Sample records for biomolecular screening applications

  1. Scanning probe and micropatterning approaches for biomolecular screening applications

    CERN Document Server

    Wilde, L M


    Force mapping using atomic force microscopy (AFM) allows for the simultaneous acquisition of topography and probe-sample interaction data. For example, AFM probes functionalised with an antigen can be employed to map the spatial distribution of recognition events on a substrate functionalised with the complementary specific antibody. However, this technique is currently limited to the detection of a single receptor-ligand species. Were the detection of multiple receptor-ligand interactions possible, AFM force mapping would offer greater scope as a sensitive tool for bioassay and screening applications. This thesis outlines developments in probe and substrate immobilisation methods to facilitate this process. We have developed an immobilisation strategy, which allows two antigen species, human serum albumin (HSA) and the beta subunit of human chorionic gonadotropin (beta hCG) to be simultaneously present on an AFM probe. Single point force spectroscopy results have revealed the ability of such probes to discri...

  2. Label-free screening of bio-molecular interactions. (United States)

    Cooper, Matthew A


    The majority of techniques currently employed to interrogate a biomolecular interaction require some type of radio- or enzymatic- or fluorescent-labelling to report the binding event. However, there is an increasing awareness of novel techniques that do not require labelling of the ligand or the receptor, and that allow virtually any complex to be screened with minimal assay development. This review focuses on three major label-free screening platforms: surface plasmon resonance biosensors, acoustic biosensors, and calorimetric biosensors. Scientists in both academia and industry are using biosensors in areas that encompass almost all areas drug discovery, diagnostics, and the life sciences. The capabilities and advantages of each technique are compared and key applications involving small molecules, proteins, oligonucleotides, bacteriophage, viruses, bacteria, and cells are reviewed. The role of the interface between the biosensor surface (in the case of SPR and acoustic biosensors) and the chemical or biological systems to be studied is also covered with attention to the covalent and non-covalent coupling chemistries commonly employed.

  3. Application of Nanodiamonds in Biomolecular Mass Spectrometry

    Directory of Open Access Journals (Sweden)

    Ping Cheng


    Full Text Available The combination of nanodiamond (ND with biomolecular mass spectrometry (MS makes rapid, sensitive detection of biopolymers from complex biosamples feasible. Due to its chemical inertness, optical transparency and biocompatibility, the advantage of NDs in MS study is unique. Furthermore, functionalization on the surfaces of NDs expands their application in the fields of proteomics and genomics for specific requirements greatly. This review presents methods of MS analysis based on solid phase extraction and elution on NDs and different application examples including peptide, protein, DNA, glycan and others. Owing to the quick development of nanotechnology, surface chemistry, new MS methods and the intense interest in proteomics and genomics, a huge increase of their applications in biomolecular MS analysis in the near future can be predicted.

  4. Application of Nanodiamonds in Biomolecular Mass Spectrometry


    Ping Cheng; Xianglei Kong


    The combination of nanodiamond (ND) with biomolecular mass spectrometry (MS) makes rapid, sensitive detection of biopolymers from complex biosamples feasible. Due to its chemical inertness, optical transparency and biocompatibility, the advantage of NDs in MS study is unique. Furthermore, functionalization on the surfaces of NDs expands their application in the fields of proteomics and genomics for specific requirements greatly. This review presents methods of MS analysis based on solid phase...

  5. Nanoarchitectonics of biomolecular assemblies for functional applications (United States)

    Avinash, M. B.; Govindaraju, T.


    The stringent processes of natural selection and evolution have enabled extraordinary structure-function properties of biomolecules. Specifically, the archetypal designs of biomolecules, such as amino acids, nucleobases, carbohydrates and lipids amongst others, encode unparalleled information, selectivity and specificity. The integration of biomolecules either with functional molecules or with an embodied functionality ensures an eclectic approach for novel and advanced nanotechnological applications ranging from electronics to biomedicine, besides bright prospects in systems chemistry and synthetic biology. Given this intriguing scenario, our feature article intends to shed light on the emerging field of functional biomolecular engineering.

  6. DockScreen: A Database of In Silico Biomolecular Interactions to Support Computational Toxicology

    Directory of Open Access Journals (Sweden)

    Michael-Rock Goldsmith


    Full Text Available We have developed DockScreen, a database of in silico biomolecular interactions designed to enable rational molecular toxicological insight within a computational toxicology framework. This database is composed of chemical/target (receptor and enzyme binding scores calculated by molecular docking of more than 1000 chemicals into 150 protein targets and contains nearly 135 thousand unique ligand/target binding scores. Obtaining this dataset was achieved using eHiTS (Simbiosys Inc., a fragment-based molecular docking approach with an exhaustive search algorithm, on a heterogeneous distributed high-performance computing framework. The chemical landscape covered in DockScreen comprises selected environmental and therapeutic chemicals. The target landscape covered in DockScreen was selected based on the availability of high-quality crystal structures that covered the assay space of phase I ToxCast in vitro assays. This in silico data provides continuous information that establishes a means for quantitatively comparing, on a structural biophysical basis, a chemical’s profile of biomolecular interactions. The combined minimum-score chemical/target matrix is provided.

  7. Electrochemical sensor for multiplex screening of genetically modified DNA: identification of biotech crops by logic-based biomolecular analysis. (United States)

    Liao, Wei-Ching; Chuang, Min-Chieh; Ho, Ja-An Annie


    Genetically modified (GM) technique, one of the modern biomolecular engineering technologies, has been deemed as profitable strategy to fight against global starvation. Yet rapid and reliable analytical method is deficient to evaluate the quality and potential risk of such resulting GM products. We herein present a biomolecular analytical system constructed with distinct biochemical activities to expedite the computational detection of genetically modified organisms (GMOs). The computational mechanism provides an alternative to the complex procedures commonly involved in the screening of GMOs. Given that the bioanalytical system is capable of processing promoter, coding and species genes, affirmative interpretations succeed to identify specified GM event in terms of both electrochemical and optical fashions. The biomolecular computational assay exhibits detection capability of genetically modified DNA below sub-nanomolar level and is found interference-free by abundant coexistence of non-GM DNA. This bioanalytical system, furthermore, sophisticates in array fashion operating multiplex screening against variable GM events. Such a biomolecular computational assay and biosensor holds great promise for rapid, cost-effective, and high-fidelity screening of GMO.

  8. Recent applications of AC electrokinetics in biomolecular analysis on microfluidic devices. (United States)

    Sasaki, Naoki


    AC electrokinetics is a generic term that refers to an induced motion of particles and fluids under nonuniform AC electric fields. The AC electric fields are formed by application of AC voltages to microelectrodes, which can be easily integrated into microfluidic devices by standard microfabrication techniques. Moreover, the magnitude of the motion is large enough to control the mass transfer on the devices. These advantages are attractive for biomolecular analysis on the microfluidic devices, in which the characteristics of small space and microfluidics have been mainly employed. In this review, I describe recent applications of AC electrokinetics in biomolecular analysis on microfluidic devices. The applications include fluid pumping and mixing by AC electrokinetic flow, and manipulation of biomolecules such as DNA and proteins by various AC electrokinetic techniques. Future prospects for highly functional biomolecular analysis on microfluidic devices with the aid of AC electrokinetics are also discussed.

  9. Rational Design of Biomolecular Templates for Synthesizing Multifunctional Noble Metal Nanoclusters toward Personalized Theranostic Applications. (United States)

    Yu, Yong; Mok, Beverly Y L; Loh, Xian Jun; Tan, Yen Nee


    Biomolecule-templated or biotemplated metal nanoclusters (NCs) are ultrasmall (<2 nm) metal (Au, Ag) particles stabilized by a certain type of biomolecular template (e.g., peptides, proteins, and DNA). Due to their unique physiochemical properties, biotemplated metal NCs have been widely used in sensing, imaging, delivery and therapy. The overwhelming applications in these individual areas imply the great promise of harnessing biotemplated metal NCs in more advanced biomedical aspects such as theranostics. Although applications of biotemplated metal NCs as theranostic agents are trending, the rational design of biomolecular templates suitable for the synthesis of multifunctional metal NCs for theranostics is comparatively underexplored. This progress report first identifies the essential attributes of biotemplated metal NCs for theranostics by reviewing the state-of-art applications in each of the four modalities of theranostics, namely sensing, imaging, delivery and therapy. To achieve high efficacy in these modalities, we elucidate the design principles underlying the use of biomolecules (proteins, peptides and nucleic acids) to control the NC size, emission color and surface chemistries for post-functionalization of therapeutic moieties. We then propose a unified strategy to engineer biomolecular templates that combine all these modalities to produce multifunctional biotemplated metal NCs that can serve as the next-generation personalized theranostic agents.

  10. Surface-enhanced Raman spectroscopy bioanalytical, biomolecular and medical applications

    CERN Document Server

    Procházka, Marek


    This book gives an overview of recent developments in RS and SERS for sensing and biosensing considering also limitations, possibilities and prospects of this technique. Raman scattering (RS) is a widely used vibrational technique providing highly specific molecular spectral patterns. A severe limitation for the application of this spectroscopic technique lies in the low cross section of RS. Surface-enhanced Raman scattering (SERS) spectroscopy overcomes this problem by 6-11 orders of magnitude enhancement compared with the standard RS for molecules in the close vicinity of certain rough metal surfaces. Thus, SERS combines molecular fingerprint specificity with potential single-molecule sensitivity. Due to the recent development of new SERS-active substrates, labeling and derivatization chemistry as well as new instrumentations, SERS became a very promising tool for many varied applications, including bioanalytical studies and sensing. Both intrinsic and extrinsic SERS biosensing schemes have been employed to...

  11. Advances in biomolecular surface meshing and its applications to mathematical modeling

    Institute of Scientific and Technical Information of China (English)

    CHEN MinXin; LU BenZhuo


    In the field of molecular modeling and simulation,molecular surface meshes are necessary for many problems,such as molecular structure visualization and analysis,docking problem and implicit solvent modeling and simulation.Recently,with the developments of advanced mathematical modeling in the field of implicit solvent modeling and simulation,providing surface meshes with good qualities efficiently for large real biomolecular systems becomes an urgent issue beyond its traditional purposes for visualization and geometry analyses for molecular structure.In this review,we summarize recent works on this issue.First,various definitions of molecular surfaces and corresponding meshing methods are introduced.Second,our recent meshing tool,TMSmesh,and its performances are presented.Finally,we show the applications of the molecular surface mesh in implicit solvent modeling and simulations using boundary element method (BEM) and finite element method (FEM).

  12. Biomolecular ligands screening using radiation damping difference WaterLOGSY spectroscopy. (United States)

    Sun, Peng; Jiang, Xianwang; Jiang, Bin; Zhang, Xu; Liu, Maili


    Water-ligand observed via gradient spectroscopy (WaterLOGSY) is a widely used nuclear magnetic resonance method for ligand screening. The crucial procedure for the effectiveness of WaterLOGSY is selective excitation of the water resonance. The selective excitation is conventionally achieved by using long selective pulse, which causes partial saturation of the water magnetization leading to reduction of sensitivity, in addition to time consuming and error prone. Therefore, many improvements have been made to enhance the sensitivity and robustness of the method. Here we propose an alternative selective excitation scheme for WaterLOGSY by utilizing radiation damping effect. The pulse scheme starts simply with a hard inversion pulse, instead of selective pulse or pulse train, followed by a pulse field gradient to control the radiation damping effect. The rest parts of the pulse scheme are similar to conventional WaterLOGSY. When the gradient pulse is applied immediately after the inversion pulse, the radiation damping effect is suppressed, and all of the magnetization is inversed. When the gradient pulse and the inversion pulse are about 10-20 ms apart, the radiation damping effect remains active and drives the water magnetization toward +z-axis, resulting in selective non-inversion of the water magnetization. By taking the differences of the spectra obtained under these two conditions, one should get the result of WaterLOGSY. The method is demonstrated to be simple, robust and sensitive for ligand screening.

  13. Designing Business Touch Screen Applications


    Čeč, Neža


    This thesis covers conversion of a business application from a standard application to a touch screen version. The first part describes basic functional characteristics of touch screen applications, like their structure and user interaction. Later on we describe technological characteristics that cover different technologies and frameworks for developing touch screen applications. These theoretic chapters are followed by a practical example of converting a business application to a touch scre...

  14. Phase sensitive spectral domain interferometry for label free biomolecular interaction analysis and biosensing applications (United States)

    Chirvi, Sajal

    Biomolecular interaction analysis (BIA) plays vital role in wide variety of fields, which include biomedical research, pharmaceutical industry, medical diagnostics, and biotechnology industry. Study and quantification of interactions between natural biomolecules (proteins, enzymes, DNA) and artificially synthesized molecules (drugs) is routinely done using various labeled and label-free BIA techniques. Labeled BIA (Chemiluminescence, Fluorescence, Radioactive) techniques suffer from steric hindrance of labels on interaction site, difficulty of attaching labels to molecules, higher cost and time of assay development. Label free techniques with real time detection capabilities have demonstrated advantages over traditional labeled techniques. The gold standard for label free BIA is surface Plasmon resonance (SPR) that detects and quantifies the changes in refractive index of the ligand-analyte complex molecule with high sensitivity. Although SPR is a highly sensitive BIA technique, it requires custom-made sensor chips and is not well suited for highly multiplexed BIA required in high throughput applications. Moreover implementation of SPR on various biosensing platforms is limited. In this research work spectral domain phase sensitive interferometry (SD-PSI) has been developed for label-free BIA and biosensing applications to address limitations of SPR and other label free techniques. One distinct advantage of SD-PSI compared to other label-free techniques is that it does not require use of custom fabricated biosensor substrates. Laboratory grade, off-the-shelf glass or plastic substrates of suitable thickness with proper surface functionalization are used as biosensor chips. SD-PSI is tested on four separate BIA and biosensing platforms, which include multi-well plate, flow cell, fiber probe with integrated optics and fiber tip biosensor. Sensitivity of 33 ng/ml for anti-IgG is achieved using multi-well platform. Principle of coherence multiplexing for multi

  15. Biomolecular interactions and tools for their recognition: focus on the quartz crystal microbalance and its diverse surface chemistries and applications. (United States)

    Cheng, Cathy I; Chang, Yi-Pin; Chu, Yen-Ho


    Interactions between molecules are ubiquitous and occur in our bodies, the food we eat, the air we breathe, and myriad additional contexts. Although numerous tools are available for the recognition of biomolecular interactions, such tools are often limited in their sensitivity, expensive, and difficult to modify for various uses. In contrast, the quartz crystal microbalance (QCM) has sub-nanogram detection capabilities, is label-free, is inexpensive to create, and can be readily modified with a number of diverse surface chemistries to detect and characterize diverse interactions. To maximize the versatility of the QCM, scientists need to know available methods by which QCM surfaces can be modified. Therefore, in addition to summarizing the various tools currently used for biomolecular recognition, explicating the fundamental principles of the QCM as a tool for biomolecular recognition, and comparing the QCM with other acoustic sensors, we systematically review the numerous types of surface chemistries-including hydrophobic bonds, ionic bonds, hydrogen bonds, self-assembled monolayers, plasma-polymerized films, photochemistry, and sensing ionic liquids-used to functionalize QCMs for various purposes. We also review the QCM's diverse applications, which include the detection of gaseous species, detection of carbohydrates, detection of nucleic acids, detection of non-enzymatic proteins, characterization of enzymatic activity, detection of antigens and antibodies, detection of cells, and detection of drugs. Finally, we discuss the ultimate goals of and potential barriers to the development of future QCMs.

  16. Global analysis of time-resolved fluorescence microspectroscopy and applications in biomolecular studies

    NARCIS (Netherlands)

    Laptenok, S.


    Understanding the properties of biomolecular networks is of central importance in life sciences. Optical microscopy has been very useful to determine the sub-cellular localisation of proteins but it cannot reveal whether proteins interact with one another. Micro-spectroscopic techniques (combining m

  17. A Theoretical Study of Distribution of First Passage Times of Biomolecular Folding and Reactions with Application to Single Molecules (United States)

    Wang, Jin; Leite, Vitor; Stell, George; Lee, Chi-Lun


    We study the distribution of first passage times of biomolecular folding and reactions through the general framework of energy landscape theory. Both the analytical and lattice simulation results show above cirtain specific temperature, the distribution of first passage time is log-normal, while under the same temperature, the distribution starts to develop fatty tails and deviate from the log-normal distribution, indicating intermittency whereas rare events might dominate the whole process. A power law distribution of first passage time was found analytically in this situation. Applications and connections to experiments on single molecule reaction dynamics are studied.

  18. Application of isothermal titration calorimetry and column chromatography for identification of biomolecular targets. (United States)

    Zhou, Xingding; Kini, R Manjunatha; Sivaraman, J


    This protocol describes a method for identifying unknown target proteins from a mixture of biomolecules for a given drug or a lead compound. This method is based on a combination of chromatography and isothermal titration calorimetry (ITC) where ITC is used as a tracking tool. The first step involves the use of ITC to confirm the binding of ligand to a component in the biomolecular mixture. Subsequently, the biomolecular mixture is fractionated by chromatography, and the binding of the ligand with individual fractions (or subfractions) is verified by ITC. The iteration of chromatographic purification on the fractions combined with ITC results in identifying the target protein. This method is useful when the target protein or ligand is unknown and/or not amenable to labeling, chemical modification or immobilization. This protocol has been successfully used by our team and by others to identify both low-abundance and highly abundant target proteins present in biomolecular mixtures. With this protocol, it takes approximately 3-5 d to identify the target protein from a mixture.

  19. Application of Frontal Affinity Chromatography to Study the Biomolecular Interactions with Trypsin. (United States)

    Hu, YuanYuan; Qian, Junqing; Guo, Hui; Jiang, ShengLan; Zhang, Zheng


    Trypsin is a serine protease that has been proposed as a potential therapeutic target for metabolic disorders and malignancy diseases, thus the identification of biomolecular interactions of compounds to trypsin could be of great therapeutic importance. In this study, trypsin was immobilized on a monolithic silica capillary column via sol-gel. The binding properties of four small molecules (daidzin, genistin, matrine and oxymatrine) to trypsin were examined using the trypsin affinity columns by frontal analysis. The results indicate that the matrine (dissociation constant, Kd = 7.904 μM) has stronger interaction with trypsin than the oxymatrine (Kd = 8.204 μM), whereas daidzin and genistin were nearly have no affinity with trypsin. The results demonstrated that the frontal affinity chromatography can be used for the direct determination of protein-protease inhibitor binding interactions and have several significant advantages, including easy fabricating, reproducible, minimal technological requirements and potential to become a reliable alternative for quantitative studies of biomolecular interactions.

  20. PUPIL: A Software Integration System for Multi-Scale QM/MM-MD Simulations and Its Application to Biomolecular Systems. (United States)

    Torras, Juan; Roberts, Benjamin P; Seabra, Gustavo M; Trickey, Samuel B


    PUPIL (Program for User Package Interfacing and Linking) implements a distinctive multi-scale approach to hybrid quantum mechanical/molecular mechanical molecular dynamics (QM/MM-MD) simulations. Originally developed to interface different external programs for multi-scale simulation with applications in the materials sciences, PUPIL is finding increasing use in the study of complex biological systems. Advanced MD techniques from the external packages can be applied readily to a hybrid QM/MM treatment in which the forces and energy for the QM region can be computed by any of the QM methods available in any of the other external packages. Here, we give a survey of PUPIL design philosophy, main features, and key implementation decisions, with an orientation to biomolecular simulation. We discuss recently implemented features which enable highly realistic simulations of complex biological systems which have more than one active site that must be treated concurrently. Examples are given.

  1. Design of Flow Systems for Improved Networking and Reduced Noise in Biomolecular Signal Processing in Biocomputing and Biosensing Applications. (United States)

    Verma, Arjun; Fratto, Brian E; Privman, Vladimir; Katz, Evgeny


    We consider flow systems that have been utilized for small-scale biomolecular computing and digital signal processing in binary-operating biosensors. Signal measurement is optimized by designing a flow-reversal cuvette and analyzing the experimental data to theoretically extract the pulse shape, as well as reveal the level of noise it possesses. Noise reduction is then carried out numerically. We conclude that this can be accomplished physically via the addition of properly designed well-mixing flow-reversal cell(s) as an integral part of the flow system. This approach should enable improved networking capabilities and potentially not only digital but analog signal-processing in such systems. Possible applications in complex biocomputing networks and various sense-and-act systems are discussed.

  2. Design of Flow Systems for Improved Networking and Reduced Noise in Biomolecular Signal Processing in Biocomputing and Biosensing Applications

    Directory of Open Access Journals (Sweden)

    Arjun Verma


    Full Text Available We consider flow systems that have been utilized for small-scale biomolecular computing and digital signal processing in binary-operating biosensors. Signal measurement is optimized by designing a flow-reversal cuvette and analyzing the experimental data to theoretically extract the pulse shape, as well as reveal the level of noise it possesses. Noise reduction is then carried out numerically. We conclude that this can be accomplished physically via the addition of properly designed well-mixing flow-reversal cell(s as an integral part of the flow system. This approach should enable improved networking capabilities and potentially not only digital but analog signal-processing in such systems. Possible applications in complex biocomputing networks and various sense-and-act systems are discussed.

  3. Grid computing and biomolecular simulation. (United States)

    Woods, Christopher J; Ng, Muan Hong; Johnston, Steven; Murdock, Stuart E; Wu, Bing; Tai, Kaihsu; Fangohr, Hans; Jeffreys, Paul; Cox, Simon; Frey, Jeremy G; Sansom, Mark S P; Essex, Jonathan W


    Biomolecular computer simulations are now widely used not only in an academic setting to understand the fundamental role of molecular dynamics on biological function, but also in the industrial context to assist in drug design. In this paper, two applications of Grid computing to this area will be outlined. The first, involving the coupling of distributed computing resources to dedicated Beowulf clusters, is targeted at simulating protein conformational change using the Replica Exchange methodology. In the second, the rationale and design of a database of biomolecular simulation trajectories is described. Both applications illustrate the increasingly important role modern computational methods are playing in the life sciences.

  4. Variational Methods for Biomolecular Modeling

    CERN Document Server

    Wei, Guo-Wei


    Structure, function and dynamics of many biomolecular systems can be characterized by the energetic variational principle and the corresponding systems of partial differential equations (PDEs). This principle allows us to focus on the identification of essential energetic components, the optimal parametrization of energies, and the efficient computational implementation of energy variation or minimization. Given the fact that complex biomolecular systems are structurally non-uniform and their interactions occur through contact interfaces, their free energies are associated with various interfaces as well, such as solute-solvent interface, molecular binding interface, lipid domain interface, and membrane surfaces. This fact motivates the inclusion of interface geometry, particular its curvatures, to the parametrization of free energies. Applications of such interface geometry based energetic variational principles are illustrated through three concrete topics: the multiscale modeling of biomolecular electrosta...

  5. Biomolecular EPR spectroscopy

    CERN Document Server

    Hagen, Wilfred Raymond


    Comprehensive, Up-to-Date Coverage of Spectroscopy Theory and its Applications to Biological SystemsAlthough a multitude of books have been published about spectroscopy, most of them only occasionally refer to biological systems and the specific problems of biomolecular EPR (bioEPR). Biomolecular EPR Spectroscopy provides a practical introduction to bioEPR and demonstrates how this remarkable tool allows researchers to delve into the structural, functional, and analytical analysis of paramagnetic molecules found in the biochemistry of all species on the planet. A Must-Have Reference in an Intrinsically Multidisciplinary FieldThis authoritative reference seamlessly covers all important bioEPR applications, including low-spin and high-spin metalloproteins, spin traps and spin lables, interaction between active sites, and redox systems. It is loaded with practical tricks as well as do's and don'ts that are based on the author's 30 years of experience in the field. The book also comes with an unprecedented set of...

  6. Stable isotope applications in biomolecular structure and mechanisms. A meeting to bring together producers and users of stable-isotope-labeled compounds to assess current and future needs

    Energy Technology Data Exchange (ETDEWEB)

    Trewhella, J.; Cross, T.A.; Unkefer, C.J. [eds.


    Knowledge of biomolecular structure is a prerequisite for understanding biomolecular function, and stable isotopes play an increasingly important role in structure determination of biological molecules. The first Conference on Stable Isotope Applications in Biomolecular Structure and Mechanisms was held in Santa Fe, New Mexico, March 27--31, 1994. More than 120 participants from 8 countries and 44 institutions reviewed significant developments, discussed the most promising applications for stable isotopes, and addressed future needs and challenges. Participants focused on applications of stable isotopes for studies of the structure and function of proteins, peptides, RNA, and DNA. Recent advances in NMR techniques neutron scattering, EPR, and vibrational spectroscopy were highlighted in addition to the production and synthesis of labeled compounds. This volume includes invited speaker and poster presentations as well as a set of reports from discussion panels that focused on the needs of the scientific community and the potential roles of private industry, the National Stable Isotope Resource, and the National High Magnetic Field Laboratory in serving those needs. This is the leading abstract. Individual papers are processed separately for the database.

  7. Application of isothermal titration calorimetry for characterizing thermodynamic parameters of biomolecular interactions: peptide self-assembly and protein adsorption case studies. (United States)

    Kabiri, Maryam; Unsworth, Larry D


    The complex nature of macromolecular interactions usually makes it very hard to identify the molecular-level mechanisms that ultimately dictate the result of these interactions. This is especially evident in the case of biological systems, where the complex interaction of molecules in various situations may be responsible for driving biomolecular interactions themselves but also has a broader effect at the cell and/or tissue level. This review will endeavor to further the understanding of biomolecular interactions utilizing the isothermal titration calorimetry (ITC) technique for thermodynamic characterization of two extremely important biomaterial systems, viz., peptide self-assembly and nonfouling polymer-modified surfaces. The advantages and shortcomings of this technique will be presented along with a thorough review of the recent application of ITC to these two areas. Furthermore, the controversies associated with the enthalpy-entropy compensation effect as well as thermodynamic equilibrium state for such interactions will be discussed.

  8. Applying Computational Scoring Functions to Assess Biomolecular Interactions in Food Science: Applications to the Estrogen Receptors

    Directory of Open Access Journals (Sweden)

    Francesca Spyrakis


    Thus, key computational medicinal chemistry methods like molecular dynamics can be used to decipher protein flexibility and to obtain stable models for docking and scoring in food-related studies, and virtual screening is increasingly being applied to identify molecules with potential to act as endocrine disruptors, food mycotoxins, and new nutraceuticals [3,4,5]. All of these methods and simulations are based on protein-ligand interaction phenomena, and represent the basis for any subsequent modification of the targeted receptor's or enzyme's physiological activity. We describe here the energetics of binding of biological complexes, providing a survey of the most common and successful algorithms used in evaluating these energetics, and we report case studies in which computational techniques have been applied to food science issues. In particular, we explore a handful of studies involving the estrogen receptors for which we have a long-term interest.

  9. Development of Cellulose-Based, Nanostructured, Conductive Paper for Biomolecular Extraction and Energy Storage Applications


    Razaq, Aamir


    Conductive paper materials consisting of conductive polymers and cellulose are promising for high-tech applications (energy storage and biosciences) due to outstanding aspects of environmental friendliness, mechanical flexibility, electrical conductivity and efficient electroactive behavior. Recently, a conductive composite paper material was developed by covering the individual nanofibers of cellulose from the green algae Cladophora with a polypyrrole (PPy) layer. The PPy-Cladophora cellulos...

  10. Conducting polymer based biomolecular electronic devices

    Indian Academy of Sciences (India)

    B D Malhotra; Rahul Singhal


    Biomolecular electronics is rapidly evolving from physics, chemistry, biology, electronics and information technology. Organic materials such as proteins, pigments and conducting polymers have been considered as alternatives for carrying out the functions that are presently being performed by semiconductor silicon. Conducting polymers such as polypyrroles, polythiophenes and polyanilines have been projected for applications for a wide range of biomolecular electronic devices such as optical, electronic, drug-delivery, memory and biosensing devices. Our group has been actively working towards the application of conducting polymers to Schottky diodes, metal–insulator–semiconductor (MIS) devices and biosensors for the past 10 years. This paper is a review of some of the results obtained at our laboratory in the area of conducting polymer biomolecular electronics.

  11. Programming in biomolecular computation

    DEFF Research Database (Denmark)

    Hartmann, Lars Røeboe; Jones, Neil; Simonsen, Jakob Grue


    Our goal is to provide a top-down approach to biomolecular computation. In spite of widespread discussion about connections between biology and computation, one question seems notable by its absence: Where are the programs? We identify a number of common features in programming that seem conspicu...

  12. Science Letters: Demonstration of a new biosensing concept for immunodiagnostic applications based on change in surface conductance of antibodies after biomolecular interactions

    Institute of Scientific and Technical Information of China (English)

    VASHIST Sandeep Kumar; KAUR Inderpreet; BAJPAI Ram Prakash; BHARADWAJ Lalit Mohan; TEWARI Rupinder; RAITERI Roberto


    We report an important observation that the surface conductivity of antibody layer immobilized on polylysine-coated glass substrate decreases upon the formation of complex with their specific antigens. This change in conductivity has been observed for both monoclonal and polyclonal antibodies. The conductance of monoclonal mouse IgG immobilized on polylysine-coated glass substrate changed from 1.02×l0-8 Ω-1 to 1.41×l0-11 Ω-1 at 10 V when complex is formed due to the specific biomolecular interactions with rabbit anti-mouse IgG F(ab')2. Similar behavior was observed when the same set up was tested in two clinical assays: (1) anti-Leishmania antigen polyclonal antibodies taken from Kala Azar positive patient serum interacting with Leishmania promastigote antigen, and (2) anti-p21 polyclonal antibodies interacting with p21 antigen. The proposed concept can represent a new immunodiagnostic technique and may have wide ranging applications in biosensors and nanobiotechnology too.

  13. Programming in biomolecular computation

    DEFF Research Database (Denmark)

    Hartmann, Lars Røeboe; Jones, Neil; Simonsen, Jakob Grue


    executable, but are also compilable and interpretable. It is universal: all computable functions can be computed (in natural ways and without arcane encodings of data and algorithm); it is also uniform: new “hardware” is not needed to solve new problems; and (last but not least) it is Turing complete......Our goal is to provide a top-down approach to biomolecular computation. In spite of widespread discussion about connections between biology and computation, one question seems notable by its absence: Where are the programs? We introduce a model of computation that is evidently programmable......, by programs reminiscent of low-level computer machine code; and at the same time biologically plausible: its functioning is defined by a single and relatively small set of chemical-like reaction rules. Further properties: the model is stored-program: programs are the same as data, so programs are not only...

  14. Programming in Biomolecular Computation

    DEFF Research Database (Denmark)

    Hartmann, Lars; Jones, Neil; Simonsen, Jakob Grue


    Our goal is to provide a top-down approach to biomolecular computation. In spite of widespread discussion about connections between biology and computation, one question seems notable by its absence: Where are the programs? We introduce a model of computation that is evidently programmable......, by programs reminiscent of low-level computer machine code; and at the same time biologically plausible: its functioning is defined by a single and relatively small set of chemical-like reaction rules. Further properties: the model is stored-program: programs are the same as data, so programs are not only...... in a strong sense: a universal algorithm exists, that is able to execute any program, and is not asymptotically inefficient. A prototype model has been implemented (for now in silico on a conventional computer). This work opens new perspectives on just how computation may be specified at the biological level....

  15. Applications of dynamic nuclear polarization to the study of reactions and reagents in organic and biomolecular chemistry. (United States)

    Hilty, Christian; Bowen, Sean


    Nuclear Magnetic Resonance (NMR) is an important spectroscopic tool for the identification and structural characterization of molecules in chemistry and biochemistry. The most significant limitation of NMR compared to other spectroscopies is its relatively low sensitivity, which thus often requires long measurement times or large amounts of sample. A way of increasing sensitivity of single scan NMR spectra by several orders of magnitude is through hyperpolarization of nuclear spins. Dynamic nuclear polarization allows hyperpolarization of most spins in small molecules encountered in chemistry and biochemistry. NMR spectra of small amounts of samples from natural source, or from chemical synthesis can readily be acquired. Perhaps more interestingly, the availability of the entire hyperpolarized NMR signal in one single scan allows the measurement of transient processes in real time, if applied together with a stopped-flow technique. Through observation of chemical shift, different reactant and product species can be distinguished, and kinetics and mechanisms, for example in enzyme catalyzed reactions, can be elucidated. Real-time hyperpolarization-enhanced NMR is uniquely amenable to correlating atomic positions not only through space, but also over time between reactant and product species. Such correlations carry mechanistic information about a reaction, and can prove reaction pathways. Applications of this technique are emerging in different areas of chemistry concerned with rapid reactions, including not only enzymatic processes, but also chemical catalysis and protein folding.

  16. Applications of ambient mass spectrometry in high-throughput screening. (United States)

    Li, Li-Ping; Feng, Bao-Sheng; Yang, Jian-Wang; Chang, Cui-Lan; Bai, Yu; Liu, Hu-Wei


    The development of rapid screening and identification techniques is of great importance for drug discovery, doping control, forensic identification, food safety and quality control. Ambient mass spectrometry (AMS) allows rapid and direct analysis of various samples in open air with little sample preparation. Recently, its applications in high-throughput screening have been in rapid progress. During the past decade, various ambient ionization techniques have been developed and applied in high-throughput screening. This review discusses typical applications of AMS, including DESI (desorption electrospray ionization), DART (direct analysis in real time), EESI (extractive electrospray ionization), etc., in high-throughput screening (HTS).

  17. Micro and Nanotechnologies Enhanced Biomolecular Sensing

    Directory of Open Access Journals (Sweden)

    Tza-Huei Wang


    Full Text Available This editorial summarizes some of the recent advances of micro and nanotechnology-based tools and devices for biomolecular detection. These include the incorporation of nanomaterials into a sensor surface or directly interfacing with molecular probes to enhance target detection via more rapid and sensitive responses, and the use of self-assembled organic/inorganic nanocomposites that inhibit exceptional spectroscopic properties to enable facile homogenous assays with efficient binding kinetics. Discussions also include some insight into microfluidic principles behind the development of an integrated sample preparation and biosensor platform toward a miniaturized and fully functional system for point of care applications.

  18. Screening of Aptamers on Microfluidic Systems for Clinical Applications


    Gwo-Bin Lee; Chao-Jyun Huang; Chen-Hsun Weng


    The use of microfluidic systems for screening of aptamers and their biomedical applications are reviewed in this paper. Aptamers with different nucleic acid sequences have been extensively studied and the results demonstrated a strong binding affinity to target molecules such that they can be used as promising candidate biomarkers for diagnosis and therapeutics. Recently, the aptamer screening protocol has been conducted with microfluidic-based devices. Furthermore, aptamer affinity screening...

  19. A mechanical Turing machine: blueprint for a biomolecular computer. (United States)

    Shapiro, Ehud


    We describe a working mechanical device that embodies the theoretical computing machine of Alan Turing, and as such is a universal programmable computer. The device operates on three-dimensional building blocks by applying mechanical analogues of polymer elongation, cleavage and ligation, movement along a polymer, and control by molecular recognition unleashing allosteric conformational changes. Logically, the device is not more complicated than biomolecular machines of the living cell, and all its operations are part of the standard repertoire of these machines; hence, a biomolecular embodiment of the device is not infeasible. If implemented, such a biomolecular device may operate in vivo, interacting with its biochemical environment in a program-controlled manner. In particular, it may 'compute' synthetic biopolymers and release them into its environment in response to input from the environment, a capability that may have broad pharmaceutical and biological applications.

  20. Smartphones for cell and biomolecular detection. (United States)

    Liu, Xiyuan; Lin, Tung-Yi; Lillehoj, Peter B


    Recent advances in biomedical science and technology have played a significant role in the development of new sensors and assays for cell and biomolecular detection. Generally, these efforts are aimed at reducing the complexity and costs associated with diagnostic testing so that it can be performed outside of a laboratory or hospital setting, requiring minimal equipment and user involvement. In particular, point-of-care (POC) testing offers immense potential for many important applications including medical diagnosis, environmental monitoring, food safety, and biosecurity. When coupled with smartphones, POC systems can offer portability, ease of use and enhanced functionality while maintaining performance. This review article focuses on recent advancements and developments in smartphone-based POC systems within the last 6 years with an emphasis on cell and biomolecular detection. These devices typically comprise multiple components, such as detectors, sample processors, disposable chips, batteries, and software, which are integrated with a commercial smartphone. One of the most important aspects of developing these systems is the integration of these components onto a compact and lightweight platform that requires minimal power. Researchers have demonstrated several promising approaches employing various detection schemes and device configurations, and it is expected that further developments in biosensors, battery technology and miniaturized electronics will enable smartphone-based POC technologies to become more mainstream tools in the scientific and biomedical communities.

  1. Screening of aptamers on microfluidic systems for clinical applications. (United States)

    Weng, Chen-Hsun; Huang, Chao-Jyun; Lee, Gwo-Bin


    The use of microfluidic systems for screening of aptamers and their biomedical applications are reviewed in this paper. Aptamers with different nucleic acid sequences have been extensively studied and the results demonstrated a strong binding affinity to target molecules such that they can be used as promising candidate biomarkers for diagnosis and therapeutics. Recently, the aptamer screening protocol has been conducted with microfluidic-based devices. Furthermore, aptamer affinity screening by a microfluidic-based method has demonstrated remarkable advantages over competing traditional methods. In this paper, we first reviewed microfluidic systems which demonstrated efficient and rapid screening of a specific aptamer. Then, the clinical applications of screened aptamers, also performed by microfluidic systems, are further reviewed. These automated microfluidic systems can provide advantages over their conventional counterparts including more compactness, faster analysis, less sample/reagent consumption and automation. An aptamer-based compact microfluidic system for diagnosis may even lead to a point-of-care device. The use of microfluidic systems for aptamer screening and diagnosis is expected to continue growing in the near future and may make a substantial impact on biomedical applications.

  2. Screening of Aptamers on Microfluidic Systems for Clinical Applications

    Directory of Open Access Journals (Sweden)

    Gwo-Bin Lee


    Full Text Available The use of microfluidic systems for screening of aptamers and their biomedical applications are reviewed in this paper. Aptamers with different nucleic acid sequences have been extensively studied and the results demonstrated a strong binding affinity to target molecules such that they can be used as promising candidate biomarkers for diagnosis and therapeutics. Recently, the aptamer screening protocol has been conducted with microfluidic-based devices. Furthermore, aptamer affinity screening by a microfluidic-based method has demonstrated remarkable advantages over competing traditional methods. In this paper, we first reviewed microfluidic systems which demonstrated efficient and rapid screening of a specific aptamer. Then, the clinical applications of screened aptamers, also performed by microfluidic systems, are further reviewed. These automated microfluidic systems can provide advantages over their conventional counterparts including more compactness, faster analysis, less sample/reagent consumption and automation. An aptamer-based compact microfluidic system for diagnosis may even lead to a point-of-care device. The use of microfluidic systems for aptamer screening and diagnosis is expected to continue growing in the near future and may make a substantial impact on biomedical applications.

  3. Biomolecular computing systems: principles, progress and potential. (United States)

    Benenson, Yaakov


    The task of information processing, or computation, can be performed by natural and man-made 'devices'. Man-made computers are made from silicon chips, whereas natural 'computers', such as the brain, use cells and molecules. Computation also occurs on a much smaller scale in regulatory and signalling pathways in individual cells and even within single biomolecules. Indeed, much of what we recognize as life results from the remarkable capacity of biological building blocks to compute in highly sophisticated ways. Rational design and engineering of biological computing systems can greatly enhance our ability to study and to control biological systems. Potential applications include tissue engineering and regeneration and medical treatments. This Review introduces key concepts and discusses recent progress that has been made in biomolecular computing.

  4. Biomolecular rods and tubes in nanotechnology (United States)

    Bittner, Alexander M.


    Biomolecules are vitally important elements in nanoscale science and also in future nanotechnology. Their shape and their chemical and physical functionality can give them a big advantage over inorganic and organic substances. While this becomes most obvious in proteins and peptides, with their complicated, but easily controlled chemistry, other biomolecular substances such as DNA, lipids and carbohydrates can also be important. In this review, the emphasis is on one-dimensional molecules and on molecules that self-assemble into linear structures, and on their potential applications. An important aspect is that biomolecules can act as templates, i.e. their shape and chemical properties can be employed to arrange inorganic substances such as metals or metal compounds on the nanometre scale. In particular, rod- and tube-like nanostructures can show physical properties that are different from those of the bulk material, and thus these structures are likely to be a basis for new technology.

