through the boronic acid–carbohydrate interaction. The MBA-biotin-AuNPs facilitated the attachment of streptavidin-conjugated alkaline phosphatase for the production of electroactive p-aminophenol from p-aminophenyl phosphate substrate. A detection limit of 8 fmol L-1 for rHuEPO detection was achieved. Other glycosylated and non-glycosylated proteins, such as horseradish peroxidase, prostate specific antigen, metallothionein, streptavidin, and thrombin showed no interference in the detection assay.Keywords: electrochemical biosensor, boronic acid, signal amplification, alkaline phosphatase

  17. Classification of protein fold classes by knot theory and prediction of folds by neural networks: A combined theoretical and experimental approach

    DEFF Research Database (Denmark)

    Ramnarayan, K.; Bohr, Henrik; Jalkanen, Karl J.

    2008-01-01

    We present different means of classifying protein structure. One is made rigorous by mathematical knot invariants that coincide reasonably well with ordinary graphical fold classification and another classification is by packing analysis. Furthermore when constructing our mathematical fold...... classifications, we utilize standard neural network methods for predicting protein fold classes from amino acid sequences. We also make an analysis of the redundancy of the structural classifications in relation to function and ligand binding. Finally we advocate the use of combining the measurement of the VA......, VCD, Raman, ROA, EA and ECD spectra with the primary sequence as a way to improve both the accuracy and reliability of fold class prediction schemes....

  18. Microalgae amino acid extraction and analysis at nanomolar level using electroporation and capillary electrophoresis with laser-induced fluorescence detection.

    Science.gov (United States)

    Nehmé, Reine; Atieh, Carla; Fayad, Syntia; Claude, Bérengère; Chartier, Agnès; Tannoury, Mona; Elleuch, Fatma; Abdelkafi, Slim; Pichon, Chantal; Morin, Philippe

    2017-01-01

    Amino acids play a key role in food analysis, clinical diagnostics, and biochemical research. Capillary electrophoresis with laser-induced fluorescence detection was used for the analysis of several amino acids. Amino acid labeling with fluorescein isothiocyanate was conducted using microwave-assisted derivatization at 80°C (680 W) during only 150 s. Good electrophoretic resolution was obtained using a background electrolyte composed of sodium tetraborate buffer (100 mM; pH 9.4) and β-cyclodextrin (10 mM), and the limits of quantification were 3-30 nM. The developed capillary electrophoresis with laser-induced fluorescence method was used to analyze amino acids in Dunaliella salina green algae grown under different conditions. A simple extraction technique based on electroporation of the cell membrane was introduced. A home-made apparatus allowed the application of direct and alternating voltages across the electrochemical compartment containing a suspension of microalgae in distilled water at 2.5 g/L. A direct voltage of 12 V applied for 4 min gave the optimum extraction yield. Results were comparable to those obtained with accelerated-solvent extraction. The efficiency of electroporation in destroying microalgae membranes was shown by examining the algae surface morphology using scanning electron microscopy. Stress conditions were found to induce the production of amino acids in Dunaliella salina cells. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Point-Counterpoint: A Nucleic Acid Amplification Test for Streptococcus pyogenes Should Replace Antigen Detection and Culture for Detection of Bacterial Pharyngitis.

    Science.gov (United States)

    Pritt, Bobbi S; Patel, Robin; Kirn, Thomas J; Thomson, Richard B

    2016-10-01

    Nucleic acid amplification tests (NAATs) have frequently been the standard diagnostic approach when specific infectious agents are sought in a clinic specimen. They can be applied for specific agents such as S. pyogenes, or commercial multiplex NAATs for detection of a variety of pathogens in gastrointestinal, bloodstream, and respiratory infections may be used. NAATs are both rapid and sensitive. For many years, S. pyogenes testing algorithms used a rapid and specific group A streptococcal antigen test to screen throat specimens, followed, in some clinical settings, by a throat culture for S. pyogenes to increase the sensitivity of its detection. Now S. pyogenes NAATs are being used with increasing frequency. Given their accuracy, rapidity, and ease of use, should they replace antigen detection and culture for the detection of bacterial pharyngitis? Bobbi Pritt and Robin Patel of the Mayo Clinic, where S. pyogenes NAATs have been used for well over a decade with great success, will explain the advantages of this approach, while Richard (Tom) Thomson and Tom Kirn of the NorthShore University HealthSystem will discuss their concerns about this approach to diagnosing bacterial pharyngitis. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  20. Understanding Protein Non-Folding

    Science.gov (United States)

    Uversky, Vladimir N.; Dunker, A. Keith

    2010-01-01

    This review describes the family of intrinsically disordered proteins, members of which fail to form rigid 3-D structures under physiological conditions, either along their entire lengths or only in localized regions. Instead, these intriguing proteins/regions exist as dynamic ensembles within which atom positions and backbone Ramachandran angles exhibit extreme temporal fluctuations without specific equilibrium values. Many of these intrinsically disordered proteins are known to carry out important biological functions which, in fact, depend on the absence of specific 3-D structure. The existence of such proteins does not fit the prevailing structure-function paradigm, which states that unique 3-D structure is a prerequisite to function. Thus, the protein structure-function paradigm has to be expanded to include intrinsically disordered proteins and alternative relationships among protein sequence, structure, and function. This shift in the paradigm represents a major breakthrough for biochemistry, biophysics and molecular biology, as it opens new levels of understanding with regard to the complex life of proteins. This review will try to answer the following questions: How were intrinsically disordered proteins discovered? Why don't these proteins fold? What is so special about intrinsic disorder? What are the functional advantages of disordered proteins/regions? What is the functional repertoire of these proteins? What are the relationships between intrinsically disordered proteins and human diseases? PMID:20117254

  1. The simple detection of neuraminic acid-containing urinary oligosaccharides in patients with glycoprotein storage diseases.

    Science.gov (United States)

    Sewell, A C

    1983-01-01

    Urine samples from patients with different types of glycoprotein storage disease were chromatographed by gel filtration and the fractions analysed for sialic acid. Patients with mucolipidoses I and II excreted the largest amounts of bound sialic acid. One patient with GM1 gangliosidosis showed an abnormal level of sialyloligosaccharide excretion. Other patients showed normal results. With the present method mucolipidoses I and II, together with GM1 gangliosidosis, are readily distinguished from other possible oligosaccharidurias.

  2. A selective voltammetric detection for dopamine using poly(gallic acid) film modified electrode

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The electrochemistry behavior of dopamine was investigated by cyclic voltammetry and differential pulse voltammetry at a poly (gallic acid) film modified glassy carbon electrode.Two electrons and two protons participated in the diffusion-controlled electrocatalytic oxidation of dopamine with a diffusion coefficient of 2.186×10~(-5) cm~2/s.The interference of ascorbic acid with the determination of dopamine could be efficiently eliminated.This work provided a simple approach to selectively and sensitively...