  5. Applications of chemogenomic library screening in drug discovery. (United States)

    Jones, Lyn H; Bunnage, Mark E


    The allure of phenotypic screening, combined with the industry preference for target-based approaches, has prompted the development of innovative chemical biology technologies that facilitate the identification of new therapeutic targets for accelerated drug discovery. A chemogenomic library is a collection of selective small-molecule pharmacological agents, and a hit from such a set in a phenotypic screen suggests that the annotated target or targets of that pharmacological agent may be involved in perturbing the observable phenotype. In this Review, we describe opportunities for chemogenomic screening to considerably expedite the conversion of phenotypic screening projects into target-based drug discovery approaches. Other applications are explored, including drug repositioning, predictive toxicology and the discovery of novel pharmacological modalities.

  6. Application of Plagiarism Screening Software in the Chemical Engineering Curriculum (United States)

    Cooper, Matthew E.; Bullard, Lisa G.


    Plagiarism is an area of increasing concern for written ChE assignments, such as laboratory and design reports, due to ease of access to text and other materials via the internet. This study examines the application of plagiarism screening software to four courses in a university chemical engineering curriculum. The effectiveness of plagiarism…

  7. Graphene Tribotronics for Electronic Skin and Touch Screen Applications. (United States)

    Khan, Usman; Kim, Tae-Ho; Ryu, Hanjun; Seung, Wanchul; Kim, Sang-Woo


    Graphene tribotronics is introduced for touch-sensing applications such as electronic skins and touch screens. The devices are based on a coplanar coupling of triboelectrification and current transport in graphene transistors. The touch sensors are ultrasensitive, fast, and stable. Furthermore, they are transparent and flexible, and can spatially map touch stimuli such as movement of a ball, multi-touch, etc.

  8. Global Langevin model of multidimensional biomolecular dynamics (United States)

    Schaudinnus, Norbert; Lickert, Benjamin; Biswas, Mithun; Stock, Gerhard


    Molecular dynamics simulations of biomolecular processes are often discussed in terms of diffusive motion on a low-dimensional free energy landscape F ( 𝒙 ) . To provide a theoretical basis for this interpretation, one may invoke the system-bath ansatz á la Zwanzig. That is, by assuming a time scale separation between the slow motion along the system coordinate x and the fast fluctuations of the bath, a memory-free Langevin equation can be derived that describes the system's motion on the free energy landscape F ( 𝒙 ) , which is damped by a friction field and driven by a stochastic force that is related to the friction via the fluctuation-dissipation theorem. While the theoretical formulation of Zwanzig typically assumes a highly idealized form of the bath Hamiltonian and the system-bath coupling, one would like to extend the approach to realistic data-based biomolecular systems. Here a practical method is proposed to construct an analytically defined global model of structural dynamics. Given a molecular dynamics simulation and adequate collective coordinates, the approach employs an "empirical valence bond"-type model which is suitable to represent multidimensional free energy landscapes as well as an approximate description of the friction field. Adopting alanine dipeptide and a three-dimensional model of heptaalanine as simple examples, the resulting Langevin model is shown to reproduce the results of the underlying all-atom simulations. Because the Langevin equation can also be shown to satisfy the underlying assumptions of the theory (such as a delta-correlated Gaussian-distributed noise), the global model provides a correct, albeit empirical, realization of Zwanzig's formulation. As an application, the model can be used to investigate the dependence of the system on parameter changes and to predict the effect of site-selective mutations on the dynamics.

  9. Integrative NMR for biomolecular research. (United States)

    Lee, Woonghee; Cornilescu, Gabriel; Dashti, Hesam; Eghbalnia, Hamid R; Tonelli, Marco; Westler, William M; Butcher, Samuel E; Henzler-Wildman, Katherine A; Markley, John L


    NMR spectroscopy is a powerful technique for determining structural and functional features of biomolecules in physiological solution as well as for observing their intermolecular interactions in real-time. However, complex steps associated with its practice have made the approach daunting for non-specialists. We introduce an NMR platform that makes biomolecular NMR spectroscopy much more accessible by integrating tools, databases, web services, and video tutorials that can be launched by simple installation of NMRFAM software packages or using a cross-platform virtual machine that can be run on any standard laptop or desktop computer. The software package can be downloaded freely from the NMRFAM software download page ( ), and detailed instructions are available from the Integrative NMR Video Tutorial page ( ).

  10. Application of neural networks to waste site screening

    Energy Technology Data Exchange (ETDEWEB)

    Dabiri, A.E.; Garrett, M.; Kraft, T.; Hilton, J.; VanHammersveld, M.


    Waste site screening requires knowledge of the actual concentrations of hazardous materials and rates of flow around and below the site with time. The present approach consists primarily of drilling boreholes near contaminated sites and chemically analyzing the extracted physical samples and processing the data. This is expensive and time consuming. The feasibility of using neural network techniques to reduce the cost of waste site screening was investigated. Two neural network techniques, gradient descent back propagation and fully recurrent back propagation were utilized. The networks were trained with data received from Westinghouse Hanford Corporation. The results indicate that the network trained with the fully recurrent technique shows satisfactory generalization capability. The predicted results are close to the results obtained from a mathematical flow prediction model. It is possible to develop a new tool to predict the waste plume, thus substantially reducing the number of the bore sites and samplings. There are a variety of applications for this technique in environmental site screening and remediation. One of the obvious applications would be for optimum well siting. A neural network trained from the existing sampling data could be utilized to decide where would be the best position for the next bore site. Other applications are discussed in the report.

  11. Mining, modeling, and evaluation of subnetworks from large biomolecular networks and its comparison study. (United States)

    Hu, Xiaohua; Ng, Michael; Wu, Fang-Xiang; Sokhansanj, Bahrad A


    In this paper, we present a novel method to mine, model, and evaluate a regulatory system executing cellular functions that can be represented as a biomolecular network. Our method consists of two steps. First, a novel scale-free network clustering approach is applied to such a biomolecular network to obtain various subnetworks. Second, computational models are generated for the subnetworks and simulated to predict their behavior in the cellular context. We discuss and evaluate some of the advanced computational modeling approaches, in particular, state-space modeling, probabilistic Boolean network modeling, and fuzzy logic modeling. The modeling and simulation results represent hypotheses that are tested against high-throughput biological datasets (microarrays and/or genetic screens) under normal and perturbation conditions. Experimental results on time-series gene expression data for the human cell cycle indicate that our approach is promising for subnetwork mining and simulation from large biomolecular networks.

  12. [Advances in biomolecular machine: methane monooxygenases]. (United States)

    Lu, Jixue; Wang, Shizhen; Fang, Baishan


    Methane monooxygenases (MMO), regarded as "an amazing biomolecular machine", catalyze the oxidation of methane to methanol under aerobic conditions. MMO catalyze the oxidation of methane elaborately, which is a novel way to catalyze methane to methanol. Furthermore, MMO can inspire the biomolecular machine design. In this review, we introduced MMO including structure, gene and catalytic mechanism. The history and the taxonomy of MMO were also introduced.

  13. Solution influence on biomolecular equilibria - Nucleic acid base associations (United States)

    Pohorille, A.; Pratt, L. R.; Burt, S. K.; Macelroy, R. D.


    Various attempts to construct an understanding of the influence of solution environment on biomolecular equilibria at the molecular level using computer simulation are discussed. First, the application of the formal statistical thermodynamic program for investigating biomolecular equilibria in solution is presented, addressing modeling and conceptual simplications such as perturbative methods, long-range interaction approximations, surface thermodynamics, and hydration shell. Then, Monte Carlo calculations on the associations of nucleic acid bases in both polar and nonpolar solvents such as water and carbon tetrachloride are carried out. The solvent contribution to the enthalpy of base association is positive (destabilizing) in both polar and nonpolar solvents while negative enthalpies for stacked complexes are obtained only when the solute-solute in vacuo energy is added to the total energy. The release upon association of solvent molecules from the first hydration layer around a solute to the bulk is accompanied by an increase in solute-solvent energy and decrease in solvent-solvent energy. The techniques presented are expectd to displace less molecular and more heuristic modeling of biomolecular equilibria in solution.

  14. Virtual screening of electron acceptor materials for organic photovoltaic applications (United States)

    Halls, Mathew D.; Djurovich, Peter J.; Giesen, David J.; Goldberg, Alexander; Sommer, Jonathan; McAnally, Eric; Thompson, Mark E.


    Virtual screening involves the generation of structure libraries, automated analysis to predict properties related to application performance and subsequent screening to identify lead systems and estimate critical structure-property limits across a targeted chemical design space. This approach holds great promise for informing experimental discovery and development efforts for next-generation materials, such as organic semiconductors. In this work, the virtual screening approach is illustrated for nitrogen-substituted pentacene molecules to identify systems for development as electron acceptor materials for use in organic photovoltaic (OPV) devices. A structure library of tetra-azapentacenes (TAPs) was generated by substituting four nitrogens for CH at 12 sites on the pentacene molecular framework. Molecular properties (e.g. ELUMO, Eg and μ) were computed for each candidate structure using hybrid DFT at the B3LYP/6-311G** level of theory. The resulting TAPs library was then analyzed with respect to intrinsic properties associated with OPV acceptor performance. Marcus reorganization energies for charge transport for the most favorable TAP candidates were then calculated to further determine suitability as OPV electron acceptors. The synthesis, characterization and OPV device testing of TAP materials is underway, guided by these results.

  15. Applications of biochromatography in the screening of bioactive natural products. (United States)

    Chen, Cen; Yang, Feng-Qing; Zuo, Hua-Li; Song, Yue-Lin; Xia, Zhi-Ning; Xiao, Wen


    Searching for bioactive compounds from natural resources such as plant materials has become a focus for study. Several models, such as animal (biofluid, organ and tissue) and cellular (several kinds of cell lines), have traditionally been used for this purpose. As a fast, economic and effective way to identify or predict bioactive compounds in complex matrices, biochromatography has developed rapidly during the past years. Combing the properties of traditional chromatography and biomaterials, biochromatographic analysis possesses features of simultaneous screening, separation and structural identification for active compounds in a complex matrix. According to the process, biochromatography can be divided into offline and online approaches. For offline bioextraction, the biomaterials are used as the extraction phase and followed by routine chromatographic analysis. For online biochromatography, the biomaterials are directly used as the stationary phase for chromatographic analysis. This paper reviews the applications of offline bioextraction followed by chromatographic analysis and online biochromatography, including molecular, cell membrane and cell, and artificial biomembrane chromatography in the screening or predicting active compounds from natural sources.

  16. Screening applications in drug discovery based on microfluidic technology. (United States)

    Eribol, P; Uguz, A K; Ulgen, K O


    Microfluidics has been the focus of interest for the last two decades for all the advantages such as low chemical consumption, reduced analysis time, high throughput, better control of mass and heat transfer, downsizing a bench-top laboratory to a chip, i.e., lab-on-a-chip, and many others it has offered. Microfluidic technology quickly found applications in the pharmaceutical industry, which demands working with leading edge scientific and technological breakthroughs, as drug screening and commercialization are very long and expensive processes and require many tests due to unpredictable results. This review paper is on drug candidate screening methods with microfluidic technology and focuses specifically on fabrication techniques and materials for the microchip, types of flow such as continuous or discrete and their advantages, determination of kinetic parameters and their comparison with conventional systems, assessment of toxicities and cytotoxicities, concentration generations for high throughput, and the computational methods that were employed. An important conclusion of this review is that even though microfluidic technology has been in this field for around 20 years there is still room for research and development, as this cutting edge technology requires ingenuity to design and find solutions for each individual case. Recent extensions of these microsystems are microengineered organs-on-chips and organ arrays.

  17. Origin of organic molecules and biomolecular homochirality. (United States)

    Podlech, J


    Theories about the origin of biomolecular homochirality, which seems to be a prerequisite for the creation of life, are discussed. First, possible terrestrial and extraterrestrial sources of organic molecules are outlined. Then, mechanisms for the formation of enantiomerically enriched compounds and for the amplification of their chirality are described.

  18. Thermodynamic properties of water solvating biomolecular surfaces (United States)

    Heyden, Matthias

    Changes in the potential energy and entropy of water molecules hydrating biomolecular interfaces play a significant role for biomolecular solubility and association. Free energy perturbation and thermodynamic integration methods allow calculations of free energy differences between two states from simulations. However, these methods are computationally demanding and do not provide insights into individual thermodynamic contributions, i.e. changes in the solvent energy or entropy. Here, we employ methods to spatially resolve distributions of hydration water thermodynamic properties in the vicinity of biomolecular surfaces. This allows direct insights into thermodynamic signatures of the hydration of hydrophobic and hydrophilic solvent accessible sites of proteins and small molecules and comparisons to ideal model surfaces. We correlate dynamic properties of hydration water molecules, i.e. translational and rotational mobility, to their thermodynamics. The latter can be used as a guide to extract thermodynamic information from experimental measurements of site-resolved water dynamics. Further, we study energy-entropy compensations of water at different hydration sites of biomolecular surfaces. This work is supported by the Cluster of Excellence RESOLV (EXC 1069) funded by the Deutsche Forschungsgemeinschaft.

  19. Computer Programming and Biomolecular Structure Studies: A Step beyond Internet Bioinformatics (United States)

    Likic, Vladimir A.


    This article describes the experience of teaching structural bioinformatics to third year undergraduate students in a subject titled "Biomolecular Structure and Bioinformatics." Students were introduced to computer programming and used this knowledge in a practical application as an alternative to the well established Internet bioinformatics…

  20. Microfluidic liquid chromatography system for proteomic applications and biomarker screening. (United States)

    Lazar, Iulia M; Trisiripisal, Phichet; Sarvaiya, Hetal A


    A microfluidic liquid chromatography (LC) system for proteomic investigations that integrates all the necessary components for stand-alone operation, i.e., pump, valve, separation column, and electrospray interface, is described in this paper. The overall size of the LC device is small enough to enable the integration of two fully functional separation systems on a 3 in. x 1 in. glass microchip. A multichannel architecture that uses electroosmotic pumping principles provides the necessary functionality for eluent propulsion and sample valving. The flow rates generated within these chips are fully consistent with the requirements of nano-LC platforms that are routinely used in proteomic applications. The microfluidic device was evaluated for the analysis of a protein digest obtained from the MCF7 breast cancer cell line. The cytosolic protein extract was processed according to a shotgun protocol, and after tryptic digestion and prefractionation using strong cation exchange chromatography (SCX), selected sample subfractions were analyzed with conventional and microfluidic LC platforms. Using similar experimental conditions, the performance of the microchip LC was comparable to that obtained with benchtop instrumentation, providing an overlap of 75% in proteins that were identified by more than two unique peptides. The microfluidic LC analysis of a protein-rich SCX fraction enabled the confident identification of 77 proteins by using conventional data filtering parameters, of 39 proteins with p screening applications.

  1. An oral multispecies biofilm model for high content screening applications (United States)

    Kommerein, Nadine; Stumpp, Sascha N.; Müsken, Mathias; Ehlert, Nina; Winkel, Andreas; Häussler, Susanne; Behrens, Peter; Buettner, Falk F. R.; Stiesch, Meike


    Peri-implantitis caused by multispecies biofilms is a major complication in dental implant treatment. The bacterial infection surrounding dental implants can lead to bone loss and, in turn, to implant failure. A promising strategy to prevent these common complications is the development of implant surfaces that inhibit biofilm development. A reproducible and easy-to-use biofilm model as a test system for large scale screening of new implant surfaces with putative antibacterial potency is therefore of major importance. In the present study, we developed a highly reproducible in vitro four-species biofilm model consisting of the highly relevant oral bacterial species Streptococcus oralis, Actinomyces naeslundii, Veillonella dispar and Porphyromonas gingivalis. The application of live/dead staining, quantitative real time PCR (qRT-PCR), scanning electron microscopy (SEM) and urea-NaCl fluorescence in situ hybridization (urea-NaCl-FISH) revealed that the four-species biofilm community is robust in terms of biovolume, live/dead distribution and individual species distribution over time. The biofilm community is dominated by S. oralis, followed by V. dispar, A. naeslundii and P. gingivalis. The percentage distribution in this model closely reflects the situation in early native plaques and is therefore well suited as an in vitro model test system. Furthermore, despite its nearly native composition, the multispecies model does not depend on nutrient additives, such as native human saliva or serum, and is an inexpensive, easy to handle and highly reproducible alternative to the available model systems. The 96-well plate format enables high content screening for optimized implant surfaces impeding biofilm formation or the testing of multiple antimicrobial treatment strategies to fight multispecies biofilm infections, both exemplary proven in the manuscript. PMID:28296966

  2. Microfluidic-Enabled Print-to-Screen Platform for High-Throughput Screening of Combinatorial Chemotherapy. (United States)

    Ding, Yuzhe; Li, Jiannan; Xiao, Wenwu; Xiao, Kai; Lee, Joyce; Bhardwaj, Urvashi; Zhu, Zijie; Digiglio, Philip; Yang, Gaomai; Lam, Kit S; Pan, Tingrui


    Since the 1960s, combination chemotherapy has been widely utilized as a standard method to treat cancer. However, because of the potentially enormous number of drug candidates and combinations, conventional identification methods of the effective drug combinations are usually associated with significantly high operational costs, low throughput screening, laborious and time-consuming procedures, and ethical concerns. In this paper, we present a low-cost, high-efficiency microfluidic print-to-screen (P2S) platform, which integrates combinatorial screening with biomolecular printing for high-throughput screening of anticancer drug combinations. This P2S platform provides several distinct advantages and features, including automatic combinatorial printing, high-throughput parallel drug screening, modular disposable cartridge, and biocompatibility, which can potentially speed up the entire discovery cycle of potent drug combinations. Microfluidic impact printing utilizing plug-and-play microfluidic cartridges is experimentally characterized with controllable droplet volume and accurate positioning. Furthermore, the combinatorial print-to-screen assay is demonstrated in a proof-of-concept biological experiment which can identify the positive hits among the entire drug combination library in a parallel and rapid manner. Overall, this microfluidic print-to-screen platform offers a simple, low-cost, high-efficiency solution for high-throughput large-scale combinatorial screening and can be applicable for various emerging applications in drug cocktail discovery.

  3. MPBEC, a Matlab Program for Biomolecular Electrostatic Calculations. (United States)

    Vergara-Perez, Sandra; Marucho, Marcelo


    One of the most used and efficient approaches to compute electrostatic properties of biological systems is to numerically solve the Poisson-Boltzmann (PB) equation. There are several software packages available that solve the PB equation for molecules in aqueous electrolyte solutions. Most of these software packages are useful for scientists with specialized training and expertise in computational biophysics. However, the user is usually required to manually take several important choices, depending on the complexity of the biological system, to successfully obtain the numerical solution of the PB equation. This may become an obstacle for researchers, experimentalists, even students with no special training in computational methodologies. Aiming to overcome this limitation, in this article we present MPBEC, a free, cross-platform, open-source software that provides non-experts in the field an easy and efficient way to perform biomolecular electrostatic calculations on single processor computers. MPBEC is a Matlab script based on the Adaptative Poisson Boltzmann Solver, one of the most popular approaches used to solve the PB equation. MPBEC does not require any user programming, text editing or extensive statistical skills, and comes with detailed user-guide documentation. As a unique feature, MPBEC includes a useful graphical user interface (GUI) application which helps and guides users to configure and setup the optimal parameters and approximations to successfully perform the required biomolecular electrostatic calculations. The GUI also incorporates visualization tools to facilitate users pre- and post- analysis of structural and electrical properties of biomolecules.

  4. MPBEC, a Matlab Program for Biomolecular Electrostatic Calculations (United States)

    Vergara-Perez, Sandra; Marucho, Marcelo


    One of the most used and efficient approaches to compute electrostatic properties of biological systems is to numerically solve the Poisson-Boltzmann (PB) equation. There are several software packages available that solve the PB equation for molecules in aqueous electrolyte solutions. Most of these software packages are useful for scientists with specialized training and expertise in computational biophysics. However, the user is usually required to manually take several important choices, depending on the complexity of the biological system, to successfully obtain the numerical solution of the PB equation. This may become an obstacle for researchers, experimentalists, even students with no special training in computational methodologies. Aiming to overcome this limitation, in this article we present MPBEC, a free, cross-platform, open-source software that provides non-experts in the field an easy and efficient way to perform biomolecular electrostatic calculations on single processor computers. MPBEC is a Matlab script based on the Adaptative Poisson-Boltzmann Solver, one of the most popular approaches used to solve the PB equation. MPBEC does not require any user programming, text editing or extensive statistical skills, and comes with detailed user-guide documentation. As a unique feature, MPBEC includes a useful graphical user interface (GUI) application which helps and guides users to configure and setup the optimal parameters and approximations to successfully perform the required biomolecular electrostatic calculations. The GUI also incorporates visualization tools to facilitate users pre- and post-analysis of structural and electrical properties of biomolecules.

  5. Biomolecular engineered sensors for diagnostic applications


    Marti Villalba, M


    Electrochemistry is a powerful technique that offers multiple possibilities and which is in constant evolution. Simple modifications of the electrode surface can result in an improvement of the selectivity and sensitivity of the method. However some situations require more complex modifications such as the incorporation of an external agent to the electrode surface, or within the actual electrode. This thesis describes the development and characterization of a range of novel electrochemical s...

  6. Improvements in continuum modeling for biomolecular systems

    CERN Document Server

    Qiao, Yu


    Modeling of biomolecular systems plays an essential role in understanding biological processes, such as ionic flow across channels, protein modification or interaction, and cell signaling. The continuum model described by the Poisson-Boltzmann (PB)/Poisson-Nernst-Planck (PNP) equations has made great contributions towards simulation of these processes. However, the model has shortcomings in its commonly used form and cannot capture (or cannot accurately capture) some important physical properties of biological systems. Considerable efforts have been made to improve the continuum model to account for discrete particle interactions and to make progress in numerical methods to provide accurate and efficient simulation. This review will summarize recent main improvements in continuum modeling for biomolecular systems, with focus on the size-modified models, the coupling of the classical density functional theory and PNP equations, the coupling of polar and nonpolar interactions, and numerical progress.

  7. A statistical mechanical description of biomolecular hydration

    Energy Technology Data Exchange (ETDEWEB)



    We present an efficient and accurate theoretical description of the structural hydration of biological macromolecules. The hydration of molecules of almost arbitrary size (tRNA, antibody-antigen complexes, photosynthetic reaction centre) can be studied in solution and in the crystal environment. The biomolecular structure obtained from x-ray crystallography, NMR, or modeling is required as input information. The structural arrangement of water molecules near a biomolecular surface is represented by the local water density analogous to the corresponding electron density in an x-ray diffraction experiment. The water-density distribution is approximated in terms of two- and three-particle correlation functions of solute atoms with water using a potentials-of-mean-force expansion.

  8. Application of an Aesthetic Evaluation Model to Data Entry Screens. (United States)

    Ngo, D. C. L.; Byrne, J. G.


    Describes a new model for quantitatively assessing screen formats. Results of applying the model to data entry screens support the use of the model. Also described is a critiquing mechanism embedded in a user interface design environment as a demonstration of this approach. (Author/AEF)

  9. Biomolecular electrostatics and solvation: a computational perspective. (United States)

    Ren, Pengyu; Chun, Jaehun; Thomas, Dennis G; Schnieders, Michael J; Marucho, Marcelo; Zhang, Jiajing; Baker, Nathan A


    An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis, and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. This review discusses the solvation of biomolecules with a computational biophysics view toward describing the phenomenon. While our main focus lies on the computational aspect of the models, we provide an overview of the basic elements of biomolecular solvation (e.g. solvent structure, polarization, ion binding, and non-polar behavior) in order to provide a background to understand the different types of solvation models.

  10. In silico screening of ligand databases: Methods and applications

    Directory of Open Access Journals (Sweden)

    Khedkar S


    Full Text Available Pressure is mounting on the pharmaceutical industry to reduce both the cost of drugs and the time to market. The large number of targets made available in the last decade has created a new area for technologies that can rapidly identify quality lead candidates. Virtual screening is one such technology that is gaining increasing importance in the drug discovery process. Virtual screening is a reliable and inexpensive method currently being employed as a complementary approach to high-throughput screening. Virtual screening can be adopted irrespective of the structural information of the target receptor. In the absence of structural data, virtual screening using pharmacophore-based search is a major in silico tool. However, when the structure of the receptor is available, virtual screening using both pharmacophore-based and docking techniques can be employed. Both of these methods can be synergistically integrated to improve the drug design and development process. In this article, we provide an overview of methods for virtual screening - in particular, docking and pharmacophore-based - along with commercial algorithms implementing these methods, and a successful example in this arena. Further, we enumerate the potential for patenting such kind of studies.

  11. Biomolecular interactions: essential instrumentation methods. (United States)

    Messina, Paula Veronica; Ruso, Juan Manuel


    The main goal of this review is to outline the basic principles and applications of the broad range of modern biophysical technical methods used to study the different aspects of protein–ligand interactions by discussing such aspects as newer systems, unusual approaches and highly used techniques.

  12. Barcoded microchips for biomolecular assays. (United States)

    Zhang, Yi; Sun, Jiashu; Zou, Yu; Chen, Wenwen; Zhang, Wei; Xi, Jianzhong Jeff; Jiang, Xingyu


    Multiplexed assay of analytes is of great importance for clinical diagnostics and other analytical applications. Barcode-based bioassays with the ability to encode and decode may realize this goal in a straightforward and consistent manner. We present here a microfluidic barcoded chip containing several sets of microchannels with different widths, imitating the commonly used barcode. A single barcoded microchip can carry out tens of individual protein/nucleic acid assays (encode) and immediately yield all assay results by a portable barcode reader or a smartphone (decode). The applicability of a barcoded microchip is demonstrated by human immunodeficiency virus (HIV) immunoassays for simultaneous detection of three targets (anti-gp41 antibody, anti-gp120 antibody, and anti-gp36 antibody) from six human serum samples. We can also determine seven pathogen-specific oligonucleotides by a single chip containing both positive and negative controls.

  13. Mussel byssus and biomolecular materials. (United States)

    Deming, T J


    Mussel adhesive proteins are remarkable materials that display an extraordinary capability to adhere to substrates underwater. Recent investigations from groups with quite diverse areas of expertise have made substantial progress in the identification of the genes and proteins that are involved in adhesive formation. These discoveries have led to the development of recombinant proteins and synthetic polypeptides that are able to reproduce the properties of mussel adhesives for applications in medicine and biotechnology.

  14. The Dutch periodontal screening index validation and its application in The Netherlands

    NARCIS (Netherlands)

    van der Velden, U.


    Objective: To provide evidence that the Dutch periodontal screening index (DPSI) is a valuable tool for the screening of the periodontal status and to evaluate the application of the DPSI by general practitioners in the Netherlands. Material and methods: To assess the validity of the DPSI, an availa

  15. Simulation of Parallel Logical Operations with Biomolecular Computing

    Directory of Open Access Journals (Sweden)

    Mahnaz Kadkhoda


    Full Text Available Biomolecular computing is the computational method that uses the potential of DNA as a parallel computing device. DNA computing can be used to solve NP-complete problems. An appropriate application of DNA computation is large-scale evaluation of parallel computation models such as Boolean Circuits. In this study, we present a molecular-based algorithm for evaluation of Nand-based Boolean Circuits. The contribution of this paper is that the proposed algorithm has been implemented using only three molecular operations and the number of passes in each level is decreased to less than half of previously addressed in the literature. Thus, the proposed algorithm is much easier to implement in the laboratory.

  16. Hybrid organic semiconductor lasers for bio-molecular sensing. (United States)

    Haughey, Anne-Marie; Foucher, Caroline; Guilhabert, Benoit; Kanibolotsky, Alexander L; Skabara, Peter J; Burley, Glenn; Dawson, Martin D; Laurand, Nicolas


    Bio-functionalised luminescent organic semiconductors are attractive for biophotonics because they can act as efficient laser materials while simultaneously interacting with molecules. In this paper, we present and discuss a laser biosensor platform that utilises a gain layer made of such an organic semiconductor material. The simple structure of the sensor and its operation principle are described. Nanolayer detection is shown experimentally and analysed theoretically in order to assess the potential and the limits of the biosensor. The advantage conferred by the organic semiconductor is explained, and comparisons to laser sensors using alternative dye-doped materials are made. Specific biomolecular sensing is demonstrated, and routes to functionalisation with nucleic acid probes, and future developments opened up by this achievement, are highlighted. Finally, attractive formats for sensing applications are mentioned, as well as colloidal quantum dots, which in the future could be used in conjunction with organic semiconductors.

  17. Biomolecular Assembly of Gold Nanocrystals

    Energy Technology Data Exchange (ETDEWEB)

    Micheel, Christine Marya [Univ. of California, Berkeley, CA (United States)


    Over the past ten years, methods have been developed to construct discrete nanostructures using nanocrystals and biomolecules. While these frequently consist of gold nanocrystals and DNA, semiconductor nanocrystals as well as antibodies and enzymes have also been used. One example of discrete nanostructures is dimers of gold nanocrystals linked together with complementary DNA. This type of nanostructure is also known as a nanocrystal molecule. Discrete nanostructures of this kind have a number of potential applications, from highly parallel self-assembly of electronics components and rapid read-out of DNA computations to biological imaging and a variety of bioassays. My research focused in three main areas. The first area, the refinement of electrophoresis as a purification and characterization method, included application of agarose gel electrophoresis to the purification of discrete gold nanocrystal/DNA conjugates and nanocrystal molecules, as well as development of a more detailed understanding of the hydrodynamic behavior of these materials in gels. The second area, the development of methods for quantitative analysis of transmission electron microscope data, used computer programs written to find pair correlations as well as higher order correlations. With these programs, it is possible to reliably locate and measure nanocrystal molecules in TEM images. The final area of research explored the use of DNA ligase in the formation of nanocrystal molecules. Synthesis of dimers of gold particles linked with a single strand of DNA possible through the use of DNA ligase opens the possibility for amplification of nanostructures in a manner similar to polymerase chain reaction. These three areas are discussed in the context of the work in the Alivisatos group, as well as the field as a whole.

  18. Electromagnetic radiation screening of semiconductor devices for long life applications (United States)

    Hall, T. C.; Brammer, W. G.


    A review is presented of the mechanism of interaction of electromagnetic radiation in various spectral ranges, with various semiconductor device defects. Previous work conducted in this area was analyzed as to its pertinence to the current problem. The task was studied of implementing electromagnetic screening methods in the wavelength region determined to be most effective. Both scanning and flooding type stimulation techniques are discussed. While the scanning technique offers a considerably higher yield of useful information, a preliminary investigation utilizing the flooding approach is first recommended because of the ease of implementation, lower cost and ability to provide go-no-go information in semiconductor screening.

  19. Protein crystallization with microseed matrix screening: application to human germline antibody Fabs

    Energy Technology Data Exchange (ETDEWEB)

    Obmolova, Galina, E-mail:; Malia, Thomas J.; Teplyakov, Alexey; Sweet, Raymond W.; Gilliland, Gary L., E-mail: [Janssen Research and Development LLC, 1400 McKean Road, Spring House, PA 19477 (United States)


    The power of microseed matrix screening is demonstrated in the crystallization of a panel of antibody Fab fragments. The crystallization of 16 human antibody Fab fragments constructed from all pairs of four different heavy chains and four different light chains was enabled by employing microseed matrix screening (MMS). In initial screening, diffraction-quality crystals were obtained for only three Fabs, while many Fabs produced hits that required optimization. Application of MMS, using the initial screens and/or refinement screens, resulted in diffraction-quality crystals of these Fabs. Five Fabs that failed to give hits in the initial screen were crystallized by cross-seeding MMS followed by MMS optimization. The crystallization protocols and strategies that resulted in structure determination of all 16 Fabs are presented. These results illustrate the power of MMS and provide a basis for developing future strategies for macromolecular crystallization.

  20. Azurin for Biomolecular Electronics: a Reliability Study (United States)

    Bramanti, Alessandro; Pompa, Pier Paolo; Maruccio, Giuseppe; Calabi, Franco; Arima, Valentina; Cingolani, Roberto; Corni, Stefano; Di Felice, Rosa; De Rienzo, Francesca; Rinaldi, Ross


    The metalloprotein azurin, used in biomolecular electronics, is investigated with respect to its resilience to high electric fields and ambient conditions, which are crucial reliability issues. Concerning the effect of electric fields, two models of different complexity agree indicating an unexpectedly high robustness. Experiments in device-like conditions confirm that no structural modifications occur, according to fluorescence spectra, even after a 40-min exposure to tens of MV/m. Ageing is then investigated experimentally, at ambient conditions and without field, over several days. Only a small conformational rearrangement is observed in the first tens of hours, followed by an equilibrium state.

  1. Nanotube-Based Chemical and Biomolecular Sensors

    Institute of Scientific and Technical Information of China (English)

    J.Koh; B.Kim; S.Hong; H.Lim; H.C.Choi


    We present a brief review about recent results regarding carbon nanotube (CNT)-based chemical and biomolecular sensors. For the fabrication of CNT-based sensors, devices containing CNT channels between two metal electrodes are first fabricated usually via chemical vapor deposition (CVD) process or "surface programmed assembly" method. Then, the CNT surfaces are often functionalized to enhance the selectivity of the sensors. Using this process, highly-sensitive CNT-based sensors can be fabricated for the selective detection of various chemical and biological molecules such as hydrogen, ammonia, carbon monoxide, chlorine gas, DNA, glucose, alcohol, and proteins.

  2. Scalable Molecular Dynamics for Large Biomolecular Systems

    Directory of Open Access Journals (Sweden)

    Robert K. Brunner


    Full Text Available We present an optimized parallelization scheme for molecular dynamics simulations of large biomolecular systems, implemented in the production-quality molecular dynamics program NAMD. With an object-based hybrid force and spatial decomposition scheme, and an aggressive measurement-based predictive load balancing framework, we have attained speeds and speedups that are much higher than any reported in literature so far. The paper first summarizes the broad methodology we are pursuing, and the basic parallelization scheme we used. It then describes the optimizations that were instrumental in increasing performance, and presents performance results on benchmark simulations.

  3. Fundamentos biomoleculares de la diabetes mellitus



    La diabetes mellitus es una enfermedad endocrina con importantes implicaciones a nivel sistémico, como: angiopatía, neuropatía, retinopatía y nefropatía, entre otras. Estas  complicaciones tienen su origen en eventos biomoleculares desencadenados por la hiperglicemia.  La presente revisión de tema trata sobre la estructura y síntesis de la insulina en las células β del páncreas; los eventos moleculares y bioquímicos que activan su secreción como respuesta a una alta concentración de glucosa e...

  4. Energy dissipation in biomolecular machines

    Energy Technology Data Exchange (ETDEWEB)

    Lervik, Anders


    The operation of a molecular pump, the calcium pump of sarcoplasmic reticulum is studied using mesoscopic non-equilibrium thermodynamics and molecular dynamics. The mesoscopic non-equilibrium thermodynamic description of the pump is compared to the description obtained in the framework of Hill for kinetic enzyme cycles. By comparing these two descriptions at isothermal conditions, they are found to be equivalent. This supports the validity of the mesoscopic approach. An extension of the mesoscopic non-equilibrium framework to also include a heat flux and the corresponding temperature difference is proposed. This can be used to model phenomena such as non-shivering thermogenesis, a process which lack a theoretical description in the kinetic cycle picture. Further, the heat transfer in the calcium pump is studied using molecular dynamics. This is done in order to obtain phenomenological parameters that can be used for the modeling of thermogenesis. A non-stationary non-equilibrium molecular dynamics approach is developed, which may be used to study heat transfer between a small object and the surrounding solvent. This methodology is applied to the calcium pump solvated in water. It is found that the thermal conductivity of the protein is low (0.2 W K-1 m-1) compared to water (0.6 WK-1 m-1). This means that the protein may sustain a large temperature gradient across its structure. The simulations also show that the protein-water surface is important for the heat transfer. The time scale for vibrational energy relaxation is found to be of order 10/100 ps which strengthens the local equilibrium assumption of mesoscopic non-equilibrium thermodynamics. Mesoscopic non-equilibrium thermodynamics is also applied to calculate the thermodynamic efficiency of the calcium pump embedded in lipid bilayers of varying length and from different tissues. This is done in order to show the applicability of mesoscopic non-equilibrium thermodynamics to interpret experimental data. The

  5. Systematic evaluation of bundled SPC water for biomolecular simulations. (United States)

    Gopal, Srinivasa M; Kuhn, Alexander B; Schäfer, Lars V


    molecules between the active site and the bulk. Our results form a basis for assessing the accuracy that can be expected from bundled SPC water models. At the same time, this study also highlights the importance of evaluating beforehand the effects of water bundling on the biomolecular system of interest for a particular multiscale simulation application.

  6. Application of neural networks to waste site screening

    Energy Technology Data Exchange (ETDEWEB)

    Dabiri, A.E.; Kraft, T.; Hilton, J.M. [Science Applications International Corp., San Diego, CA (United States)


    Waste site screening requires knowledge of the actual concentrations of hazardous materials and rates of flow around and below the site with time. The present approach to site screening consists primarily of drilling, boreholes near contaminated site and chemically analyzing the extracted physical samples and processing the data. In addition, hydraulic and geochemical soil properties are obtained so that numerical simulation models can be used to interpret and extrapolate the field data. The objective of this work is to investigate the feasibility of using neural network techniques to reduce the cost of waste site screening. A successful technique may lead to an ability to reduce the number of boreholes and the number of samples analyzed from each borehole to properly screen the waste site. The analytic tool development described here is inexpensive because it makes use of neural network techniques that can interpolate rapidly and which can learn how to analyze data rather than having to be explicitly programmed. In the following sections, data collection and data analyses will be described, followed by a section on different neural network techniques used. The results will be presented and compared with mathematical model. Finally, the last section will summarize the research work performed and make several recommendations for future work.

  7. Hazard screening application guide. Safety Analysis Report Update Program

    Energy Technology Data Exchange (ETDEWEB)



    The basic purpose of hazard screening is to group precesses, facilities, and proposed modifications according to the magnitude of their hazards so as to determine the need for and extent of follow on safety analysis. A hazard is defined as a material, energy source, or operation that has the potential to cause injury or illness in human beings. The purpose of this document is to give guidance and provide standard methods for performing hazard screening. Hazard screening is applied to new and existing facilities and processes as well as to proposed modifications to existing facilities and processes. The hazard screening process evaluates an identified hazards in terms of the effects on people, both on-site and off-site. The process uses bounding analyses with no credit given for mitigation of an accident with the exception of certain containers meeting DOT specifications. The process is restricted to human safety issues only. Environmental effects are addressed by the environmental program. Interfaces with environmental organizations will be established in order to share information.

  8. Improvements in continuum modeling for biomolecular systems (United States)

    Yu, Qiao; Ben-Zhuo, Lu


    Modeling of biomolecular systems plays an essential role in understanding biological processes, such as ionic flow across channels, protein modification or interaction, and cell signaling. The continuum model described by the Poisson- Boltzmann (PB)/Poisson-Nernst-Planck (PNP) equations has made great contributions towards simulation of these processes. However, the model has shortcomings in its commonly used form and cannot capture (or cannot accurately capture) some important physical properties of the biological systems. Considerable efforts have been made to improve the continuum model to account for discrete particle interactions and to make progress in numerical methods to provide accurate and efficient simulations. This review will summarize recent main improvements in continuum modeling for biomolecular systems, with focus on the size-modified models, the coupling of the classical density functional theory and the PNP equations, the coupling of polar and nonpolar interactions, and numerical progress. Project supported by the National Natural Science Foundation of China (Grant No. 91230106) and the Chinese Academy of Sciences Program for Cross & Cooperative Team of the Science & Technology Innovation.

  9. Quantitative characterization of biomolecular assemblies and interactions using atomic force microscopy. (United States)

    Yang, Yong; Wang, Hong; Erie, Dorothy A


    Atomic force microscopy (AFM) has been applied in many biological investigations in the past 15 years. This review focuses on the application of AFM for quantitatively characterizing the structural and thermodynamic properties of protein-protein and protein-nucleic acid complexes. AFM can be used to determine the stoichiometries and association constants of multiprotein assemblies and to quantify changes in conformations of proteins and protein-nucleic acid complexes. In addition, AFM in solution permits the observation of the dynamic properties of biomolecular complexes and the measurement of intermolecular forces between biomolecules. Recent advances in cryogenic AFM, AFM on two-dimensional crystals, carbon nanotube probes, solution imaging, high-speed AFM, and manipulation capabilities enhance these applications by improving AFM resolution and the dynamic and operative capabilities of the AFM. These developments make AFM a powerful tool for investigating the biomolecular assemblies and interactions that govern gene regulation.