  3. Electrochemical detection of uric acid using ruthenium-dioxide-coated carbon nanotube directly grown onto Si wafer

    Science.gov (United States)

    Shih, Yi-Ting; Lee, Kuei-Yi; Lin, Chung-Kuang

    2015-12-01

    Carbon nanotubes (CNTs) directly grown onto a Si substrate by thermal chemical vapor deposition were used in uric acid (UA) detection. The process is simple and formation is easy without the need for additional chemical treatments. However, CNTs lack selectivity and sensitivity to UA. To enhance the electrochemical analysis, ruthenium oxide was used as a catalytic mediator in the modification of electrodes. The electrochemical results show that RuO2 nanostructures coated onto CNTs can strengthen the UA signal. The peak currents of RuO2 nanostructures coated onto CNTs linearly increase with increasing UA concentration, meaning that they can work as electrodes for UA detection. The lowest detection limit and highest sensitivity were 55 nM and 4.36 µA/µM, respectively. Moreover, the characteristics of RuO2 nanostructures coated onto CNTs were examined by scanning electron microscopy, transmission electron microscopy, and Raman spectroscopy.

  4. In situ detection of denitrifying bacteria by mRNA-targeted nucleic acid probes and catalyzed reporter deposition

    DEFF Research Database (Denmark)

    Kofoed, Michael Vedel; Stief, Peter; Poulsen, Morten

    In situ detection of denitrifying bacteria by mRNA-targeted nucleic acid probes and catalyzed reporter deposition   Michael V.W. Kofoed, Peter Stief, Morten Poulsen, and Andreas Schramm Department of Biological Sciences, Microbiology, University of Aarhus, Denmark Denitrification, the sequential...... reductase) and nosZ (encoding nitrous oxide reductase), to detect nitrate-reducing and completely denitrifying bacteria, respectively. Enzyme-labelled oligonucleotide probes and digoxygenin-labelled polynucleotide probes were evaluated for in situ hybridization in combination with immunochemical detection...... reduction of nitrate to dinitrogen gas, is essential for the removal of fixed nitrogen from natural and engineered ecosystems. However, community structure and activity dynamics of denitrifying bacteria in most systems are poorly understood, partially due to difficulties in identifying and quantifying...

  5. Simultaneous determination of 3-methoxy-4-hydroxyphenylglycol, 5-hydroxyindoleacetic acid, and homovanillic acid in cerebrospinal fluid with high-performance liquid chromatography using electrochemical detection.

    Science.gov (United States)

    Scheinin, M; Chang, W H; Kirk, K L; Linnoila, M

    1983-05-01

    An improved high-performance liquid chromatographic method with electrochemical detection (HPLC-EC) for the simultaneous determination of 3-methoxy-4-hydroxyphenylglycol (MHPG), 5-hydroxyindoleacetic acid (5-HIAA), and homovanillic acid (HVA) in cerebrospinal fluid (CSF) of humans and nonhuman primates is described. Quantitation is based on the use of an internal standard, 5-fluoro-HVA. Sample preparation consists of mixing an aliquot of CSF with a solution of the internal standard followed by ultrafiltration. The precision of the method is high, with within-run and between-run coefficients of variation of 2-6% and less than 10%, respectively, in the concentration ranges of the metabolites encountered in human lumbar CSF. Accuracy was tested by comparing the present HPLC method with specific gas chromatographic-mass spectrometric (GS-MS) assays for MHPG and HVA and a GC-MS-validated HPLC assay for 5-HIAA: the correlations obtained were 0.968 for MHPG, 0.989 for 5-HIAA, and 0.999 for HVA, with no systematic bias between the methods. The use of ascorbate as a preserving agent for monoamine metabolites in CSF was not found to be necessary when proper care was exercised in sample handling and storage. The analysis of samples with up to 2% ascorbic acid was possible as well, but MHPG had to be assayed separately using an extraction procedure and an alternative internal standard, 3-ethoxy-4-hydroxyphenylglycol.

  6. [Determination of nabumetone and 6-methoxy-2-naphthylacetic acid in plasma using HPLC with UV and MS detection].

    Science.gov (United States)

    Nespesná, Lenka; Stícha, Martin; Matousková, Olga; Perlík, Frantisek; Slanar, Ondrej

    2011-02-01

    The study aimed to establish and validate an analytical method for the determination of nabumetone and 6-methoxy-2-naphthylacetic acid (6-MNA) in human plasma after a single therapeutic dose of the drug. Two methods based on HPLC with UV and MS detection were compared. Optimal results in sample preparation were achieved using solid phase extraction. The recovery reached approximately 84% and 86-90% for nabumetone and 6-MNA, respectively. A reverse C18 column was used for HPLC separation of the analytes. The limit of UV detection was 50 nM and 0.1 microM for 6-MNA and nabumetone, respectively. The limit of MS detection was 1 microM and 0.5 microM for 6-MNA and nabumetone, respectively. Precision ranged between 4.2-14.4% and 4.6-8.5% using UV and MS detection for nabumetone, respectively. The respective values for 6-MNA were 2.4-12.5% and 2.1-9.4%. Accuracy ranged between 93.4-109.6% in UV detection and 86.2-107.9% using UV and MS detection for nabumetone, respectively. The respective values for 6-MNA were 87.8-107.4% and 86.3-106.4%. The method was subsequently applied to determine the pharmacokinetic parameters of nabumetone and 6-MNA in a group of 24 healthy volunteers.

  7. Direct detection of circulating free DNA extracted from serum samples of breast cancer using locked nucleic acid molecular beacon.

    Science.gov (United States)

    Gui, Zhen; Wang, Quanbo; Li, Jinchang; Zhu, Mingchen; Yu, Lili; Xun, Tang; Yan, Feng; Ju, Huangxian

    2016-07-01

    As an emerging noninvasive blood biomarker, circulating free DNA (cfDNA) can be utilized to assess diagnosis, progression and evaluate prognosis of cancer. However, cfDNAs are not "naked", they can be part of complexes, or are bound to the surface of the cells via proteins, which make the detection more challenging. Here, a simple method for the detection of Ubiquitin-like with PHD and ring finger domains 1 (UHRF1) DNA exacted from serum of breast cancer (BC) has been developed using a novel locked nucleic acid molecular beacon (LNA-MB). In order to enhance the stability and detection efficiency of the probe in biofluids, we design a shared-stem molecular beacon containing a 27-mer loop and a 4-mer stem with DNA/LNA alternating bases. The fluorescence is released in the presence of target. The detection procedure is simple and can be completed within 1h. This method shows a sensitive response to UHRF1 DNA with a dynamic range of 3 orders of magnitude. The limit of detection is 11nM (S/N=3) with excellent selectivity. It can discriminate UHRF1 DNA from three-base mismatched DNA with a high specificity. More importantly, this method can distinguish the expression of serum UHRF1 DNA among 5 breast cancer patients and 5 healthy controls. The mentioned superiority may suggest that this assay can be served as a promising noninvasive detection tool for early BC diagnosis and monitoring.

  8. Capillary electrophoresis with capacitively coupled contactless conductivity detection for the determination of cis/trans isomers of octadec-9-enoic acid and other long chain fatty acids.

    Science.gov (United States)

    Wong, Yong Foo; Saad, Bahruddin; Makahleh, Ahmad

    2013-05-17

    A capillary electrophoresis (CE)-capacitively coupled contactless conductivity detection (C(4)D) method for the simultaneous separation of eleven underivatized fatty acids (FAs), namely, lauric, myristic, tridecanoic (internal standard), pentadecanoic, palmitic, stearic, oleic, elaidic, linoleic, linolenic and arachidic acids is described. The separation was carried out in normal polarity mode at 20 °C, 30 kV and using hydrodynamic injection (50 mbar for 1 s). The separation was achieved in a bare fused-silica capillary (70 cm × 75 μm i.d.) using a background electrolyte of methyl-β-cyclodextrin (~6 mM) and heptakis-(2,3,6-tri-O-methyl)-β-cyclodextrin (~8 mM) dissolved in a mixture of Na2HPO4/KH2PO4 (5 mM, pH 7.4):ACN:MeOH:n-octanol (3:4:2.5:0.5, v/v/v/v). C(4)D parameters were set at fixed amplitude of 100 V and frequency of 1000 kHz. The developed method was validated. Calibration curves of the ten FAs were well correlated (r(2)>0.99) within the range of 5-250 μg mL(-1) for lauric acid, and 3-250 μg mL(-1) for the other FAs. The method was simple and sensitive with detection limits (S/N=3) of 0.9-1.9 μg mL(-1) and good relative standard deviations of intra- and inter-day for migration times and peak areas (≤9.7%) were achieved. The method was applied to the determination of FAs in margarine samples. The proposed method offers distinct advantages over the GC and HPLC methods, especially in terms of simplicity (without derivatization) and sensitivity.

  9. 3D fold growth in transpression

    Science.gov (United States)

    Frehner, Marcel

    2016-12-01

    Geological folds in transpression are inherently 3D structures; hence their growth and rotation behavior is studied using 3D numerical finite-element simulations. Upright single-layer buckle folds in Newtonian materials are considered, which grow from an initial point-like perturbation due to a combination of in-plane shortening and shearing (i.e., transpression). The resulting fold growth exhibits three components: (1) fold amplification (vertical), (2) fold elongation (parallel to fold axis), and (3) sequential fold growth (perpendicular to axial plane) of new anti- and synforms adjacent to the initial fold. Generally, the fold growth rates are smaller for shearing-dominated than for shortening-dominated transpression. In spite of the growth rate, the folding behavior is very similar for the different convergence angles. The two lateral directions always exhibit similar growth rates implying that the bulk fold structure occupies an increasing roughly circular area. Fold axes are always parallel to the major horizontal principal strain axis (λ→max, i.e., long axis of the horizontal finite strain ellipse), which is initially also parallel to the major horizontal instantaneous stretching axis (ISA→max). After initiation, the fold axes rotate together with λ→max. Sequential folds appearing later do not initiate parallel to ISA→max, but parallel to λ→max, i.e. parallel to the already existing folds, and also rotate with λ→max. Therefore, fold axes do not correspond to passive material lines and hinge migration takes place as a consequence. The fold axis orientation parallel to λ→max is independent of convergence angle and viscosity ratio. Therefore, a triangular relationship between convergence angle, amount of shortening, and fold axis orientation exists. If two of these values are known, the third can be determined. This relationship is applied to the Zagros fold-and-thrust-belt to estimate the degree of strain partitioning between the Simply

  10. Functional stimuli responsive hydrogel devices by self-folding

    Science.gov (United States)

    Yoon, ChangKyu; Xiao, Rui; Park, JaeHyun; Cha, Jaepyeong; Nguyen, Thao D.; Gracias, David H.

    2014-09-01

    We describe a photolithographic approach to create functional stimuli responsive, self-folding, microscale hydrogel devices using thin, gradient cross-linked hinges and thick, fully cross-linked panels. The hydrogels are composed of poly (N-isopropylacrylamide-co-acrylic acid) (pNIPAM-AAc) with reversible stimuli responsive properties just below physiological temperatures. We show that a variety of three-dimensional structures can be formed and reversibly actuated by temperature or pH. We experimentally characterized the swelling and mechanical properties of pNIPAM-AAc and developed a finite element model to rationalize self-folding and its variation with hinge thickness and swelling ratio. Finally, we highlight applications of this approach in the creation of functional devices such as self-folding polymeric micro-capsules, untethered micro-grippers and thermally steered micro-mirror systems.

  11. Anatomy and Histology of an Epicanthal Fold.

    Science.gov (United States)

    Park, Jae Woo; Hwang, Kun

    2016-06-01

    The aim of this study is to elucidate the precise anatomical and histological detail of the epicanthal fold.Thirty-two hemifaces of 16 Korean adult cadavers were used in this study (30 hemifaces with an epicanthal fold, 2 without an epicanthal fold). In 2 patients who had an epicanthoplasty, the epicanthal folds were sampled.In a dissection, the periorbital skin and subcutaneous tissues were removed and the epicanthal fold was observed in relation to each part of the orbicularis oculi muscle. Specimens including the epicanthal fold were embeddedin in paraffin, sectioned at 10 um, and stained with Hematoxylin-Eosin. The horizontal section in the level of the paplebral fissure was made and the prepared slides were observed under a light microscope.In the specimens without an epicanthal fold, no connection between the upper preseptal muscle and the lower preseptal muscle was found. In the specimens with an epicanthal fold, a connection of the upper preseptal muscle to the lower preseptal muscle was observed. It was present in all 15 hemifaces (100%). There was no connection between the pretarsal muscles. In a horizontal section, the epicanthal fold was composed of 3 compartments: an outer skin lining, a core structure, and an innerskin lining. The core structure was mainly composed of muscular fibers and fibrotic tissue and they were intermingled.Surgeons should be aware of the anatomical details of an epicanthal fold. In removing or reconstructing an epicanthal fold, the fibromuscular core band should also be removed or reconstructed.