  10. [Research on the Screening Method of Soil Remediation Technology at Contaminated Sites and Its Application]. (United States)

    Bai, Li-ping; Luo, Yun; Liu, Li; Zhou, You-ya; Yan, Zeng-guang; Li, Fa-sheng


    Soil remediation technology screening is an important procedure in the supervision of contaminated sites. The efficiency and costs of contaminated site remediation will be directly affected by the applicability of soil remediation technology. The influencing factors include characteristics of contaminants, site conditions, remediation time and costs should be considered to determine the most applicable remediation technology. The remediation technology screening was commonly evaluated by the experienced expert in China, which limited the promotion and application of the decision making method. Based on the supervision requirements of contaminated sites and the research status at home and abroad, the screening method includes preliminary screening and explicit evaluation was suggested in this paper. The screening index system was constructed, and the extension theory was used to divide the technology grade. The extension theory could solve the problem of human interference in the evaluation process and index value assignment. A chromium residue contaminated site in China was selected as the study area, and the applicable remediation technologies were suggested by the screening method. The research results could provide a scientific and technological support for the supervision and management of contaminated sites in China.

  11. Electromagnetic radiation screening of microcircuits for long life applications (United States)

    Brammer, W. G.; Erickson, J. J.; Levy, M. E.


    The utility of X-rays as a stimulus for screening high reliability semiconductor microcircuits was studied. The theory of the interaction of X-rays with semiconductor materials and devices was considered. Experimental measurements of photovoltages, photocurrents, and effects on specified parameters were made on discrete devices and on microcircuits. The test specimens included discrete devices with certain types of identified flaws and symptoms of flaws, and microcircuits exhibiting deviant electrical behavior. With a necessarily limited sample of test specimens, no useful correlation could be found between the X-ray-induced electrical response and the known or suspected presence of flaws.

  12. Computational Screening of Materials for Water Splitting Applications

    DEFF Research Database (Denmark)

    Castelli, Ivano Eligio

    Design new materials for energy production in a photoelectrochemical cell, where water is split into hydrogen and oxygen by solar light, is one possible solution to the problem of increasing energy demand and storage. A screening procedure based on ab-initio density functional theory calculations...... from Sun is using a photovoltaic cell that converts solar light into electricity. The absorption spectra of 70 experimentally known compounds, that are expected to be useful for light-to-electricity generation, have been calculated. 17 materials have been predicted to be promising for a single......-layer solar cell and 11 for a double-layer device....

  13. Stochastic Simulation of Biomolecular Reaction Networks Using the Biomolecular Network Simulator Software (United States)


    investigate the simulation of a biomolecular reaction network with BNS, a simple model of a generic self-assembling catalytic ligation reaction in a...Amino Acid Pools Nucleotide Triphosphate Pools Nucleotide Monophosphate Pools Ligation Reaction 1551 517 7 RESULTS Simulation of exemplar...and reaction r8 is the catalytic ligation reaction . In figures 5(B) through 5(F), both the time-averaged event rate for a single simulation run

  14. The application of tandem mass spectrometry to neonatal screening for inherited disorders of intermediary metabolism. (United States)

    Chace, Donald H; Kalas, Theodore A; Naylor, Edwin W


    This review is intended to serve as a practical guide for geneticists to current applications of tandem mass spectrometry to newborn screening. By making dried-blood spot analysis more sensitive, specific, reliable, and inclusive, tandem mass spectrometry has improved the newborn detection of inborn errors of metabolism. Its innate ability to detect and quantify multiple analytes from one prepared blood specimen in a single analysis permits broad recognition of amino acid, fatty acid, and organic acid disorders. An increasing number of newborn screening programs are either utilizing or conducting pilot studies with tandem mass spectrometry. It is therefore imperative that the genetics community be familiar with tandem mass spectrometric newborn screening.

  15. CRISPR-Cas9 for medical genetic screens: applications and future perspectives. (United States)

    Xue, Hui-Ying; Ji, Li-Juan; Gao, Ai-Mei; Liu, Ping; He, Jing-Dong; Lu, Xiao-Jie


    CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats-CRISPR associated nuclease 9) systems have emerged as versatile and convenient (epi)genome editing tools and have become an important player in medical genetic research. CRISPR-Cas9 and its variants such as catalytically inactivated Cas9 (dead Cas9, dCas9) and scaffold-incorporating single guide sgRNA (scRNA) have been applied in various genomic screen studies. CRISPR screens enable high-throughput interrogation of gene functions in health and diseases. Compared with conventional RNAi screens, CRISPR screens incur less off-target effects and are more versatile in that they can be used in multiple formats such as knockout, knockdown and activation screens, and can target coding and non-coding regions throughout the genome. This powerful screen platform holds the potential of revolutionising functional genomic studies in the near future. Herein, we introduce the mechanisms of (epi)genome editing mediated by CRISPR-Cas9 and its variants, introduce the procedures and applications of CRISPR screen in functional genomics, compare it with conventional screen tools and at last discuss current challenges and opportunities and propose future directions.

  16. Biomolecular Markers in Cancer of the Tongue

    Directory of Open Access Journals (Sweden)

    Daris Ferrari


    Full Text Available The incidence of tongue cancer is increasing worldwide, and its aggressiveness remains high regardless of treatment. Genetic changes and the expression of abnormal proteins have been frequently reported in the case of head and neck cancers, but the little information that has been published concerning tongue tumours is often contradictory. This review will concentrate on the immunohistochemical expression of biomolecular markers and their relationships with clinical behaviour and prognosis. Most of these proteins are associated with nodal stage, tumour progression and metastases, but there is still controversy concerning their impact on disease-free and overall survival, and treatment response. More extensive clinical studies are needed to identify the patterns of molecular alterations and the most reliable predictors in order to develop tailored anti-tumour strategies based on the targeting of hypoxia markers, vascular and lymphangiogenic factors, epidermal growth factor receptors, intracytoplasmatic signalling and apoptosis.

  17. Nonequilibrium phase transitions in biomolecular signal transduction (United States)

    Smith, Eric; Krishnamurthy, Supriya; Fontana, Walter; Krakauer, David


    We study a mechanism for reliable switching in biomolecular signal-transduction cascades. Steady bistable states are created by system-size cooperative effects in populations of proteins, in spite of the fact that the phosphorylation-state transitions of any molecule, by means of which the switch is implemented, are highly stochastic. The emergence of switching is a nonequilibrium phase transition in an energetically driven, dissipative system described by a master equation. We use operator and functional integral methods from reaction-diffusion theory to solve for the phase structure, noise spectrum, and escape trajectories and first-passage times of a class of minimal models of switches, showing how all critical properties for switch behavior can be computed within a unified framework.

  18. Fundamentos biomoleculares de la diabetes mellitus

    Directory of Open Access Journals (Sweden)

    Katiana Mendoza


    Full Text Available La diabetes mellitus es una enfermedad endocrina con importantes implicaciones a nivel sistémico, como: angiopatía, neuropatía, retinopatía y nefropatía, entre otras. Estas  complicaciones tienen su origen en eventos biomoleculares desencadenados por la hiperglicemia.  La presente revisión de tema trata sobre la estructura y síntesis de la insulina en las células β del páncreas; los eventos moleculares y bioquímicos que activan su secreción como respuesta a una alta concentración de glucosa en sangre; la cascada de señalización generada por la unión de la insulina a su receptor sobre células diana; y las alteraciones metabólicas que los diferentes tipos de diabetes mellitus producen.

  19. Specificity quantification of biomolecular recognition and its implication for drug discovery (United States)

    Yan, Zhiqiang; Wang, Jin


    Highly efficient and specific biomolecular recognition requires both affinity and specificity. Previous quantitative descriptions of biomolecular recognition were mostly driven by improving the affinity prediction, but lack of quantification of specificity. We developed a novel method SPA (SPecificity and Affinity) based on our funneled energy landscape theory. The strategy is to simultaneously optimize the quantified specificity of the ``native'' protein-ligand complex discriminating against ``non-native'' binding modes and the affinity prediction. The benchmark testing of SPA shows the best performance against 16 other popular scoring functions in industry and academia on both prediction of binding affinity and ``native'' binding pose. For the target COX-2 of nonsteroidal anti-inflammatory drugs, SPA successfully discriminates the drugs from the diversity set, and the selective drugs from non-selective drugs. The remarkable performance demonstrates that SPA has significant potential applications in identifying lead compounds for drug discovery.

  20. Climate risk screening tools and their application: A guide to the guidance

    Energy Technology Data Exchange (ETDEWEB)

    Traerup, S.; Olhoff, A.


    Climate risk screening is an integral part of efforts to ascertain current and future vulnerabilities and risks related to climate change. It is a prerequisite for identifying and designing adaptation measures, and an important element in the process of integrating, or mainstreaming, climate change adaptation into development project, planning and policy processes. There is an increasing demand and attention among national stakeholders in developing countries to take into account potential implications of climate variability and change for planning and prioritizing of development strategies and activities. Subsequently, there is a need for user friendly guidance on climate risk screening tools and their potentials for application that targets developing country stakeholders. This need is amplified by the sheer volume of climate change mainstreaming guidance documents and risk screening and assessment tools available and currently under development. Against this background, this paper sets out to provide potential users in developing countries, including project and programme developers and managers, with an informational entry point to climate risk screening tools. The emphasis in this report is on providing: 1) An overview of available climate risk screening and assessment tools along with indications of the tools available and relevant for specific purposes and contexts (Section 3). 2) Examples of application of climate risk screening and assessment tools along with links to further information (Section 4). Before turning to the respective sections on available climate risk screening tools and examples of their application, a delimitation of the tools included in this paper is included in Section 2. This section also provides a brief overview of how climate screening and related tools fit into decision making steps at various planning and decision making levels in conjunction with an outline of overall considerations to make when choosing a tool. The paper is

  1. The fidelity of dynamic signaling by noisy biomolecular networks.

    Directory of Open Access Journals (Sweden)

    Clive G Bowsher

    Full Text Available Cells live in changing, dynamic environments. To understand cellular decision-making, we must therefore understand how fluctuating inputs are processed by noisy biomolecular networks. Here we present a general methodology for analyzing the fidelity with which different statistics of a fluctuating input are represented, or encoded, in the output of a signaling system over time. We identify two orthogonal sources of error that corrupt perfect representation of the signal: dynamical error, which occurs when the network responds on average to other features of the input trajectory as well as to the signal of interest, and mechanistic error, which occurs because biochemical reactions comprising the signaling mechanism are stochastic. Trade-offs between these two errors can determine the system's fidelity. By developing mathematical approaches to derive dynamics conditional on input trajectories we can show, for example, that increased biochemical noise (mechanistic error can improve fidelity and that both negative and positive feedback degrade fidelity, for standard models of genetic autoregulation. For a group of cells, the fidelity of the collective output exceeds that of an individual cell and negative feedback then typically becomes beneficial. We can also predict the dynamic signal for which a given system has highest fidelity and, conversely, how to modify the network design to maximize fidelity for a given dynamic signal. Our approach is general, has applications to both systems and synthetic biology, and will help underpin studies of cellular behavior in natural, dynamic environments.

  2. Mobile applications for handheld devices to screen and randomize acute stroke patients in clinical trials. (United States)

    Qureshi, Ai; Connelly, B; Abbott, Ei; Maland, E; Kim, J; Blake, J


    The availability of internet connectivity and mobile application software used by low-power handheld devices makes smart phones of unique value in time-sensitive clinical trials. Trial-specific applications can be downloaded by investigators from various mobile software distribution platforms or web applications delivered over HTTP. The Antihypertensive Treatment in Acute Cerebral Hemorrhage (ATACH) II investigators in collaboration with MentorMate released the ATACH-II Patient Recruitment mobile application available on iPhone, Android, and Blackberry in 2011. The mobile application provides tools for pre-screening, assessment of eligibility, and randomization of patients. Since the release of ATACH-II mobile application, the CLEAR-IVH (Clot Lysis Evaluating Accelerated Resolution of Intraventricular Hemorrhage) trial investigators have also adopted such a mobile application. The video-conferencing capabilities of the most recent mobile devices open up additional opportunities to involve central coordinating centers in the recruitment process in real time.

  3. Introduction and Application of Electrochemical Sensors Based on Screen-Printed Technology

    Institute of Scientific and Technical Information of China (English)


    @@ We report here the development of chemical sensors based on screen-printed technology in our research group to solve major analytical problems in environmental and clinical aspects. The purpose of the research is aimed at the enhancement of selectivity and sensitivity for analysis and monitoring of pollutants and analytes using novel chenically modified screen-printed electrodes. For example, an enzyme reactor coupled with a copper-plated screen-printed carbon electrode (CuSPE) was developed for glucose sensing. The electrocatalytic reduction of enzymatically produced H2O2 at the CuSPE was determined by flow injection analysis (FIA) in pH 7.4 PBS. The proposed method was applied to determine glucose content in fruit juice and clinical sample and satisfactory results with good recoveries were obtained. A thoroughly kinetics and mechanism study was also done for those systems that are verified in analytical applications.

  4. Introduction and Application of Electrochemical Sensors Based on Screen-Printed Technology

    Institute of Scientific and Technical Information of China (English)

    ZEN; Jyh-Myng


    We report here the development of chemical sensors based on screen-printed technology in our research group to solve major analytical problems in environmental and clinical aspects. The purpose of the research is aimed at the enhancement of selectivity and sensitivity for analysis and monitoring of pollutants and analytes using novel chenically modified screen-printed electrodes. For example, an enzyme reactor coupled with a copper-plated screen-printed carbon electrode (CuSPE) was developed for glucose sensing. The electrocatalytic reduction of enzymatically produced H2O2 at the CuSPE was determined by flow injection analysis (FIA) in pH 7.4 PBS. The proposed method was applied to determine glucose content in fruit juice and clinical sample and satisfactory results with good recoveries were obtained. A thoroughly kinetics and mechanism study was also done for those systems that are verified in analytical applications.  ……

  5. Biomolecular Modification of Inorganic Crystal Growth

    Energy Technology Data Exchange (ETDEWEB)

    De Yoreo, J J


    The fascinating shapes and hierarchical designs of biomineralized structures are an inspiration to materials scientists because of the potential they suggest for biomolecular control over materials synthesis. Conversely, the failure to prevent or limit tissue mineralization in the vascular, skeletal, and urinary systems is a common source of disease. Understanding the mechanisms by which organisms direct or limit crystallization has long been a central challenge to the biomineralization community. One prevailing view is that mineral-associated macromolecules are responsible for either inhibiting crystallization or initiating and stabilizing non-equilibrium crystal polymorphs and morphologies through interactions between anionic moieties and cations in solution or at mineralizing surfaces. In particular, biomolecules that present carboxyl groups to the growing crystal have been implicated as primary modulators of growth. Here we review the results from a combination of in situ atomic force microscopy (AFM) and molecular modeling (MM) studies to investigate the effect of specific interactions between carboxylate-rich biomolecules and atomic steps on crystal surfaces during the growth of carbonates, oxalates and phosphates of calcium. Specifically, we how the growth kinetics and morphology depend on the concentration of additives that include citrate, simple amino acids, synthetic Asp-rich polypeptides, and naturally occurring Asp-rich proteins found in both functional and pathological mineral tissues. The results reveal a consistent picture of shape modification in which stereochemical matching of modifiers to specific atomic steps drives shape modification. Inhibition and other changes in growth kinetics are shown to be due to a range of mechanisms that depend on chemistry and molecular size. Some effects are well described by classic crystal growth theories, but others, such as step acceleration due to peptide charge and hydrophylicity, were previously unrealized

  6. Screen printable flexible conductive nanocomposite polymer with applications to wearable sensors (United States)

    Chung, D.; Khosla, A.; Gray, B. L.


    We have developed a conductive nanocomposite polymer that possesses both good conductivity and flexibility, and screen printed it onto fabric to realize wearable flexible electrodes and electronic routing. The conductive polymer consists of dispersed silver nanoparticles (90~210nm) in a screen printable plastisol polymer. The conductive polymer is conductive for weight-percentages above approximately 61 wt-% of Ag nanoparticles, and has a resistivity of 2.12×10-6 ohm·m at 70 wt-% of Ag nanoparticles. To test the screen printed conductive polymer's flexibility and its effect on conductivity, we measured the resistivity of the Ag-doped composite polymer at different bending angles (-90˚ ~ 90˚) with a 10° step angle at different wt-% of silver particles, and compared the results. We also tested washability of the screen printed conductive polymer as applied to fabric for long-term use in wearable sensors systems. We also used the screen printed Ag composite polymer to realize an example wearable system. Flexible wearable dry electrocardiogram (ECG) electrodes were developed and ECG signal was measured via the electrodes. The sensing ECG electrodes (3mm diameter circle) were chloridized to form Ag/AgCl electrodes. We measured an ECG signal using a simple right-leg driven ECG circuit and observed normal ECG signals even without application of electrolyte gel.

  7. Discoveries and application of prostate-specific antigen, and some proposals to optimize prostate cancer screening

    Directory of Open Access Journals (Sweden)

    Tokudome S


    Full Text Available Shinkan Tokudome,1 Ryosuke Ando,2 Yoshiro Koda,3 1Department of Nutritional Epidemiology, National Institute of Health and Nutrition, Shinjuku-ku, Tokyo, 2Department of Nephro-urology, Nagoya City University Graduate School of Medical Sciences, Mizuho-ku, Nagoya, 3Department of Forensic Medicine and Human Genetics, Kurume University School of Medicine, Kurume, Japan Abstract: The discoveries and application of prostate-specific antigen (PSA have been much appreciated because PSA-based screening has saved millions of lives of prostate cancer (PCa patients. Historically speaking, Flocks et al first identified antigenic properties in prostate tissue in 1960. Then, Barnes et al detected immunologic characteristics in prostatic fluid in 1963. Hara et al characterized γ-semino-protein in semen in 1966, and it has been proven to be identical to PSA. Subsequently, Ablin et al independently reported the presence of precipitation antigens in the prostate in 1970. Wang et al purified the PSA in 1979, and Kuriyama et al first applied an enzyme-linked immunosorbent assay for PSA in 1980. However, the positive predictive value with a cutoff figure of 4.0 ng/mL appeared substantially low (~30%. There are overdiagnoses and overtreatments for latent/low-risk PCa. Controversies exist in the PCa mortality-reducing effects of PSA screening between the European Randomized Study of Screening for Prostate Cancer (ERSPC and the US Prostate, Lung, Colorectal, and Ovarian (PLCO Cancer Screening Trial. For optimizing PCa screening, PSA-related items may require the following: 1 adjustment of the cutoff values according to age, as well as setting limits to age and screening intervals; 2 improving test performance using doubling time, density, and ratio of free: total PSA; and 3 fostering active surveillance for low-risk PCa with monitoring by PSA value. Other items needing consideration may include the following: 1 examinations of cell proliferation and cell cycle markers

  8. In situ monitoring of biomolecular processes in living systems using surface-enhanced Raman scattering (United States)

    Altunbek, Mine; Kelestemur, Seda; Culha, Mustafa


    Surface-enhanced Raman scattering (SERS) continues to strive to gather molecular level information from dynamic biological systems. It is our ongoing effort to utilize the technique for understanding of the biomolecular processes in living systems such as eukaryotic and prokaryotic cells. In this study, the technique is investigated to identify cell death mechanisms in 2D and 3D in vitro cell culture models, which is a very important process in tissue engineering and pharmaceutical applications. Second, in situ biofilm formation monitoring is investigated to understand how microorganisms respond to the environmental stimuli, which inferred information can be used to interfere with biofilm formation and fight against their pathogenic activity.

  9. Acoustic Droplet Ejection Applications for High-Throughput Screening of Infectious Agents. (United States)

    Rasmussen, Lynn; White, E Lucile; Bostwick, James R


    When acoustic droplet ejection technology was first introduced for high-throughput applications, it was used primarily for dispensing compounds dissolved in DMSO. The high precision and accuracy achieved for low-volume transfers in this application were noted by those working outside of the compound management area, and interest was generated in expanding the scope of the technology to include other liquid types. Later-generation instruments included calibrations for several aqueous buffers that were applicable to the life sciences. The High Throughput Screening Center at Southern Research has made use of this range of liquid calibrations for the Infectious Disease Program. The original calibration for DMSO has allowed the preparation of assay-ready plates that can be sent to remote locations. This process was used as part of the collaboration between Southern Research and Galveston National Laboratory, University of Texas Medical Branch, to develop high-throughput screening for biological safety level 4 containment and to provide compounds for two pilot screens that were run there with BSL-4-level pathogens. The aqueous calibrations have been instrumental in miniaturizing assays used for infectious disease, such as qPCR, tissue culture infectious dose 50, and bacterial motility, to make them compatible with HTS operations.

  10. The use of haptic interfaces and web services in crystallography: an application for a 'screen to beam' interface. (United States)

    Bruno, Andrew E; Soares, Alexei S; Owen, Robin L; Snell, Edward H


    Haptic interfaces have become common in consumer electronics. They enable easy interaction and information entry without the use of a mouse or keyboard. The work presented here illustrates the application of a haptic interface to crystallization screening in order to provide a natural means for visualizing and selecting results. By linking this to a cloud-based database and web-based application program interface, the same application shifts the approach from 'point and click' to 'touch and share', where results can be selected, annotated and discussed collaboratively. In the crystallographic application, given a suitable crystallization plate, beamline and robotic end effector, the resulting information can be used to close the loop between screening and X-ray analysis, allowing a direct and efficient 'screen to beam' approach. The application is not limited to the area of crystallization screening; 'touch and share' can be used by any information-rich scientific analysis and geographically distributed collaboration.

  11. Development and applicability of a ready-to-use PCR system for GMO screening. (United States)

    Rosa, Sabrina F; Gatto, Francesco; Angers-Loustau, Alexandre; Petrillo, Mauro; Kreysa, Joachim; Querci, Maddalena


    With the growing number of GMOs introduced to the market, testing laboratories have seen their workload increase significantly. Ready-to-use multi-target PCR-based detection systems, such as pre-spotted plates (PSP), reduce analysis time while increasing capacity. This paper describes the development and applicability to GMO testing of a screening strategy involving a PSP and its associated web-based Decision Support System. The screening PSP was developed to detect all GMOs authorized in the EU in one single PCR experiment, through the combination of 16 validated assays. The screening strategy was successfully challenged in a wide inter-laboratory study on real-life food/feed samples. The positive outcome of this study could result in the adoption of a PSP screening strategy across the EU; a step that would increase harmonization and quality of GMO testing in the EU. Furthermore, this system could represent a model for other official control areas where high-throughput DNA-based detection systems are needed.

  12. The Effect of Screen Size on Mobile Phone User Comprehension of Health Information and Application Structure: An Experimental Approach. (United States)

    Al Ghamdi, Ebtisam; Yunus, Faisal; Da'ar, Omar; El-Metwally, Ashraf; Khalifa, Mohamed; Aldossari, Bakheet; Househ, Mowafa


    This research analyzes the impact of mobile phone screen size on user comprehension of health information and application structure. Applying experimental approach, we asked randomly selected users to read content and conduct tasks on a commonly used diabetes mobile application using three different mobile phone screen sizes. We timed and tracked a number of parameters, including correctness, effectiveness of completing tasks, content ease of reading, clarity of information organization, and comprehension. The impact of screen size on user comprehension/retention, clarity of information organization, and reading time were mixed. It is assumed on first glance that mobile screen size would affect all qualities of information reading and comprehension, including clarity of displayed information organization, reading time and user comprehension/retention of displayed information, but actually the screen size, in this experimental research, did not have significant impact on user comprehension/retention of the content or on understanding the application structure. However, it did have significant impact on clarity of information organization and reading time. Participants with larger screen size took shorter time reading the content with a significant difference in the ease of reading. While there was no significant difference in the comprehension of information or the application structures, there were a higher task completion rate and a lower number of errors with the bigger screen size. Screen size does not directly affect user comprehension of health information. However, it does affect clarity of information organization, reading time and user's ability to recall information.

  13. Time-resolved methods in biophysics. 9. Laser temperature-jump methods for investigating biomolecular dynamics. (United States)

    Kubelka, Jan


    Many important biochemical processes occur on the time-scales of nanoseconds and microseconds. The introduction of the laser temperature-jump (T-jump) to biophysics more than a decade ago opened these previously inaccessible time regimes up to direct experimental observation. Since then, laser T-jump methodology has evolved into one of the most versatile and generally applicable methods for studying fast biomolecular kinetics. This perspective is a review of the principles and applications of the laser T-jump technique in biophysics. A brief overview of the T-jump relaxation kinetics and the historical development of laser T-jump methodology is presented. The physical principles and practical experimental considerations that are important for the design of the laser T-jump experiments are summarized. These include the Raman conversion for generating heating pulses, considerations of size, duration and uniformity of the temperature jump, as well as potential adverse effects due to photo-acoustic waves, cavitation and thermal lensing, and their elimination. The laser T-jump apparatus developed at the NIH Laboratory of Chemical Physics is described in detail along with a brief survey of other laser T-jump designs in use today. Finally, applications of the laser T-jump in biophysics are reviewed, with an emphasis on the broad range of problems where the laser T-jump methodology has provided important new results and insights into the dynamics of the biomolecular processes.

  14. Biomolecular detection using a metal semiconductor field effect transistor (United States)

    Estephan, Elias; Saab, Marie-Belle; Buzatu, Petre; Aulombard, Roger; Cuisinier, Frédéric J. G.; Gergely, Csilla; Cloitre, Thierry


    In this work, our attention was drawn towards developing affinity-based electrical biosensors, using a MESFET (Metal Semiconductor Field Effect Transistor). Semiconductor (SC) surfaces must be prepared before the incubations with biomolecules. The peptides route was adapted to exceed and bypass the limits revealed by other types of surface modification due to the unwanted unspecific interactions. As these peptides reveal specific recognition of materials, then controlled functionalization can be achieved. Peptides were produced by phage display technology using a library of M13 bacteriophage. After several rounds of bio-panning, the phages presenting affinities for GaAs SC were isolated; the DNA of these specific phages were sequenced, and the peptide with the highest affinity was synthesized and biotinylated. To explore the possibility of electrical detection, the MESFET fabricated with the GaAs SC were used to detect the streptavidin via the biotinylated peptide in the presence of the bovine Serum Albumin. After each surface modification step, the IDS (current between the drain and the source) of the transistor was measured and a decrease in the intensity was detected. Furthermore, fluorescent microscopy was used in order to prove the specificity of this peptide and the specific localisation of biomolecules. In conclusion, the feasibility of producing an electrical biosensor using a MESFET has been demonstrated. Controlled placement, specific localization and detection of biomolecules on a MESFET transistor were achieved without covering the drain and the source. This method of functionalization and detection can be of great utility for biosensing application opening a new way for developing bioFETs (Biomolecular Field-Effect Transistor).

  15. The HADDOCK web server for data-driven biomolecular docking

    NARCIS (Netherlands)

    de Vries, S.J.; van Dijk, M.; Bonvin, A.M.J.J.


    Computational docking is the prediction or modeling of the three-dimensional structure of a biomolecular complex, starting from the structures of the individual molecules in their free, unbound form. HADDOC K is a popular docking program that takes a datadriven approach to docking, with support for

  16. Transient response characteristics in a biomolecular integral controller. (United States)

    Sen, Shaunak


    The cellular behaviour of perfect adaptation is achieved through the use of an integral control element in the underlying biomolecular circuit. It is generally unclear how integral action affects the important aspect of transient response in these biomolecular systems, especially in light of the fact that it typically deteriorates the transient response in engineering contexts. To address this issue, the authors investigated the transient response in a computational model of a simple biomolecular integral control system involved in bacterial signalling. They find that the transient response can actually speed up as the integral gain parameter increases. On further analysis, they find that the underlying dynamics are composed of slow and fast modes and the speed-up of the transient response is because of the speed-up of the slow-mode dynamics. Finally, they note how an increase in the integral gain parameter also leads to a decrease in the amplitude of the transient response, consistent with the overall improvement in the transient response. These results should be useful in understanding the overall effect of integral action on system dynamics, particularly for biomolecular systems.

  17. Exposing biomolecular properties one molecule at a time

    NARCIS (Netherlands)

    Elmalk, Abdalmohsen


    The work described in this thesis was aimed at the study of the functional properties of (isolated and purified) biomolecular systems at the single-molecule level. Two prerequisites are essential for successfully achieving this goal. First of all, single biomolecules should be observable, which mean

  18. From dynamics to structure and function of model biomolecular systems

    NARCIS (Netherlands)

    Fontaine-Vive-Curtaz, F.


    The purpose of this thesis was to extend recent works on structure and dynamics of hydrogen bonded crystals to model biomolecular systems and biological processes. The tools that we have used are neutron scattering (NS) and density functional theory (DFT) and force field (FF) based simulation method

  19. Biomolecular recognition mechanisms studied by NMR spectroscopy and MD simulations

    NARCIS (Netherlands)

    Hsu, Shang-Te Danny


    This thesis describes the use of solution Nuclear Magnetic Resonance (NMR) spectroscopy and Molecular Dynamics (MD) simulations to study the mechanism of biomolecular recognition with two model systems: i) lipid II-binding lantibiotics (lanthionine-containing antibiotics) and ii) the human immunodef

  20. Screening and metamodeling of computer experiments with functional outputs. Application to thermal-hydraulic computations

    CERN Document Server

    Auder, Benjamin; Iooss, Bertrand; Marques, Michel


    To perform uncertainty, sensitivity or optimization analysis on scalar variables calculated by a cpu time expensive computer code, a widely accepted methodology consists in first identifying the most influential uncertain inputs (by screening techniques), and then in replacing the cpu time expensive model by a cpu inexpensive mathematical function, called a metamodel. This paper extends this methodology to the functional output case, for instance when the model output variables are curves. The screening approach is based on the analysis of variance and principal component analysis of output curves. The functional metamodeling consists in a curve classification step, a dimension reduction step, then a classical metamodeling step. An industrial nuclear reactor application (dealing with uncertainties in the pressurized thermal shock analysis) illustrates all these steps.

  1. Interacting with the biomolecular solvent accessible surface via a haptic feedback device

    Directory of Open Access Journals (Sweden)

    Hayward Steven


    Full Text Available Abstract Background From the 1950s computer based renderings of molecules have been produced to aid researchers in their understanding of biomolecular structure and function. A major consideration for any molecular graphics software is the ability to visualise the three dimensional structure of the molecule. Traditionally, this was accomplished via stereoscopic pairs of images and later realised with three dimensional display technologies. Using a haptic feedback device in combination with molecular graphics has the potential to enhance three dimensional visualisation. Although haptic feedback devices have been used to feel the interaction forces during molecular docking they have not been used explicitly as an aid to visualisation. Results A haptic rendering application for biomolecular visualisation has been developed that allows the user to gain three-dimensional awareness of the shape of a biomolecule. By using a water molecule as the probe, modelled as an oxygen atom having hard-sphere interactions with the biomolecule, the process of exploration has the further benefit of being able to determine regions on the molecular surface that are accessible to the solvent. This gives insight into how awkward it is for a water molecule to gain access to or escape from channels and cavities, indicating possible entropic bottlenecks. In the case of liver alcohol dehydrogenase bound to the inhibitor SAD, it was found that there is a channel just wide enough for a single water molecule to pass through. Placing the probe coincident with crystallographic water molecules suggests that they are sometimes located within small pockets that provide a sterically stable environment irrespective of hydrogen bonding considerations. Conclusion By using the software, named HaptiMol ISAS (available from, one can explore the accessible surface of biomolecules using a three-dimensional input device to gain insights into the shape and water

  2. Development of design, qualification, screening, and application requirements for plastic encapsulated solid-state devices for space applications (United States)


    Test data were collected on 1035 plastic encapsulated devices and 75 hermetically scaled control group devices that were purchased from each of five different manufacturers in the categories of (1) low power Schottsky TTL (bipolar) digital circuits; (2) CMOS digital circuits; (3) operational amplifier linear circuits; and (4) NPN transistors. These parts were subjected to three different initial screening conditions, then to extended life testing, to determine any possible advantages or trends for any particular screen. Several tests were carried out in the areas of flammability testing, humidity testing, high pressure steam (auroclave) testing, and high temperature storage testing. Test results are presented. Procurement and application considerations for use of plastic encapsulated semiconductors are presented and a statistical analysis program written to study the log normal distributions resulting from life testing is concluded.

  3. Biomolecular detection at ssDNA-conjugated nanoparticles by nano-impact electrochemistry. (United States)

    Karimi, Anahita; Hayat, Akhtar; Andreescu, Silvana


    We describe the use of ssDNA functionalized silver nanoparticle (AgNP) probes for quantitative investigation of biorecognition and real time detection of biomolecular targets using nano-impact electrochemistry. The method is based on measurements of the individual collision events between ssDNA aptamer-functionalized AgNPs and a carbon fiber miroelectrode (CFME). Specific binding events of target analyte induced collision frequency changes enabling ultrasensitive detection of the aptamer target in a single step. These changes are assigned to the surface coverage of the NP by the ssDNA aptamers and subsequent conformational changes of the aptamer probe which affect the electron transfer between the NP and the electrode surface. The method enables sensitive and selective detection of ochratoxin A (OTA), chosen here as a model target, with a limit of detection of 0.05nM and a relative standard deviation of 4.9%. The study provides a means of characterizing bioconjugation of AgNPs with aptamers and assessing biomolecular recognition events with high sensitivity and without the use of exogenous reagents or enzyme amplification steps. This methodology can be broadly applicable to other bioconjugated systems, biosensing and related bioanalytical applications.

  4. Engineering intracellular active transport systems as in vivo biomolecular tools.

    Energy Technology Data Exchange (ETDEWEB)

    Bachand, George David; Carroll-Portillo, Amanda


    Active transport systems provide essential functions in terms of cell physiology and metastasis. These systems, however, are also co-opted by invading viruses, enabling directed transport of the virus to and from the cell's nucleus (i.e., the site of virus replication). Based on this concept, fundamentally new approaches for interrogating and manipulating the inner workings of living cells may be achievable by co-opting Nature's active transport systems as an in vivo biomolecular tool. The overall goal of this project was to investigate the ability to engineer kinesin-based transport systems for in vivo applications, specifically the collection of effector proteins (e.g., transcriptional regulators) within single cells. In the first part of this project, a chimeric fusion protein consisting of kinesin and a single chain variable fragment (scFv) of an antibody was successfully produced through a recombinant expression system. The kinesin-scFv retained both catalytic and antigenic functionality, enabling selective capture and transport of target antigens. The incorporation of a rabbit IgG-specific scFv into the kinesin established a generalized system for functionalizing kinesin with a wide range of target-selective antibodies raised in rabbits. The second objective was to develop methods of isolating the intact microtubule network from live cells as a platform for evaluating kinesin-based transport within the cytoskeletal architecture of a cell. Successful isolation of intact microtubule networks from two distinct cell types was demonstrated using glutaraldehyde and methanol fixation methods. This work provides a platform for inferring the ability of kinesin-scFv to function in vivo, and may also serve as a three-dimensional scaffold for evaluating and exploiting kinesin-based transport for nanotechnological applications. Overall, the technology developed in this project represents a first-step in engineering active transport system for in vivo

  5. Screening of As-accumulating plants using a foliar application and a native accumulation of As. (United States)

    Zhang, Z; Sugawara, K; Hatayama, M; Huang, Y; Inoue, Chihiro


    The discovery of novel accumulating plants is useful for efficient phytoremediation due to the demands of various conditions of impacted sites such as land use, soil properties, concentration of pollutants, and climate. In the present study, we investigated foliar application or a field with highly bioavailable arsenic (As) to screen As-accumulating plants. Plants grown in the downstream of a hot springs area were analyzed for native As accumulation and As foliar application, and the rhizosphere soils were collected. The water-soluble As in the rhizosphere soils had a high average, 144 microg/kg, whereas total As was similar to normal soil in Japan. Among 34 herbaceous plants and 17 woody plants, Chelidonium majus var. asiaticum accumulated a relatively high As level, 8.07 mg/kg DW (93.6% of As added), that was not revealed by native accumulation. In a further pot experiment, C. majus accumulated a moderately high As level (314 mg/kg DW) in the roots but not in the shoot (30.1 mg/kg DW), and exhibited a low transfer factor (TF = 0.096). Thus, a foliar application would be a simple and high-throughput method to screen plants that accumulate and tolerate As. C. majus would be useful as a tool for phytostabilization of As.

  6. Applications in radiation therapy of a scintillating screen viewed by a CCD camera

    CERN Document Server

    Schippers, J M; Luijk, P V


    A two-dimensional (2D) dosimetry system has been designed for position-sensitive dose-measurement applications in modern radiation therapy. The system consists of a scintillating screen (Gd sub 2 O sub 2 S : Tb), observed by a low-noise CCD camera with a long integration time. The system allows reliable and accurate simultaneous 2D imaging of therapeutic dose distributions in the scintillator with sub millimeter spatial resolution. This system has been applied successfully at different applications in radiation therapy. Results of dose measurements in a treatment modality using a scanning proton beam are reported. It is shown that a quick and reliable measurement can be done. The screen+CCD system has proven to perform accurate dosimetry in applications where beams with a small (1-5 mm) diameter are used and where absolute dosimetry by means of standard ionization chambers is not possible due to their relatively large size. For the routine measurements of the alignment of therapeutic beams with respect to the...

  7. Considerations for the design and reporting of enzyme assays in high-throughput screening applications

    Directory of Open Access Journals (Sweden)

    Michael G. Acker


    Full Text Available This review describes the key steps and methods which are used to develop enzyme assays suitable for high-throughput screening (HTS applications. The goals of HTS enzyme assays are defined relative to lower-throughput bench top assays and important aspects which go into constructing robust and sensitive enzyme assays are described. Methods that have been applied to common enzyme classes are reviewed and pitfalls related to assay artifacts are discussed. We also suggest a reporting format to describe the steps in HTS enzyme assays.

  8. Cathode material for lithium ion accumulators prepared by screen printing for Smart Textile applications (United States)

    Syrový, T.; Kazda, T.; Syrová, L.; Vondrák, J.; Kubáč, L.; Sedlaříková, M.


    The presented study is focused on the development of LiFePO4 based cathode for thin and flexible screen printed secondary lithium based accumulators. An ink formulation was developed for the screen printing technique, which enabled mass production of accumulator's cathode for Smart Label and Smart Textile applications. The screen printed cathode was compared with an electrode prepared by the bar coating technique using an ink formulation based on the standard approach of ink composition. Obtained LiFePO4 cathode layers were characterized by scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDS) and galvanostatic charge/discharge measurements at different loads. The discharge capacity, capacity retention and stability at a high C rate of the LiFePO4 cathode were improved when Super P and PVDF were replaced by conductive polymers PEDOT:PSS. The achieved capacity during cycling at various C rates was approximately the same at the beginning and at the end, and it was about 151 mAh/g for cycling under 1C. The obtained results of this novelty electrode layer exceed the parameters of several electrode layers based on LiFePO4 published in literature in terms of capacity, cycling stability and overcomes them in terms of simplicity/industrial process ability of cathode layer fabrication and electrode material preparation.

  9. Survey and screening of intermediate-size photovoltaic total energy and electric applications

    Energy Technology Data Exchange (ETDEWEB)

    Rattin, E.J.


    One of the principal objectives of this photovoltaic mission analysis effort has been to identify and evaluate applications for photovoltaic solar energy conversion that could lead to significant contributions to the national energy supply and that would provide attractive opportunities for application experiments aimed at stimulating the adoption of photovoltaic technology. The scope of the study has included applications both for electric-only photovoltaic (PV) systems and for photovoltaic total energy systems (PTES), i.e., systems that provide both photovoltaic electricity and solar thermal energy to meet all or part of the energy demand at a single load point or a group of related load points. In either case, both flat-plate and concentrating systems have been considered and it has been assumed that the thermal energy is collected in and transported by the fluid used in an active cooling system for the photovoltaic cells. Because the efficiency of photovoltaic devices decreases rapidly with increasing temperature and because the operational lifetime of such devices is reduced by prolonged operation at elevated temperatures, a practical upper limit of about 200/sup 0/C (400/sup 0/F) was assumed for the temperature at which arrays can be allowed to be operated. This limitation, in turn, places an upper bound on the temperature at which solar thermal energy is available in PTES applications. An initial screening aimed at identifying the most promising applications has therefore been required, with the expectation that detailed evaluation will be made of only the higher-ranking candidates. A description of the screening procedure that was adopted and a discussion of the results are presented.