  12. Exploiting the downhill folding regime via experiment

    Science.gov (United States)

    Muñoz, Victor; Sadqi, Mourad; Naganathan, Athi N.; de Sancho, David

    2008-01-01

    Traditionally, folding experiments have been directed at determining equilibrium and relaxation rate constants of proteins that fold with two-state-like kinetics. More recently, the combination of free energy surface approaches inspired by theory with the discovery of proteins that fold in the downhill regime has greatly widened the battlefield for experimentalists. Downhill folding proteins cross very small or no free energy barrier at all so that all relevant partially folded conformations become experimentally accessible. From these combined efforts we now have tools to estimate the height of thermodynamic and kinetic folding barriers. Procedures to measure with atomic resolution the structural heterogeneity of conformational ensembles at varying unfolding degrees are also available. Moreover, determining the dynamic modes driving folding and how they change as folding proceeds is finally at our fingertips. These developments allow us to address via experiment fundamental questions such as the origin of folding cooperativity, the relationship between structure and stability, or how to engineer folding barriers. Moreover, the level of detail attained in this new breed of experiments should provide powerful benchmarks for computer simulations of folding and force-field refinement. PMID:19436488

  13. k-fold coloring of planar graphs

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    A k-fold n-coloring of G is a mapping φ: V (G) → Zk(n) where Zk(n) is the collection of all ksubsets of {1,2,...,n} such that φ(u) ∩φ(v) = φ if uv ∈ E(G).If G has a k-fold n-coloring,i.e.,G is k-fold n-colorable.Let the smallest integer n such that G is k-fold n-colorable be the k-th chromatic number,denoted by χk(G).In this paper,we show that any outerplanar graph is k-fold 2k-colorable or k-fold χk(C*)-colorable,where C* is a shortest odd cycle of G.Moreover,we investigate that every planar graph with odd girth at least 10k-9(k 3) can be k-fold (2k + 1)-colorable.

  14. Electrochemical Co-Reduction Synthesis of AuPt Bimetallic Nanoparticles-Graphene Nanocomposites for Selective Detection of Dopamine in the Presence of Ascorbic Acid and Uric Acid

    Directory of Open Access Journals (Sweden)

    Zongya Zhao

    2015-07-01

    Full Text Available In this paper, AuPt bimetallic nanoparticles-graphene nanocomposites were obtained by electrochemical co-reduction of graphene oxide (GO, HAuCl4 and H2PtCl6. The as-prepared AuPt bimetallic nanoparticles-graphene nanocomposites were characterized by scanning electron microscopy (SEM, electrochemical impedance spectroscopy (EIS and other electrochemical methods. The morphology and composition of the nanocomposite could be easily controlled by adjusting the HAuCl4/H2PtCl6 concentration ratio. The electrochemical experiments showed that when the concentration ratio of HAuCl4/H2PtCl6 was 1:1, the obtained AuPt bimetallic nanoparticles-graphene nanocomposite (denoted as Au1Pt1NPs-GR possessed the highest electrocatalytic activity toward dopamine (DA. As such, Au1Pt1NPs-GR nanocomposites were used to detect DA in the presence of ascorbic acid (AA and uric acid (UA using the differential pulse voltammetry (DPV technique and on the modified electrode, there were three separate DPV oxidation peaks with the peak potential separations of 177 mV, 130 mV and 307 mV for DA and AA, DA and UA, AA and UA, respectively. The linear range of the constructed DA sensor was from 1.6 μM to 39.7 μM with a detection limit of 0.1 μM (S/N = 3. The obtained DA sensor with good stability, high reproducibility and excellent selectivity made it possible to detect DA in human urine samples.

  15. Electrochemical Co-Reduction Synthesis of AuPt Bimetallic Nanoparticles-Graphene Nanocomposites for Selective Detection of Dopamine in the Presence of Ascorbic Acid and Uric Acid.

    Science.gov (United States)

    Zhao, Zongya; Zhang, Mingming; Chen, Xiang; Li, Youjun; Wang, Jue

    2015-07-09

    In this paper, AuPt bimetallic nanoparticles-graphene nanocomposites were obtained by electrochemical co-reduction of graphene oxide (GO), HAuCl4 and H2PtCl6. The as-prepared AuPt bimetallic nanoparticles-graphene nanocomposites were characterized by scanning electron microscopy (SEM), electrochemical impedance spectroscopy (EIS) and other electrochemical methods. The morphology and composition of the nanocomposite could be easily controlled by adjusting the HAuCl4/H2PtCl6 concentration ratio. The electrochemical experiments showed that when the concentration ratio of HAuCl4/H2PtCl6 was 1:1, the obtained AuPt bimetallic nanoparticles-graphene nanocomposite (denoted as Au1Pt1NPs-GR) possessed the highest electrocatalytic activity toward dopamine (DA). As such, Au1Pt1NPs-GR nanocomposites were used to detect DA in the presence of ascorbic acid (AA) and uric acid (UA) using the differential pulse voltammetry (DPV) technique and on the modified electrode, there were three separate DPV oxidation peaks with the peak potential separations of 177 mV, 130 mV and 307 mV for DA and AA, DA and UA, AA and UA, respectively. The linear range of the constructed DA sensor was from 1.6 μM to 39.7 μM with a detection limit of 0.1 μM (S/N = 3). The obtained DA sensor with good stability, high reproducibility and excellent selectivity made it possible to detect DA in human urine samples.

  16. A spatio-temporal mining approach towards summarizing and analyzing protein folding trajectories

    Directory of Open Access Journals (Sweden)

    Ucar Duygu

    2007-04-01

    Full Text Available Abstract Understanding the protein folding mechanism remains a grand challenge in structural biology. In the past several years, computational theories in molecular dynamics have been employed to shed light on the folding process. Coupled with high computing power and large scale storage, researchers now can computationally simulate the protein folding process in atomistic details at femtosecond temporal resolution. Such simulation often produces a large number of folding trajectories, each consisting of a series of 3D conformations of the protein under study. As a result, effectively managing and analyzing such trajectories is becoming increasingly important. In this article, we present a spatio-temporal mining approach to analyze protein folding trajectories. It exploits the simplicity of contact maps, while also integrating 3D structural information in the analysis. It characterizes the dynamic folding process by first identifying spatio-temporal association patterns in contact maps, then studying how such patterns evolve along a folding trajectory. We demonstrate that such patterns can be leveraged to summarize folding trajectories, and to facilitate the detection and ordering of important folding events along a folding path. We also show that such patterns can be used to identify a consensus partial folding pathway across multiple folding trajectories. Furthermore, we argue that such patterns can capture both local and global structural topology in a 3D protein conformation, thereby facilitating effective structural comparison amongst conformations. We apply this approach to analyze the folding trajectories of two small synthetic proteins-BBA5 and GSGS (or Beta3S. We show that this approach is promising towards addressing the above issues, namely, folding trajectory summarization, folding events detection and ordering, and consensus partial folding pathway identification across trajectories.

  17. A reliable and inexpensive method of nucleic acid extraction for the PCR-based detection of diverse plant pathogens.

    Science.gov (United States)

    Li, R; Mock, R; Huang, Q; Abad, J; Hartung, J; Kinard, G

    2008-12-01

    A reliable extraction method is described for the preparation of total nucleic acids from at least ten plant genera for subsequent detection of plant pathogens by PCR-based techniques. The method combined a modified CTAB (cetyltrimethylammonium bromide) extraction protocol with a semi-automatic homogenizer (FastPrep) instrument) for rapid sample processing and low potential of cross contamination. The method was applied to sample preparation for PCR-based detection of 28 different RNA and DNA viruses, six viroids, two phytoplasmas and two bacterial pathogens from a range of infected host plants including sweet potato, small fruits and fruit trees. The procedure is cost-effective and the qualities of the nucleic acid preparations are comparable to those prepared by commonly used commercial kits. The efficiency of the procedure permits processing of numerous samples and the use of a single nucleic acid preparation for testing both RNA and DNA genomes by PCR, making this an appealing method for testing multiple pathogens in certification and quarantine programs.