  10. A method to screen and evaluate tissue adhesives for joint repair applications

    Directory of Open Access Journals (Sweden)

    Dehne Tilo


    Full Text Available Abstract Background Tissue adhesives are useful means for various medical procedures. Since varying requirements cause that a single adhesive cannot meet all needs, bond strength testing remains one of the key applications used to screen for new products and study the influence of experimental variables. This study was conducted to develop an easy to use method to screen and evaluate tissue adhesives for tissue engineering applications. Method Tissue grips were designed to facilitate the reproducible production of substrate tissue and adhesive strength measurements in universal testing machines. Porcine femoral condyles were used to generate osteochondral test tissue cylinders (substrates of different shapes. Viability of substrates was tested using PI/FDA staining. Self-bonding properties were determined to examine reusability of substrates (n = 3. Serial measurements (n = 5 in different operation modes (OM were performed to analyze the bonding strength of tissue adhesives in bone (OM-1 and cartilage tissue either in isolation (OM-2 or under specific requirements in joint repair such as filling cartilage defects with clinical applied fibrin/PLGA-cell-transplants (OM-3 or tissues (OM-4. The efficiency of the method was determined on the basis of adhesive properties of fibrin glue for different assembly times (30 s, 60 s. Seven randomly generated collagen formulations were analyzed to examine the potential of method to identify new tissue adhesives. Results Viability analysis of test tissue cylinders revealed vital cells (>80% in cartilage components even 48 h post preparation. Reuse (n = 10 of test substrate did not significantly change adhesive characteristics. Adhesive strength of fibrin varied in different test settings (OM-1: 7.1 kPa, OM-2: 2.6 kPa, OM-3: 32.7 kPa, OM-4: 30.1 kPa and was increasing with assembly time on average (2.4-fold. The screening of the different collagen formulations revealed a substance with significant

  11. fireball/amber: An Efficient Local-Orbital DFT QM/MM Method for Biomolecular Systems. (United States)

    Mendieta-Moreno, Jesús I; Walker, Ross C; Lewis, James P; Gómez-Puertas, Paulino; Mendieta, Jesús; Ortega, José


    In recent years, quantum mechanics/molecular mechanics (QM/MM) methods have become an important computational tool for the study of chemical reactions and other processes in biomolecular systems. In the QM/MM technique, the active region is described by means of QM calculations, while the remainder of the system is described using a MM approach. Because of the complexity of biomolecules and the desire to achieve converged sampling, it is important that the QM method presents a good balance between accuracy and computational efficiency. Here, we report on the implementation of a QM/MM technique that combines a DFT approach specially designed for the study of complex systems using first-principles molecular dynamics simulations (fireball) with the amber force fields and simulation programs. We also present examples of the application of this QM/MM approach to three representative biomolecular systems: the analysis of the effect of electrostatic embedding in the behavior of a salt bridge between an aspartic acid and a lysine residue, a study of the intermediate states for the triosephosphate isomerase catalyzed conversion of dihydroxyacetone phosphate into glyceraldehyde 3-phosphate, and the detailed description, using DFT QM/MM molecular dynamics, of the cleavage of a phosphodiester bond in RNA catalyzed by the enzyme RNase A.

  12. The interplay of intrinsic and extrinsic bounded noises in biomolecular networks.

    Directory of Open Access Journals (Sweden)

    Giulio Caravagna

    Full Text Available After being considered as a nuisance to be filtered out, it became recently clear that biochemical noise plays a complex role, often fully functional, for a biomolecular network. The influence of intrinsic and extrinsic noises on biomolecular networks has intensively been investigated in last ten years, though contributions on the co-presence of both are sparse. Extrinsic noise is usually modeled as an unbounded white or colored gaussian stochastic process, even though realistic stochastic perturbations are clearly bounded. In this paper we consider Gillespie-like stochastic models of nonlinear networks, i.e. the intrinsic noise, where the model jump rates are affected by colored bounded extrinsic noises synthesized by a suitable biochemical state-dependent Langevin system. These systems are described by a master equation, and a simulation algorithm to analyze them is derived. This new modeling paradigm should enlarge the class of systems amenable at modeling. We investigated the influence of both amplitude and autocorrelation time of a extrinsic Sine-Wiener noise on: (i the Michaelis-Menten approximation of noisy enzymatic reactions, which we show to be applicable also in co-presence of both intrinsic and extrinsic noise, (ii a model of enzymatic futile cycle and (iii a genetic toggle switch. In (ii and (iii we show that the presence of a bounded extrinsic noise induces qualitative modifications in the probability densities of the involved chemicals, where new modes emerge, thus suggesting the possible functional role of bounded noises.

  13. Combining vibrational biomolecular spectroscopy with chemometric techniques for the study of response and sensitivity of molecular structures/functional groups mainly related to lipid biopolymer to various processing applications. (United States)

    Yu, Gloria Qingyu; Yu, Peiqiang


    The objectives of this project were to (1) combine vibrational spectroscopy with chemometric multivariate techniques to determine the effect of processing applications on molecular structural changes of lipid biopolymer that mainly related to functional groups in green- and yellow-type Crop Development Centre (CDC) pea varieties [CDC strike (green-type) vs. CDC meadow (yellow-type)] that occurred during various processing applications; (2) relatively quantify the effect of processing applications on the antisymmetric CH3 ("CH3as") and CH2 ("CH2as") (ca. 2960 and 2923 cm(-1), respectively), symmetric CH3 ("CH3s") and CH2 ("CH2s") (ca. 2873 and 2954 cm(-1), respectively) functional groups and carbonyl C=O ester (ca. 1745 cm(-1)) spectral intensities as well as their ratios of antisymmetric CH3 to antisymmetric CH2 (ratio of CH3as to CH2as), ratios of symmetric CH3 to symmetric CH2 (ratio of CH3s to CH2s), and ratios of carbonyl C=O ester peak area to total CH peak area (ratio of C=O ester to CH); and (3) illustrate non-invasive techniques to detect the sensitivity of individual molecular functional group to the various processing applications in the recently developed different types of pea varieties. The hypothesis of this research was that processing applications modified the molecular structure profiles in the processed products as opposed to original unprocessed pea seeds. The results showed that the different processing methods had different impacts on lipid molecular functional groups. Different lipid functional groups had different sensitivity to various heat processing applications. These changes were detected by advanced molecular spectroscopy with chemometric techniques which may be highly related to lipid utilization and availability. The multivariate molecular spectral analyses, cluster analysis, and principal component analysis of original spectra (without spectral parameterization) are unable to fully distinguish the structural differences in the

  14. Solid electrodes in electroanalytical chemistry: present applications and prospects for high throughput screening of drug compounds. (United States)

    Uslu, Bengi; Ozkan, Sibel A


    This review summarizes recent progress in the development and application of solid electrodes to the screening of pharmaceutical dosage forms and biological fluids. Recent trends and advances in the electroanalytical chemistry of solid electrodes, microelectrodes and electrochemical sensors are reviewed. The varieties of solid electrodes and their basic physico-chemical properties and some specific characteristics including some supramolecular phenomena at their surface are surveyed. This review also includes some selected designs and their applications. Despite many reviews about individual solid electrodes in the literature, this review offers the first comprehensive report on all forms of solid electrodes. Special attention is paid to the possibilities of solid electrodes in high throughput electroanalytical investigation of drug dosage forms and biological samples using modern electroanalytical techniques. Various selected studies on these subjects since 1996 are reviewed in this paper.

  15. Characterization of SPAD Array for Multifocal High-Content Screening Applications

    Directory of Open Access Journals (Sweden)

    Anthony Tsikouras


    Full Text Available Current instruments used to detect specific protein-protein interactions in live cells for applications in high-content screening (HCS are limited by the time required to measure the lifetime. Here, a 32 × 1 single-photon avalanche diode (SPAD array was explored as a detector for fluorescence lifetime imaging (FLIM in HCS. Device parameters and characterization results were interpreted in the context of the application to determine if the SPAD array could satisfy the requirements of HCS-FLIM. Fluorescence lifetime measurements were performed using a known fluorescence standard; and the recovered fluorescence lifetime matched literature reported values. The design of a theoretical 32 × 32 SPAD array was also considered as a detector for a multi-point confocal scanning microscope.

  16. Graphene-based screen-printed electrochemical (bio)sensors and their applications: Efforts and criticisms. (United States)

    Cinti, Stefano; Arduini, Fabiana


    K.S. Novoselov in his Nobel lecture (December 8, 2010), described graphene as "more than just a flat crystal" and summarized the best possible impression of graphene with (i) it is the first example of 2D atomic crystals, (ii) it demonstrated unique electronic properties, thanks to charge carriers which mimic massless relativistic particles, and (iii) it has promise for a number of applications. The fascinating and unusual properties of this 2D material were indeed recently investigated and exploited in several disciplines including physics, medicine, and chemistry, indicating the extremely versatile and polyedric aspect of this nanomaterial. The utilization of nanomaterials, printed technology, and microfluidics in electroanalysis has resulted in a period that can be called the "Electroanalysis Renaissance" (Escarpa, 2012) in which graphene is without any doubt a forefront nanomaterial. The rise in affordable fabrication processes, along with the great dispersing attitude in a plenty of matrices, have made graphene powerful in large-scale production of electrochemical platforms. Herein, we overview the employment of graphene to customize and/or fabricate printable based (bio)sensors over the past 5 years, including several modification approaches such as drop casting, screen- and inkjet-printing, different strategies of graphene-based sensing, and applications as well. The objective of this review is to provide a critical perspective related to advantages and disadvantages of using graphene in biosensing tools, based on screen-printed sensors.

  17. Physics at the biomolecular interface fundamentals for molecular targeted therapy

    CERN Document Server

    Fernández, Ariel


    This book focuses primarily on the role of interfacial forces in understanding biological phenomena at the molecular scale. By providing a suitable statistical mechanical apparatus to handle the biomolecular interface, the book becomes uniquely positioned to address core problems in molecular biophysics. It highlights the importance of interfacial tension in delineating a solution to the protein folding problem, in unravelling the physico-chemical basis of enzyme catalysis and protein associations, and in rationally designing molecular targeted therapies. Thus grounded in fundamental science, the book develops a powerful technological platform for drug discovery, while it is set to inspire scientists at any level in their careers determined to address the major challenges in molecular biophysics. The acknowledgment of how exquisitely the structure and dynamics of proteins and their aqueous environment are related attests to the overdue recognition that biomolecular phenomena cannot be effectively understood w...

  18. Single-Molecule Pull-down FRET (SiMPull-FRET) to dissect the mechanisms of biomolecular machines (United States)

    Kahlscheuer, Matthew L.; Widom, Julia; Walter, Nils G.


    Spliceosomes are multi-megadalton RNA-protein complexes responsible for the faithful removal of non-coding segments (introns) from pre-messenger RNAs (pre-mRNAs), a process critical for the maturation of eukaryotic mRNAs for subsequent translation by the ribosome. Both the spliceosome and ribosome, as well as many other RNA and DNA processing machineries, contain central RNA components that endow biomolecular complexes with precise, sequence-specific nucleic acid recognition and versatile structural dynamics. Single molecule fluorescence (or Förster) resonance energy transfer (smFRET) microscopy is a powerful tool for the study of local and global conformational changes of both simple and complex biomolecular systems involving RNA. The integration of biochemical tools such as immunoprecipitation with advanced methods in smFRET microscopy and data analysis has opened up entirely new avenues towards studying the mechanisms of biomolecular machines isolated directly from complex biological specimens such as cell extracts. Here we detail the general steps for using prism-based total internal reflection fluorescence (TIRF) microscopy in exemplary single molecule pull-down FRET (SiMPull-FRET) studies of the yeast spliceosome and discuss the broad application potential of this technique. PMID:26068753

  19. Quantum dynamics of bio-molecular systems in noisy environments


    Huelga S.F.; Plenio M.B.


    We discuss three different aspects of the quantum dynamics of bio-molecular systems and more generally complex networks in the presence of strongly coupled environments. Firstly, we make a case for the systematic study of fundamental structural elements underlying the quantum dynamics of these systems, identify such elements and explore the resulting interplay of quantum dynamics and environmental decoherence. Secondly, we critically examine some existing approaches to the numerical descripti...

  20. Biomolecular recognition and detection using gold-based nanoprobes (United States)

    Crew, Elizabeth

    The ability to control the biomolecular interactions is important for developing bioanalytical probes used in biomolecule and biomarker detections. This work aims at a fundamental understanding of the interactions and reactivities involving DNA, miRNA, and amino acids using gold-based nanoparticles as nanoprobes, which has implications for developing new strategies for the early detection of diseases, such as cancer, and controlled delivery of drugs. Surface modifications of the nanoprobes with DNA, miRNA, and amino acids and the nanoprobe directed biomolecular reactivities, such as complementary-strand binding, enzymatic cutting and amino acid interactions, have been investigated. Among various analytical techniques employed for the analysis of the biomolecule-nanoprobe interactions, surface enhanced Raman scattering spectroscopy (SERS) has been demonstrated to provide a powerful tool for real time monitoring of the DNA assembly and enzymatic cutting processes in solutions. This demonstration harnesses the "hot-spot" characteristic tuned by the interparticle biomolecular-regulated interactions and distances. The assembly of gold nanoparticles has also been exploited as sensing thin films on chemiresistor arrays for the detection of volatile organic compounds, including biomarker molecules associated with diabetes. Important findings of the nanoprobes in delivering miRNA to cells, detecting DNA hybridization kinetics, discerning chiral recognition with enantiomeric cysteines, and sensing biomarker molecules with the nanostructured thin films will be discussed, along with their implications to enhancing sensitivity, selectivity and limits of detection.

  1. Retroactivity in the Context of Modularly Structured Biomolecular Systems (United States)

    Pantoja-Hernández, Libertad; Martínez-García, Juan Carlos


    Synthetic biology has intensively promoted the technical implementation of modular strategies in the fabrication of biological devices. Modules are considered as networks of reactions. The behavior displayed by biomolecular systems results from the information processes carried out by the interconnection of the involved modules. However, in natural systems, module wiring is not a free-of-charge process; as a consequence of interconnection, a reactive phenomenon called retroactivity emerges. This phenomenon is characterized by signals that propagate from downstream modules (the modules that receive the incoming signals upon interconnection) to upstream ones (the modules that send the signals upon interconnection). Such retroactivity signals, depending of their strength, may change and sometimes even disrupt the behavior of modular biomolecular systems. Thus, analysis of retroactivity effects in natural biological and biosynthetic systems is crucial to achieve a deeper understanding of how this interconnection between functionally characterized modules takes place and how it impacts the overall behavior of the involved cell. By discussing the modules interconnection in natural and synthetic biomolecular systems, we propose that such systems should be considered as quasi-modular. PMID:26137457

  2. Screening CO

    NARCIS (Netherlands)

    Ramírez, A.; Hagedoorn, S.; Kramers, L.; Wildenborg, T.; Hendriks, C.


    This paper describes the development and application of a methodology to screen and rank Dutch reservoirs suitable for long-term large scale CO2 storage. The screening focuses on off- and on-shore individual aquifers, gas and oil fields. In total 176 storage reservoirs have been taken int

  3. Printable Electrochemical Biosensors: A Focus on Screen-Printed Electrodes and Their Application. (United States)

    Yamanaka, Keiichiro; Vestergaard, Mun'delanji C; Tamiya, Eiichi


    In this review we present electrochemical biosensor developments, focusing on screen-printed electrodes (SPEs) and their applications. In particular, we discuss how SPEs enable simple integration, and the portability needed for on-field applications. First, we briefly discuss the general concept of biosensors and quickly move on to electrochemical biosensors. Drawing from research undertaken in this area, we cover the development of electrochemical DNA biosensors in great detail. Through specific examples, we describe the fabrication and surface modification of printed electrodes for sensitive and selective detection of targeted DNA sequences, as well as integration with reverse transcription-polymerase chain reaction (RT-PCR). For a more rounded approach, we also touch on electrochemical immunosensors and enzyme-based biosensors. Last, we present some electrochemical devices specifically developed for use with SPEs, including USB-powered compact mini potentiostat. The coupling demonstrates the practical use of printable electrode technologies for application at point-of-use. Although tremendous advances have indeed been made in this area, a few challenges remain. One of the main challenges is application of these technologies for on-field analysis, which involves complicated sample matrices.

  4. A Sensor-Enabled Smartphone Application to Collect Eating Behavior Data for Population Screening. (United States)

    Maramis, Christos; Moulos, Ioannis; Ioakeimidis, Ioannis; Nolstam, Jenny; Lekka, Irini; Bergh, Cecilia; Maglaveras, Nicos


    The worldwide extent of obesity and eating disorders (ED) today highlights the necessity for efficient treatment, but also early prevention of eating-related diseases. A promising category of therapeutic and preventive interventions comes from the domain of behavioral informatics (BI), whose purpose is to monitor and modify harmful behaviors - unhealthy eating in the particular case - with the help of information and communication technologies. Smartphones have already shown great promise in delivering such BI interventions in the field of obesity and ED. In fact, plenty of smartphone applications aiming to monitor and support the change of eating behavior with the help of built-in or external sensors have been proposed in the scientific literature. However, to the best of our knowledge, no smartphone application up to date has been designed to collect eating behavior data for the purpose of population screening against obesity or ED. In this work we describe a novel, sensor-enabled smartphone application that captures in-meal behavioral data from multiple subjects in a brief data collection process, with the end goal of recording, in detail, the user's eating style throughout a cooked meal. These data can later be employed for assessing the subjects' risk for obesity or ED. The proposed application has undergone preliminary evaluation with respect to its usability and technical soundness, yielding promising results.

  5. Printable Electrochemical Biosensors: A Focus on Screen-Printed Electrodes and Their Application

    Directory of Open Access Journals (Sweden)

    Keiichiro Yamanaka


    Full Text Available In this review we present electrochemical biosensor developments, focusing on screen-printed electrodes (SPEs and their applications. In particular, we discuss how SPEs enable simple integration, and the portability needed for on-field applications. First, we briefly discuss the general concept of biosensors and quickly move on to electrochemical biosensors. Drawing from research undertaken in this area, we cover the development of electrochemical DNA biosensors in great detail. Through specific examples, we describe the fabrication and surface modification of printed electrodes for sensitive and selective detection of targeted DNA sequences, as well as integration with reverse transcription-polymerase chain reaction (RT-PCR. For a more rounded approach, we also touch on electrochemical immunosensors and enzyme-based biosensors. Last, we present some electrochemical devices specifically developed for use with SPEs, including USB-powered compact mini potentiostat. The coupling demonstrates the practical use of printable electrode technologies for application at point-of-use. Although tremendous advances have indeed been made in this area, a few challenges remain. One of the main challenges is application of these technologies for on-field analysis, which involves complicated sample matrices.

  6. Applicability of Screening Tests for Oxytetracycline in the Milk of Three Breeds of Goats. (United States)

    Attaie, Rahmat; Bsharat, Mohammed; Mora-Gutierrez, Adela


    Antibiotics are widely used in animal husbandry, and the presence of antibiotic residues in milk is a health hazard. The objectives of this study were to determine residual amounts of oxytetracycline in the milk of three breeds of goats using high-pressure liquid chromatography (HPLC) analysis and screening tests. It was also essential to explore the safe withdrawal period of oxytetracycline in lactating goats and examine the applicability of Charm ROSA and SNAP screening tests. The qualitative results of these tests were compared with the quantitative results of the HPLC method. Fifteen milking does, five each from the Alpine, LaMancha, and Nubian breeds, were selected from the herd at Prairie View A&M University. Milk samples containing antibiotic residues were deproteinized by HCl and acetonitrile, and then oxytetracycline was extracted from the supernatant. The residues of oxytetracycline in goat's milk up to 110 h after injection were qualitatively detected using the Charm ROSA test. Similarly, the SNAP test detected the antibiotic residues in milk up to 110 h after treatment. The HPLC results indicated that oxytetracycline residues in milk from Alpine goats were below the tolerance level (300 ng/ml) 82 h after drug treatment (72 h for LaManchas, 58 h for Nubians); however, the results of the screening tests would indicate longer withdrawal periods for milk from the breeds of goats studied, which would result in economic losses to goat's milk producers. The results of this study also indicated that oxytetracycline was not stable in raw goat's milk at refrigeration temperature or during pasteurization and that the concentrations decreased significantly. Commercial goat's milk is usually exposed to several hours of refrigeration and then to pasteurization. The results of this study indicated that, if oxytetracycline was present in raw goat's milk, the concentration would decrease significantly before it was marketed.

  7. Automated toxicological screening reports of modified Agilent MSD Chemstation combined with Microsoft Visual Basic application programs. (United States)

    Choe, Sanggil; Kim, Suncheun; Choi, Hyeyoung; Choi, Hwakyoung; Chung, Heesun; Hwang, Bangyeon


    Agilent GC-MS MSD Chemstation offers automated library search report for toxicological screening using total ion chromatogram (TIC) and mass spectroscopy in normal mode. Numerous peaks appear in the chromatogram of biological specimen such as blood or urine and often large migrating peaks obscure small target peaks, in addition, any target peaks of low abundance regularly give wrong library search result or low matching score. As a result, retention time and mass spectrum of all the peaks in the chromatogram have to be checked to see if they are relevant. These repeated actions are very tedious and time-consuming to toxicologists. MSD Chemstation software operates using a number of macro files which give commands and instructions on how to work on and extract data from the chromatogram and spectroscopy. These macro files are developed by the own compiler of the software. All the original macro files can be modified and new macro files can be added to the original software by users. To get more accurate results with more convenient method and to save time for data analysis, we developed new macro files for reports generation and inserted new menus in the Enhanced Data Analysis program. Toxicological screening reports generated by these new macro files are in text mode or graphic mode and these reports can be generated with three different automated subtraction options. Text reports have Brief mode and Full mode and graphic reports have the option with or without mass spectrum mode. Matched mass spectrum and matching score for detected compounds are printed in reports by modified library searching modules. We have also developed an independent application program named DrugMan. This program manages drug groups, lists and parameters that are in use in MSD Chemstation. The incorporation of DrugMan with modified macro modules provides a powerful tool for toxicological screening and save a lot of valuable time on toxicological work.

  8. A fluorescence-based bioassay for antibacterials and its application in screening natural product extracts. (United States)

    Michels, Katharina; Heinke, Ramona; Schöne, Pia; Kuipers, Oscar P; Arnold, Norbert; Wessjohann, Ludger A


    The reliable assessment of the biological activity of a minor component embedded in a complex matrix of several hundred compounds is a difficult but common task in the search for natural product-based antibiotics, for example, by bioassay-guided fractionation. To quantify the antibiotic properties, it is necessary to assess the cell viability. Direct measurements use CFU counts, OD measurements or detection via fluorescent or reducible dyes. However, natural extracts often already possess intrinsic dye, fluorescent, reducing or protein denaturing properties, or they contain insoluble compounds or general protein-binding (tanning) polyphenols as disturbing features, while at the same time very little of the selective antibiotic sought after is present. A promising alternative is provided by intrinsically produced bright fluorescent proteins. In this paper, a rapid, robust and concentration-dependent assay for screening antibiotics with genetically modified mutants of Bacillus subtilis 168 (PabrB-iyfp) is presented. The Gram-positive bacteria exhibit a native fluorescence during their exponential growth phase due to the expression of improved yellow fluorescent protein. To demonstrate the applicability in the field of natural product research, several compounds and extracts were screened for antibacterial activity, with an emphasis on those from the fungal genus Hygrophorus (waxy caps).

  9. Expanding the Diversity of Imaging-Based RNAi Screen Applications Using Cell Spot Microarrays. (United States)

    Rantala, Juha K; Kwon, Sunjong; Korkola, James; Gray, Joe W


    Over the past decade, great strides have been made in identifying gene aberrations and deregulated pathways that are associated with specific disease states. These association studies guide experimental studies aimed at identifying the aberrant genes and networks that cause the disease states. This requires functional manipulation of these genes and networks in laboratory models of normal and diseased cells. One approach is to assess molecular and biological responses to high-throughput RNA interference (RNAi)-induced gene knockdown. These responses can be revealed by immunofluorescent staining for a molecular or cellular process of interest and quantified using fluorescence image analysis. These applications are typically performed in multiwell format, but are limited by high reagent costs and long plate processing times. These limitations can be mitigated by analyzing cells grown in cell spot microarray (CSMA) format. CSMAs are produced by growing cells on small (~200 mm diameter) spots with each spot carrying an siRNA with transfection reagent. The spacing between spots is only a few hundred micrometers, thus thousands of cell spots can be arranged on a single cell culture surface. These high-density cell cultures can be immunofluorescently stained with minimal reagent consumption and analyzed quickly using automated fluorescence microscopy platforms. This review covers basic aspects of imaging-based CSMA technology, describes a wide range of immunofluorescence assays that have already been implemented successfully for CSMA screening and suggests future directions for advanced RNAi screening experiments.

  10. Optical oxygen sensing systems for drug discovery applications: Respirometric Screening Technology (RST) (United States)

    Papkovsky, Dmitri B.; Hynes, James; Fernandes, Richard


    Quenched-fluorescence oxygen sensing allows non-chemical, reversible, real-time monitoring of molecular oxygen and rates of oxygen consumption in biological samples. Using this approach we have developed Respirometric Screening Technology (RST); a platform which facilitates the convenient analysis of cellular oxygen uptake. This in turn allows the investigation of compounds and processes which affect respiratory activity. The RST platform employs soluble phosphorescent oxygen-sensitive probes, which may be assessed in standard microtitter plates on a fluorescence plate reader. New formats of RST assays and time-resolved fluorescence detection instrumentation developed by Luxcel provide improvements in assay sensitivity, miniaturization and overall performance. RST has a diverse range of applications in drug discovery area including high throughput analysis of mitochondrial function; studies of mechanisms of toxicity and apoptosis; cell and animal based screening of compound libraries and environmental samples; and, sterility testing. RST has been successfully validated with a range of practical targets and adopted by several leading pharmaceutical companies.

  11. Efficient Theoretical Screening of Solid Sorbents for CO2 Capture Applications*

    Energy Technology Data Exchange (ETDEWEB)

    Duan, Yuhua; Luebke, David; Pennline, Henry


    By combining thermodynamic database mining with first principles density functional theory and phonon lattice dynamics calculations, a theoretical screening methodology to identify the most promising CO2 sorbent candidates from the vast array of possible solid materials has been proposed and validated. The ab initio thermodynamic technique has the advantage of allowing identification of thermodynamic properties of CO2 capture reactions without any experimental input beyond crystallographic structural information of the solid phases involved. For a given solid, the first step is to attempt to extract thermodynamic properties from thermodynamic databases and the available literatures. If the thermodynamic properties of the compound of interest are unknown, an ab initio thermodynamic approach is used to calculate them. These properties expressed conveniently as chemical potentials and heat of reactions, which obtained either from databases or from calculations, are further used for computing the thermodynamic reaction equilibrium properties of the CO2 absorption/desorption cycles. Only those solid materials for which lower capture energy costs are predicted at the desired process conditions are selected as CO2 sorbent candidates and are further considered for experimental validations. Solid sorbents containing alkali and alkaline earth metals have been reported in several previous studies to be good candidates for CO2 sorbent applications due to their high CO2 absorption capacity at moderate working temperatures. In addition to introducing our computational screening procedure, in this presentation we will summarize our results for solid systems composed by alkali and alkaline earth metal oxides, hydroxides, and carbon- ates/bicarbonates to validate our methodology. Additionally, applications of our computational method to mixed solid systems of Li2O with SiO2/ZrO2 with different mixing ratios, our preliminary results showed that increasing the Li2O/SiO2 ratio in

  12. Label-free screening of single biomolecules through resistive pulse sensing technology for precision medicine applications (United States)

    Harrer, S.; Kim, S. C.; Schieber, C.; Kannam, S.; Gunn, N.; Moore, S.; Scott, D.; Bathgate, R.; Skafidas, S.; Wagner, J. M.


    systems genomics has to be accompanied by an equally strong effort to develop next-generation DNA-sequencing and next-generation drug screening and design platforms. In that context lab-on-a-chip devices utilizing nanopore- and nanochannel based resistive pulse-sensing technology for DNA-sequencing and protein screening applications occupy a key role. This paper describes the status quo of resistive pulse sensing technology for these two application areas with a special focus on current technology trends and challenges ahead.

  13. Self-chemisorption of azurin on functionalized oxide surfaces for the implementation of biomolecular devices

    Energy Technology Data Exchange (ETDEWEB)

    Biasco, A.; Maruccio, G.; Visconti, P.; Bramanti, A.; Calogiuri, P.; Cingolani, R.; Rinaldi, R


    In this work, we investigate the formation of redox protein Azurin (Az) monolayers on functionalized oxygen exposing surfaces. These metallo-proteins mediate electron transfer in the denitrifying chain of Pseudomonas bacteria and exhibit self-assembly properties, therefore they are good candidates for bio-electronic applications. Azurin monolayers are self-assembled onto silane functionalized surfaces and characterized by atomic force microscopy (AFM). We show also that a biomolecular field effect transistor (FET) in the solid state can be implemented by interconnecting an Azurin monolayer immobilized on SiO{sub 2} with two gold nanoelectrodes. Transport experiments, carried out at room temperature and ambient pressure, show FET behavior with conduction modulated by the gate potential.

  14. In situ characterization of nanoparticle biomolecular interactions in complex biological media by flow cytometry (United States)

    Lo Giudice, Maria Cristina; Herda, Luciana M.; Polo, Ester; Dawson, Kenneth A.


    Nanoparticles interacting with, or derived from, living organisms are almost invariably coated in a variety of biomolecules presented in complex biological milieu, which produce a bio-interface or `biomolecular corona' conferring a biological identity to the particle. Biomolecules at the surface of the nanoparticle-biomolecule complex present molecular fragments that may be recognized by receptors of cells or biological barriers, potentially engaging with different biological pathways. Here we demonstrate that using intense fluorescent reporter binders, in this case antibodies bound to quantum dots, we can map out the availability of such recognition fragments, allowing for a rapid and meaningful biological characterization. The application in microfluidic flow, in small detection volumes, with appropriate thresholding of the detection allows the study of even complex nanoparticles in realistic biological milieu, with the emerging prospect of making direct connection to conditions of cell level and in vivo experiments.

  15. Computer programming and biomolecular structure studies: A step beyond internet bioinformatics. (United States)

    Likić, Vladimir A


    This article describes the experience of teaching structural bioinformatics to third year undergraduate students in a subject titled Biomolecular Structure and Bioinformatics. Students were introduced to computer programming and used this knowledge in a practical application as an alternative to the well established Internet bioinformatics approach that relies on access to the Internet and biological databases. This was an ambitious approach considering that the students mostly had a biological background. There were also time constraints of eight lectures in total and two accompanying practical sessions. The main challenge was that students had to be introduced to computer programming from a beginner level and in a short time provided with enough knowledge to independently solve a simple bioinformatics problem. This was accomplished with a problem directly relevant to the rest of the subject, concerned with the structure-function relationships and experimental techniques for the determination of macromolecular structure.

  16. Screening Systems and Decision Making at the Preschool Level: Application of a Comprehensive Validity Framework (United States)

    Kettler, Ryan J.; Feeney-Kettler, Kelly A.


    Universal screening is designed to be an efficient method for identifying preschool students with mental health problems, but prior to use, screening systems must be evaluated to determine their appropriateness within a specific setting. In this article, an evidence-based validity framework is applied to four screening systems for identifying…

  17. Scanning probe and optical tweezer investigations of biomolecular interactions

    Energy Technology Data Exchange (ETDEWEB)

    Rigby-Singleton, Shellie


    A complex array of intermolecular forces controls the interactions between and within biological molecules. The desire to empirically explore the fundamental forces has led to the development of several biophysical techniques. Of these, the atomic force microscope (AFM) and the optical tweezers have been employed throughout this thesis to monitor the intermolecular forces involved in biomolecular interactions. The AFM is a well-established force sensing technique capable of measuring biomolecular interactions at a single molecule level. However, its versatility has not been extrapolated to the investigation of a drug-enzyme complex. The energy landscape for the force induced dissociation of the DHFR-methotrexate complex was studied. Revealing an energy barrier to dissociation located {approx}0.3 nm from the bound state. Unfortunately, the AFM has a limited range of accessible loading rates and in order to profile the complete energy landscape alternative force sensing instrumentation should be considered, for example the BFP and optical tweezers. Thus, this thesis outlines the development and construction an optical trap capable of measuring intermolecular forces between biomolecules at the single molecule level. To demonstrate the force sensing abilities of the optical set up, proof of principle measurements were performed which investigate the interactions between proteins and polymer surfaces subjected to varying degrees of argon plasma treatment. Complementary data was gained from measurements performed independently by the AFM. Changes in polymer resistance to proteins as a response to changes in polymer surface chemistry were detected utilising both AFM and optical tweezers measurements. Finally, the AFM and optical tweezers were employed as ultrasensitive biosensors. Single molecule investigations of the antibody-antigen interaction between the cardiac troponin I marker and its complementary antibody, reveals the impact therapeutic concentrations of heparin

  18. Engineering biomolecular microenvironments for cell instructive biomaterials. (United States)

    Custódio, Catarina A; Reis, Rui L; Mano, João F


    Engineered cell instructive microenvironments with the ability to stimulate specific cellular responses are a topic of high interest in the fabrication and development of biomaterials for application in tissue engineering. Cells are inherently sensitive to the in vivo microenvironment that is often designed as the cell "niche." The cell "niche" comprising the extracellular matrix and adjacent cells, influences not only cell architecture and mechanics, but also cell polarity and function. Extensive research has been performed to establish new tools to fabricate biomimetic advanced materials for tissue engineering that incorporate structural, mechanical, and biochemical signals that interact with cells in a controlled manner and to recapitulate the in vivo dynamic microenvironment. Bioactive tunable microenvironments using micro and nanofabrication have been successfully developed and proven to be extremely powerful to control intracellular signaling and cell function. This Review is focused in the assortment of biochemical signals that have been explored to fabricate bioactive cell microenvironments and the main technologies and chemical strategies to encode them in engineered biomaterials with biological information.

  19. Application of pre-participation cardiovascular screening guidelines to novice older runners and endurance athletes

    Directory of Open Access Journals (Sweden)

    Justin R Abbatemarco


    Full Text Available Objectives: Despite robust growth in participation in marathons and endurance sports among older individuals, guidance regarding pre-participation cardiovascular evaluation of these athletes is lacking. The objective of this study was to assess the utility of currently available pre-participation cardiovascular evaluation guidelines as applied to a cohort of older novice endurance athletes. Methods: We applied data from 1457 novice runners and endurance athletes aged 35 years and older to two pre-participation screening tools, the American Heart Association/American College of Sports Medicine Pre-Participation Questionnaire and the 2001 Working Group recommendations for pre-participation screening of masters athletes (2001 Masters. Results: Application of the American Heart Association/American College of Sports Medicine Pre-Participation Questionnaire identified 42.1% for which pre-participation cardiovascular evaluation was indicated. Of those who met criteria, 51.5% reported completion of a healthcare evaluation. Application of the 2001 Masters guidelines identified 75.2% who qualified for pre-participation electrocardiogram and 34.0% for pre-participation stress testing. Of those who met 2001 Masters criteria for pre-participation testing, 43.7% and 24.6% underwent recommended electrocardiogram and stress testing, respectively. While there was modest concordance with recommendations for pre-participation evaluations based on both American Heart Association/American College of Sports Medicine Pre-Participation Questionnaire and 2001 Masters, only athlete age was independently associated with completion of a pre-participation healthcare evaluation and only athlete age and athlete’s participation in marathons were independently associated with pre-participation stress testing. Conclusion: Among older novice endurance athletes, application of the American Heart Association/American College of Sports Medicine Pre-Participation Questionnaire

  20. Application of pre-participation cardiovascular screening guidelines to novice older runners and endurance athletes (United States)

    Abbatemarco, Justin R; Bennett, Courtney; Bell, Adrian J; Dunne, Laura; Matsumura, Martin E


    Objectives: Despite robust growth in participation in marathons and endurance sports among older individuals, guidance regarding pre-participation cardiovascular evaluation of these athletes is lacking. The objective of this study was to assess the utility of currently available pre-participation cardiovascular evaluation guidelines as applied to a cohort of older novice endurance athletes. Methods: We applied data from 1457 novice runners and endurance athletes aged 35 years and older to two pre-participation screening tools, the American Heart Association/American College of Sports Medicine Pre-Participation Questionnaire and the 2001 Working Group recommendations for pre-participation screening of masters athletes (2001 Masters). Results: Application of the American Heart Association/American College of Sports Medicine Pre-Participation Questionnaire identified 42.1% for which pre-participation cardiovascular evaluation was indicated. Of those who met criteria, 51.5% reported completion of a healthcare evaluation. Application of the 2001 Masters guidelines identified 75.2% who qualified for pre-participation electrocardiogram and 34.0% for pre-participation stress testing. Of those who met 2001 Masters criteria for pre-participation testing, 43.7% and 24.6% underwent recommended electrocardiogram and stress testing, respectively. While there was modest concordance with recommendations for pre-participation evaluations based on both American Heart Association/American College of Sports Medicine Pre-Participation Questionnaire and 2001 Masters, only athlete age was independently associated with completion of a pre-participation healthcare evaluation and only athlete age and athlete’s participation in marathons were independently associated with pre-participation stress testing. Conclusion: Among older novice endurance athletes, application of the American Heart Association/American College of Sports Medicine Pre-Participation Questionnaire and 2001 Masters

  1. Theoretical description of biomolecular hydration - Application to A-DNA

    Energy Technology Data Exchange (ETDEWEB)

    Garcia, A.E.; Hummer, G. [Los Alamos National Laboratory, NM (United States); Soumpasis, D.M. [Max Planck Inst. for Biophysical Chemistry, Goettingen (Germany)


    The local density of water molecules around a biomolecule is constructed from calculated two- and three-points correlation functions of polar solvents in water using a Potential-of-Mean-Force (PMF) expansion. As a simple approximation, the hydration of all polar (including charged) groups in a biomolecule is represented by the hydration of water oxygen in bulk water, and the effect of non-polar groups on hydration are neglected, except for excluded volume effects. Pair and triplet correlation functions are calculated by molecular dynamics simulations. We present calculations of the structural hydration for ideal A-DNA molecules with sequences [d(CG){sub 5}]{sub 2} and [d(C{sub 5}G{sub 5})]{sub 2}. We find that this method can accurately reproduce the hydration patterns of A-DNA observed in neutron diffraction experiments on oriented DNA fibers.

  2. First-principles screening of complex transition metal hydrides for high temperature applications. (United States)

    Nicholson, Kelly M; Sholl, David S


    Metal hydrides with enhanced thermodynamic stability with respect to the associated binary hydrides are useful for high temperature applications in which highly stable materials with low hydrogen overpressures are desired. Though several examples of complex transition metal hydrides (CTMHs) with such enhanced stability are known, little thermodynamic or phase stability information is available for this materials class. In this work, we use semiautomated thermodynamic and phase diagram calculations based on density functional theory (DFT) and grand canonical linear programming (GCLP) methods to screen 102 ternary and quaternary CTMHs and 26 ternary saline hydrides in a library of over 260 metals, intermetallics, binary, and higher hydrides to identify materials that release hydrogen at higher temperatures than the associated binary hydrides and at elevated temperatures, T > 1000 K, for 1 bar H2 overpressure. For computational efficiency, we employ a tiered screening approach based first on solid phase ground state energies with temperature effects controlled via H2 gas alone and second on the inclusion of phonon calculations that correct solid phase free energies for temperature-dependent vibrational contributions. We successfully identified 13 candidate CTMHs including Eu2RuH6, Yb2RuH6, Ca2RuH6, Ca2OsH6, Ba2RuH6, Ba3Ir2H12, Li4RhH4, NaPd3H2, Cs2PtH4, K2PtH4, Cs3PtH5, Cs3PdH3, and Rb2PtH4. The most stable CTMHs tend to crystallize in the Sr2RuH6 cubic prototype structure and decompose to the pure elements and hydrogen rather than to intermetallic phases.

  3. A Seoul-Fluor-based bioprobe for lipid droplets and its application in image-based high throughput screening. (United States)

    Kim, Eunha; Lee, Sanghee; Park, Seung Bum


    We developed a novel fluorescent bioprobe (SF44) that can specifically visualize the cellular lipid droplets in in vitro and in vivo systems and illustrated the mechanistic rationale of its fluorogenic property. Its application to image-based high throughput screening led us to the identification of a new small-molecule modulator of lipid droplet formation.

  4. Knowledge based cluster ensemble for cancer discovery from biomolecular data. (United States)

    Yu, Zhiwen; Wongb, Hau-San; You, Jane; Yang, Qinmin; Liao, Hongying


    The adoption of microarray techniques in biological and medical research provides a new way for cancer diagnosis and treatment. In order to perform successful diagnosis and treatment of cancer, discovering and classifying cancer types correctly is essential. Class discovery is one of the most important tasks in cancer classification using biomolecular data. Most of the existing works adopt single clustering algorithms to perform class discovery from biomolecular data. However, single clustering algorithms have limitations, which include a lack of robustness, stability, and accuracy. In this paper, we propose a new cluster ensemble approach called knowledge based cluster ensemble (KCE) which incorporates the prior knowledge of the data sets into the cluster ensemble framework. Specifically, KCE represents the prior knowledge of a data set in the form of pairwise constraints. Then, the spectral clustering algorithm (SC) is adopted to generate a set of clustering solutions. Next, KCE transforms pairwise constraints into confidence factors for these clustering solutions. After that, a consensus matrix is constructed by considering all the clustering solutions and their corresponding confidence factors. The final clustering result is obtained by partitioning the consensus matrix. Comparison with single clustering algorithms and conventional cluster ensemble approaches, knowledge based cluster ensemble approaches are more robust, stable and accurate. The experiments on cancer data sets show that: 1) KCE works well on these data sets; 2) KCE not only outperforms most of the state-of-the-art single clustering algorithms, but also outperforms most of the state-of-the-art cluster ensemble approaches.