  18. Electrodes Modification Based on Metal-Free Phthalocyanine: Example of Electrochemical Sensors for the Detection of Acetic Acid

    Directory of Open Access Journals (Sweden)

    Amadou L. Ndiaye

    2015-01-01

    Full Text Available Electroanalytical properties of tetra-tert-butyl phthalocyanine (PcH2-tBu modified electrodes are studied by cyclic voltammetry (CV. The modified electrodes are obtained by CV deposition techniques on gold (Au and glassy carbon (C screen-printed electrodes (SPEs and used for the electrochemical detection of acetic acid (AA. Based on the CV experiments, the electrodeposition mechanism is detailed. The modified PcH2-tBu electrodes reveal one oxidation and one reduction peak within the potential window of the working electrodes. In the presence of the analyte (acetic acid, the modified electrodes show sensitivity in the range of 10 mM to 400 mM. For the PcH2-tBu modified Au electrode, a limit of detection (LOD of 5.89 mM (based on the +0.06 V peak was obtained while for the PcH2-tBu modified C electrode a LOD of 17.76 mM (based on the +0.07 V peak was achieved. A signal decay of 17%, based on 20 experiments, is obtained when gold is used as working electrode. If carbon is used as working electrode a value of 7% is attained. A signal decay is observed after more than 50 cycles of experiments and is more pronounced when higher concentrations of acetic acid are used. A mechanism of sensing is proposed at the end.

  19. UV-Visible Spectroscopy Detection of Iron(III) Ion on Modified Gold Nanoparticles With a Hydroxamic Acid

    Science.gov (United States)

    Karami, C.; Alizadeh, A.; Taher, M. A.; Hamidi, Z.; Bahrami, B.

    2016-09-01

    The present work describes the preparation of gold nanoparticles (AuNPs) functionalized with hydroxamic acid and the use of them in UV-visible spectroscopy detection of iron(III) ions. The prepared AuNPs were thoroughly characterized by using UV-visible spectroscopy, TEM, and 1H NMR techniques. The newly synthesized hydroxamic acid-AuNPs are brown in color due to the intense surface plasmon absorption band centered at 527 nm. In the presence of Fe(III), the surface plasmon absorption band is centered at 540 nm. However, the sensitivity of hydroxamic acid-AuNPs towards other metal ions such as Mg(II), Ca(II), Ag(I), Cu(II), Mn(II), Cr(II), Ni(II), Co(II),Fe(II), Hg(II), and Pb(II) can be negligible. This highly selective sensor allows a direct quantitative assay of Fe(III) with a UVvisible spectroscopy detection limited to 45.8 nM.

  20. Detection of Elevated Signaling Amino Acids in Human Diabetic Vitreous by Rapid Capillary Electrophoresis

    Directory of Open Access Journals (Sweden)

    Miao-Jen Lu

    2007-01-01

    Full Text Available Elevated glutamate is implicated in the pathology of PDR. The ability to rapidly assess the glutamate and amino acid content of vitreous provides a more complete picture of the chemical changes occurring at the diabetic retina and may lead to a better understanding of the pathology of PDR. Vitreous humor was collected following vitrectomies of patients with PDR and control conditions of macular hole or epiretinal membrane. A capillary electrophoresis method was developed to quantify glutamate and arginine. The analysis is relatively fast (<6 minutes and utilizes a poly(ethyleneoxide and sodium dodecylsulfate run buffer. Both amino acid levels show significant increases in PDR patients versus controls and are comparable to other reports. The levels of vitreal glutamate vary inversely with the degree of observed hemorrhage. The results demonstrate a rapid method for assessment of a number of amino acids to characterize the chemical changes at the diabetic retina to better understand tissue changes and potentially identify new treatments.

  1. Nucleic acid-based methods for the early detection of sepsis in heart transplant recipients

    Directory of Open Access Journals (Sweden)

    Sarvesh Pal Singh

    2016-01-01

    Full Text Available Nucleic acid-based tests (NABTs were developed to decrease the time required to identify microorganism in the pathological specimens. The commercially available NABTs are of two types – one those can be applied to positive cultures grown in blood culture bottles and other those can be applied directly to blood samples. The latter tests are polymerase chain reaction (PCR-based assays which can amplify the existing load of microorganism nucleic acids many a times like a culture in a blood culture bottle. Both tests then identify the pathogenic organisms with the use of specific nucleic acid probes. These tests have proven useful in management of heart transplant sepsis management.

  2. Fast mapping of global protein folding states by multivariate NMR: a GPS for proteins

    DEFF Research Database (Denmark)

    Malmendal, Anders; Underhaug, Jarl; Otzen, Daniel E

    2010-01-01

    , protein-folding state maps. The method is fast, sensitive, and robust, and it works without isotope-labelling. The unique capabilities of GPS NMR to identify different folding states and to compare different unfolding processes are demonstrated by mapping of the equilibrium folding space of bovine alpha......-lactalbumin in the presence of the anionic surfactant sodium dodecyl sulfate, SDS, and compare these with other surfactants, acid, denaturants and heat....

  3. Detection of cancer cells using a peptide nanotube–folic acid modified graphene electrode

    DEFF Research Database (Denmark)

    Castillo, John J.; Svendsen, Winnie Edith; Rozlosnik, Noemi

    2013-01-01

    by fluorescence microscopy and atomic force microscopy. The peptide nanotube–folic acid modified graphene electrode was characterized by scanning electron microscopy and cyclic voltammetry. The modification of the graphene electrode with peptide nanotube–folic acid led to an increase in the current signal....... The human cervical cancer cells were bound to the modified electrode through the folic acid–folate receptor interaction. Cyclic voltammograms in the presence of [Fe(CN)6]3/4 as a redox species demonstrated that the binding of the folate receptor from human cervical cancer cells to the peptide nanotube...

  4. Sensitive detection of nucleic acids by PNA hybridization directed co-localization of fluorescent beads

    DEFF Research Database (Denmark)

    Shiraishi, Takehiko; Deborggraeve, Stijn; Büscher, Philippe;

    2011-01-01

    We have designed a pair of biotinylated peptide nucleic acid (PNA) probes targeting two sequences in 18S rRNA (from the parasite Trypanosoma brucei) at a distance of 191 nt (corresponding to maximum distance of ca. 60 nm) from each other. The PNA probes were individually bound to (strept)avidin-c......We have designed a pair of biotinylated peptide nucleic acid (PNA) probes targeting two sequences in 18S rRNA (from the parasite Trypanosoma brucei) at a distance of 191 nt (corresponding to maximum distance of ca. 60 nm) from each other. The PNA probes were individually bound to (strept...