  5. Photochirogenesis: Photochemical Models on the Origin of Biomolecular Homochirality

    Directory of Open Access Journals (Sweden)

    Cornelia Meinert


    Full Text Available Current research focuses on a better understanding of the origin of biomolecular asymmetry by the identification and detection of the possibly first chiral molecules that were involved in the appearance and evolution of life on Earth. We have reasons to assume that these molecules were specific chiral amino acids. Chiral amino acids have been identified in both chondritic meteorites and simulated interstellar ices. Present research reasons that circularly polarized electromagnetic radiation was identified in interstellar environments and an asymmetric interstellar photon-molecule interaction might have triggered biomolecular symmetry breaking. We review on the possible prebiotic interaction of ‘chiral photons’ in the form of circularly polarized light, with early chiral organic molecules. We will highlight recent studies on enantioselective photolysis of racemic amino acids by circularly polarized light and experiments on the asymmetric photochemical synthesis of amino acids from only one C and one N containing molecules by simulating interstellar environments. Both approaches are based on circular dichroic transitions of amino acids that will be presented as well.

  6. Programming in Biomolecular Computation: Programs, Self-Interpretation and Visualisation

    Directory of Open Access Journals (Sweden)

    J.G. Simonsen


    Full Text Available Our goal is to provide a top-down approach to biomolecular computation. In spite of widespread discussion about connections between biology and computation, one question seems notable by its absence: Where are the programs? We identify a number of common features in programming that seem conspicuously absent from the literature on biomolecular computing; to partially redress this absence, we introduce a model of computation that is evidently programmable, by programs reminiscent of low-level computer machine code; and at the same time biologically plausible: its functioning is defined by a single and relatively small set of chemical-like reaction rules. Further properties: the model is stored-program: programs are the same as data, so programs are not only executable, but are also compilable and interpretable. It is universal: all computable functions can be computed (in natural ways and without arcane encodings of data and algorithm; it is also uniform: new ``hardware'' is not needed to solve new problems; and (last but not least it is Turing complete in a strong sense: a universal algorithm exists, that is able to execute any program, and is not asymptotically inefficient.

  7. REPROVIS-DB: a benchmark system for ligand-based virtual screening derived from reproducible prospective applications. (United States)

    Ripphausen, Peter; Wassermann, Anne Mai; Bajorath, Jürgen


    Benchmark calculations are essential for the evaluation of virtual screening (VS) methods. Typically, classes of known active compounds taken from the medicinal chemistry literature are divided into reference molecules (search templates) and potential hits that are added to background databases assumed to consist of compounds not sharing this activity. Then VS calculations are carried out, and the recall of known active compounds is determined. However, conventional benchmarking is affected by a number of problems that reduce its value for method evaluation. In addition to often insufficient statistical validation and the lack of generally accepted evaluation standards, the artificial nature of typical benchmark settings is often criticized. Retrospective benchmark calculations generally overestimate the potential of VS methods and do not scale with their performance in prospective applications. In order to provide additional opportunities for benchmarking that more closely resemble practical VS conditions, we have designed a publicly available compound database (DB) of reproducible virtual screens (REPROVIS-DB) that organizes information from successful ligand-based VS applications including reference compounds, screening databases, compound selection criteria, and experimentally confirmed hits. Using the currently available 25 hand-selected compound data sets, one can attempt to reproduce successful virtual screens with other than the originally applied methods and assess their potential for practical applications.

  8. Application of experimental modal analysis technique to structural design of linear vibrating screen

    Institute of Scientific and Technical Information of China (English)

    LI Wen-ying(李文英); MI Zhao-yang(米朝阳); WU Wang-guo(武望国); XIONG Shi-bo(熊诗波)


    A large model of the screen was mounted in the laboratory for studying its modal performance. The model is suspended with steel ropes. Modal test was carried out with artificially exciting by 500 g impacting hammer and 100 kg exciting force shaker respectively. Synthesis and correction of the modal parameters are obtained from both testing methods. Design faults of vibrating screen were determined based on the analysis and dynamic correction of structure approaches about the screen was put forward finally.

  9. The Application of Eddy Current Transducer for Testing Movement Locus of Shaker Screen

    Institute of Scientific and Technical Information of China (English)

    Zhu Pingyu; Lao Chuanjun; Zhang Wei; Li Xuejun


    Shaker screen is one of important equipments in the industry of oil, metallurgy, coal and timbering. The movement locus of shaker screen affects the capacity and efficiency of shaker screen to split the solid particle from crude ore directly .To test movement of shaker locus, two eddy current transducers are employed. A discussion of the usage of these eddy current transducer to test and acceleration sensors will be made. The experiment results from a real elliptic shaker screen have good agree with the design requirements.

  10. Development and application of a general plasmid reference material for GMO screening. (United States)

    Wu, Yuhua; Li, Jun; Wang, Yulei; Li, Xiaofei; Li, Yunjing; Zhu, Li; Li, Jun; Wu, Gang

    The use of analytical controls is essential when performing GMO detection through screening tests. Additionally, the presence of taxon-specific sequences is analyzed mostly for quality control during GMO detection. In this study, 11 commonly used genetic elements involving three promoters (P-35S, P-FMV35S and P-NOS), four marker genes (Bar, NPTII, HPT and Pmi), and four terminators (T-NOS, T-35S, T-g7 and T-e9), together with the reference gene fragments from six major crops of maize, soybean, rapeseed, rice, cotton and wheat, were co-integrated into the same single plasmid to construct a general reference plasmid pBI121-Screening. The suitability test of pBI121-Screening plasmid as reference material indicated that the non-target sequence on the pBI121-Screening plasmid did not affect the PCR amplification efficiencies of screening methods and taxon-specific methods. The sensitivity of screening and taxon-specific assays ranged from 5 to 10 copies of pBI121-Screening plasmid, meeting the sensitivity requirement of GMO detection. The construction of pBI121-Screening solves the lack of a general positive control for screening tests, thereby reducing the workload and cost of preparing a plurality of the positive control.

  11. Applications of a catch and release electrospray ionization mass spectrometry assay for carbohydrate library screening. (United States)

    El-Hawiet, Amr; Shoemaker, Glen K; Daneshfar, Rambod; Kitova, Elena N; Klassen, John S


    Applications of a catch and release electrospray ionization mass spectrometry (CaR-ESI-MS) assay for screening carbohydrate libraries against target proteins are described. Direct ESI-MS measurements were performed on solutions containing a target protein (a single chain antibody, an antigen binding fragment, or a fragment of a bacterial toxin) and a library of carbohydrates containing multiple specific ligands with affinities in the 10(3) to 10(6) M(-1) range. Ligands with moderate affinity (10(4) to 10(6) M(-1)) were successfully detected from mixtures containing >200 carbohydrates (at concentrations as low as 0.25 μM each). Additionally, the absolute affinities were estimated from the abundance of free and ligand-bound protein ions determined from the ESI mass spectrum. Multiple low affinity ligands (~10(3) M(-1)) were successfully detected in mixtures containing >20 carbohydrates (at concentrations of ~10 μM each). However, identification of specific interactions required the use of the reference protein method to correct the mass spectrum for the occurrence of nonspecific carbohydrate-protein binding during the ESI process. The release of the carbohydrate ligands, as ions, was successfully demonstrated using collision-induced dissociation performed on the deprotonated ions of the protein-carbohydrate complexes. The use of ion mobility separation, performed on deprotonated carbohydrate ions following their release from the complex, allowed for the positive identification of isomeric ligands.

  12. Applicability of ELISA to screen for dioxin-like PCBs in retail fish

    Energy Technology Data Exchange (ETDEWEB)

    Tsutsumi, T.; Amakura, Y.; Sasaki, K.; Maitani, T. [National Institute of Health Sciences, Tokyo (Japan); Okuyama, A.; Mizukami, H. [EnBioTec Laboratories Co., Ltd., Tokyo (Japan); Tanioka, Y.; Ueda, K.; Sakata, K. [Daiichi Fine Chemical Co., Ltd., Toyama (Japan)


    The group of dioxin-like PCBs, consisting of four non-ortho PCBs and eight mono-ortho PCBs, is classified among the dioxins. Humans are considerably exposed to dioxin through consumption of fish in Japan. The TEQ contribution of dioxin-like PCBs in fish is dominant, contributing about 70% of the total TEQ. Therefore, it is important to reveal TEQ levels of dioxin-like PCBs as well as PCDD/Fs in retail fish. HRGC/HRMS is currently the most widely used method to determine levels of dioxin-like PCBs. This method is very reliable and highly sensitive, but it is also timeconsuming and requires expensive equipment and highly trained analysts. One possible alternative method for screening dioxin-like PCBs is a bioassay, such as an ELISA. We recently developed an ELISA kit using a monoclonal antibody (MAb) specific to 2,3{sup '},4,4{sup '},5-pentachlorobiphenyl (PCB 118). PCB 118 is generally the most abundant isomer among dioxin-like PCBs in fish, although it has a relatively small contribution to the total TEQ derived from dioxin-like PCBs. Based on our HRGC/HRMS data, we found that the concentrations of PCB 118 correlated well to the TEQ levels of dioxin-like PCBs in retail fish (r>0.85, n = 181). Here, we examined the application of the ELISA kit in determining TEQ levels of dioxin-like PCBs in retail fish.

  13. Establishment of a P-glycoprotein substrate screening model and its preliminary application

    Institute of Scientific and Technical Information of China (English)

    Yi Wang; Jiang Cao; Su Zeng


    AIM: To establish a high P-glycoprotein (P-gp) expressing cell line as a model for studying drug absorption and distribution, and to explore the preliminary application of this screening model.METHODS: A full-length MDR1 cDNA fragment in plasmid pMDRA1 was first subcloned into plasmid pET28a(+), then MDR1 cDNA was cut from the recombinant plasmid with double-digestion and ligated into the mammalian expression vector pcDNA3.1(+). The recombinant plasmid pcDNA3.1(+)/MDR1 was transfected into breast cancer cell line Bcap37using the Superfect transfection reagent. Several stably transfected clones were obtained after selection with G418.Real-time fluorescent quantitative RT- PCR and Western blot methods were used to detect the expression of P-gp, and the cellular location of the expressed protein was determined by immunohistochemical staining. Drug sensitivity assay was used to evaluate the biological function of expressed P-gp.Concentration of quercetin in cells was determined by highperformance liquid chromatography (HPLC).RESULTS: The recombinant plasmid was confirmed to be inserted in the correct orientation by restrictive enzyme digestion and DNA sequencing. Real-time fluorescent quantitative RT-PCR showed a higher level of P-cp mRNA in transfected cells compared to that in the control cells, and the Western blot result also indicated that P-gp expression in transfected cells was higher than that in control cells. The immunohistochemical staining showed that the expressed P-gp was localized on cell membranes. Drug sensitivity assay showed that the IC50 for adriamycin and colchicine of the transfected cells was higher than that of the control cells.The concentration of quercetin in model cells was lower than that in control cells by HPLC. After P-gp inhibitor verapamil was administered, the concentration of quercetin in model cells was increased.CONCLUSION: A high P-gp expressing ceil line can be established, which could provide a suitable in vitro model system for

  14. An ontology for pharmaceutical ligands and its application for in silico screening and library design. (United States)

    Schuffenhauer, Ansgar; Zimmermann, Jürg; Stoop, Ruedi; van der Vyver, Jan-Jan; Lecchini, Steffano; Jacoby, Edgar


    Annotation efforts in biosciences have focused in past years mainly on the annotation of genomic sequences. Only very limited effort has been put into annotation schemes for pharmaceutical ligands. Here we propose annotation schemes for the ligands of four major target classes, enzymes, G protein-coupled receptors (GPCRs), nuclear receptors (NRs), and ligand-gated ion channels (LGICs), and outline their usage for in silico screening and combinatorial library design. The proposed schemes cover ligand functionality and hierarchical levels of target classification. The classification schemes are based on those established by the EC, GPCRDB, NuclearDB, and LGICDB. The ligands of the MDL Drug Data Report (MDDR) database serve as a reference data set of known pharmacologically active compounds. All ligands were annotated according to the schemes when attribution was possible based on the activity classification provided by the reference database. The purpose of the ligand-target classification schemes is to allow annotation-based searching of the ligand database. In addition, the biological sequence information of the target is directly linkable to the ligand, hereby allowing sequence similarity-based identification of ligands of next homologous receptors. Ligands of specified levels can easily be retrieved to serve as comprehensive reference sets for cheminformatics-based similarity searches and for design of target class focused compound libraries. Retrospective in silico screening experiments within the MDDR01.1 database, searching for structures binding to dopamine D2, all dopamine receptors and all amine-binding class A GPCRs using known dopamine D2 binding compounds as a reference set, have shown that such reference sets are in particular useful for the identification of ligands binding to receptors closely related to the reference system. The potential for ligand identification drops with increasing phylogenetic distance. The analysis of the focus of a tertiary

  15. A bivariate binormal ROC methodology for comparing new methods to an existing standard for screening applications (United States)

    Abbey, Craig K.; Insana, Michael F.; Eckstein, Miguel P.; Boone, John M.


    Validating the use of new imaging technologies for screening large patient populations is an important and very challenging area of diagnostic imaging research. A particular concern in ROC studies evaluating screening technologies is the problem of verification bias, in which an independent verification of disease status is only available for a subpopulation of patients, typically those with positive results by a current screening standard. For example, in screening mammography, a study might evaluate a new approach using a sample of patients that have undergone needle biopsy following a standard mammogram and subsequent work-up. This case sampling approach provides accurate independent verification of ground truth and increases the prevalence of disease cases. However, the selection criteria will likely bias results of the study. In this work we present an initial exploration of an approach to correcting this bias within the parametric framework of binormal assumptions. We posit conditionally bivariate normal distributions on the latent decision variable for both the new methodology as well as the screening standard. In this case, verification bias can be seen as the effect of missing data from an operating point in the screening standard. We examine the magnitude of this bias in the setting of breast cancer screening with mammography, and we derive a maximum likelihood approach to estimating bias corrected ROC curves in this model.

  16. Insights into cancer severity from biomolecular interaction mechanisms (United States)

    Raimondi, Francesco; Singh, Gurdeep; Betts, Matthew J.; Apic, Gordana; Vukotic, Ranka; Andreone, Pietro; Stein, Lincoln; Russell, Robert B.


    To attain a deeper understanding of diseases like cancer, it is critical to couple genetics with biomolecular mechanisms. High-throughput sequencing has identified thousands of somatic mutations across dozens of cancers, and there is a pressing need to identify the few that are pathologically relevant. Here we use protein structure and interaction data to interrogate nonsynonymous somatic cancer mutations, identifying a set of 213 molecular interfaces (protein-protein, -small molecule or –nucleic acid) most often perturbed in cancer, highlighting several potentially novel cancer genes. Over half of these interfaces involve protein-small-molecule interactions highlighting their overall importance in cancer. We found distinct differences in the predominance of perturbed interfaces between cancers and histological subtypes and presence or absence of certain interfaces appears to correlate with cancer severity. PMID:27698488

  17. Structure and Interactions of Isolated Biomolecular Building Blocks. (United States)

    de Vries, Mattanjah


    We investigate biomolecular building blocks and their clusters with each other and with water on a single molecular level. The motivation is the need to distinguish between intrinsic molecular properties and those that result from the biological environment. This is achieved by a combination of laser desorption and jet cooling, applied to aromatic amino acids, small peptides containing those, nucleobases and nucleosides. This approach is coupled with a number of laser spectroscopic techniques, including resonant multi-photon ionization, spectral hole burning and infra-red ion-dip spectroscopy. We will discuss examples illustrating how information can be obtained on spatial structure of individual biomolecules, including peptide conformations and details of DNA base-pairing.

  18. Orientation of biomolecular assemblies in a microfluidic jet

    Energy Technology Data Exchange (ETDEWEB)

    Priebe, M; Kalbfleisch, S; Tolkiehn, M; Salditt, T [Institut fuer Roentgenphysik, Universitaet Goettingen, Goettingen (Germany); Koester, S [Courant Research Centre Nano-Spectroscopy and X-Ray Imaging, Universitaet Goettingen, Goettingen (Germany); Abel, B [Institut fuer Physikalische Chemie, Universitaet Goettingen, Goettingen (Germany); Davies, R J, E-mail: tsalditt@gwdg.d [ID13, ESRF, Grenoble (France)


    We have investigated multilamellar lipid assemblies in a microfluidic jet, operating at high shear rates of the order of 10{sup 7} s{sup -1}. Compared to classical Couette cells or rheometers, the shear rate was increased by at least 2-3 orders of magnitude, and the sample volume was scaled down correspondingly. At the same time, the jet is characterized by high extensional stress due to elongational flow. A focused synchrotron x-ray beam was used to measure the structure and orientation of the lipid assemblies in the jet. The diffraction patterns indicate conventional multilamellar phases, aligned with the membrane normals oriented along the velocity gradient of the jet. The results indicate that the setup may be well suited for coherent diffractive imaging of oriented biomolecular assemblies and macromolecules at the future x-ray free electron laser (XFEL) sources.

  19. Biomolecular Network-Based Synergistic Drug Combination Discovery

    Directory of Open Access Journals (Sweden)

    Xiangyi Li


    Full Text Available Drug combination is a powerful and promising approach for complex disease therapy such as cancer and cardiovascular disease. However, the number of synergistic drug combinations approved by the Food and Drug Administration is very small. To bridge the gap between urgent need and low yield, researchers have constructed various models to identify synergistic drug combinations. Among these models, biomolecular network-based model is outstanding because of its ability to reflect and illustrate the relationships among drugs, disease-related genes, therapeutic targets, and disease-specific signaling pathways as a system. In this review, we analyzed and classified models for synergistic drug combination prediction in recent decade according to their respective algorithms. Besides, we collected useful resources including databases and analysis tools for synergistic drug combination prediction. It should provide a quick resource for computational biologists who work with network medicine or synergistic drug combination designing.

  20. Biomolecular decision-making process for self assembly.

    Energy Technology Data Exchange (ETDEWEB)

    Osbourn, Gordon Cecil


    The brain is often identified with decision-making processes in the biological world. In fact, single cells, single macromolecules (proteins) and populations of molecules also make simple decisions. These decision processes are essential to survival and to the biological self-assembly and self-repair processes that we seek to emulate. How do these tiny systems make effective decisions? How do they make decisions in concert with a cooperative network of other molecules or cells? How can we emulate the decision-making behaviors of small-scale biological systems to program and self-assemble microsystems? This LDRD supported research to answer these questions. Our work included modeling and simulation of protein populations to help us understand, mimic, and categorize molecular decision-making mechanisms that nonequilibrium systems can exhibit. This work is an early step towards mimicking such nanoscale and microscale biomolecular decision-making processes in inorganic systems.

  1. The biomolecular corona of nanoparticles in circulating biological media (United States)

    Pozzi, D.; Caracciolo, G.; Digiacomo, L.; Colapicchioni, V.; Palchetti, S.; Capriotti, A. L.; Cavaliere, C.; Zenezini Chiozzi, R.; Puglisi, A.; Laganà, A.


    When nanoparticles come into contact with biological media, they are covered by a biomolecular `corona', which confers a new identity to the particles. In all the studies reported so far nanoparticles are incubated with isolated plasma or serum that are used as a model for protein adsorption. Anyway, bodily fluids are dynamic in nature so the question arises on whether the incubation protocol, i.e. dynamic vs. static incubation, could affect the composition and structure of the biomolecular corona. Here we let multicomponent liposomes interact with fetal bovine serum (FBS) both statically and dynamically, i.e. in contact with circulating FBS (~40 cm s-1). The structure and composition of the liposome-protein corona, as determined by dynamic light scattering, electrophoretic light scattering and liquid chromatography tandem mass spectrometry, were found to be dependent on the incubation protocol. Specifically, following dynamic exposure to FBS, multicomponent liposomes were less enriched in complement proteins and appreciably more enriched in apolipoproteins and acute phase proteins (e.g. alpha-1-antitrypsin and inter-alpha-trypsin inhibitor heavy chain H3) that are involved in relevant interactions between nanoparticles and living systems. Supported by our results, we speculate that efficient predictive modeling of nanoparticle behavior in vivo will require accurate knowledge of nanoparticle-specific protein fingerprints in circulating biological media.When nanoparticles come into contact with biological media, they are covered by a biomolecular `corona', which confers a new identity to the particles. In all the studies reported so far nanoparticles are incubated with isolated plasma or serum that are used as a model for protein adsorption. Anyway, bodily fluids are dynamic in nature so the question arises on whether the incubation protocol, i.e. dynamic vs. static incubation, could affect the composition and structure of the biomolecular corona. Here we let

  2. Computational and theoretical aspects of biomolecular structure and dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Garcia, A.E.; Berendzen, J.; Catasti, P., Chen, X. [and others


    This is the final report for a project that sought to evaluate and develop theoretical, and computational bases for designing, performing, and analyzing experimental studies in structural biology. Simulations of large biomolecular systems in solution, hydrophobic interactions, and quantum chemical calculations for large systems have been performed. We have developed a code that implements the Fast Multipole Algorithm (FMA) that scales linearly in the number of particles simulated in a large system. New methods have been developed for the analysis of multidimensional NMR data in order to obtain high resolution atomic structures. These methods have been applied to the study of DNA sequences in the human centromere, sequences linked to genetic diseases, and the dynamics and structure of myoglobin.

  3. Quantum dynamics of bio-molecular systems in noisy environments

    CERN Document Server

    Plenio, M B


    We discuss three different aspects of the quantum dynamics of bio-molecular systems and more generally complex networks in the presence of strongly coupled environments. Firstly, we make a case for the systematic study of fundamental structural elements underlying the quantum dynamics of these systems, identify such elements and explore the resulting interplay of quantum dynamics and environmental decoherence. Secondly, we critically examine some existing approaches to the numerical description of system-environment interaction in the non-perturbative regime and present a promising new method that can overcome some limitations of existing methods. Thirdly, we present an approach towards deciding and quantifying the non-classicality of the action of the environment and the observed system-dynamics. We stress the relevance of these tools for strengthening the interplay between theoretical and experimental research in this field.

  4. Design and implementation of a biomolecular concentration tracker. (United States)

    Hsiao, Victoria; de los Santos, Emmanuel L C; Whitaker, Weston R; Dueber, John E; Murray, Richard M


    As a field, synthetic biology strives to engineer increasingly complex artificial systems in living cells. Active feedback in closed loop systems offers a dynamic and adaptive way to ensure constant relative activity independent of intrinsic and extrinsic noise. In this work, we use synthetic protein scaffolds as a modular and tunable mechanism for concentration tracking through negative feedback. Input to the circuit initiates scaffold production, leading to colocalization of a two-component system and resulting in the production of an inhibitory antiscaffold protein. Using a combination of modeling and experimental work, we show that the biomolecular concentration tracker circuit achieves dynamic protein concentration tracking in Escherichia coli and that steady state outputs can be tuned.

  5. Ion irradiation and biomolecular radiation damage II. Indirect effect

    CERN Document Server

    Wang, Wei; Su, Wenhui


    It has been reported that damage of genome in a living cell by ionizing radiation is about one-third direct and two-thirds indirect. The former which has been introduced in our last paper, concerns direct energy deposition and ionizing reactions in the biomolecules; the latter results from radiation induced reactive species (mainly radicals) in the medium (mainly water) surrounding the biomolecules. In this review, a short description of ion implantation induced radical formation in water is presented. Then we summarize the aqueous radical reaction chemistry of DNA, protein and their components, followed by a brief introduction of biomolecular damage induced by secondary particles (ions and electron). Some downstream biological effects are also discussed.

  6. Microfluidic Plastic Devices for Single-use Applications in High-Throughput Screening and DNA-Analysis


    Gerlach, Andreas; Knebel, Günther; Guber, A. E.; Heckele, M.; Herrmann, D; Muslija, A.; Schaller, T.


    Microfluidic devices fabricated by mass production offer an immense potential of applications such as high-throughput drug screening, clinical diagnostics and gene analysis [1]. The low unit production costs of plastic substrates make it possible to produce single-use devices, eliminating the need for cleaning and reuse [2]. Fabrication of microfluidic devices can be applied by microtechnical fabrication processes in combination with plastic molding techniques [3]. Basically, replication...


    Institute of Scientific and Technical Information of China (English)

    Yong-jing Guan; Hua-wei Ling; Ke-min Chen


    Objective To investigate the feasibility of whole body diffusion weighted imaging (WB-DWI) in screening metastasis.Methods WB-DWI was performed in 24 patients diagnosed with various types of primary tumors. The three-dimensional maximum intensity projection reconstruction and black-and-white flip technique were used to observe metastatic lesions, and the results were compared with those of bone scintigraphy. Results By WB-DWI scanning sequence at b = 800 s/mm2, all the bone lesions found by bone scintigraphy in the cohort were well identified, and other lesions of soft tissue and organs were also well demonstrated. Its screening capability was equivalent with bone scintigraphy in screening metastases in bones (P = 0.062). Conclusion WB-DWI was practicable with the parameter settings attempted in metastases screening.

  8. The Statistical Precision of Medical Screening Procedures: Application to Polygraph and AIDS Antibodies Test Data


    Gastwirth, Joseph L.


    The increased use of screening tests for drug use or antibodies to the HTLV-III (AIDS) virus, as well as pre-employment polygraph testing, has raised concerns about the reliability of the results of these procedures. This paper reviews the mathematical model underlying the analysis of data from screening tests. In addition to the known formulas for the proportion of positive (negative) classifications that are correct, we provide a large sample approximation to their standard errors. The resu...

  9. High-throughput screening normalized to biological response: application to antiviral drug discovery. (United States)

    Patel, Dhara A; Patel, Anand C; Nolan, William C; Huang, Guangming; Romero, Arthur G; Charlton, Nichole; Agapov, Eugene; Zhang, Yong; Holtzman, Michael J


    The process of conducting cell-based phenotypic screens can result in data sets from small libraries or portions of large libraries, making accurate hit picking from multiple data sets important for efficient drug discovery. Here, we describe a screen design and data analysis approach that allow for normalization not only between quadrants and plates but also between screens or batches in a robust, quantitative fashion, enabling hit selection from multiple data sets. We independently screened the MicroSource Spectrum and NCI Diversity Set II libraries using a cell-based phenotypic high-throughput screening (HTS) assay that uses an interferon-stimulated response element (ISRE)-driven luciferase-reporter assay to identify interferon (IFN) signal enhancers. Inclusion of a per-plate, per-quadrant IFN dose-response standard curve enabled conversion of ISRE activity to effective IFN concentrations. We identified 45 hits based on a combined z score ≥2.5 from the two libraries, and 25 of 35 available hits were validated in a compound concentration-response assay when tested using fresh compound. The results provide a basis for further analysis of chemical structure in relation to biological function. Together, the results establish an HTS method that can be extended to screening for any class of compounds that influence a quantifiable biological response for which a standard is available.

  10. Video Screen Capture Basics (United States)

    Dunbar, Laura


    This article is an introduction to video screen capture. Basic information of two software programs, QuickTime for Mac and BlueBerry Flashback Express for PC, are also discussed. Practical applications for video screen capture are given.

  11. Application effect of TruScreen system in cervical cancer screening%TruScreen系统在宫颈癌筛查中的应用效果

    Institute of Scientific and Technical Information of China (English)

    李佩; 王金声; 康媛


    Objective To investigate the effect of TruScreen (TS) system as applied in cervical cancer screening. Method 368 patients were included in the retrospective analysis, and were randomized into TS group or TCT group, with 184 cases in each. The TS group was tested with TS detection, while the TCT group was administered with Thin Prep cytology test (TCT), and the effect of the two tests were compared with histopathology as the diagnostic standard. Result The detection sensitivity, specificity and the positive rate of the TS and TCT group were 93.2%and 100%, 76.0%and 75.0%, 64.7% and 55.7%, respectively. Conclusion TS detection is as good as TCT detection in cervical cancer screening, which is clinically applicable.%目的:探讨宫颈癌筛查系统TruScreen(TS)在宫颈癌筛查中的应用效果。方法回顾性分析368例检查者,分为TS检测组和TCT检测组,每组184例,TS检测组行TS检测,TCT检测组行液基薄层细胞学(TCT)检测,以组织病理学为诊断标准,比较TS与TCT检查在宫颈癌筛查中的应用效果。结果 TS检测组与TCT检测组检测敏感度分别为93.2%、100%,特异度分别为76.0%、75.0%,阳性符合率分别为64.7%、55.7%。结论 TS检测与TCT检测在宫颈癌筛查中具有相似的检测效果,值得临床推广和运用。

  12. Pushing back the frontiers of mercury speciation using a combination of biomolecular and isotopic signatures: challenge and perspectives. (United States)

    Pedrero, Zoyne; Donard, Olivier F X; Amouroux, David


    Mercury (Hg) pollution is considered a major environmental problem due to the extreme toxicity of Hg. However, Hg metabolic pathways in biota remain elusive. An understanding of these pathways is crucial to elucidating the (eco)toxic effects of Hg and its biogeochemical cycle. The development of a new analytical methodology based on both speciation and natural isotopic fractionation represents a promising approach for metabolic studies of Hg and other metal(loid)s. Speciation provides valuable information about the reactivity and potential toxicity of metabolites, while the use of natural isotopic signature analysis adds a complementary dynamic dimension that allows the life history of the target element to be probed, the source of the target element (i.e., the source of pollution) to be identified, and reactions to be tracked. The resulting combined (bio)molecular and isotopic signature affords precious insight into the behavior of Hg in biota and Hg detoxification mechanisms. In the long term, this highly innovative methodology could be used in life and environmental science studies of metal(loid)s to push back the frontiers of our knowledge in this field. This paper summarizes the current status of the application of Hg speciation and the isotopic signature of Hg at the biomolecular level in living organisms, and discusses potential future uses of this combination of techniques.

  13. Thin-Film Thermoelectric Module for Power Generator Applications Using a Screen-Printing Method (United States)

    Lee, Heon-Bok; Yang, Hyun Jeong; We, Ju Hyung; Kim, Kukjoo; Choi, Kyung Cheol; Cho, Byung Jin


    A new process for fabricating a low-cost thermoelectric module using a screen-printing method has been developed. Thermoelectric properties of screen-printed ZnSb films were investigated in an effort to develop a thermoelectric module with low cost per watt. The screen-printed Zn x Sb1- x films showed a low carrier concentration and high Seebeck coefficient when x was in the range of 0.5 to 0.57 and the annealing temperature was kept below 550°C. When the annealing temperature was higher than 550°C, the carrier concentration of the Zn x Sb1- x films reached that of a metal, leading to a decrease of the Seebeck coefficient. In the present experiment, the optimized carrier concentration of screen-printed ZnSb was 7 × 1018/cm3. The output voltage and power density of the ZnSb film were 10 mV and 0.17 mW/cm2, respectively, at Δ T = 50 K. A thermoelectric module was produced using the proposed screen-printing approach with ZnSb and CoSb3 as p-type and n-type thermoelectric materials, respectively, and copper as the pad metal.

  14. Differential geometry-based solvation and electrolyte transport models for biomolecular modeling: a review


    Wei, Guo Wei; Baker, Nathan A.


    This chapter reviews the differential geometry-based solvation and electrolyte transport for biomolecular solvation that have been developed over the past decade. A key component of these methods is the differential geometry of surfaces theory, as applied to the solvent-solute boundary. In these approaches, the solvent-solute boundary is determined by a variational principle that determines the major physical observables of interest, for example, biomolecular surface area, enclosed volume, el...

  15. Modeling Structural Dynamics of Biomolecular Complexes by Coarse-Grained Molecular Simulations. (United States)

    Takada, Shoji; Kanada, Ryo; Tan, Cheng; Terakawa, Tsuyoshi; Li, Wenfei; Kenzaki, Hiroo


    Due to hierarchic nature of biomolecular systems, their computational modeling calls for multiscale approaches, in which coarse-grained (CG) simulations are used to address long-time dynamics of large systems. Here, we review recent developments and applications of CG modeling methods, focusing on our methods primarily for proteins, DNA, and their complexes. These methods have been implemented in the CG biomolecular simulator, CafeMol. Our CG model has resolution such that ∼10 non-hydrogen atoms are grouped into one CG particle on average. For proteins, each amino acid is represented by one CG particle. For DNA, one nucleotide is simplified by three CG particles, representing sugar, phosphate, and base. The protein modeling is based on the idea that proteins have a globally funnel-like energy landscape, which is encoded in the structure-based potential energy function. We first describe two representative minimal models of proteins, called the elastic network model and the classic Go̅ model. We then present a more elaborate protein model, which extends the minimal model to incorporate sequence and context dependent local flexibility and nonlocal contacts. For DNA, we describe a model developed by de Pablo's group that was tuned to well reproduce sequence-dependent structural and thermodynamic experimental data for single- and double-stranded DNAs. Protein-DNA interactions are modeled either by the structure-based term for specific cases or by electrostatic and excluded volume terms for nonspecific cases. We also discuss the time scale mapping in CG molecular dynamics simulations. While the apparent single time step of our CGMD is about 10 times larger than that in the fully atomistic molecular dynamics for small-scale dynamics, large-scale motions can be further accelerated by two-orders of magnitude with the use of CG model and a low friction constant in Langevin dynamics. Next, we present four examples of applications. First, the classic Go̅ model was used to

  16. Application of ICP-DRC-MS to screening test of strontium and plutonium in environmental samples at Fukushima. (United States)

    Sakama, M; Nagano, Y; Saze, T; Higaki, S; Kitade, T; Izawa, N; Shikino, O; Nakayama, S


    An application of sequential automated SPE separation equipment coupled to the quadrupole-based ICPMS instrumentation with a dynamic reaction cell such as a screening test system of (90)Sr and Pu isotopes in environmental samples was developed in this work. So far, during the course of a large number of reports as to various specific radioactivities in environmental samples surveyed at radioactive contaminated area around the Fukushima Daiichi Nuclear Power Plants (FDNPP), there is a much smaller number of reports on (90)Sr and Pu isotopes than that of (134)Cs and (137)Cs since the FDNPP accident, and then it would be expected to develop the simple analysis method of these isotopes instead of radiation measurements currently in use. In particular, a screening for (90)Sr in environmental samples has been accomplished using an isotopic ratio measurement mode in comparison with the characterization on the Solid Phase Elution (SPE) separation between strontium and zirconium isotopes around the mass-90 fraction. As a result, for a trial analysis of environmental samples of a muddy snow water and a soil which were collected at Fukushima, it was found that the present developed system makes it applicable for achieving up to the specific activity levels of several hundreds Bq/kg ((90)Sr) and about 1-2Bq/kg (Pu isotopes) as the screening test system.

  17. Application of isothermal titration calorimeter for screening bitterness-suppressing molecules of quinine. (United States)

    Zhang, Yifan; Zhu, Youwei; Zhao, Na; Wu, Jinhui; Hu, Yiqiao


    Bitterness-suppressing molecules have drawn ever-increasing attention these years for some unique advantages like low molecular weight, tastelessness and no interference on drug bioavailability. L-Arg was reported to suppress the bitterness of quinine, and we happened to find that the suppressing effects could be demonstrated by isothermal titration calorimeter (ITC). In this study, we investigated the possibility of using ITC to screen bitterness-suppressing molecules for quinine. Among the amino acids we screened, L-Lys bond quinine with high affinity. The results of ITC correlated well with the results of human sensory experiments. L-Arg and L-Lys could suppress the bitterness of quinine while other amino acids could not. Therefore, ITC has the potential to screen bitterness-suppressing molecules.

  18. 大屏幕拼接技术及其应用%Large-Screen Splicing Technology and Its Applications

    Institute of Scientific and Technical Information of China (English)



    大屏幕拼接技术是现代计算机图形处理技术和各种显示技术的有机结合,实现多路独立视频信号和计算机信号同时直通显示,单元无级缩放、画中画显示,网络计算机信号快速显示,高分辨率全屏显示,灵活缩放显示、大画面跨屏清晰显示,超高分辨率图像、视频、计算机、网络信号综合显示等.广泛用于部队、武警、公安指挥中心、政府视频会议系统、企业生产调度中心等场合.该文主要介绍DLP、MPDP、LED三种主流大屏幕拼接技术的原理、结构和实际运用.%Splicing technology is a large-screen graphics of modern computer technology and the organic integration of display technology to achieve an independent multi-channel video signal and computer signal through at the same time show that no unit-level zoom, pic-ture-in-picture display, network computer signal quickly revealed that high-resolution the rate of full-screen display, flexible scaling showed that the screen to clearly indicate that cross-screen, ultra-high-resohition images, video, computer, network signal integrated dis-play. Widely used in troops, armed police, public security command center, the Government Video Conference System, business centers, production scheduling occasions. In this paper, DLP, MPDP, LED splicing of three large-screen technology to mainstream the principles, structure and practical appli-cation.

  19. Application of LC-high-resolution MS with 'intelligent' data mining tools for screening reactive drug metabolites. (United States)

    Ma, Shuguang; Chowdhury, Swapan K


    Biotransformation of chemically stable compounds to reactive metabolites that can bind covalently to macromolecules (such as proteins and DNA) is considered an undesirable property of drug candidates. Due to the possible link, which has not yet been conclusively demonstrated, between reactive metabolites and adverse drug reactions, screening for metabolic activation of lead compounds through in vitro chemical trapping experiments has become an integral part of the drug discovery process in many laboratories. In this review, we provide an overview of the recent advances in the application of high-resolution MS. These advances facilitated the development of accurate-mass-based data mining tools for high-throughput screening of reactive drug metabolites in drug discovery.


    NARCIS (Netherlands)



    Solid-phase extraction (SPE) by means of disposable columns has become a widely accepted technique for sample pretreatment in toxicology, both for directed analyses and for screening analyses. However, the sample capacity in SPE is usually limited to a few millilitres. Therefore, we have investigate

  1. Application value of OSCAR syetem in prenatal screen of chromosome disease and severeα-thalassemia

    Institute of Scientific and Technical Information of China (English)

    Yi Ling; Song Jin; Chun-Xia Hu; Rui-XiANan; Fu Huo; Ning Zhang; Tu-Zhao Xie; Qun-Hua Shi


    Objective:To study the value of combining serum and ultrasound nuchal translucency thickness (NT) measurement for One-stop Clinic of Risk Assessment (OSCAR) in Hainan Province in prenatal diagnose of chromosomal disorders and thalassemia diagnosis.Methods:The patients of 11-13+ 6 weeks in our hospital for regularly standardized checking were selected for OSCAR prenatal screening, the patients of the Down's and severe thalassemia at high risk were selected for prenatal diagnosis of fetal karyotype and thalassemia gene checking, then pregnancy outcomes was followed up. Rate of OSCAR in fetal chromosomal disease and the diagnostic value in fetal thalassemia was detected.Results:The positive rate of OSCAR Down's screening was 9.8%, the detection rate was 90%. The incidence of chromosomal abnormalities and severe alpha thalassemia were increased as NT thickening and tricuspid or venous ductus regurgitation.Conclusions: OSCAR Down's screening system for early pregnancy is noninvasive, affordable and it is preferred prenatal screening through comprehensive evaluation.

  2. Natural language processing of clinical trial announcements: exploratory-study of building an automated screening application. (United States)

    Solti, Imre; Gennari, John H; Payne, Thomas; Payne, Tom; Solti, Magdolna; Tarczy-Hornoch, Peter


    Clinical trials are important for the advancement of medical research. Despite of the benefits clinical trial enrollment is low. We study the feasibility of using NLP to assist with automatic eligibility screening by extracting medical diagnoses from the inclusion and exclusion criteria of cancer clinical trial announcements posted on the internet. We compare the performances of the system versus an oncologist.

  3. Screening for the important factors in large discrete-event simulation: sequential bifurcation and its applications

    NARCIS (Netherlands)

    Kleijnen, J.P.C.; Bettonvil, B.; Persson, F.


    Screening in simulation experiments to find the most important factors, from a very large number of factors, is discussed. The method of sequential bifurcation in the presence of random noise is described and is demonstrated through a case study from the mobile telecommunications industry. The case

  4. Justifying age thresholds for mammographic screening: an application of pragma-dialectical argumentation theory

    NARCIS (Netherlands)

    Schulz, P.J.; Meuffels, B.