  5. Protein Collapse is Encoded in the Folded State Architecture

    CERN Document Server

    Samanta, Himadri S; Hinczewski, Michael; Hori, Naoto; Chakrabarti, Shaon; Thirumalai, D

    2016-01-01

    Natural protein sequences that self-assemble to form globular structures are compact with high packing densities in the folded states. It is known that proteins unfold upon addition of denaturants, adopting random coil structures. The dependence of the radii of gyration on protein size in the folded and unfolded states obeys the same scaling laws as synthetic polymers. Thus, one might surmise that the mechanism of collapse in proteins and polymers ought to be similar. However, because the number of amino acids in single domain proteins is not significantly greater than about two hundred, it has not been resolved if the unfolded states of proteins are compact under conditions that favor the folded states - a problem at the heart of how proteins fold. By adopting a theory used to derive polymer-scaling laws, we find that the propensity for the unfolded state of a protein to be compact is universal and is encoded in the contact map of the folded state. Remarkably, analysis of over 2000 proteins shows that protei...

  6. Efficient procedure for isolating methylated catechins from green tea and effective simultaneous analysis of ten catechins, three purine alkaloids, and gallic acid in tea by high-performance liquid chromatography with diode array detection.

    Science.gov (United States)

    Hu, Bing; Wang, Lin; Zhou, Bei; Zhang, Xin; Sun, Yi; Ye, Hong; Zhao, Liyan; Hu, Qiuhui; Wang, Guoxiang; Zeng, Xiaoxiong

    2009-04-10

    Monomers of (-)-epigallocatechin (EGC), (-)-epigallocatechin gallate (EGCG), (-)-epicatechin (EC), (-)-epicatechin gallate (ECG), (-)-epigallocatechin 3-O-(3-O-methyl) gallate (EGCG3''Me) and (-)-3-O-methyl epicatechin gallate (ECG3'Me) (purity, >97%) were successfully prepared from extract of green tea by two-time separation with Toyopearl HW-40S column chromatography eluted by 80% ethanol. In addition, monomers of (-)-catechin (C), (-)-gallocatechin (GC), (-)-gallocatechin gallate (GCG), and (-)-catechin gallate (CG) (purity, >98%) were prepared from EC, EGC, EGCG, and ECG by heat-epimerization and semi-preparative HPLC chromatography. With the prepared catechin standards, an effective and simultaneous HPLC method for the analysis of gallic acid, tea catechins, and purine alkaloids in tea was developed in the present study. Using an ODS-100Z C(18) reversed-phase column, fourteen compounds were rapidly separated within 15min by a linear gradient elution of formic acid solution (pH 2.5) and methanol. A 2.5-7-fold reduction in HPLC analysis time was obtained from existing analytical methods (40-105min) for gallic acid, tea catechins including O-methylated catechins and epimers of epicatechins, as well as purine alkaloids. Detection limits were generally on the order of 0.1-1.0ng for most components at the applied wavelength of 280nm. Method replication generally resulted in intraday and interday peak area variation of catechins.

  7. Comparison of culture and acid-fast bacilli stain to PCR for detection of Mycobacterium tuberculosis in clinical samples.

    Science.gov (United States)

    Aslanzadeh, J; de la Viuda, M; Fille, M; Smith, W B; Namdari, H

    1998-08-01

    The major drawback in effective use of polymerase chain reaction (PCR) for detecting Mycobacterium tuberculosis (MTB) in clinical samples is the presence of PCR inhibitors and unique cell components of the organism that complicate DNA extraction and subsequent PCR amplification. A PCR assay with a unique multistep DNA extraction method that minimizes these problems was compared in a prospective study to acid-fast bacilli stain (AFBS) and culture for detecting MTB in clinical samples. A total of 254 clinical specimens in two separate studies were processed for MTB by these techniques. While PCR and culture were 100% sensitive and specific, culture required up to 8 weeks of incubation and additional time to perform biochemical testing to identify the isolated micro-organism. Acid-fast bacilli stain had a specificity of about 87% and did not differentiate among Mycobacterial species. In contrast, the results from PCR were available within 48 h and did not require additional testing to attain a final result. Polymerase chain reaction was highly reliable for detection and confirmation and interpretation of positive AFBS results. The assay was easy to perform with a turn around time of about 2 days.

  8. A Nicotinamide Adenine Dinucleotide Dispersed Multi-walled Carbon Nanotubes Electrode for Direct and Selective Electrochemical Detection of Uric Acid.

    Science.gov (United States)

    Chen, Yan; Li, Yiwei; Ma, Yaohong; Meng, Qingjun; Yan, Yan; Shi, Jianguo

    2015-01-01

    A nanocomposite platform built with multi-walled carbon nanotubes (MWCNTs) and nicotinamide adenine dinucleotide (NAD(+)) via a noncovalent interaction between the large π systems in NAD(+) molecules and MWCNTs on a glassy carbon substrate was successfully developed for the sensitive and selective detection of uric acid (UA) in the presence of ascorbic acid (AA), dopamine (DA). NAD(+) has an adenine subunit and a nicotinamide subunit, which enabled interaction with the purine subunit of UA through a strong π-π interaction to enhance the specificity of UA. Compared with a bare glassy carbon electrode (GCE) and MWCNTs/GCE, the MWCNTs-NAD(+)/GCE showed a low background current and a remarkable enhancement of the oxidation peak current of UA. Using differential pulse voltammetry (DPV), a high sensitivity for the determination of UA was explored for the MWCNTs-NAD(+) modified electrode. A linear relationship between the DPV peak current of UA and its concentration could be obtained in the range of 0.05 - 10 μM with the detection limit as low as 10 nM (S/N = 3). This present strategy provides a novel and promising platform for the detection of UA in human urine and serum samples.

  9. Detection of Staphylococcus epidermidis by a Quartz Crystal Microbalance Nucleic Acid Biosensor Array Using Au Nanoparticle Signal Amplification

    Directory of Open Access Journals (Sweden)

    Weiling Fu

    2008-10-01

    Full Text Available Staphylococcus epidermidis is a critical pathogen of nosocomial blood infections, resulting in significant morbidity and mortality. A piezoelectric quartz crystal microbalance (QCM nucleic acid biosensor array using Au nanoparticle signal amplification was developed to rapidly detect S. epidermidis in clinical samples. The synthesized thiolated probes specific targeting S. epidermidis 16S rRNA gene were immobilized on the surface of QCM nucleic acid biosensor arrays. Hybridization was induced by exposing the immobilized probes to the PCR amplified fragments of S. epidermidis, resulting in a mass change and a consequent frequency shift of the QCM biosensor. To further enhance frequency shift results from above described hybridizations, streptavidin coated Au nanoparticles were conjugated to the PCR amplified fragments. The results showed that the lowest detection limit of current QCM system was 1.3×103 CFU/mL. A linear correlation was found when the concentration of S. epidermidis varied from 1.3×103 to 1.3×107 CFU/mL. In addition, 55 clinical samples were detected with both current QCM biosensor system and conventional clinical microbiological method, and the sensitivity and specificity of current QCM biosensor system were 97.14% and 100%, respectively. In conclusion, the current QCM system is a rapid, low-cost and sensitive method that can be used to identify infection of S. epidermidis in clinical samples.