    Information campaigns on breast cancer screening in the Netherlands need to convince women above 50 years of age to have biannual mammography, and women below 50 years of age that regular mammograms are not recommended for them. This article reports the results of two experiments in which the constr

  5. Application of multimedia models for screening assessment of long-range transport potential and overall persistence.

    NARCIS (Netherlands)

    Klasmeier, Jörg; Matthies, Michael; Macleod, Matthew; Fenner, Kathrin; Scheringer, Martin; Stroebe, Maximilian; Gall, Anne Christine le; McKone, Thomas; Meent, Dik van de; Wania, Frank


    We propose a multimedia model-based methodology to evaluate whether a chemical substance qualifies as POP-like based on overall persistence (Pov) and potential for long-range transport (LRTP). It relies upon screening chemicals against the Pov and LRTP characteristics of selected reference chemicals

  6. Construction of the Application Systems for Universal Education in Architectural Heritage – Multimedia Touch Screen Desk System

    Directory of Open Access Journals (Sweden)

    Sato Reika


    Full Text Available The importance of popular education in architectural heritage is well known. It is an effective method for public education to develop applications that utilize digital copy of architectural heritage. We provide a case study focusing on the historical buildings of Toji Temple in Kyoto, Japan. We digitize the historical buildings in both overall construction and detailed structures. We build a demonstration and operating system using multimedia technologies such as multimedia touch screen desk system. The system will produce 3D digital models of architectural heritage with high resolution and use advanced technology to develop a variety of demonstration applications that can enhance your presentation and ease operation. The users can also have more opportunities and ways to improve their interests in learning and understanding about the architectural heritage knowledge, hence finding new ways to further improve the methodology of architectural heritage education with the application of multimedia interactive technologies and digital copy of historical buildings.

  7. [Biobanking and Biomolecular Resources Research Infrastructure (BBMRI). Implications for pathology]. (United States)

    Viertler, C; Zatloukal, K


    High quality human biological samples (e.g. blood, tissue or DNA) with associated, well documented clinical and research data are key resources for advancement of life sciences, biotechnology, clinical medicine, drug development and also molecular pathology. Millions of samples of diseased tissues have been collected in the context of routine histopathological diagnosis and are stored in the archives of hospitals and institutes of pathology. A concerted effort is necessary to overcome the current fragmentation of the European biobanking community in order to tap the full research potential of existing biobanks. A pan-European research infrastructure for biobanking and biomolecular resources (BBMRI) is currently in its planning phase. The mission is to link and provide access to local biobanks of different formats, including tissue collections, harmonize standards, establish operational procedures which properly consider ethical, legal, societal aspects, and to secure sustainable funding. Pathology plays a key role in development and administration of tissue banks and is, thus, a major partner for collaboration, expertise and construction of this pan-European research infrastructure.

  8. Biomolecular Evidence of Silk from 8,500 Years Ago. (United States)

    Gong, Yuxuan; Li, Li; Gong, Decai; Yin, Hao; Zhang, Juzhong


    Pottery, bone implements, and stone tools are routinely found at Neolithic sites. However, the integrity of textiles or silk is susceptible to degradation, and it is therefore very difficult for such materials to be preserved for 8,000 years. Although previous studies have provided important evidence of the emergence of weaving skills and tools, such as figuline spinning wheels and osseous lamellas with traces of filament winding, there is a lack of direct evidence proving the existence of silk. In this paper, we explored evidence of prehistoric silk fibroin through the analysis of soil samples collected from three tombs at the Neolithic site of Jiahu. Mass spectrometry was employed and integrated with proteomics to characterize the key peptides of silk fibroin. The direct biomolecular evidence reported here showed the existence of prehistoric silk fibroin, which was found in 8,500-year-old tombs. Rough weaving tools and bone needles were also excavated, indicating the possibility that the Jiahu residents may possess the basic weaving and sewing skills in making textile. This finding may advance the study of the history of silk, and the civilization of the Neolithic Age.

  9. Stochastic Simulation of Biomolecular Networks in Dynamic Environments.

    Directory of Open Access Journals (Sweden)

    Margaritis Voliotis


    Full Text Available Simulation of biomolecular networks is now indispensable for studying biological systems, from small reaction networks to large ensembles of cells. Here we present a novel approach for stochastic simulation of networks embedded in the dynamic environment of the cell and its surroundings. We thus sample trajectories of the stochastic process described by the chemical master equation with time-varying propensities. A comparative analysis shows that existing approaches can either fail dramatically, or else can impose impractical computational burdens due to numerical integration of reaction propensities, especially when cell ensembles are studied. Here we introduce the Extrande method which, given a simulated time course of dynamic network inputs, provides a conditionally exact and several orders-of-magnitude faster simulation solution. The new approach makes it feasible to demonstrate-using decision-making by a large population of quorum sensing bacteria-that robustness to fluctuations from upstream signaling places strong constraints on the design of networks determining cell fate. Our approach has the potential to significantly advance both understanding of molecular systems biology and design of synthetic circuits.

  10. Microscale thermophoresis quantifies biomolecular interactions under previously challenging conditions. (United States)

    Seidel, Susanne A I; Dijkman, Patricia M; Lea, Wendy A; van den Bogaart, Geert; Jerabek-Willemsen, Moran; Lazic, Ana; Joseph, Jeremiah S; Srinivasan, Prakash; Baaske, Philipp; Simeonov, Anton; Katritch, Ilia; Melo, Fernando A; Ladbury, John E; Schreiber, Gideon; Watts, Anthony; Braun, Dieter; Duhr, Stefan


    Microscale thermophoresis (MST) allows for quantitative analysis of protein interactions in free solution and with low sample consumption. The technique is based on thermophoresis, the directed motion of molecules in temperature gradients. Thermophoresis is highly sensitive to all types of binding-induced changes of molecular properties, be it in size, charge, hydration shell or conformation. In an all-optical approach, an infrared laser is used for local heating, and molecule mobility in the temperature gradient is analyzed via fluorescence. In standard MST one binding partner is fluorescently labeled. However, MST can also be performed label-free by exploiting intrinsic protein UV-fluorescence. Despite the high molecular weight ratio, the interaction of small molecules and peptides with proteins is readily accessible by MST. Furthermore, MST assays are highly adaptable to fit to the diverse requirements of different biomolecules, such as membrane proteins to be stabilized in solution. The type of buffer and additives can be chosen freely. Measuring is even possible in complex bioliquids like cell lysate allowing close to in vivo conditions without sample purification. Binding modes that are quantifiable via MST include dimerization, cooperativity and competition. Thus, its flexibility in assay design qualifies MST for analysis of biomolecular interactions in complex experimental settings, which we herein demonstrate by addressing typically challenging types of binding events from various fields of life science.

  11. A fast mollified impulse method for biomolecular atomistic simulations (United States)

    Fath, L.; Hochbruck, M.; Singh, C. V.


    Classical integration methods for molecular dynamics are inherently limited due to resonance phenomena occurring at certain time-step sizes. The mollified impulse method can partially avoid this problem by using appropriate filters based on averaging or projection techniques. However, existing filters are computationally expensive and tedious in implementation since they require either analytical Hessians or they need to solve nonlinear systems from constraints. In this work we follow a different approach based on corotation for the construction of a new filter for (flexible) biomolecular simulations. The main advantages of the proposed filter are its excellent stability properties and ease of implementation in standard softwares without Hessians or solving constraint systems. By simulating multiple realistic examples such as peptide, protein, ice equilibrium and ice-ice friction, the new filter is shown to speed up the computations of long-range interactions by approximately 20%. The proposed filtered integrators allow step sizes as large as 10 fs while keeping the energy drift less than 1% on a 50 ps simulation.

  12. Development and application of an aerosol screening model for size-resolved urban aerosols. (United States)

    Stanier, Charles O; Lee, Sang-Rin


    Predictive models of vehicular ultrafine particles less than 0.1 microm in diameter (UFPs*) and other urban pollutants with high spatial and temporal variation are useful and important in applications such as (1) decision support for infrastructure projects, emissions controls, and transportation-mode shifts; (2) the interpretation and enhancement of observations (e.g., source apportionment, extrapolation, interpolation, and gap-filling in space and time); and (3) the generation of spatially and temporally resolved exposure estimates where monitoring is unfeasible. The objective of the current study was to develop, test, and apply the Aerosol Screening Model (ASM), a new physically based vehicular UFP model for use in near-road environments. The ASM simulates hourly average outdoor concentrations of roadway-derived aerosols and gases. Its distinguishing features include user-specified spatial resolution; use of the Weather Research and Forecasting (WRF) meteorologic model for winds estimates; use of a database of more than 100,000 road segments in the Los Angeles, California, region, including freeway ramps and local streets; and extensive testing against more than 9000 hours of observed particle concentrations at 11 sites. After initialization of air parcels at an upwind boundary, the model solves for vehicle emissions, dispersion, coagulation, and deposition using a Lagrangian modeling framework. The Lagrangian parcel of air is subdivided vertically (into 11 levels) and in the crosswind direction (into 3 parcels). It has overall dimensions of 10 m (downwind), 300 m (vertically), and 2.1 km (crosswind). The simulation is typically started 4 km upwind from the receptor, that is, the location at which the exposure is to be estimated. As parcels approach the receptor, depending on the user-specified resolution, step size is decreased, and crosswind resolution is enhanced through subdivision of parcels in the crosswind direction. Hourly concentrations and size

  13. Solving the 0/1 Knapsack Problem by a Biomolecular DNA Computer

    Directory of Open Access Journals (Sweden)

    Hassan Taghipour


    Full Text Available Solving some mathematical problems such as NP-complete problems by conventional silicon-based computers is problematic and takes so long time. DNA computing is an alternative method of computing which uses DNA molecules for computing purposes. DNA computers have massive degrees of parallel processing capability. The massive parallel processing characteristic of DNA computers is of particular interest in solving NP-complete and hard combinatorial problems. NP-complete problems such as knapsack problem and other hard combinatorial problems can be easily solved by DNA computers in a very short period of time comparing to conventional silicon-based computers. Sticker-based DNA computing is one of the methods of DNA computing. In this paper, the sticker based DNA computing was used for solving the 0/1 knapsack problem. At first, a biomolecular solution space was constructed by using appropriate DNA memory complexes. Then, by the application of a sticker-based parallel algorithm using biological operations, knapsack problem was resolved in polynomial time.

  14. A Quick-responsive DNA Nanotechnology Device for Bio-molecular Homeostasis Regulation. (United States)

    Wu, Songlin; Wang, Pei; Xiao, Chen; Li, Zheng; Yang, Bing; Fu, Jieyang; Chen, Jing; Wan, Neng; Ma, Cong; Li, Maoteng; Yang, Xiangliang; Zhan, Yi


    Physiological processes such as metabolism, cell apoptosis and immune responses, must be strictly regulated to maintain their homeostasis and achieve their normal physiological functions. The speed with which bio-molecular homeostatic regulation occurs directly determines the ability of an organism to adapt to conditional changes. To produce a quick-responsive regulatory system that can be easily utilized for various types of homeostasis, a device called nano-fingers that facilitates the regulation of physiological processes was constructed using DNA origami nanotechnology. This nano-fingers device functioned in linked open and closed phases using two types of DNA tweezers, which were covalently coupled with aptamers that captured specific molecules when the tweezer arms were sufficiently close. Via this specific interaction mechanism, certain physiological processes could be simultaneously regulated from two directions by capturing one biofactor and releasing the other to enhance the regulatory capacity of the device. To validate the universal application of this device, regulation of the homeostasis of the blood coagulant thrombin was attempted using the nano-fingers device. It was successfully demonstrated that this nano-fingers device achieved coagulation buffering upon the input of fuel DNA. This nano-device could also be utilized to regulate the homeostasis of other types of bio-molecules.

  15. Nanoscale Biomolecular Detection Limit for Gold Nanoparticles Based on Near-Infrared Response

    Directory of Open Access Journals (Sweden)

    Mario D’Acunto


    Full Text Available Gold nanoparticles have been widely used during the past few years in various technical and biomedical applications. In particular, the resonance optical properties of nanometer-sized particles have been employed to design biochips and biosensors used as analytical tools. The optical properties of nonfunctionalized gold nanoparticles and core-gold nanoshells play a crucial role for the design of biosensors where gold surface is used as a sensing component. Gold nanoparticles exhibit excellent optical tunability at visible and near-infrared frequencies leading to sharp peaks in their spectral extinction. In this paper, we study how the optical properties of gold nanoparticles and core-gold nanoshells are changed as a function of different sizes, shapes, composition, and biomolecular coating with characteristic shifts towards the near-infrared region. We show that the optical tenability can be carefully tailored for particle sizes falling in the range 100–150 nm. The results should improve the design of sensors working at the detection limit.

  16. Co-Immobilization of Proteins and DNA Origami Nanoplates to Produce High-Contrast Biomolecular Nanoarrays. (United States)

    Hager, Roland; Burns, Jonathan R; Grydlik, Martyna J; Halilovic, Alma; Haselgrübler, Thomas; Schäffler, Friedrich; Howorka, Stefan


    The biofunctionalization of nanopatterned surfaces with DNA origami nanostructures is an important topic in nanobiotechnology. An unexplored challenge is, however, to co-immobilize proteins with DNA origami at pre-determined substrate sites in high contrast relative to the nontarget areas. The immobilization should, in addition, preferably be achieved on a transparent substrate to allow ultrasensitive optical detection. If successful, specific co-binding would be a step towards stoichiometrically defined arrays with few to individual protein molecules per site. Here, we successfully immobilize with high specificity positively charged avidin proteins and negatively charged DNA origami nanoplates on 100 nm-wide carbon nanoislands while suppressing undesired adsorption to surrounding nontarget areas. The arrays on glass slides achieve unprecedented selectivity factors of up to 4000 and allow ultrasensitive fluorescence read-out. The co-immobilization onto the nanoislands leads to layered biomolecular architectures, which are functional because bound DNA origami influences the number of capturing sites on the nanopatches for other proteins. The novel hybrid DNA origami-protein nanoarrays allow the fabrication of versatile research platforms for applications in biosensing, biophysics, and cell biology, and, in addition, represent an important step towards single-molecule protein arrays.

  17. Potential-of-mean-force description of ionic interactions and structural hydration in biomolecular systems

    Energy Technology Data Exchange (ETDEWEB)

    Hummer, G.; Garcia, A.E. [Los Alamos National Lab., NM (United States). Theoretical Biology and Biophysics Group; Soumpasis, D.M. [Max-Planck-Inst for Biophysical Chemistry, Goettingen (Germany). Biocomputation Group


    To understand the functioning of living organisms on a molecular level, it is crucial to dissect the intricate interplay of the immense number of biological molecules. Most of the biochemical processes in cells occur in a liquid environment formed mainly by water and ions. This solvent environment plays an important role in biological systems. The potential-of-mean-force (PMF) formalism attempts to describe quantitatively the interactions of the solvent with biological macromolecules on the basis of an approximate statistical-mechanical representation. At its current status of development, it deals with ionic effects on the biomolecular structure and with the structural hydration of biomolecules. The underlying idea of the PMF formalism is to identify the dominant sources of interactions and incorporate these interactions into the theoretical formalism using PMF`s (or particle correlation functions) extracted from bulk-liquid systems. In the following, the authors shall briefly outline the statistical-mechanical foundation of the PMF formalism and introduce the PMF expansion formalism, which is intimately linked to superposition approximations for higher-order particle correlation functions. The authors shall then sketch applications, which describe the effects of the ionic environment on nucleic-acid structure. Finally, the authors shall present the more recent extension of the PMF idea to describe quantitatively the structural hydration of biomolecules. Results for the interface of ice and water and for the hydration of deoxyribonucleic acid (DNA) will be discussed.

  18. Computational Recipe for Efficient Description of Large-Scale Conformational Changes in Biomolecular Systems. (United States)

    Moradi, Mahmoud; Tajkhorshid, Emad


    Characterizing large-scale structural transitions in biomolecular systems poses major technical challenges to both experimental and computational approaches. On the computational side, efficient sampling of the configuration space along the transition pathway remains the most daunting challenge. Recognizing this issue, we introduce a knowledge-based computational approach toward describing large-scale conformational transitions using (i) nonequilibrium, driven simulations combined with work measurements and (ii) free energy calculations using empirically optimized biasing protocols. The first part is based on designing mechanistically relevant, system-specific reaction coordinates whose usefulness and applicability in inducing the transition of interest are examined using knowledge-based, qualitative assessments along with nonequilirbrium work measurements which provide an empirical framework for optimizing the biasing protocol. The second part employs the optimized biasing protocol resulting from the first part to initiate free energy calculations and characterize the transition quantitatively. Using a biasing protocol fine-tuned to a particular transition not only improves the accuracy of the resulting free energies but also speeds up the convergence. The efficiency of the sampling will be assessed by employing dimensionality reduction techniques to help detect possible flaws and provide potential improvements in the design of the biasing protocol. Structural transition of a membrane transporter will be used as an example to illustrate the workings of the proposed approach.

  19. Application of screening model for assessing subsurface NAPL contamination and remediation

    Energy Technology Data Exchange (ETDEWEB)

    MacFarlane, S.; Shiu, W.Y. [Univ. of Toronto, Ontario (Canada); Mackay, D. [Trent Univ., Peterborough, Ontario (Canada)


    To select the most appropriate technique for remediating non-aqueous phase liquids (NAPL)-contaminated sites a full understanding is required of the characteristics of the site, the contaminant, and the effectiveness of the remedial measure. A screening model has been developed (MacFarlane and Mackay, in press) for evaluating the partitioning of components of NAPLs present in the subsurface environment and for providing order of magnitude estimates of the effectiveness, in terms of recovery time, of a variety of remedial technologies including water and solvent flushing, air and steam stripping, and enhanced degradation. The model calculations employ the fugacity concept which is found to simplify and clarify the calculations. Two types of calculations are employed in the screening assessment. Level 1 fugacity calculations are simple multimedia equilibrium calculations that deduce how a chemical partitions between media or phases in a defined environment. Level 2 fugacity calculations account for or quantify losses of chemical being conveyed out of the environment by advective flows in phases such as air or water or by degradation by chemical or biochemical reactions. The screening model was originally applied to an existing fractured bedrock site in Smithville, Ontario which is contaminated with a NAPL containing polychlorinated biphenyls, trichlorobenzene, and trichloroethylene. In this paper, the model approach is illustrated for vinyl chloride which may be present at the site due to biochemical reactions occurring in the subsurface. It is their aim to show that this approach can provide screening level insights into the behavior and remediation of NAPLs and can serve as a first step and justification towards more detailed modeling.

  20. Application of stress susceptibility index for drought tolerance screening of tomato populations

    Directory of Open Access Journals (Sweden)

    Zdravković Jasmina


    Full Text Available Investigation comprised 41 tomato genotypes originating from the population of domestic and domesticated genotypes collected in Serbia and belonging to the tomato collection of the Institute of Vegetable Crop Science, Smederevska Palanka. The aim of collection screening was to choose the genotypes tolerant to drought during plant intensive growth stage, whereby the process of selection would set out to obtain the recombinant genotypes for this abiotic factor. The screening criteria were established for genotype divergence in plant height and shoot-root ratio under conditions of optimal irrigation regime and drought. Divergence was estimated using cluster analysis with Euclidean distance as a measure of distance, with a complete gene attachment to grouping. Drought tolerance is expressed by the stress susceptibility index (SSI. Various results were obtained based on the screening of genotypes grown under optimal and dry conditions. As a measure of stress susceptibility, based on SSI, genotypes having different drought tolerance level were determined. On the grounds of the analyses carried out, 10 genotypes were segregated (G102, G104, G107, G109, G110, G119, G125, G126, G128 and G141 to represent a basis to obtain the recombinant genotypes and to initiate the selection for drought resistance. [Projekat Ministarstva nauke Republike Srbije, br. TR 31005 i br. TR 31059

  1. FINDSITE(X): a structure-based, small molecule virtual screening approach with application to all identified human GPCRs. (United States)

    Zhou, Hongyi; Skolnick, Jeffrey


    We have developed FINDSITE(X), an extension of FINDSITE, a protein threading based algorithm for the inference of protein binding sites, biochemical function and virtual ligand screening, that removes the limitation that holo protein structures (those containing bound ligands) of a sufficiently large set of distant evolutionarily related proteins to the target be solved; rather, predicted protein structures and experimental ligand binding information are employed. To provide the predicted protein structures, a fast and accurate version of our recently developed TASSER(VMT), TASSER(VMT)-lite, for template-based protein structural modeling applicable up to 1000 residues is developed and tested, with comparable performance to the top CASP9 servers. Then, a hybrid approach that combines structure alignments with an evolutionary similarity score for identifying functional relationships between target and proteins with binding data has been developed. By way of illustration, FINDSITE(X) is applied to 998 identified human G-protein coupled receptors (GPCRs). First, TASSER(VMT)-lite provides updates of all human GPCR structures previously modeled in our lab. We then use these structures and the new function similarity detection algorithm to screen all human GPCRs against the ZINC8 nonredundant (TC identity > 30% to the target from the binding data library) on a 168 human GPCR set with known binding data, the average enrichment factor in the top 1% of the compound library (EF(0.01)) is 22.7, whereas EF(0.01) by FINDSITE is 7.1. For virtual screening when just the target and its native ligands are excluded, the average EF(0.01) reaches 41.4. We also analyze off-target interactions for the 168 protein test set. All predicted structures, virtual screening data and off-target interactions for the 998 human GPCRs are available at .

  2. A Systematic Strategy for Screening and Application of Specific Biomarkers in Hepatotoxicity Using Metabolomics Combined With ROC Curves and SVMs. (United States)

    Li, Yubo; Wang, Lei; Ju, Liang; Deng, Haoyue; Zhang, Zhenzhu; Hou, Zhiguo; Xie, Jiabin; Wang, Yuming; Zhang, Yanjun


    Current studies that evaluate toxicity based on metabolomics have primarily focused on the screening of biomarkers while largely neglecting further verification and biomarker applications. For this reason, we used drug-induced hepatotoxicity as an example to establish a systematic strategy for screening specific biomarkers and applied these biomarkers to evaluate whether the drugs have potential hepatotoxicity toxicity. Carbon tetrachloride (5 ml/kg), acetaminophen (1500 mg/kg), and atorvastatin (5 mg/kg) are established as rat hepatotoxicity models. Fifteen common biomarkers were screened by multivariate statistical analysis and integration analysis-based metabolomics data. The receiver operating characteristic curve was used to evaluate the sensitivity and specificity of the biomarkers. We obtained 10 specific biomarker candidates with an area under the curve greater than 0.7. Then, a support vector machine model was established by extracting specific biomarker candidate data from the hepatotoxic drugs and nonhepatotoxic drugs; the accuracy of the model was 94.90% (92.86% sensitivity and 92.59% specificity) and the results demonstrated that those ten biomarkers are specific. 6 drugs were used to predict the hepatotoxicity by the support vector machines model; the prediction results were consistent with the biochemical and histopathological results, demonstrating that the model was reliable. Thus, this support vector machine model can be applied to discriminate the between the hepatic or nonhepatic toxicity of drugs. This approach not only presents a new strategy for screening-specific biomarkers with greater diagnostic significance but also provides a new evaluation pattern for hepatotoxicity, and it will be a highly useful tool in toxicity estimation and disease diagnoses.

  3. Computational methods to study the structure and dynamics of biomolecules and biomolecular processes from bioinformatics to molecular quantum mechanics

    CERN Document Server


    Since the second half of the 20th century machine computations have played a critical role in science and engineering. Computer-based techniques have become especially important in molecular biology, since they often represent the only viable way to gain insights into the behavior of a biological system as a whole. The complexity of biological systems, which usually needs to be analyzed on different time- and size-scales and with different levels of accuracy, requires the application of different approaches, ranging from comparative analysis of sequences and structural databases, to the analysis of networks of interdependence between cell components and processes, through coarse-grained modeling to atomically detailed simulations, and finally to molecular quantum mechanics. This book provides a comprehensive overview of modern computer-based techniques for computing the structure, properties and dynamics of biomolecules and biomolecular processes. The twenty-two chapters, written by scientists from all over t...

  4. Network target for screening synergistic drug combinations with application to traditional Chinese medicine

    Directory of Open Access Journals (Sweden)

    Zhang Ningbo


    Full Text Available Abstract Background Multicomponent therapeutics offer bright prospects for the control of complex diseases in a synergistic manner. However, finding ways to screen the synergistic combinations from numerous pharmacological agents is still an ongoing challenge. Results In this work, we proposed for the first time a “network target”-based paradigm instead of the traditional "single target"-based paradigm for virtual screening and established an algorithm termed NIMS (Network target-based Identification of Multicomponent Synergy to prioritize synergistic agent combinations in a high throughput way. NIMS treats a disease-specific biological network as a therapeutic target and assumes that the relationship among agents can be transferred to network interactions among the molecular level entities (targets or responsive gene products of agents. Then, two parameters in NIMS, Topology Score and Agent Score, are created to evaluate the synergistic relationship between each given agent combinations. Taking the empirical multicomponent system traditional Chinese medicine (TCM as an illustrative case, we applied NIMS to prioritize synergistic agent pairs from 63 agents on a pathological process instanced by angiogenesis. The NIMS outputs can not only recover five known synergistic agent pairs, but also obtain experimental verification for synergistic candidates combined with, for example, a herbal ingredient Sinomenine, which outperforms the meet/min method. The robustness of NIMS was also showed regarding the background networks, agent genes and topological parameters, respectively. Finally, we characterized the potential mechanisms of multicomponent synergy from a network target perspective. Conclusions NIMS is a first-step computational approach towards identification of synergistic drug combinations at the molecular level. The network target-based approaches may adjust current virtual screen mode and provide a systematic paradigm for facilitating the

  5. Functional genomic screening approaches in mechanistic toxicology and potential future applications of CRISPR-Cas9. (United States)

    Shen, Hua; McHale, Cliona M; Smith, Martyn T; Zhang, Luoping


    Characterizing variability in the extent and nature of responses to environmental exposures is a critical aspect of human health risk assessment. Chemical toxicants act by many different mechanisms, however, and the genes involved in adverse outcome pathways (AOPs) and AOP networks are not yet characterized. Functional genomic approaches can reveal both toxicity pathways and susceptibility genes, through knockdown or knockout of all non-essential genes in a cell of interest, and identification of genes associated with a toxicity phenotype following toxicant exposure. Screening approaches in yeast and human near-haploid leukemic KBM7 cells have identified roles for genes and pathways involved in response to many toxicants but are limited by partial homology among yeast and human genes and limited relevance to normal diploid cells. RNA interference (RNAi) suppresses mRNA expression level but is limited by off-target effects (OTEs) and incomplete knockdown. The recently developed gene editing approach called clustered regularly interspaced short palindrome repeats-associated nuclease (CRISPR)-Cas9, can precisely knock-out most regions of the genome at the DNA level with fewer OTEs than RNAi, in multiple human cell types, thus overcoming the limitations of the other approaches. It has been used to identify genes involved in the response to chemical and microbial toxicants in several human cell types and could readily be extended to the systematic screening of large numbers of environmental chemicals. CRISPR-Cas9 can also repress and activate gene expression, including that of non-coding RNA, with near-saturation, thus offering the potential to more fully characterize AOPs and AOP networks. Finally, CRISPR-Cas9 can generate complex animal models in which to conduct preclinical toxicity testing at the level of individual genotypes or haplotypes. Therefore, CRISPR-Cas9 is a powerful and flexible functional genomic screening approach that can be harnessed to provide

  6. Assessment of the potential for refinery applications of inorganic membrane technology: An identification and screening analysis. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, H.E.; Schulman, B.L.


    Commercial application of membrane technology in the separation of gas, liquid, and solid streams has grown to a business with worldwide revenues exceeding $1 billion annually. Use of organic membranes for industrial gas separation, particularly in the refining industry, is one of the major growth areas. However, organic membranes based on polymeric separation barriers, are susceptible to damage by liquids, and careful precautions must be taken to retain the system integrity. Researchers are currently developing small pore sized inorganic membranes which may substantially increase the efficiency and economics in selected refinery separation applications. Expected advantages of these advanced inorganic membranes include high permeability, high selectivity, and low manufacturing cost. SFA Pacific conducted a screening analysis to identify applications for inorganic membrane technology in the petroleum refining industry and their potential cost advantages over competing separation systems. Two meetings were held in connection with this project. Copies of Viewgraphs presented by SFA Pacific at these meetings are attached in Appendices A and C. Potential high priority applications and market impacts of advanced inorganic membrane technology in the refining industry are addressed in this report, and include the following areas: Competitive separation technologies; application of those technologies; incentives for inorganic membranes; market benefits and impacts of inorganic membranes.

  7. Bases biomoleculares do fotoenvelhecimento Molecular basis of photoaging

    Directory of Open Access Journals (Sweden)

    Suelen Montagner


    Full Text Available Com o aumento da expectativa de vida, o estudo do processo de envelhecimento orgânico tem sido estimulado. O envelhecimento da pele, órgão que espelha os sinais do tempo, é processo de deterioração progressiva, tempo-dependente, e pode ser intensificado pela exposição solar, então designado fotoenvelhecimento. O dano das radiações sobre diversas estruturas celulares e cutâneas leva a alterações morfológicas nesses componentes, fruto de modificações biomoleculares. Muitas pesquisas são desenvolvidas com o intuito de combater ou minimizar os efeitos do fotoenvelhecimento, porém a principal estratégia nesse sentido continua sendo a prevenção, só conseguida pelo progressivo desvendar dos mecanismos fisiopatogênicos envolvidos nesse processo.As a result of the increase in life expectancy, the study of the organic process of aging has been stimulated. Skin ageing, which reflects the signs of time, is a time-dependent process of progressive deterioration that can be intensified by sun exposure, which is known as photoaging. The damage of radiation on various cell structures and on the skin results in molecular and morphological changes to these components. Many research studies are performed to try to minimize the effects of photoaging; however, the main strategy to manage it is still prevention, which will only be achieved once we learn about the mechanisms involved in the process.

  8. Bridging Nano- and Microtribology in Mechanical and Biomolecular Layers (United States)

    Tomala, Agnieszka; Göçerler, Hakan; Gebeshuber, Ille C.

    The physical and chemical composition of surfaces determine various important properties of solids such as corrosion rates, adhesive properties, frictional properties, catalytic activity, wettability, contact potential and - finally and most importantly - failure mechanisms. Very thin, weak layers (of man-made and biological origin) on much harder substrates that reduce friction are the focus of the micro- and nanotribological investigations presented in this chapter.Biomolecular layers fulfil various functions in organs of the human body. Examples comprise the skin that provides a protective physical barrier between the body and the environment, preventing unwanted inward and outward passage of water and electrolytes, reducing penetration by destructive chemicals, arresting the penetration of microorganisms and external antigens and absorbing radiation from the sun, or the epithelium of the cornea that blocks the passage of foreign material, such as dust, water and bacteria, into the eye and that contributes to the lubrication layer that ensures smooth movement of the eyelids over the eyeballs.Monomolecular thin films, additive-derived reaction layers and hard coatings are widely used to tailor tribological properties of surfaces. Nanotribological investigations on these substrates can reveal novel properties regarding the orientation of chemisorbed additive layers, development of rubbing films with time and the relation of frictional properties to surface characteristics in diamond coatings.Depending on the questions to be answered with the tribological research, various micro- and nanotribological measurement methods are applied, including scanning probe microscopy (AFM, FFM), scanning electron microscopy, microtribometer investigations, angle-resolved photoelectron spectroscopy and optical microscopy. Thoughts on the feasibility of a unified approach to energy-dissipating systems and how it might be reached (touching upon new ways of scientific publishing

  9. Screening Protocol for Iodine-Specific Getters in YMP-Related Invert Applications

    Energy Technology Data Exchange (ETDEWEB)

    J.L. Krumhansl; J.D. Pless; J.B. Chwirka


    This document defines a standardized screening protocol for use in developing iodine ''getters'' for placement in the proposed YMP-repository invert. The work was funded by the US Department of Energy (DOE), Office of Civilian Radioactive Waste Management (OCRWM), Office of Science and Technology International (S&T) during 2004-2005. First, the likely environmental conditions in the invert are reviewed as a basis for defining the thermal and geochemical regimes in which a getter must function. These considerations, then, served as the basis for laying out a hierarchy of materials screening tests (Table 1). An experimental design for carrying out these screening tests follows next. Finally, the latter half of the document develops methods for preparing test solutions with chemistries that relate to various aspects of the YMP-repository environment (or, at least to such representations as were available from program documents late in 2004). Throughout the document priority was given to defining procedures that would quickly screen out unpromising candidate materials with a minimum amount of labor. Hence, the proposed protocol relies on batch tests over relatively short times, and on a hierarchy of short pre-test conditioning steps. So as not to repeat the mistakes (and frustrations) encountered in the past (notably in preparing WIPP test brines) particular care was also given to developing standardized test solution recipes that could be prepared easily and reproducibly. This document is principally intended for use as a decision-making tool in evaluating and planning research activities. It is explicitly NOT a roadmap for qualifying getters for actual placement in the repository. That would require a comprehensive test plan and a substantial consensus building effort. This document is also not intended to provide a complete list of all the tests that individuals may wish to carry out. Various materials will have their own peculiar concerns that

  10. Index-matched indium tin oxide electrodes for capacitive touch screen panel applications. (United States)

    Hong, Chan-Hwa; Shin, Jae-Heon; Ju, Byeong-Kwon; Kim, Kyung-Hyun; Park, Nae-Man; Kim, Bo-Sul; Cheong, Woo-Seok


    Index-matched indium tin oxide (ITO) electrodes for capacitive touch screen panels have been fabricated to improve optical transmittance and reduce the difference of reflectance (deltaR) between the etched and un-etched regions. 8.5 nm Nb2O5 and 49 nm SiO2 thin films were deposited by magnetron sputtering as index-matching layers between an ITO electrode and a glass substrate. In case of 30 nm ITO electrode, a 4.3% improvement in the optical transmittance and a deltaR of less than 1% were achieved, along with a low sheet resistance of 90 omega/square.

  11. High voltage series resonant inverter ion engine screen supply. [SCR series resonant inverter for space applications (United States)

    Biess, J. J.; Inouye, L. Y.; Shank, J. H.


    A high-voltage, high-power LC series resonant inverter using SCRs has been developed for an Ion Engine Power Processor. The inverter operates within 200-400Vdc with a maximum output power of 2.5kW. The inverter control logic, the screen supply electrical and mechanical characteristics, the efficiency and losses in power components, regulation on the dual feedback principle, the SCR waveforms and the component weight are analyzed. Efficiency of 90.5% and weight density of 4.1kg/kW are obtained.

  12. In vitro application of integrated selection index for screening drought tolerant genotypes in common wheat

    Directory of Open Access Journals (Sweden)

    Ezatollah FARSHADFAR


    Full Text Available This experiment was conducted on 20 wheat genotypes during 2010-2011 growing season at the Razi University, Kermanshah, Iran. A completely randomized design with six replications was used for callus induction and a 20 × 2 factorial experiment with three replications was used for response of genotypes to in vitro drought stress. ANOVA exhibited highly significant differences among the genotypes for callus growth rate, relative fresh mass growth, relative growth rate, callus water content, percent of callus chlorosis and proline content under stress condition (15 % PEG. PCA showed that the integrated selection index was correlated with callus growth index, relative fresh mass growth, relative growth rate and proline content indicating that these screening techniques can be useful for selecting drought tolerant genotypes. Screening drought tolerant genotypes and in vitro indicators of drought tolerance using mean rank, standard deviation of ranks and biplot analysis, discriminated genotypes 2, 18 and 10 as the most drought tolerant. Therefore they are recommended to be used as parents for genetic analysis, gene mapping and improvement of drought tolerance.

  13. Toward the discovery of functional transthyretin amyloid inhibitors: application of virtual screening methods. (United States)

    Simões, Carlos J V; Mukherjee, Trishna; Brito, Rui M M; Jackson, Richard M


    Inhibition of amyloid fibril formation by stabilization of the native form of the protein transthyretin (TTR) is a viable approach for the treatment of familial amyloid polyneuropathy that has been gaining momentum in the field of amyloid research. The TTR stabilizer molecules discovered to date have shown efficacy at inhibiting fibrilization in vitro but display impairing issues of solubility, affinity for TTR in the blood plasma and/or adverse effects. In this study we present a benchmark of four protein- and ligand-based virtual screening (VS) methods for identifying novel TTR stabilizers: (i) two-dimensional (2D) similarity searches with chemical hashed, pharmacophore, and UNITY fingerprints, (ii) 3D searches based on shape, chemical, and electrostatic similarity, (iii) LigMatch, a new ligand-based method which uses multiple templates and combines 3D geometric hashing with a 2D preselection process, and (iv) molecular docking to consensus X-ray crystal structures of TTR. We illustrate the potential of the best-performing VS protocols to retrieve promising new leads by ranking a tailored library of 2.3 million commercially available compounds. Our predictions show that the top-scoring molecules possess distinctive features from the known TTR binders, holding better solubility, fraction of halogen atoms, and binding affinity profiles. To the best of our knowledge, this is the first attempt to rationalize the utilization of a large battery of in silico screening techniques toward the identification of a new generation of TTR amyloid inhibitors.

  14. Isolation, screening and identification of novel isolates of Actinomycetes from India for antimicrobial applications

    Directory of Open Access Journals (Sweden)

    Vineeta Singh


    Full Text Available The search for novel bioactive compounds from the natural environment has been rapidly increased with the increase in multi-drug resistant (MDR pathogens. In the present study, the antimicrobial potential of novel actinomycetes has been evaluated by initial screening of six soil samples. Primary and secondary screening was performed against Bacillus subtilis, Staphylococcus aureus, Escherichia coli, Candida albicans, Candida tropicalis, Trichophyton rubrum, and other MDR bacterial and fungal test strains, and at the end thirteen active isolates were selected for further study. Microbial strains were identified on the basis of growth conditions and other biochemical characters. Five most active microbial strains were identified using 16S rRNA sequence homology and designated as Streptomyces xanthophaeus MTCC 11938, Streptomyces variabilis MTCC 12266, Streptomyces xanthochromogenes MTCC 11937, Streptomyces levis EU 124569 and Streptomyces sp. NCIM 5500. Four antibacterial and three antifungal compounds isolated from the above five isolates were purified and partially characterized using UV absorption and IR spectra. Two antibacterial metabolites, belong to chromone and peptide antibiotic, respectively. The antifungal compounds were found to be of non-polyene nature. In conclusion, we study the isolation of novel bacterial strains of actinomycetes for producing novel compounds having antibacterial and antifungal activities from the unexplored agro-ecological niches of India. Also, this study paves the way for further characterization of these isolates of Streptomyces sp. for their optimum utilization for antimicrobial purposes.

  15. Droplet Microfluidic System with On-Demand Trapping and Releasing of Droplet for Drug Screening Applications. (United States)

    Courtney, Matthew; Chen, Xiaoming; Chan, Sarah; Mohamed, Tarek; Rao, Praveen P N; Ren, Carolyn L


    96-Well plate has been the traditional method used for screening drug compounds libraries for potential bioactivity. Although this method has been proven successful in testing dose-response analysis, the microliter consumption of expensive reagents and hours of reaction and analysis time call for innovative methods for improvements. This work demonstrates a droplet microfluidic platform that has the potential to significantly reduce the reagent consumption and shorten the reaction and analysis time by utilizing nanoliter-sized droplets as a replacement of wells. This platform is evaluated by applying it to screen drug compounds that inhibit the tau-peptide aggregation, a phenomena related to Alzheimer's disease. In this platform, sample reagents are first dispersed into nanolitre-sized droplets by an immiscible carrier oil and then these droplets are trapped on-demand in the downstream of the microfluidic device. The relative decrease in fluorescence through drug inhibition is characterized using an inverted epifluorescence microscope. Finally, the trapped droplets are released on-demand after each test by manipulating the applied pressures to the channel network which allows continuous processing. The testing results agree well with that obtained from 96-well plates with much lower sample consumption (∼200 times lower than 96-well plate) and reduced reaction time due to increased surface volume ratio (2.5 min vs 2 h).

  16. Development of Screen-Printed Texture-Barrier Paste for Single-Side Texturization of Interdigitated Back-Contact Silicon Solar Cell Applications


    Chi-Cheng Chen; Chin-Lung Cheng; Thou-Jen Whang; Yu-Shun Chiu


    Continuous cost reduction of silicon-based solar cells is needed to lower the process time and increase efficiency. To achieve lower costs, screen-printed texture-barrier (SPTB) paste was first developed for single-side texturization (ST) of the interdigitated back-contact (IBC) for silicon-based solar cell applications. The SPTB paste was screen-printed on silicon substrates. The SPTB paste was synthesized from intermixed silicate glass (75 wt %), a resin binder (ethyl cellulose ethoce: 20 w...

  17. Sop-GPU: accelerating biomolecular simulations in the centisecond timescale using graphics processors. (United States)

    Zhmurov, A; Dima, R I; Kholodov, Y; Barsegov, V


    Theoretical exploration of fundamental biological processes involving the forced unraveling of multimeric proteins, the sliding motion in protein fibers and the mechanical deformation of biomolecular assemblies under physiological force loads is challenging even for distributed computing systems. Using a C(α)-based coarse-grained self organized polymer (SOP) model, we implemented the Langevin simulations of proteins on graphics processing units (SOP-GPU program). We assessed the computational performance of an end-to-end application of the program, where all the steps of the algorithm are running on a GPU, by profiling the simulation time and memory usage for a number of test systems. The ∼90-fold computational speedup on a GPU, compared with an optimized central processing unit program, enabled us to follow the dynamics in the centisecond timescale, and to obtain the force-extension profiles using experimental pulling speeds (v(f) = 1-10 μm/s) employed in atomic force microscopy and in optical tweezers-based dynamic force spectroscopy. We found that the mechanical molecular response critically depends on the conditions of force application and that the kinetics and pathways for unfolding change drastically even upon a modest 10-fold increase in v(f). This implies that, to resolve accurately the free energy landscape and to relate the results of single-molecule experiments in vitro and in silico, molecular simulations should be carried out under the experimentally relevant force loads. This can be accomplished in reasonable wall-clock time for biomolecules of size as large as 10(5) residues using the SOP-GPU package.

  18. Application of consensus scoring and principal component analysis for virtual screening against β-secretase (BACE-1.

    Directory of Open Access Journals (Sweden)

    Shu Liu

    Full Text Available BACKGROUND: In order to identify novel chemical classes of β-secretase (BACE-1 inhibitors, an alternative scoring protocol, Principal Component Analysis (PCA, was proposed to summarize most of the information from the original scoring functions and re-rank the results from the virtual screening against BACE-1. METHOD: Given a training set (50 BACE-1 inhibitors and 9950 inactive diverse compounds, three rank-based virtual screening methods, individual scoring, conventional consensus scoring and PCA, were judged by the hit number in the top 1% of the ranked list. The docking poses were generated by Surflex, five scoring functions (Surflex_Score, D_Score, G_Score, ChemScore, and PMF_Score were used for pose extraction. For each pose group, twelve scoring functions (Surflex_Score, D_Score, G_Score, ChemScore, PMF_Score, LigScore1, LigScore2, PLP1, PLP2, jain, Ludi_1, and Ludi_2 were used for the pose rank. For a test set, 113,228 chemical compounds (Sigma-Aldrich® corporate chemical directory were docked by Surflex, then ranked by the same three ranking methods motioned above to select the potential active compounds for experimental test. RESULTS: For the training set, the PCA approach yielded consistently superior rankings compared to conventional consensus scoring and single scoring. For the test set, the top 20 compounds according to conventional consensus scoring were experimentally tested, no inhibitor was found. Then, we relied on PCA scoring protocol to test another different top 20 compounds and two low micromolar inhibitors (S450588 and 276065 were emerged through the BACE-1 fluorescence resonance energy transfer (FRET assay. CONCLUSION: The PCA method extends the conventional consensus scoring in a quantitative statistical manner and would appear to have considerable potential for chemical screening applications.

  19. Immobilization of Acetylcholinesterase on Screen-Printed Electrodes. Application to the Determination of Arsenic(III

    Directory of Open Access Journals (Sweden)

    M. Julia Arcos-Martínez


    Full Text Available Enzymatic amperometric procedures for measuring arsenic, based on the inhibitive action of this metal on acetylcholinesterase enzyme activity, have been developed. Screen-printed carbon electrodes (SPCEs were used with acetylcholinesterase covalently bonded directly to its surface. The amperometric response of acetylcholinesterase was affected by the presence of arsenic ions, which caused a decrease in the current intensity. The experimental optimum working conditions of pH, substrate concentration and potential applied, were established. Under these conditions, repeatability and reproducibility of biosensors were determined, reaching values below 4% in terms of relative standard deviation. The detection limit obtained for arsenic was 1.1 × 10−8 M for Ach/SPCE biosensor. Analysis of the possible effect of the presence of foreign ions in the solution was performed. The method was applied to determine levels of arsenic in spiked tap water samples.

  20. Application of remote Raman screening to processing of mixed wastes in drums (United States)

    Crawford, Beverly A.; Jewett, James R.; Parker, K. E.; Petersen, C. A.; Petty, Chris J.


    Transuranic (TRU) and low-level drum waste disposal involves decisions based on transportation restrictions, conditions for acceptance, and federal and state regulations. To support the decisions made concerning final disposition of these wastes, characterization protocols must be established to help define the environmental impact. One promising screening technique involves applying near infrared (IR) Fourier Transform Raman (FT- Raman) spectroscopy using remote fiber optic probes for identifying unknown salts, sludges, and solids in wastes. It is proposed that FT-Raman spectroscopy be used in conjunction with real-time radiography and visual documentation. Developing an extensive solid waste library is a key element in the deployment of this technology in the process environment of solid waste drums. The feasibility for such library generation is also demonstrated.

  1. Screening for ligninolytic enzymes from autochthonous fungi and applications for decolorization of Remazole Marine Blue (United States)

    Erden, Emre; Ucar, M. Cigdem; Gezer, Tekin; Pazarlioglu, Nurdan Kasikara


    This study presents new and alternative fungal strains for the production of ligninolytic enzymes which have great potential to use in industrial and biotechnological processes. Thirty autochthonous fungal strains were harvested from Bornova-Izmir in Turkiye. In the fresh fruitbody extracts laccase, manganese peroxidase and lignin peroxidase activities, which are the principal enzymes responsible for ligninocellulose degradation by Basidiomycetes, were screened. Spores of some of the basidiomycetes species such as Cortinarius sp., Trametes versicolor, Pleurotus ostreatus, Abortiporus biennis, Lyophyllum subglobisporium, Ramaria stricta, Ganoderma carnosum, Lactarius delicious ve Lepista nuda were isolated and investigated optimum cultivation conditions in submerged fermentation for high yields of ligninolytic enzyme production. In addition, isolated fungal strains were monitored on agar plates whether having the capability of decolorization of a textile dye Remazol Marine Blue. PMID:24031371

  2. Low-coherence enhanced backscattering: review of principles and applications for colon cancer screening (United States)

    Kim, Young L.; Liu, Yang; Turzhitsky, Vladimir M.; Roy, Hemant K.; Wali, Ramesh K.; Subramanian, Hariharan; Pradhan, Prabhakar; Backman, Vadim


    The phenomenon of enhanced backscattering (EBS) of light, also known as coherent backscattering (CBS) of light, has been the object of intensive investigation in nonbiological media over the last two decades. However, there have been only a few attempts to explore EBS for tissue characterization and diagnosis. We have recently made progress in the EBS measurements in tissue by taking advantage of low spatial coherence illumination, which has led us to the development of low-coherence enhanced backscattering (LEBS) spectroscopy. In this work, we review the current state of research on LEBS. After a brief discussion of the basic principle of EBS and LEBS, we present an overview of the unique features of LEBS for tissue characterization, and show that LEBS enables depth-selective spectroscopic assessment of mucosal tissue. Then, we demonstrate the potential of LEBS spectroscopy for predicting the risk of colon carcinogenesis and colonoscopy-free screening for colorectal cancer (CRC).

  3. In vivo models of cardiac diseases: application to drug development and screening. (United States)

    Rokutan, Hirofumi; Anker, Stefan D; Springer, Jochen


    Cardiac disease is the top cause of human mortality in the Western world. Current drug therapy for cardiac disease has been established via experimental studies using a variety of in vivo animal models. The purpose of this review is to discuss the features (advantages and limitations) of the mainly used in vivo models of cardiac disease and provide the reader with an overview of how they can be utilized in the development and screening of cardiac drugs. A search for articles focusing on and including in vivo models for the main areas of cardiac diseases was performed on PubMed. We also searched the reference lists of identified articles for further original articles. Large and small animal models including genetically modified ones have made accomplishments in the process of cardiac drug development with different clinical relevance. However, there is still a clear need for lessening the gap between human and experimental models by improving in vivo models.

  4. Screening and Improving the Recombinant Nitrilases and Application in Biotransformation of Iminodiacetonitrile to Iminodiacetic Acid.

    Directory of Open Access Journals (Sweden)

    Zhi-Qiang Liu

    Full Text Available In this study, several nitrilase genes from phylogenetically distinct organisms were expressed and purified in E. coli in order to study their ability to mediate the biotransformation of nitriles. We identified three nitrilases: Acidovorax facilis nitrilase (AcN; Alcaligenes fecalis nitrilase (AkN; and Rhodococcus rhodochrous nitrilase (RkN, which catalyzed iminodiacetonitrile (IDAN to iminodiacetic acid (IDA. AcN demonstrated 8.8-fold higher activity for IDAN degradation as compared to AkN and RkN. Based on homology modeling and previously described 'hot spot' mutations, several AcN mutants were screened for improved activity. One mutant M3 (F168V/L201N/S192F was identified, which demonstrates a 41% enhancement in the conversion as well as a 2.4-fold higher catalytic efficiency towards IDAN as compared to wild-type AcN.

  5. iBIOMES: managing and sharing biomolecular simulation data in a distributed environment. (United States)

    Thibault, Julien C; Facelli, Julio C; Cheatham, Thomas E


    Biomolecular simulations, which were once batch queue or compute limited, have now become data analysis and management limited. In this paper we introduce a new management system for large biomolecular simulation and computational chemistry data sets. The system can be easily deployed on distributed servers to create a mini-grid at the researcher's site. The system not only offers a simple data deposition mechanism but also a way to register data into the system without moving the data from their original location. Any registered data set can be searched and downloaded using a set of defined metadata for molecular dynamics and quantum mechanics and visualized through a dynamic Web interface.

  6. Output-input ratio in thermally fluctuating biomolecular machines. (United States)

    Kurzynski, Michal; Torchala, Mieczyslaw; Chelminiak, Przemyslaw


    Biological molecular machines are proteins that operate under isothermal conditions and hence are referred to as free energy transducers. They can be formally considered as enzymes that simultaneously catalyze two chemical reactions: the free energy-donating (input) reaction and the free energy-accepting (output) one. Most if not all biologically active proteins display a slow stochastic dynamics of transitions between a variety of conformational substates composing their native state. This makes the description of the enzymatic reaction kinetics in terms of conventional rate constants insufficient. In the steady state, upon taking advantage of the assumption that each reaction proceeds through a single pair (the gate) of transition conformational substates of the enzyme-substrates complex, the degree of coupling between the output and the input reaction fluxes has been expressed in terms of the mean first-passage times on a conformational transition network between the distinguished substates. The theory is confronted with the results of random-walk simulations on the five-dimensional hypercube. The formal proof is given that, for single input and output gates, the output-input degree of coupling cannot exceed unity. As some experiments suggest such exceeding, looking for the conditions for increasing the degree of coupling value over unity challenges the theory. Performed simulations of random walks on several model networks involving more extended gates indicate that the case of the degree of coupling value higher than 1 is realized in a natural way on critical branching trees extended by long-range shortcuts. Such networks are scale-free and display the property of the small world. For short-range shortcuts, the networks are scale-free and fractal, representing a reasonable model for biomolecular machines displaying tight coupling, i.e., the degree of coupling equal exactly to unity. A hypothesis is stated that the protein conformational transition networks, as

  7. Organic-resistant screen-printed graphitic electrodes: Application to on-site monitoring of liquid fuels

    Energy Technology Data Exchange (ETDEWEB)

    Almeida, Eduardo S.; Silva, Luiz A.J.; Sousa, Raquel M.F.; Richter, Eduardo M. [Universidade Federal de Uberlândia, Universidade Federal de Uberlândia, Av. João Naves de Ávila, 2121, Uberlândia, MG, 38408100 (Brazil); Foster, Christopher W.; Banks, Craig E. [Manchester Metropolitan University, Faculty of Science and the Environment, School of Science and the Environment, Division of Chemistry and Environmental Science, Manchester, M1 5GD, England (United Kingdom); Munoz, Rodrigo A.A., E-mail: [Universidade Federal de Uberlândia, Universidade Federal de Uberlândia, Av. João Naves de Ávila, 2121, Uberlândia, MG, 38408100 (Brazil)


    This work presents the potential application of organic-resistant screen-printed graphitic electrodes (SPGEs) for fuel analysis. The required analysis of the antioxidant 2,6-di-tert-butylphenol (2,6-DTBP) in biodiesel and jet fuel is demonstrated as a proof-of-concept. The screen-printing of graphite, Ag/AgCl and insulator inks on a polyester substrate (250 μm thickness) resulted in SPGEs highly compatible with liquid fuels. SPGEs were placed on a batch-injection analysis (BIA) cell, which was filled with a hydroethanolic solution containing 99% v/v ethanol and 0.1 mol L{sup −1} HClO{sub 4} (electrolyte). An electronic micropipette was connected to the cell to perform injections (100 μL) of sample or standard solutions. Over 200 injections can be injected continuously without replacing electrolyte and SPGE strip. Amperometric detection (+1.1 V vs. Ag/AgCl) of 2,6-DTBP provided fast (around 8 s) and precise (RSD = 0.7%, n = 12) determinations using an external calibration curve. The method was applied for the analysis of biodiesel and aviation jet fuel samples and comparable results with liquid and gas chromatographic analyses, typically required for biodiesel and jet fuel samples, were obtained. Hence, these SPGE strips are completely compatible with organic samples and their combination with the BIA cell shows great promise for routine and portable analysis of fuels and other organic liquid samples without requiring sophisticated sample treatments. - Highlights: • Organic-resistant screen-printed graphitic electrodes (SPGE) for (bio)fuels. • Screen-printing of conductive and insulator inks on thin polyester substrate. • Continuous detection of antioxidants in electrolyte with 99% v/v ethanol. • SPGE coupled with batch-injection analysis allows over 200 injections (100 μL). • Similar results to GC and HPLC analyses of biodiesel and aviation jet fuels.

  8. Development and Application of a New Microarray- Based Method for High-Throughput Screening of Carbohydrate Active Enzymes

    DEFF Research Database (Denmark)

    Vidal Melgosa, Silvia

    biological roles in plants and in addition to biofuel production they are extensively used in other industrial processes including in detergents, textiles, paper and the food industry. A vast repertoire of CAZymes exists in nature but there is a growing disparity between our ability to putatively identify....... The applicability of the method to identify the substrate specificities of purified uncharacterised enzymes as well as for screening CAZyme activities in complex enzyme mixtures, such as crude culture broths and plant extracts, is shown by examples presented in this thesis. We envisage that the method......The effective and sustainable use of plant biomass for second generation biofuels is of vital importance for reducing dependence on fossil fuels. Carbohydrate-active enzymes (CAZymes) that degrade lignocellulosic plant cell wall material are an important part of this effort. CAZymes have multiple...

  9. A commentary on iPS cells: potential applications in autologous transplantation, study of illnesses and drug screening. (United States)

    Romano, Gaetano; Morales, Fátima; Marino, Ignazio R; Giordano, Antonio


    Undoubtedly, the focus of the field of stem cell research is predominantly aimed at the artificial reprogramming of human somatic cells for the production of induced pluripotent stem (iPS) cells. This relatively new technology may circumvent the ethical issues of using human embryonic stem (hES) cells for the potential applications in cell replacement therapy. Besides such ethical issues, iPS cell technology offers the advantage of obtaining patient-derived tissues and/or cells, which may be utilized for autologous transplantation and tissue regeneration, investigation of a variety of human illnesses and for the screening of new drugs. The field of stem cell research has placed a major emphasis in understanding the genetic and epigenetic codes for pluripotency, in order to control and optimize autologous transplantation techniques and avoid teratoma formation.

  10. Design and experimental analysis of a screened heat pipe for solar applications (United States)

    Jafari, D.; Filippeschi, S.; Franco, A.; Di Marco, P.


    This paper summarizes the design, the construction and the preliminary results of a transient and steady state investigation of the heat transfer mechanisms of a horizontal heat pipe (HP). The experiments are performed using a custom-made HP constituted by copper tube with outer diameter and length as 35 mm and 510 mm, respectively, with the inner surface covered by three layers stainless steel mesh wick (100 mesh/inch). Water is used as a working fluid. The evaporator section is heated by electrical resistances wrapped around the tube and the cooling system consists of an insulated water manifold with inner diameter of 39 mm, connected to chilled water bath to maintain the inlet temperature of the circulating cooling water at 25 °C for various heat loads (30-100 W). The aims of this activity is to obtain data to verify the steady state HP analytical model already presented by authors at a fixed filling volume and to determine the effect of the heat transfer load on the heat transfer performance of screen mesh HPs. The heat transfer coefficients are determined using thermocouples on the outer wall and within the core of the HP. The agreement between the analytical results and the preliminary experimental data appears to be very good.

  11. An optimized TALEN application for mutagenesis and screening in Drosophila melanogaster. (United States)

    Lee, Han B; Sebo, Zachary L; Peng, Ying; Guo, Yi


    Transcription activator-like effector nucleases (TALENs) emerged as powerful tools for locus-specific genome engineering. Due to the ease of TALEN assembly, the key to streamlining TALEN-induced mutagenesis lies in identifying efficient TALEN pairs and optimizing TALEN mRNA injection concentrations to minimize the effort to screen for mutant offspring. Here we present a simple methodology to quantitatively assess bi-allelic TALEN cutting, as well as approaches that permit accurate measures of somatic and germline mutation rates in Drosophila melanogaster. We report that percent lethality from pilot injection of candidate TALEN mRNAs into Lig4 null embryos can be used to effectively gauge bi-allelic TALEN cutting efficiency and occurs in a dose-dependent manner. This timely Lig4-dependent embryonic survival assay also applies to CRISPR/Cas9-mediated targeting. Moreover, the somatic mutation rate of individual G0 flies can be rapidly quantitated using SURVEYOR nuclease and capillary electrophoresis, and germline transmission rate determined by scoring progeny of G0 outcrosses. Together, these optimized methods provide an effective step-wise guide for routine TALEN-mediated gene editing in the fly.

  12. Screening efficiency and screen length of a linear vibrating screen using DEM 3D simulation

    Institute of Scientific and Technical Information of China (English)

    Wang Guifeng; Tong Xin


    The effect of screen length on the screening efficiency of particles is studied under various single parameter conditions including frequency,amplitude,vibration angle,and screen inclination.The Discrete Element Method (DEM) has been used to simulate the screening process.A functional relationship between screening efficiency and screen length is established.It is shown that screening efficiency and screen length have a complicated exponential relationship.Relationships between them are profoundly discussed and conclusions are easily drawn:low values of the parameters do not benefit screening; screening efficiency generally increases with screen length; screening efficiency reaches a plateau when these parameters are in range frequently encountered in practical applications.

  13. Simultaneous formation of fine and large-area electrode patterns using screen-offset printing and its application to the patterning on adhesive materials (United States)

    Nomura, Ken-ichi; Ushijima, Hirobumi; Nagase, Kazuro; Ikedo, Hiroaki; Mitsui, Ryosuke; Sato, Junya; Takahashi, Seiya; Nakajima, Shin-ichiro; Arai, Masahiro; Kurata, Yuji; Iwata, Shiro


    Additive-type printing techniques such as gravure-offset printing and screen printing are effective for low-cost and ecofriendly electrode pattern formation. Gravure-offset printing is effective for fine pattern formation with widths on the order of 10-20 µm, whereas screen printing is effective for the formation of large-area patterns. However, it is difficult to simultaneously form fine and large-area patterns using these printing techniques. In this study, we demonstrate that fine (minimum width of 15 µm) and medium- as well as large-area patterns can be formed simultaneously using our developed screen-offset printing technique, which is a combination of screen printing on a silicone blanket and transfer printing from the blanket to a substrate. Furthermore, we demonstrate the application of our method to printing on adhesive materials, which allows electrode formation without applying heat to the film substrate.

  14. Screening the CIP potato collection for response to in-season calcium application (United States)

    Potato growers in many parts of the US now routinely use in-season calcium to improve production and tuber quality. Our recent studies have shown that native potatoes grown in the Peruvian Highlands also respond positively to calcium application resulting in increased yield and tuber size. However, ...

  15. Biomolecular and epidemiological aspects of human papillomavirus induced cervical carcinogenesis

    NARCIS (Netherlands)

    Vermeulen, Christine Frederike Wilhelmine


    Cervical cancer remains one of the leading causes of death from cancer among women worldwide. Organised screening programmes aim to trace precursor lesions in order to reduce cervical cancer incidence. Human papillomavirus (HPV) is a necessary cause for cervical carcinogenesis. Most HPV infections a

  16. Wet Chemical Synthesis and Screening of Thick Porous Oxide Films for Resistive Gas Sensing Applications

    Directory of Open Access Journals (Sweden)

    Wilhelm F. Maier


    Full Text Available A method of wet chemical synthesis suitable for high throughput and combinatorial applications has been developed for the synthesis of porous resistive thick-film gas sensors. This method is based on the robot-controlled application of unstable metal oxide suspensions on an array of 64 inter-digital electrodes positioned on an Al2O3 substrate. SnO2, WO3, ZrO2, TiO2, CeO2, In2O3 and Bi2O3 were chosen as base oxides, and were optimised by doping or mixed oxide formation. The parallel synthesis of mixed oxide sensors is illustrated by representative examples. The electrical characteristics and the sensor performance of the films were measured by high-throughput impedance spectroscopy while supplying various test gases (H2, CO, NO, NO2, propene. Data collection, data mining techniques applied and the best potential sensor materials discovered are presented.

  17. Mechanical and analytical screening of braided composites for transport fuselage applications (United States)

    Fedro, Mark J.; Gunther, Christian; Ko, Frank K.


    The mechanics of materials progress in support of the goal of understanding the application of braided composites in a transport aircraft fuselage are summarized. Composites consisting of both 2-D and 3-D braid patterns are investigated. Both consolidation of commingled graphite/PEEK and resin transfer molding of graphite-epoxy braided composite processes are studied. Mechanical tests were used to examine unnotched tension, open hole tension, compression, compression after impact, in-plane shear, out-of-plane tension, bearing, and crippling. Analytical methods are also developed and applied to predict the stiffness and strengths of test specimens. A preliminary study using the test data and analytical results is performed to assess the applicability of braided composites to a commercial aircraft fuselage.

  18. Development and validation of a high-throughput screen for inhibitors of SARS CoV and its application in screening of a 100,000-compound library. (United States)

    Severson, William E; Shindo, Nice; Sosa, Mindy; Fletcher, Thomas; White, E Lucile; Ananthan, Subramaniam; Jonsson, Colleen B


    The authors have developed a high-throughput screen (HTS) that allows for the identification of potential inhibitors of the severe acute respiratory syndrome coronavirus (SARS CoV) from large compound libraries. The luminescent-based assay measures the inhibition of SARS CoV-induced cytopathic effect (CPE) in Vero E6 cells. The assay was validated in 96-well plates in a BSL3 containment facility. The assay is sensitive and robust, with Z values > 0.6, signal to background (S/B) > 16, and signal to noise (S/N) > 3. The assay was further validated with 2 different diversity sets of compounds against the SARS CoV. The "hit" rate for both libraries was approximately 0.01%. The validated HTS assay was then employed to screen a 100,000-compound library against SARS CoV. The hit rate for the library in a single-dose format was determined to be approximately 0.8%. Screening of the 3 libraries resulted in the identification of several novel compounds that effectively inhibited the CPE of SARS CoV in vitro-compounds which will serve as excellent lead candidates for further evaluation. At a 10-microM concentration, 3 compounds with selective indexes (SI50) of > 53 were discovered.

  19. Immune cell-based screening assay for response to anticancer agents: applications in pharmacogenomics

    Directory of Open Access Journals (Sweden)

    Frick A


    Full Text Available Amber Frick,1 Yuri Fedoriw,2 Kristy Richards,3,4 Blossom Damania,3,5 Bethany Parks,6 Oscar Suzuki,1 Cristina S Benton,1 Emmanuel Chan,1 Russell S Thomas,7 Tim Wiltshire1,3 1Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, 2Department of Pathology and Laboratory Medicine, School of Medicine, 3Lineberger Comprehensive Cancer Center, School of Medicine, 4Department of Genetics, School of Medicine, 5Department of Microbiology and Immunology, School of Medicine, University of North Carolina, Chapel Hill, NC, USA; 6The Hamner Institutes for Health Sciences, 7Environmental Protection Agency, Research Triangle Park, NC, USA Background: Interpatient variability in immune and chemotherapeutic cytotoxic responses is likely due to complex genetic differences and is difficult to ascertain in humans. Through the use of a panel of genetically diverse mouse inbred strains, we developed a drug screening platform aimed at examining interstrain differences in viability on normal, noncancerous immune cells following chemotherapeutic cytotoxic insult. Drug effects were investigated by comparing selective chemotherapeutic agents, such as BEZ-235 and selumetinib, against conventional cytotoxic agents targeting multiple pathways, including doxorubicin and idarubicin. Methods: Splenocytes were isolated from 36 isogenic strains of mice using standard procedures. Of note, the splenocytes were not stimulated to avoid attributing responses to pathways involved with cellular stimulation rather than toxicity. Cells were incubated with compounds on a nine-point logarithmic dosing scale ranging from 15 nM to 100 µM (37°C, 5% CO2. At 4 hours posttreatment, cells were labeled with antibodies and physiological indicator dyes and fixed with 4% paraformaldehyde. Cellular phenotypes (eg, viability were collected and analyzed using flow cytometry. Dose-response curves with response normalized to the zero dose as a function of log concentration

  20. Screening of various low-grade biomass materials for low temperature gasification: Method development and application

    DEFF Research Database (Denmark)

    Thomsen, Tobias Pape; Ravenni, Giulia; Holm, Jens Kai;


    method and the subsequent use of the method to identify promising e but currently unproven, low-grade biomass resources for conversion in Pyroneer systems. The technical assessment is conducted by comparing the results from a series of physical-mechanical and thermochemical experiments to a set of proven...... references. The technical assessment is supplemented by an evaluation of practical application and overall energy balance. Applying the developed method to 4 references and 18 unproven low-grade potential fuels, indicated that one of these unproven candidates was most likely unsuited for Pyroneer...

  1. Application of high-throughput affinity-selection mass spectrometry for screening of chemical compound libraries in lead discovery. (United States)

    Zehender, Hartmut; Mayr, Lorenz M


    High-throughput screening of chemical libraries for compounds that interfere with a particular molecular target is among the most powerful methodologies applied in lead discovery at present. In this review, the authors describe a label-free, homogeneous, affinity-selection-based technology developed at Novartis, termed SpeedScreen, which is compared with similar technologies used for high-throughput screening in the pharmaceutical and biotechnology industries. The focus at present of SpeedScreen is twofold: first, this technology is applied to orphan genomic targets and to those targets that are non-tractable by a functional assay; second, this technology is applied complementary to the well-established traditional methodologies for the screening of molecular targets. In summary, the authors discuss the value of affinity-selection-based high-throughput screening as a complementary technology to the common functional screening platforms and the benefits as well as the limitations of this new technology are outlined.

  2. Screening-engineered Field-effect Photovoltaics and Synthesis, Characterization, and Applications of Carbon-based and Related Nanomaterials (United States)

    Regan, William Raymond

    Carbon nanomaterials, and especially graphene (a 2D carbon allotrope), possess unique electronic, optical, and mechanical properties and allow access to both new physical phenomena and reinventions of familiar technologies. In the first part of this thesis (chapter 2), the low carrier density and high conductivity of graphene are used to repurpose the electric field effect (used for many decades in transistors) into a universally-applicable doping method for electrically-contacted semiconductors. This method, referred to as "screening-engineered field-effect photovoltaics" as the electric field doping is enabled by a carefully-designed poorly-screening electrode (e.g. graphene), is shown to open up many new low-cost and abundant semiconductors for use in high efficiency solar cells. We extend this method beyond ultrathin materials such as graphene and show that 1D nanowire electrodes made of any material also allow penetration of applied electric fields. The next part of this thesis (chapter 3) focuses on the fundamental properties of graphene -- its structure, synthesis, characterization, and manipulation -- and on using graphene as a building block for other nanostructures: grafold, graphene sandwiches and veils, and graphritos. In chapter 4, various graphene electronics are constructed and tested. Graphene field-effect transistors (FETs) and p-n junctions are fabricated to study the influence of the substrate on graphene carrier mobility and doping. Graphene nanoribbons and grafold FETs are made to investigate the effects of additional confinement on electronic transport. Chapter 5 summarizes synthesis methods and additional experiments with other nanomaterials, including dichalcogenides and chalcogenides (magnesium diboride, gallium selenide, and tin sulfide), carbon nanomaterials (carbon nanotubes and graphene), and copper oxide. Additional measurement and fabrication methods are discussed in appendix A.

  3. Relaxing the electrostatic screening effect by patterning vertically-aligned silicon nanowire arrays into bundles for field emission application

    Energy Technology Data Exchange (ETDEWEB)

    Hung, Yung-Jr, E-mail: [Department of Electronic Engineering, National Taiwan University of Science and Technology, No. 43, Sec. 4, Keelung Rd., Taipei 106, Taiwan, ROC (China); Department of Photonics, National Sun Yat-sen University, No. 70, Lienhai Rd., Kaohsiung 80424, Taiwan, ROC (China); Graduate Institute of Electro-Optical Engineering, National Taiwan University of Science and Technology, No. 43, Sec. 4, Keelung Rd., Taipei 106, Taiwan, ROC (China); Lee, San-Liang [Department of Electronic Engineering, National Taiwan University of Science and Technology, No. 43, Sec. 4, Keelung Rd., Taipei 106, Taiwan, ROC (China); Graduate Institute of Electro-Optical Engineering, National Taiwan University of Science and Technology, No. 43, Sec. 4, Keelung Rd., Taipei 106, Taiwan, ROC (China); Beng, Looi Choon [Faculty of Engineering, Multimedia University, Jalan Multimedia, 63100 Cyberjaya, Selangor (Malaysia); Chang, Hsuan-Chen [Department of Electronic Engineering, National Taiwan University of Science and Technology, No. 43, Sec. 4, Keelung Rd., Taipei 106, Taiwan, ROC (China); Graduate Institute of Electro-Optical Engineering, National Taiwan University of Science and Technology, No. 43, Sec. 4, Keelung Rd., Taipei 106, Taiwan, ROC (China); Huang, Yung-Jui [Graduate Institute of Electro-Optical Engineering, National Taiwan University of Science and Technology, No. 43, Sec. 4, Keelung Rd., Taipei 106, Taiwan, ROC (China); Lee, Kuei-Yi; Huang, Ying-Sheng [Department of Electronic Engineering, National Taiwan University of Science and Technology, No. 43, Sec. 4, Keelung Rd., Taipei 106, Taiwan, ROC (China); Graduate Institute of Electro-Optical Engineering, National Taiwan University of Science and Technology, No. 43, Sec. 4, Keelung Rd., Taipei 106, Taiwan, ROC (China)


    Top-down fabrication strategies are proposed and demonstrated to realize arrays of vertically-aligned silicon nanowire bundles and bundle arrays of carbon nanotube–silicon nanowire (CNT–SiNW) heterojunctions, aiming for releasing the electrostatic screening effect and improving the field emission characteristics. The trade-off between the reduction in the electrostatic screening effect and the decrease of emission sites leads to an optimal SiNW bundle arrangement which enables the lowest turn-on electric field of 1.4 V/μm and highest emission current density of 191 μA/cm{sup 2} among all testing SiNW samples. Benefiting from the superior thermal and electrical properties of CNTs and the flexible patterning technologies available for SiNWs, bundle arrays of CNT–SiNW heterojunctions show improved and highly-uniform field emission with a lower turn-on electric field of 0.9 V/μm and higher emission current density of 5.86 mA/cm{sup 2}. The application of these materials and their corresponding fabrication approaches is not limited to the field emission but can be used for a variety of emerging fields like nanoelectronics, lithium-ion batteries, and solar cells. - Highlights: • Aligned silicon nanowire (SiNW) bundle arrays are realized with top-down methods. • Growing carbon nanotubes atop SiNW bundle arrays enable uniform field emission. • A turn-on field of 0.9 V/μm and an emission current of > 5 mA/cm{sup 2} are achieved.

  4. Development and Implementation of a Smartphone Application to Promote Physical Activity and Reduce Screen-time in Adolescent Boys

    Directory of Open Access Journals (Sweden)

    David Revalds Lubans


    Full Text Available Purpose: The primary aim is to describe the development and implementation of a smartphone application (app designed to promote physical activity and reduce screen-time in adolescent boys ‘at risk’ of obesity from low-income communities.Methods: An app was developed to support the delivery of a face-to-face school-based obesity prevention program known as the ‘Active Teen Leaders Avoiding Screen-time’ (ATLAS program. ATLAS was guided by self-determination theory and social cognitive theory and evaluated using a cluster randomized controlled trial with 361 boys (12.7± 0.5 years in 14 secondary schools. Following the completion of the study, participants in the intervention group completed a process evaluation questionnaire and focus groups were conducted with 42 students to explore their general perceptions of the ATLAS program and their experience with the smartphone app. Barriers and challenges encountered in the development, implementation and evaluation of the app are also described.Results: Participation in the study was not contingent on ownership of a smartphone, but 70% of participants in the intervention group reported having access to a smartphone or tablet device. Focus group participants reported an enjoyment of the program, and felt that it had provided them with new skills, techniques, and routines for the future. However, their engagement with the smartphone app was limited, due to a variety of reasons. Barriers to the implementation and evaluation of the app included limited access to smartphone devices, technical problems with the push notifications, lack of access to usage data and the challenges of maintaining participants’ interest in using the app.Conclusions: Although participants reported high levels of satisfaction with the ATLAS program in general, the smartphone app was not used extensively. Additional strategies and features may be needed to enhance engagement in adolescent boys.

  5. Screening on binary Ti alloy with excellent mechanical property and castability for dental prosthesis application (United States)

    Li, H. F.; Qiu, K. J.; Yuan, W.; Zhou, F. Y.; Wang, B. L.; Li, L.; Zheng, Y. F.; Liu, Y. H.


    In the present study, the microstructure, mechanical property, castability, corrosion behavior and in vitro cytocompatibility of binary Ti-2X alloys with various alloying elements, including Ag, Bi, Ga, Ge, Hf, In, Mo, Nb, Sn and Zr, were systematically investigated, in order to assess their potential applications in dental field. The experimental results showed that all binary Ti‒2X alloys consisted entirely α-Ti phase. The tensile strength and microhardness of Ti were improved by adding alloying elements. The castability of Ti was significantly improved by separately adding 2 wt.% Bi, Ga, Hf, Mo, Nb, Sn and Zr. The corrosion resistance of Ti in both normal artificial saliva solution (AS) and extreme artificial saliva solution (ASFL, AS with 0.2 wt.% NaF and 0.3 wt.% lactic acid) has been improved by separately adding alloying elements. In addition, the extracts of studied Ti‒2X alloys produced no significant deleterious effect to both fibroblasts L929 cells and osteoblast-like MG63 cells, indicating a good in vitro cytocompatibility, at the same level as pure Ti. The combination of enhanced mechanical properties, castability, corrosion behavior, and in vitro cytocompatibility make the developed Ti‒2X alloys have great potential for future stomatological applications.

  6. Convection-diffusion driven concentration gradients in nanolitre droplets for microfluidic screening applications (United States)

    Thakur, Raviraj; Amin, Ahmed; Wereley, Steven


    Ability to generate a concentration gradients in emulsified aqueous droplets is a highly desired feature for several lab-on-chip applications. Numerous schemes exists for generating concentration gradients in continuous flow devices such as Y junctions, split-and-recombine techniques, etc. However, varying the sample concentration in emulsified droplets is quite challenging. In this work, we have developed a scheme for generating and controlling concentration gradients in programmable multi-layer PDMS microfluidic chips. Briefly, a high concentration sample is injected into a steady stream of buffer. The buffer with the sample pulse and an immiscible oil phase are flowed through a T-junction in an alternate manner. As the sample pulse advances, the combined effect of diffusion and convection produced dispersion of sample pulse in streamwise direction. This continuous gradient stream is split into discrete droplets at the T-junction. Pulsatile flow condition are maintained using on-chip diaphragm peristaltic pumps. The problem can be thought of an extension of Taylor-Aris dispersion with laminar pulsatile flow in rectangular channels. The concentration profile is found to be dependent upon the frequency of pulsatile flow and thus can be fine-tuned according to application needs. Theoretical framework is established for pump regimes that correlates the diffusion coefficients of the input samples with the resultant concentration profiles.

  7. The Nonmydriatic Fundus Camera in Diabetic Retinopathy Screening: A Cost-Effective Study with Evaluation for Future Large-Scale Application (United States)

    Scarpa, Giuseppe; Urban, Francesca; Tessarin, Michele; Gallo, Giovanni; Midena, Edoardo


    Aims. The study aimed to present the experience of a screening programme for early detection of diabetic retinopathy (DR) using a nonmydriatic fundus camera, evaluating the feasibility in terms of validity, resources absorption, and future advantages of a potential application, in an Italian local health authority. Methods. Diabetic patients living in the town of Ponzano, Veneto Region (Northern Italy), were invited to be enrolled in the screening programme. The “no prevention strategy” with the inclusion of the estimation of blindness related costs was compared with screening costs in order to evaluate a future extensive and feasible implementation of the procedure, through a budget impact approach. Results. Out of 498 diabetic patients eligible, 80% was enrolled in the screening programme. 115 patients (34%) were referred to an ophthalmologist and 9 cases required prompt treatment for either proliferative DR or macular edema. Based on the pilot data, it emerged that an extensive use of the investigated screening programme, within the Greater Treviso area, could prevent 6 cases of blindness every year, resulting in a saving of €271,543.32 (−13.71%). Conclusions. Fundus images obtained with a nonmydriatic fundus camera could be considered an effective, cost-sparing, and feasible screening tool for the early detection of DR, preventing blindness as a result of diabetes. PMID:27885337

  8. Decision-making in healthcare: a practical application of partial least square path modelling to coverage of newborn screening programmes

    Directory of Open Access Journals (Sweden)

    Fischer Katharina E


    Full Text Available Abstract Background Decision-making in healthcare is complex. Research on coverage decision-making has focused on comparative studies for several countries, statistical analyses for single decision-makers, the decision outcome and appraisal criteria. Accounting for decision processes extends the complexity, as they are multidimensional and process elements need to be regarded as latent constructs (composites that are not observed directly. The objective of this study was to present a practical application of partial least square path modelling (PLS-PM to evaluate how it offers a method for empirical analysis of decision-making in healthcare. Methods Empirical approaches that applied PLS-PM to decision-making in healthcare were identified through a systematic literature search. PLS-PM was used as an estimation technique for a structural equation model that specified hypotheses between the components of decision processes and the reasonableness of decision-making in terms of medical, economic and other ethical criteria. The model was estimated for a sample of 55 coverage decisions on the extension of newborn screening programmes in Europe. Results were evaluated by standard reliability and validity measures for PLS-PM. Results After modification by dropping two indicators that showed poor measures in the measurement models’ quality assessment and were not meaningful for newborn screening, the structural equation model estimation produced plausible results. The presence of three influences was supported: the links between both stakeholder participation or transparency and the reasonableness of decision-making; and the effect of transparency on the degree of scientific rigour of assessment. Reliable and valid measurement models were obtained to describe the composites of ‘transparency’, ‘participation’, ‘scientific rigour’ and ‘reasonableness’. Conclusions The structural equation model was among the first applications of PLS-PM to

  9. Screening of matrices and fibers for reinforced thermoplastics intended for dental applications. (United States)

    Goldberg, A J; Burstone, C J; Hadjinikolaou, I; Jancar, J


    Plastics reinforced with continuous fibers (FRC) are being developed for dental applications, such as prosthodontic frameworks and orthodontic retainers. Flexure properties, stress relaxation and hydrolytic stability of FRC based on six thermoplastic matrices, three types of fibers, and three fiber volume fractions were evaluated. Samples with clinically relevant dimensions were tested. Polycarbonate was the preferred matrix material. Polycarbonate reinforced with 42 volume percent glass fibers exhibited the highest combination of flexure modulus (17.9 +/- 2.6 GPa), flexure strength (426 +/- 40 MPa), reinforcing efficiency (0.79), and resistance to stress relaxation. No statistically significant difference was observed between E and S2 glass reinforced composites under the experimental conditions used. Kevlar reinforced materials exhibited a low flexure modulus and strength. The apparent flexure moduli of all composites decreased with span length in the range of clinical interest. Generally, the prevalent mode of failure for all FRC investigated was brittle failure under flexure loading. Relatively large sample-to-sample variation in both composition and properties indicated that improved fabrication methods will be needed in future studies. The combination of good flexure properties, formability, and translucency suggests that novel appliance designs for dentistry are feasible with FRC, but further studies of its properties and particularly the effects of fiber/matrix interfacial quality are needed.

  10. Screening Carbohydrate Libraries for Protein Interactions Using the Direct ESI-MS Assay. Applications to Libraries of Unknown Concentration (United States)

    Kitova, Elena N.; El-Hawiet, Amr; Klassen, John S.