  10. Simultaneous determination of amino acids in tea leaves by micellar electrokinetic chromatography with laser-induced fluorescence detection.

    Science.gov (United States)

    Yan, Jin; Cai, Yuanli; Wang, Yufei; Lin, Xia; Li, Hui

    2014-01-15

    A rapid and effective method of micellar electrokinetic chromatography with laser-induced fluorescence detection was developed for the simultaneous determination of amino acids in tea leaves. Pre-column derivatization of the analytes used 4-chloro-7-nitrobenzofurazan (NDB-Cl). Optimal separation was achieved at +20kV using an uncoated fused silica capillary (40.0cm effective length, 50.2cm total length, 75μm internal diameter), as well as 20mM sodium borate (pH 8.5), 20mM Brij 35, and acetonitrile 10% (v/v) as running buffers. Within 11min, 15 amino acids were separated completely. The optimized method demonstrated good linearity (r(2)⩾0.9990), precision (⩽6.65%), accuracy (85.50-112.74%), and sensitivity (0.1ng/mL-100ng/mL). The method successfully determined the quantity of amino acids in five different tea leaves; furthermore, theanine was identified as the most abundant amino acid in teas. The proposed method showed great potential in further investigations on the biofunctions of different tea samples.

  11. Detection of Glutamic Acid in Oilseed Rape Leaves Using Near Infrared Spectroscopy and the Least Squares-Support Vector Machine

    Science.gov (United States)

    Bao, Yidan; Kong, Wenwen; Liu, Fei; Qiu, Zhengjun; He, Yong

    2012-01-01

    Amino acids are quite important indices to indicate the growth status of oilseed rape under herbicide stress. Near infrared (NIR) spectroscopy combined with chemometrics was applied for fast determination of glutamic acid in oilseed rape leaves. The optimal spectral preprocessing method was obtained after comparing Savitzky-Golay smoothing, standard normal variate, multiplicative scatter correction, first and second derivatives, detrending and direct orthogonal signal correction. Linear and nonlinear calibration methods were developed, including partial least squares (PLS) and least squares-support vector machine (LS-SVM). The most effective wavelengths (EWs) were determined by the successive projections algorithm (SPA), and these wavelengths were used as the inputs of PLS and LS-SVM model. The best prediction results were achieved by SPA-LS-SVM (Raw) model with correlation coefficient r = 0.9943 and root mean squares error of prediction (RMSEP) = 0.0569 for prediction set. These results indicated that NIR spectroscopy combined with SPA-LS-SVM was feasible for the fast and effective detection of glutamic acid in oilseed rape leaves. The selected EWs could be used to develop spectral sensors, and the important and basic amino acid data were helpful to study the function mechanism of herbicide. PMID:23203052

  12. Two-stage sample-to-answer system based on nucleic acid amplification approach for detection of malaria parasites.

    Science.gov (United States)

    Liu, Qing; Nam, Jeonghun; Kim, Sangho; Lim, Chwee Teck; Park, Mi Kyoung; Shin, Yong

    2016-08-15

    Rapid, early, and accurate diagnosis of malaria is essential for effective disease management and surveillance, and can reduce morbidity and mortality associated with the disease. Although significant advances have been achieved for the diagnosis of malaria, these technologies are still far from ideal, being time consuming, complex and poorly sensitive as well as requiring separate assays for sample processing and detection. Therefore, the development of a fast and sensitive method that can integrate sample processing with detection of malarial infection is desirable. Here, we report a two-stage sample-to-answer system based on nucleic acid amplification approach for detection of malaria parasites. It combines the Dimethyl adipimidate (DMA)/Thin film Sample processing (DTS) technique as a first stage and the Mach-Zehnder Interferometer-Isothermal solid-phase DNA Amplification (MZI-IDA) sensing technique as a second stage. The system can extract DNA from malarial parasites using DTS technique in a closed system, not only reducing sample loss and contamination, but also facilitating the multiplexed malarial DNA detection using the fast and accurate MZI-IDA technique. Here, we demonstrated that this system can deliver results within 60min (including sample processing, amplification and detection) with high sensitivity (malaria in low-resource settings.

  13. Sensitive Detection of Capsaicinoids Using a Surface Plasmon Resonance Sensor with Anti-Homovanillic Acid Polyclonal Antibodies

    Directory of Open Access Journals (Sweden)

    Kiyoshi Toko

    2013-11-01

    Full Text Available Recently, highly functional biosensors have been developed in preparation for possible large-scale terrorist attacks using chemical warfare agents. Practically applicable sensors are required to have various abilities, such as high portability and operability, the capability of performing rapid and continuous measurement, as well as high sensitivity and selectivity. We developed the detection method of capsaicinoids, the main component of some lachrymators, using a surface plasmon resonance (SPR immunosensor as an on-site detection sensor. Homovanillic acid, which has a vanillyl group similar to capsaicinoids such as capsaicin and dihydrocapsaicin, was bound to Concholepas concholepas hemocyanin (CCH for use as an immunogen to generate polyclonal antibodies. An indirect competitive assay was carried out to detect capsaicinoids using SPR sensor chips on which different capsaicin analogues were immobilized. For the sensor chip on which 4-hydroxy-3-methoxybenzylamine hydrochloride was immobilized, a detection limit of 150 ppb was achieved. We found that the incubation time was not required and the detection can be completed in five minutes.

  14. Folic acid functionalized silver nanoparticles with sensitivity and selectivity colorimetric and fluorescent detection for Hg2+ and efficient catalysis

    Science.gov (United States)

    Su, Dongyue; Yang, Xin; Xia, Qingdong; Zhang, Qi; Chai, Fang; Wang, Chungang; Qu, Fengyu

    2014-09-01

    In this research, folic acid functionalized silver nanoparticles (FA-AgNPs) were selected as a colorimetric and a ‘turn on’ fluorescent sensor for detecting Hg2+. After being added into Hg2+, AgNPs can emit stable fluorescence at 440 nm when the excitation wavelength is selected at 275 nm. The absorbance and fluorescence of the FA-AgNPs could reflect the concentration of the Hg2+ ions. Thus, we developed a simple, sensitive analytical method to detect Hg2+ based on the colorimetric and fluorescence enhancement of FA-AgNPs. The sensor exhibits two linear response ranges between absorbance and fluorescence intensity with Hg2+ concentration, respectively. Meanwhile, a detection limit of 1 nM is estimated based on the linear relationship between responses with a concentration of Hg2+. The high specificity of Hg2+ with FA-AgNPs interactions provided the excellent selectivity towards detecting Hg2+ over other metal ions (Pb2+, Mg2+, Zn2+, Ni2+, Cu2+, Co2+, Ca2+, Mn2+, Fe2+, Cd2+, Ba2+, Cr6+ and Cr3+). This will provide a simple, effective and multifunctional colorimetric and fluorescent sensor for on-site and real-time Hg2+ ion detection. The proposed method can be applied to the analysis of trace Hg2+ in lake water. Additionally, the FA-AgNPs can be used as efficient catalyst for the reduction of 4-nitrophenol and potassium hexacyanoferrate (III).

  15. Rapid Detection of miRNA Using Nucleic Acids-templated AgNCs

    DEFF Research Database (Denmark)

    Shah, Pratik

    such as cancer, diabetes, cardiovascular disease and Alzheimer’s disease. MiRNAs, thus, can be useful markers for disease diagnosis, prognosis, and treatment. Because of its attractive optical properties such as brightness, tuneable emission wavelengths and photo-stability, DNA stabilized silver nano......-clusters (AgNCs) has increasingly been used to create nanoscale bio-sensing systems for selective and specific detection of bio-molecules. During the course of my Ph.D., I have focused on developing a novel diagnostic tool for miRNA detection using the fluorescent properties of DNA encapsulated AgNCs (DNA/Ag......NCs). I have showed that rapid, simple, sensitive and specific miRNA detection is possible. Two aspects of my research are 1) the implication of DNA secondary structure on the photoluminescence properties of DNA/AgNCs, 2) the development of a novel tool for miRNA detection in complex biological samples...

  16. Kinetic partitioning mechanism of HDV ribozyme folding

    Science.gov (United States)

    Chen, Jiawen; Gong, Sha; Wang, Yujie; Zhang, Wenbing

    2014-01-01

    RNA folding kinetics is directly tied to RNA biological functions. We introduce here a new approach for predicting the folding kinetics of RNA secondary structure with pseudoknots. This approach is based on our previous established helix-based method for predicting the folding kinetics of RNA secondary structure. In this approach, the transition rates for an elementary step: (1) formation, (2) disruption of a helix stem, and (3) helix formation with concomitant partial melting of an incompatible helix, are calculated with the free energy landscape. The folding kinetics of the Hepatitis delta virus (HDV) ribozyme and the mutated sequences are studied with this method. The folding pathways are identified by recursive searching the states with high net flux-in(out) population starting from the native state. The theory results are in good agreement with that of the experiments. The results indicate that the bi-phasic folding kinetics for the wt HDV sequence is ascribed to the kinetic partitioning mechanism: Part of the population will quickly fold to the native state along the fast pathway, while another part of the population will fold along the slow pathway, in which the population is trapped in a non-native state. Single mutation not only changes the folding rate but also the folding pathway.

  17. Viscoelastic properties of the false vocal fold

    Science.gov (United States)

    Chan, Roger W.

    2004-05-01

    The biomechanical properties of vocal fold tissues have been the focus of many previous studies, as vocal fold viscoelasticity critically dictates the acoustics and biomechanics of phonation. However, not much is known about the viscoelastic response of the ventricular fold or false vocal fold. It has been shown both clinically and in computer simulations that the false vocal fold may contribute significantly to the aerodynamics and sound generation processes of human voice production, with or without flow-induced oscillation of the false fold. To better understand the potential role of the false fold in phonation, this paper reports some preliminary measurements on the linear and nonlinear viscoelastic behavior of false vocal fold tissues. Linear viscoelastic shear properties of human false fold tissue samples were measured by a high-frequency controlled-strain rheometer as a function of frequency, and passive uniaxial tensile stress-strain response of the tissue samples was measured by a muscle lever system as a function of strain and loading rate. Elastic moduli (Young's modulus and shear modulus) of the false fold tissues were calculated from the measured data. [Work supported by NIH.

  18. Kinetic partitioning mechanism of HDV ribozyme folding

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Jiawen; Gong, Sha; Wang, Yujie; Zhang, Wenbing, E-mail: wbzhang@whu.edu.cn [Department of Physics, Wuhan University, Wuhan, Hubei 430072 (China)

    2014-01-14

    RNA folding kinetics is directly tied to RNA biological functions. We introduce here a new approach for predicting the folding kinetics of RNA secondary structure with pseudoknots. This approach is based on our previous established helix-based method for predicting the folding kinetics of RNA secondary structure. In this approach, the transition rates for an elementary step: (1) formation, (2) disruption of a helix stem, and (3) helix formation with concomitant partial melting of an incompatible helix, are calculated with the free energy landscape. The folding kinetics of the Hepatitis delta virus (HDV) ribozyme and the mutated sequences are studied with this method. The folding pathways are identified by recursive searching the states with high net flux-in(out) population starting from the native state. The theory results are in good agreement with that of the experiments. The results indicate that the bi-phasic folding kinetics for the wt HDV sequence is ascribed to the kinetic partitioning mechanism: Part of the population will quickly fold to the native state along the fast pathway, while another part of the population will fold along the slow pathway, in which the population is trapped in a non-native state. Single mutation not only changes the folding rate but also the folding pathway.

  19. Some aspects of vocal fold bowing.

    Science.gov (United States)

    Tanaka, S; Hirano, M; Chijiwa, K

    1994-05-01

    Bowing of the vocal fold frequently occurs in patients with vocal fold paralysis (VFP), those with sulcus vocalis, and those who have had laser surgery. Additionally, there are vocal folds that present bowing with no noticeable organic lesion. For the purpose of investigating the causes and mechanisms of vocal fold bowing, consecutive fiberscopic videorecordings of 127 patients with VFP, 33 with sulcus vocalis, 33 with laser surgery, and 33 with dysphonia having no clinically noticeable organic lesion were reviewed. Sixty-nine percent of the paralyzed vocal folds had bowing, and the occurrence of bowing was significantly related to the activity of the thyroarytenoid muscle as measured by electromyography. The cricothyroid activity had no significant relationship to vocal fold bowing. All vocal folds with sulcus presented with bowing. Thirty-five percent of the vocal folds that had had laser surgery had bowing. The extent of tissue removal was closely related to the occurrence of bowing. Twelve cases with no organic lesion had vocal fold bowing. Of these 12 patients, 8 were male and 9 were older than 60 years. Some aging process in the mucosa was presumed to be the cause of the bowing in this age group of patients without clinically noticeable organic lesions. Causes of vocal fold bowing in the younger group of patients without organic lesions were not determined in this study.

  20. 2-Acetylaminofluorene-modified probes for the indirect hybridocytochemical detection of specific nucleic acid sequences.

    NARCIS (Netherlands)

    J.E. Landegent; N. Jansen in de Wal; R.A. Baan; J.H.J. Hoeijmakers (Jan); M. van der Ploeg

    1984-01-01

    textabstractA new approach is presented for the indirect hybridocytochemical localization of specific nucleic acid sequences in microscopic preparations. The method is based on the application of probes modified with N-acetoxy-2-acetylaminofluorene. After hybridization, the 2-acetylaminofluorene-lab