    A semiquantitative electrospray ionization mass spectrometry (ESI-MS) binding assay suitable for analyzing mixtures of oligosaccharides, at unknown concentrations, for interactions with target proteins is described. The assay relies on the differences in the ratio of the relative abundances of the ligand-bound and free protein ions measured by ESI-MS at two or more initial protein concentrations to distinguish low affinity (≤103 M-1) ligands from moderate and high affinity (>105 M-1) ligands present in the library and to rank their affinities. Control experiments were performed on solutions of a single chain antibody and a mixture of synthetic oligosaccharides, with known affinities, in the absence and presence of a 40-component carbohydrate library to demonstrate the implementation and reliability of the assay. The application of the assay for screening natural libraries of carbohydrates against proteins is also demonstrated using mixtures of human milk oligosaccharides, isolated from breast milk, and fragments of a bacterial toxin and human galectin 3.

  11. The Rapid and Sensitive Quantitative Determination of Galactose by Combined Enzymatic and Colorimetric Method: Application in Neonatal Screening. (United States)

    Kianmehr, Anvarsadat; Mahrooz, Abdolkarim; Ansari, Javad; Oladnabi, Morteza; Shahbazmohammadi, Hamid


    The quantitative measurement of galactose in blood is essential for the early diagnosis, treatment, and dietary monitoring of galactosemia patients. In this communication, we aimed to develop a rapid, sensitive, and cost-effective combined method for galactose determination in dry blood spots. This procedure was based on the combination of enzymatic reactions of galactose dehydrogenase (GalDH), dihydrolipoyl dehydrogenase (DLD), and alkaline phosphates with a colorimetric system. The incubation time and the concentration of enzymes used in new method were also optimized. The analytical performance was studied by the precision, recovery, linearity, and sensitivity parameters. Statistical analysis was applied to method comparison experiment. The regression equation and correlation coefficient (R (2)) were Y = 0.0085x + 0.032 and R (2) = 0.998, respectively. This assay exhibited a recovery in the range of 91.7-114.3 % and had the limit detection of 0.5 mg/dl for galactose. The between-run coefficient of variation (CV) was between 2.6 and 11.1 %. The within-run CV was between 4.9 and 9.2 %. Our results indicated that the new and reference methods were in agreement because no significant biases exist between them. Briefly, a quick and reliable combined enzymatic and colorimetric assay was presented for application in newborn mass screening and monitoring of galactosemia patients.

  12. A Simplified Method for Gene Knockout and Direct Screening of Recombinant Clones for Application in Paenibacillus polymyxa.

    Directory of Open Access Journals (Sweden)

    Seong-Bin Kim

    Full Text Available Paenibacillus polymyxa is a bacterium widely used in agriculture, industry, and environmental remediation because it has multiple functions including nitrogen fixation and produces various biologically active compounds. Among these compounds are the antibiotics polymyxins, and the bacterium is currently being reassessed for medical application. However, a lack of genetic tools for manipulation of P. polymyxa has limited our understanding of the biosynthesis of these compounds.To facilitate an understanding of the genetic determinants of the bacterium, we have developed a system for marker exchange mutagenesis directly on competent cells of P. polymyxa under conditions where homologous recombination is enhanced by denaturation of the suicide plasmid DNA. To test this system, we targeted P. polymyxa α-and β-amylase genes for disruption. Chloramphenicol or erythromycin resistance genes were inserted into the suicide plasmid pGEM7Z-f+ (Promega. To mediate homologous recombination and replacement of the targeted genes with the antibiotic resistance genes nucleotide sequences of the α-and β-amylase genes were cloned into the plasmid flanking the antibiotic resistance genes.We have created a simple system for targeted gene deletion in P. polymyxa E681. We propose that P. polymyxa isogenic mutants could be developed using this system of marker exchange mutagenesis. α-and β-amylase genes provide a useful tool for direct recombinant screening in P. polymyxa.

  13. Applicability of the ankle-brachial-index measurement as screening device for high cardiovascular risk: an observational study

    Directory of Open Access Journals (Sweden)

    Bendermacher Bianca LW


    Full Text Available Abstract Background Screening with ankle-brachial index (ABI measurement could be clinically relevant to avoid cardiovascular events in subjects with asymptomatic atherosclerosis. To assess the practical impact of guidelines regarding the use of ABI as a screening tool in general practice, the corresponding number needed to screen, including the required time investment, and the feasibility of ABI performance, was assessed. Methods An observational study was performed in the setting of 955 general practices in the Netherlands. Overall, 13,038 subjects of ≥55 years presenting with symptoms of intermittent claudication and/or presenting with ≥ one vascular risk factor were included. Several guidelines recommend the ABI as an additional measurement in selected populations for risk assessment for cardiovascular morbidity. Results Screening of the overall population of ≥50 years results in ≈862 subjects per general practice who should be screened, resulting in a time-requirement of approximately 6 weeks of full time work. Using an existing clinical prediction model, 247 patients per general practice should be screened for PAD by ABI measurement. Conclusion Screening the entire population of ≥50 years will in our opinion not be feasible in general practice. A more rationale and efficient approach might be screening of subsets of the population of ≥55 years based on a clinical prediction model.

  14. The urgent need for universally applicable simple screening procedures and diagnostic criteria for gestational diabetes mellitus – lessons from projects funded by the World Diabetes Foundation

    Directory of Open Access Journals (Sweden)

    Maximilian de Courten


    Full Text Available Background: To address the risks of adverse pregnancy outcomes and future type 2 diabetes associated with gestational diabetes mellitus (GDM, its early detection and timely treatment is essential. In the absence of an international consensus, multiple different guidelines on screening and diagnosis of GDM have existed for a long time. This may be changing with the publication of the recommendations by the International Association of Diabetes and Pregnancy Study Groups. However, none of these guidelines take into account evidence from or ground realities of resource-poor settings. Objective: This study aimed to investigate whether GDM projects supported by the World Diabetes Foundation in developing countries utilize any of the internationally recommended guidelines for screening and diagnosis of GDM, explore experiences on applicability and usefulness of the guidelines and barriers if any, in implementing the guidelines. These projects have reached out to thousands of pregnant women through capacity building and improvement of access to GDM screening and diagnosis in the developing world and therefore provide a rich field experience on the applicability of the guidelines in resource-poor settings. Design: A mixed methods approach using questionnaires and interviews was utilised to review 11 GDM projects. Two projects were conducted by the same partner; interviews were conducted in person or via phone by the first author with nine project partners and one responded via email. The interviews were analysed using content analysis. Results: The projects use seven different screening procedures and diagnostic criteria and many do not completely adhere to one guideline alone. Various challenges in adhering to the recommendations emerged in the interviews, including problems with screening women during the recommended time period, applicability of some of the listed risk factors used for (pre-screening, difficulties with reaching women for testing in

  15. PREFACE: India-Japan Workshop on Biomolecular Electronics & Organic Nanotechnology for Environment Preservation (United States)

    Onoda, Mitsuyoshi; Malhotra, Bansi D.


    The 'India-Japan Workshop on Biomolecular Electronics & Organic Nanotechnology for Environment Preservation' (IJWBME 2011) will be held on 7-10 December 2011 at EGRET Himeji, Himeji, Hyogo, Japan. This workshop was held for the first time on 17-19 December 2009 at NPL, New Delhi. Keeping in mind the importance of organic nanotechnology and biomolecular electronics for environmental preservation and their anticipated impact on the economics of both the developing and the developed world, IJWBME 2009 was jointly organized by the Department of Biological Functions, Graduate School of Life Sciences and Systems Engineering, the Kyushu Institute of Technology (KIT), Kitakyushu, Japan, and the Department of Science & Technology Centre on Biomolecular Electronics (DSTCBE), National Physical Laboratory (NPL). Much progress in the field of biomolecular electronics and organic nanotechnology for environmental preservation is expected for the 21st Century. Organic optoelectronic devices, such as organic electroluminescent devices, organic thin-film transistors, organic sensors, biological systems and so on have especially attracted much attention. The main purpose of this workshop is to provide an opportunity for researchers interested in biomolecular electronics and organic nanotechnology for environmental preservation, to come together in an informal and friendly atmosphere and exchange technical knowledge and experience. We are sure that this workshop will be very useful and fruitful for all participants in summarizing the recent progress in biomolecular electronics and organic nanotechnology for environmental preservation and preparing new ground for the next generation. Many papers have been submitted from India and Japan and more than 30 papers have been accepted for presentation. The main topics of interest are as follows: Bioelectronics Biomolecular Electronics Fabrication Techniques Self-assembled Monolayers Nano-sensors Environmental Monitoring Organic Devices

  16. Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks

    DEFF Research Database (Denmark)

    Soberano de Oliveira, Ana Paula; Patil, Kiran Raosaheb; Nielsen, Jens


    Background: Uncovering the operating principles underlying cellular processes by using 'omics' data is often a difficult task due to the high-dimensionality of the solution space that spans all interactions among the bio-molecules under consideration. A rational way to overcome this problem...... is to use the topology of bio-molecular interaction networks in order to constrain the solution space. Such approaches systematically integrate the existing biological knowledge with the 'omics' data. Results: Here we introduce a hypothesis-driven method that integrates bio-molecular network topology...... with transcriptome data, thereby allowing the identification of key biological features (Reporter Features) around which transcriptional changes are significantly concentrated. We have combined transcriptome data with different biological networks in order to identify Reporter Gene Ontologies, Reporter Transcription...

  17. Biochemical filter with sigmoidal response: increasing the complexity of biomolecular logic. (United States)

    Privman, Vladimir; Halámek, Jan; Arugula, Mary A; Melnikov, Dmitriy; Bocharova, Vera; Katz, Evgeny


    The first realization of a designed, rather than natural, biochemical filter process is reported and analyzed as a promising network component for increasing the complexity of biomolecular logic systems. Key challenge in biochemical logic research has been achieving scalability for complex network designs. Various logic gates have been realized, but a "toolbox" of analog elements for interconnectivity and signal processing has remained elusive. Filters are important as network elements that allow control of noise in signal transmission and conversion. We report a versatile biochemical filtering mechanism designed to have sigmoidal response in combination with signal-conversion process. Horseradish peroxidase-catalyzed oxidation of chromogenic electron donor by H(2)O(2) was altered by adding ascorbate, allowing to selectively suppress the output signal, modifying the response from convex to sigmoidal. A kinetic model was developed for evaluation of the quality of filtering. The results offer improved capabilities for design of scalable biomolecular information processing systems.

  18. Constructing Bio-molecular Databases on a DNA-based Computer

    CERN Document Server

    Chang, Weng-Long; Ho,; Guo, Minyi


    Codd [Codd 1970] wrote the first paper in which the model of a relational database was proposed. Adleman [Adleman 1994] wrote the first paper in which DNA strands in a test tube were used to solve an instance of the Hamiltonian path problem. From [Adleman 1994], it is obviously indicated that for storing information in molecules of DNA allows for an information density of approximately 1 bit per cubic nm (nanometer) and a dramatic improvement over existing storage media such as video tape which store information at a density of approximately 1 bit per 1012 cubic nanometers. This paper demonstrates that biological operations can be applied to construct bio-molecular databases where data records in relational tables are encoded as DNA strands. In order to achieve the goal, DNA algorithms are proposed to perform eight operations of relational algebra (calculus) on bio-molecular relational databases, which include Cartesian product, union, set difference, selection, projection, intersection, join and division. Fu...

  19. Out-of-equilibrium biomolecular interactions monitored by picosecond fluorescence in microfluidic droplets. (United States)

    Maillot, Sacha; Carvalho, Alain; Vola, Jean-Pierre; Boudier, Christian; Mély, Yves; Haacke, Stefan; Léonard, Jérémie


    We developed a new experimental approach combining Time-Resolved Fluorescence (TRF) spectroscopy and Droplet Microfluidics (DμF) to investigate the relaxation dynamics of structurally heterogeneous biomolecular systems. Here DμF was used to produce with minimal material consumption an out-of-equilibrium, fluorescently labeled biomolecular complex by rapid mixing within the droplets. TRF detection was implemented with a streak camera to monitor the time evolution of the structural heterogeneity of the complex along its relaxation towards equilibrium while it propagates inside the microfluidic channel. The approach was validated by investigating the fluorescence decay kinetics of a model interacting system of bovine serum albumin and Patent Blue V. Fluorescence decay kinetics are acquired with very good signal-to-noise ratio and allow for global, multicomponent fluorescence decay analysis, evidencing heterogeneous structural relaxation over several 100 ms.

  20. Charge transport through biomolecular wires in a solvent: bridging molecular dynamics and model Hamiltonian approaches. (United States)

    Gutiérrez, R; Caetano, R A; Woiczikowski, B P; Kubar, T; Elstner, M; Cuniberti, G


    We present a hybrid method based on a combination of classical molecular dynamics simulations, quantum-chemical calculations, and a model Hamiltonian approach to describe charge transport through biomolecular wires with variable lengths in presence of a solvent. The core of our approach consists in a mapping of the biomolecular electronic structure, as obtained from density-functional based tight-binding calculations of molecular structures along molecular dynamics trajectories, onto a low-dimensional model Hamiltonian including the coupling to a dissipative bosonic environment. The latter encodes fluctuation effects arising from the solvent and from the molecular conformational dynamics. We apply this approach to the case of pG-pC and pA-pT DNA oligomers as paradigmatic cases and show that the DNA conformational fluctuations are essential in determining and supporting charge transport.

  1. Conformation of bovine submaxillary mucin layers on hydrophobic surface as studied by biomolecular probes

    DEFF Research Database (Denmark)

    Pakkanen, Kirsi I.; Madsen, Jan Busk; Lee, Seunghwan


    In the present study, the conformational changes of bovine submaxillary mucin (BSM) adsorbed on a hydrophobic surface (polystyrene (PS)) as a function of concentration in bulk solution (up to 2mg/mL) have been investigated with biomolecular probe-based approaches, including bicinchoninic acid (BCA...... solution. Adsorbed masses of BSM onto hydrophobic surface, as probe by BCA, showed a continuously increasing trend up to 2mg/mL. But, the signals from EIA and ELLA, which probe the concentration of available unglycosylatedC-terminals and the central glycosylated regions, respectively, showed complicated...... non-linear responses with increasing surface concentration. The results from this study support the conventional amphiphilic, triblock model of BSM in the adsorption onto hydrophobic surface from aqueous solution.The biomolecular probe-based approaches employed in this study, however, provided further...

  2. Effects of Application of Social Marketing Theory and the Health Belief Model in Promoting Cervical Cancer Screening among Targeted Women in Sisaket Province, Thailand. (United States)

    Wichachai, Suparp; Songserm, Nopparat; Akakul, Theerawut; Kuasiri, Chanapong


    Cervical cancer is a major public health problem in Thailand, being ranked second only to breast cancer. Thai women have been reported to have a low rate of cervical cancer screening (27.7% of the 80% goal of WHO). We therefore aimed to apply the social marketing theory and health belief model in promoting cervical cancer screening in Kanthararom District, Sisaket Province. A total of 92 from 974 targeted women aged 3060 years were randomly divided into two groups. The experimental group underwent application of social marketing theory and a health belief model program promoting cervical cancer screening while the control group received normal services. Two research tools were used: (1) application of social marketing theory and health belief model program and (2) questionnaire used to evaluate perceptions of cervical cancer. Descriptive and inferential statistics including paired sample ttest and independent ttest were used to analyze the data. After the program had been used, the mean score of perception of cervical cancer of experimental group was at a higher level (x=4.09; S.D. =0.30), than in the control group (x=3.82; S.D. =0.20) with statistical significance (psocial marketing and the health belief model be used to promote cervical cancer screening in targeted women and it can be promoted as a guideline for other health services, especially in health promotion and disease prevention.

  3. Parity Violation in Chiral Molecules: From Theory towards Spectroscopic Experiment and the Evolution of Biomolecular Homochirality

    CERN Document Server

    CERN. Geneva


    The observation of biomolecular homochirality can be considered as a quasi-fossil of the evolution of life [1], the interpretation of which has been an open question for more than a century, with numerous related hypotheses, but no definitive answers. We shall briefly discuss the current status and the relation to the other two questions. The discovery of parity violation led to important developm...

  4. Accelerated search for biomolecular network models to interpret high-throughput experimental data

    Directory of Open Access Journals (Sweden)

    Sokhansanj Bahrad A


    Full Text Available Abstract Background The functions of human cells are carried out by biomolecular networks, which include proteins, genes, and regulatory sites within DNA that encode and control protein expression. Models of biomolecular network structure and dynamics can be inferred from high-throughput measurements of gene and protein expression. We build on our previously developed fuzzy logic method for bridging quantitative and qualitative biological data to address the challenges of noisy, low resolution high-throughput measurements, i.e., from gene expression microarrays. We employ an evolutionary search algorithm to accelerate the search for hypothetical fuzzy biomolecular network models consistent with a biological data set. We also develop a method to estimate the probability of a potential network model fitting a set of data by chance. The resulting metric provides an estimate of both model quality and dataset quality, identifying data that are too noisy to identify meaningful correlations between the measured variables. Results Optimal parameters for the evolutionary search were identified based on artificial data, and the algorithm showed scalable and consistent performance for as many as 150 variables. The method was tested on previously published human cell cycle gene expression microarray data sets. The evolutionary search method was found to converge to the results of exhaustive search. The randomized evolutionary search was able to converge on a set of similar best-fitting network models on different training data sets after 30 generations running 30 models per generation. Consistent results were found regardless of which of the published data sets were used to train or verify the quantitative predictions of the best-fitting models for cell cycle gene dynamics. Conclusion Our results demonstrate the capability of scalable evolutionary search for fuzzy network models to address the problem of inferring models based on complex, noisy biomolecular

  5. Colloid-in-Liquid Crystal Gels that Respond to Biomolecular Interactions


    Agarwal, Ankit; Sidiq, Sumyra; Setia, Shilpa; Bukusoglu, Emre; de Pablo, Juan J.; Pal, Santanu Kumar; Abbott, Nicholas L.


    This paper advances the design of stimuli-responsive materials based on colloidal particles dispersed in liquid crystals (LCs). Specifically, we report that thin films of colloid-in-liquid crystal (CLC) gels can undergo easily visualized ordering transitions in response to reversible and irreversible (enzymatic) biomolecular interactions occurring at aqueous interfaces of the gels. In particular, we demonstrate that LC ordering transitions can propagate across the entire thickness of the gels...

  6. Assembly of single wall carbon nanotube-metal nanohybrids using biomolecular components (United States)

    Kim, Sang Nyon; Slocik, Joseph M.; Naik, Rajesh R.


    Biomaterials such as nucleic acids and proteins can be exploited to create higher order structures. The biomolecular components such as DNA and peptides have been used to assemble nanoparticles with high fidelity. Here, we use DNA and peptides, and their preferential interaction with inorganic and carbon nanomaterials to form homogeneous hybrids. The enhanced binding of Pt ions to both DNA and peptide functionalized nanoparticles mediates the assembly of carbon nanotubes functionalized with DNA with peptide coated gold nanoparticles.

  7. New product development with the innovative biomolecular sublingual immunotherapy formulations for the management of allergic rhinitis

    Directory of Open Access Journals (Sweden)

    Frati F


    Full Text Available Franco Frati,1 Lorenzo Cecchi,2,3 Enrico Scala,4 Erminia Ridolo,5 Ilaria Dell'Albani,1 Eleni Makrì,6 Giovanni Pajno,7 Cristoforo Incorvaia6 1Medical and Scientific Department, Stallergenes, Milan, Italy; 2Interdepartmental Centre of Bioclimatology, University of Florence, Florence, Italy; 3Allergy and Clinical Immunology Section, Azienda Sanitaria di Prato, Prato, Italy; 4Experimental Allergy Unit, IDI-IRCCS, Rome, Italy; 5Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy; 6Allergy/Pulmonary Rehabilitation, ICP Hospital, Milan, Italy; 7Department of Pediatrics, Allergy Unit, University of Messina, Messina, Italy Abstract: The molecular allergy technique, currently defined as component-resolved diagnosis, significantly improved the diagnosis of allergy, allowing for differentiation between molecules actually responsible for clinical symptoms (genuine sensitizers and those simply cross-reacting or shared by several sources (panallergens, thus influencing the appropriate management of a patient's allergy. This also concerns allergen immunotherapy (AIT, which may be prescribed more precisely based on the component-resolved diagnosis results. However, the advance in diagnosis needs to be mirrored in AIT. According to consensus documents and to expectations of specialists, therapy should be based on standardized extracts containing measured amounts of the clinically relevant molecules, ie, the major allergens. The new generation of extracts for sublingual immunotherapy fulfills these requirements and are thus defined as biomolecular (BM. BM refers to natural extracts with a defined content of major allergens in micrograms. All Staloral BM products are indicated for the treatment of allergic rhinitis with or without asthma. The effectiveness of AIT is related to its ability to modify the immunological response of allergic subjects. The 5-grass and house dust mite extracts were evaluated addressing the T helper 1, T

  8. Changes in biomolecular profile in a single nucleolus during cell fixation. (United States)

    Kuzmin, Andrey N; Pliss, Artem; Prasad, Paras N


    Fixation of biological sample is an essential technique applied in order to "freeze" in time the intracellular molecular content. However, fixation induces changes of the cellular molecular structure, which mask physiological distribution of biomolecules and bias interpretation of results. Accurate, sensitive, and comprehensive characterization of changes in biomolecular composition, occurring during fixation, is crucial for proper analysis of experimental data. Here we apply biomolecular component analysis for Raman spectra measured in the same nucleoli of HeLa cells before and after fixation by either formaldehyde solution or by chilled ethanol. It is found that fixation in formaldehyde does not strongly affect the Raman spectra of nucleolar biomolecular components, but may significantly decrease the nucleolar RNA concentration. At the same time, ethanol fixation leads to a proportional increase (up to 40%) in concentrations of nucleolar proteins and RNA, most likely due to cell shrinkage occurring in the presence of coagulant fixative. Ethanol fixation also triggers changes in composition of nucleolar proteome, as indicated by an overall reduction of the α-helical structure of proteins and increase in the concentration of proteins containing the β-sheet conformation. We conclude that cross-linking fixation is a more appropriate protocol for mapping of proteins in situ. At the same time, ethanol fixation is preferential for studies of RNA-containing macromolecules. We supplemented our quantitative Raman spectroscopic measurements with mapping of the protein and lipid macromolecular groups in live and fixed cells using coherent anti-Stokes Raman scattering nonlinear optical imaging.

  9. Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks

    Directory of Open Access Journals (Sweden)

    Nielsen Jens


    Full Text Available Abstract Background Uncovering the operating principles underlying cellular processes by using 'omics' data is often a difficult task due to the high-dimensionality of the solution space that spans all interactions among the bio-molecules under consideration. A rational way to overcome this problem is to use the topology of bio-molecular interaction networks in order to constrain the solution space. Such approaches systematically integrate the existing biological knowledge with the 'omics' data. Results Here we introduce a hypothesis-driven method that integrates bio-molecular network topology with transcriptome data, thereby allowing the identification of key biological features (Reporter Features around which transcriptional changes are significantly concentrated. We have combined transcriptome data with different biological networks in order to identify Reporter Gene Ontologies, Reporter Transcription Factors, Reporter Proteins and Reporter Complexes, and use this to decipher the logic of regulatory circuits playing a key role in yeast glucose repression and human diabetes. Conclusion Reporter Features offer the opportunity to identify regulatory hot-spots in bio-molecular interaction networks that are significantly affected between or across conditions. Results of the Reporter Feature analysis not only provide a snapshot of the transcriptional regulatory program but also are biologically easy to interpret and provide a powerful way to generate new hypotheses. Our Reporter Features analyses of yeast glucose repression and human diabetes data brings hints towards the understanding of the principles of transcriptional regulation controlling these two important and potentially closely related systems.

  10. Nanogap biosensors for electrical and label-free detection of biomolecular interactions

    Energy Technology Data Exchange (ETDEWEB)

    Kyu Kim, Sang; Cho, Hyunmin; Park, Hye-Jung; Kwon, Dohyoung; Min Lee, Jeong; Hyun Chung, Bong, E-mail: [BioNanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, PO Box 115, Yuseong, Daejeon 305-600 (Korea, Republic of)


    We demonstrate nanogap biosensors for electrical and label-free detection of biomolecular interactions. Parallel fabrication of nanometer distance gaps has been achieved using a silicon anisotropic wet etching technique on a silicon-on-insulator (SOI) wafer with a finely controllable silicon device layer. Since silicon anisotropic wet etching resulted in a trapezoid-shaped structure whose end became narrower during the etching, the nanogap structure was simply fabricated on the device layer of a SOI wafer. The nanogap devices were individually addressable and a gap size of less than 60 nm was obtained. We demonstrate that the nanogap biosensors can electrically detect biomolecular interactions such as biotin/streptavidin and antigen/antibody pairs. The nanogap devices show a current increase when the proteins are bound to the surface. The current increases proportionally depending upon the concentrations of the molecules in the range of 100 fg ml{sup -1}-100 ng ml{sup -1} at 1 V bias. It is expected that the nanogap developed here could be a highly sensitive biosensor platform for label-free detection of biomolecular interactions.

  11. An improved simple polarisable water model for use in biomolecular simulation

    Energy Technology Data Exchange (ETDEWEB)

    Bachmann, Stephan J.; Gunsteren, Wilfred F. van, E-mail: [Laboratory of Physical Chemistry, ETH Zürich, CH-8093 Zürich (Switzerland)


    The accuracy of biomolecular simulations depends to some degree on the accuracy of the water model used to solvate the biomolecules. Because many biomolecules such as proteins are electrostatically rather inhomogeneous, containing apolar, polar, and charged moieties or side chains, a water model should be able to represent the polarisation response to a local electrostatic field, while being compatible with the force field used to model the biomolecules or protein. The two polarisable water models, COS/G2 and COS/D, that are compatible with the GROMOS biomolecular force fields leave room for improvement. The COS/G2 model has a slightly too large dielectric permittivity and the COS/D model displays a much too slow dynamics. The proposed COS/D2 model has four interaction sites: only one Lennard-Jones interaction site, the oxygen atom, and three permanent charge sites, the two hydrogens, and one massless off-atom site that also serves as charge-on-spring (COS) polarisable site with a damped or sub-linear dependence of the induced dipole on the electric field strength for large values of the latter. These properties make it a cheap and yet realistic water model for biomolecular solvation.

  12. Depression Screening (United States)

    ... Centers Diseases + Condition Centers Mental Health Medical Library Depression Screening (PHQ-9) - Instructions The following questions are ... this tool, there is also text-only version . Depression Screening - Manual Instructions The following questions are a ...

  13. Genome-wide screening and identification of new Trypanosoma cruzi antigens with potential application for chronic Chagas disease diagnosis.

    Directory of Open Access Journals (Sweden)

    João Luís Reis-Cunha

    Full Text Available The protozoan Trypanosoma cruzi is the etiologic agent of Chagas disease, an infection that afflicts approximately 8 million people in Latin America. Diagnosis of chronic Chagas disease is currently based on serological tests because this condition is usually characterized by high anti-T. cruzi IgG titers and low parasitemia. The antigens used in these assays may have low specificity due to cross reactivity with antigens from related parasite infections, such as leishmaniasis, and low sensitivity caused by the high polymorphism among T. cruzi strains. Therefore, the identification of new T. cruzi-specific antigens that are conserved among the various parasite discrete typing units (DTUs is still required. In the present study, we have explored the hybrid nature of the T. cruzi CL Brener strain using a broad genome screening approach to select new T. cruzi antigens that are conserved among the different parasite DTUs and that are absent in other trypanosomatid species. Peptide arrays containing the conserved antigens with the highest epitope prediction scores were synthesized, and the reactivity of the peptides were tested by immunoblot using sera from C57BL/6 mice chronically infected with T. cruzi strains from the TcI, TcII or TcVI DTU. The two T. cruzi proteins that contained the most promising peptides were expressed as recombinant proteins and tested in ELISA experiments with sera from chagasic patients with distinct clinical manifestations: those infected with T. cruzi from different DTUs and those with cutaneous or visceral leishmaniasis. These proteins, named rTc_11623.20 and rTc_N_10421.310, exhibited 94.83 and 89.66% sensitivity, 98.2 and 94.6% specificity, respectively, and a pool of these 2 proteins exhibited 96.55% sensitivity and 98.18% specificity. This work led to the identification of two new antigens with great potential application in the diagnosis of chronic Chagas disease.

  14. Application of parallel liquid chromatography/mass spectrometry for high throughput microsomal stability screening of compound libraries. (United States)

    Xu, Rongda; Nemes, Csaba; Jenkins, Kelly M; Rourick, Robyn A; Kassel, Daniel B; Liu, Charles Z C


    Solution-phase and solid-phase parallel synthesis and high throughput screening have enabled biologically active and selective compounds to be identified at an unprecedented rate. The challenge has been to convert these hits into viable development candidates. To accelerate the conversion of these hits into lead development candidates, early assessment of the physicochemical and pharmacological properties of these compounds is being made. In particular, in vitro absorption, distribution, metabolism, and elimination (ADME) assays are being conducted at earlier and earlier stages of discovery with the goal of reducing the attrition rate of these potential drug candidates as they progress through development. In this report, we present an eight-channel parallel liquid chromatography/mass spectrometry (LC/MS) system in combination with custom Visual Basic and Applescript automated data processing applications for high throughput early ADME. The parallel LC/MS system was configured with one set of gradient LC pumps and an eight-channel multiple probe autosampler. The flow was split equivalently into eight streams before the multiple probe autosampler and recombined after the eight columns and just prior to the mass spectrometer ion source. The system was tested for column-to-column variation and for reproducibility over a 17 h period (approximately 500 injections per column). The variations in retention time and peak area were determined to be less than 2 and 10%, respectively, in both tests. The parallel LC/MS system described permits time-course microsomal incubations (t(o), t5, t15, t30) to be measured in triplicate and enables estimations of t 1/2 microsomal stability. The parallel LC/MS system is capable of analyzing up to 240 samples per hour and permits the complete profiling up to two microtiter plates of compounds per day (i.e., 176 test substrate compounds + sixteen controls).

  15. Cancer Screening

    Directory of Open Access Journals (Sweden)

    Krishna Prasad


    Full Text Available Cancer screening is a means to detect cancer early with the goal of decreasing morbidity and mortality. At present, there is a reasonable consensus regarding screening for breast, cervical and colorectal cances and the role of screening is under trial in case of cancers of the lung,  ovaries and prostate. On the other hand, good screening tests are not available for some of the commonest cancers in India like the oral, pharyngeal, esophageal and stomach cancers.

  16. Biomolecular coronas provide the biological identity of nanosized materials

    NARCIS (Netherlands)

    Monopoli, Marco P; Åberg, Christoffer; Salvati, Anna; Dawson, Kenneth A


    The search for understanding the interactions of nanosized materials with living organisms is leading to the rapid development of key applications, including improved drug delivery by targeting nanoparticles, and resolution of the potential threat of nanotechnological devices to organisms and the en

  17. Imaging and chemical surface analysis of biomolecular functionalization of monolithically integrated on silicon Mach-Zehnder interferometric immunosensors (United States)

    Gajos, Katarzyna; Angelopoulou, Michailia; Petrou, Panagiota; Awsiuk, Kamil; Kakabakos, Sotirios; Haasnoot, Willem; Bernasik, Andrzej; Rysz, Jakub; Marzec, Mateusz M.; Misiakos, Konstantinos; Raptis, Ioannis; Budkowski, Andrzej


    Time-of-flight secondary ion mass spectrometry (imaging, micro-analysis) has been employed to evaluate biofunctionalization of the sensing arm areas of Mach-Zehnder interferometers monolithically integrated on silicon chips for the immunochemical (competitive) detection of bovine κ-casein in goat milk. Biosensor surfaces are examined after: modification with (3-aminopropyl)triethoxysilane, application of multiple overlapping spots of κ-casein solutions, blocking with 100-times diluted goat milk, and reaction with monoclonal mouse anti-κ-casein antibodies in blocking solution. The areas spotted with κ-casein solutions of different concentrations are examined and optimum concentration providing homogeneous coverage is determined. Coverage of biosensor surfaces with biomolecules after each of the sequential steps employed in immunodetection is also evaluated with TOF-SIMS, supplemented by Atomic force microscopy and X-ray photoelectron spectroscopy. Uniform molecular distributions are observed on the sensing arm areas after spotting with optimum κ-casein concentration, blocking and immunoreaction. The corresponding biomolecular compositions are determined with a Principal Component Analysis that distinguished between protein amino acids and milk glycerides, as well as between amino acids characteristic for Mabs and κ-casein, respectively. Use of the optimum conditions (κ-casein concentration) for functionalization of chips with arrays of ten Mach-Zehnder interferometers provided on-chips assays with dramatically improved both intra-chip response repeatability and assay detection sensitivity.

  18. Colon cancer screening (United States)

    Screening for colon cancer; Colonoscopy - screening; Sigmoidoscopy - screening; Virtual colonoscopy - screening; Fecal immunochemical test; Stool DNA test; sDNA test; Colorectal cancer - screening; Rectal ...

  19. A Barcode-Free Combinatorial Screening Platform for Matrix Metalloproteinase Screening


    Rane, Tushar D.; Zec, Helena C.; Wang, Tza-Huei


    Application of droplet microfluidics to combinatorial screening applications remains elusive because of the need for composition-identifying unique barcodes. Here we propose a barcode-free continuous flow droplet microfluidic platform to suit the requirements of combinatorial screening applications. We demonstrate robust and repeatable functioning of this platform with matrix metalloproteinase activity screening as a sample application.

  20. A barcode-free combinatorial screening platform for matrix metalloproteinase screening. (United States)

    Rane, Tushar D; Zec, Helena C; Wang, Tza-Huei


    Application of droplet microfluidics to combinatorial screening applications remains elusive because of the need for composition-identifying unique barcodes. Here we propose a barcode-free continuous flow droplet microfluidic platform to suit the requirements of combinatorial screening applications. We demonstrate robust and repeatable functioning of this platform with matrix metalloproteinase activity screening as a sample application.

  1. Label-free high-throughput screening via mass spectrometry: a single cystathionine quantitative method for multiple applications. (United States)

    Holt, Tom G; Choi, Bernard K; Geoghagen, Neil S; Jensen, Kristian K; Luo, Qi; LaMarr, William A; Makara, Gergely M; Malkowitz, Lorraine; Ozbal, Can C; Xiong, Yusheng; Dufresne, Claude; Luo, Ming-Juan


    Label-free mass spectrometric (MS) technologies are particularly useful for enzyme assay design for drug discovery screens. MS permits the selective detection of enzyme substrates or products in a wide range of biological matrices without need for derivatization, labeling, or capture technologies. As part of a cardiovascular drug discovery effort aimed at finding modulators of cystathionine beta-synthase (CBS), we used the RapidFire((R)) label-free high-throughput MS (HTMS) technology to develop a high-throughput screening (HTS) assay for CBS activity. The in vitro assay used HTMS to quantify the unlabeled product of the CBS reaction, cystathionine. Cystathionine HTMS analyses were carried out with a throughput of 7 s per sample and quantitation over a linear range of 80-10,000 nM. A compound library of 25,559 samples (or 80 384-well plates) was screened as singlets using the HTMS assay in a period of 8 days. With a hit rate of 0.32%, the actives showed a 90% confirmation rate. The in vitro assay was applied to secondary screens in more complex matrices with no additional analytical development. Our results show that the HTMS method was useful for screening samples containing serum, for cell-based assays, and for liver explants. The novel extension of the in vitro analytical method, without modification, to secondary assays resulted in a significant and advantageous economy of development time for the drug discovery project.

  2. Virtual screening against obesity. (United States)

    Markt, P; Herdlinger, S; Schuster, D


    The development of novel drugs against obesity is one of the top priorities of worldwide drug research. In recent years, it has been facilitated by the application of virtual screening methods. In this review, we give a short introduction into obesity-related protein targets and computer-aided drug design techniques. Furthermore, we highlight the most successful virtual screening studies, outline their results, and provide suggestions for future anti-obesity drug development.

  3. Comparing neural-network scoring functions and the state of the art: applications to common library screening. (United States)

    Durrant, Jacob D; Friedman, Aaron J; Rogers, Kathleen E; McCammon, J Andrew


    We compare established docking programs, AutoDock Vina and Schrödinger's Glide, to the recently published NNScore scoring functions. As expected, the best protocol to use in a virtual-screening project is highly dependent on the target receptor being studied. However, the mean screening performance obtained when candidate ligands are docked with Vina and rescored with NNScore 1.0 is not statistically different than the mean performance obtained when docking and scoring with Glide. We further demonstrate that the Vina and NNScore docking scores both correlate with chemical properties like small-molecule size and polarizability. Compensating for these potential biases leads to improvements in virtual screen performance. Composite NNScore-based scoring functions suited to a specific receptor further improve performance. We are hopeful that the current study will prove useful for those interested in computer-aided drug design.

  4. Calculation of the importance of quality factors in braille application process on labels by screen UV-varnishes

    Directory of Open Access Journals (Sweden)

    Vyacheslav Repeta


    Full Text Available Oriented graph has been drawn in the article according to fixed factors of the quality of applying Braille screen printing on the label by screen UV-varnishes. Using hierarchical representation of relationships between factors in the form of oriented graphs we have ranked the factors of the screen printing process of Braille elements by UV-varnishes and calculated their corresponding coefficients. We have found that the most ranked are such factors as the surface energy of the printing material, the printing speed, the temperature of UV-varnish and its viscosity. Received results of ranking will enable to synthesize the model of the process’ priority factors and to reveal the possibilities of regulations of geometrical parameters of the tactile font elements.

  5. Microfluidic geometric metering-based multi-reagent mixture generator for robust live cell screening array. (United States)

    Wang, Han; Kim, Jeongyun; Jayaraman, Arul; Han, Arum


    Microfluidic live cell arrays with integrated concentration gradient or mixture generators have been utilized in screening cellular responses to various biomolecular cues. Microfluidic network-based gradient generators that can create concentration gradients by repeatedly splitting and mixing different solutions using networks of serpentine channels are commonly used. However, in this method the generation of concentration gradients relies on the continuous flow of sample solutions at optimized flow rates, which poses challenges in maintaining the pressure and flow stability throughout the entire assay period. Here we present a microfluidic live cell screening array with an on-demand multi-reagent mixture generator where the mixing ratios, thus generated concentrations, are hard-wired into the chip itself through a geometric metering method. This platform showed significantly improved robustness and repeatability in generating concentration gradients of fluorescent dyes (average coefficient of variance C.V. = 9 %) compared to the conventional network-based gradient generators (average C.V. = 21 %). In studying the concentration dependent effects of the environmental toxicant 3-methylcholanthrene (3MC) on the activation of cytochrome P450 1A1 (Cyp 1A1) enzyme in H4IIE rat hepatoma cells, statistical variation of the Cyp 1A1 response was significantly lower (C.V. = 5 %) when using the developed mixture generator compared to that using the conventional gradient generator (C.V. = 12 %). Reduction in reagent consumption by 12-times was also achieved. This robust, accurate, and scalable multi-reagent mixture generator integrated with a cell culture array as a live cell assay platform can be readily implemented into various screening applications where repeatability, robustness, and low reagent consumptions over long periods of assay time are of importance.

  6. Application of a cocktail approach to screen cytochrome P450 BM3 libraries for metabolic activity and diversity. (United States)

    Reinen, Jelle; Postma, Geert; Tump, Cornelis; Bloemberg, Tom; Engel, Jasper; Vermeulen, Nico P E; Commandeur, Jan N M; Honing, Maarten


    In the present study, the validity of using a cocktail screening method in combination with a chemometrical data mining approach to evaluate metabolic activity and diversity of drug-metabolizing bacterial Cytochrome P450 (CYP) BM3 mutants was investigated. In addition, the concept of utilizing an in-house-developed library of CYP BM3 mutants as a unique biocatalytic synthetic tool to support medicinal chemistry was evaluated. Metabolic efficiency of the mutant library towards a selection of CYP model substrates, being amitriptyline (AMI), buspirone (BUS), coumarine (COU), dextromethorphan (DEX), diclofenac (DIC) and norethisterone (NET), was investigated. First, metabolic activity of a selection of CYP BM3 mutants was screened against AMI and BUS. Subsequently, for a single CYP BM3 mutant, the effect of co-administration of multiple drugs on the metabolic activity and diversity towards AMI and BUS was investigated. Finally, a cocktail of AMI, BUS, COU, DEX, DIC and NET was screened against the whole in-house CYP BM3 library. Different validated quantitative and qualitative (U)HPLC-MS/MS-based analytical methods were applied to screen for substrate depletion and targeted product formation, followed by a more in-depth screen for metabolic diversity. A chemometrical approach was used to mine all data to search for unique metabolic properties of the mutants and allow classification of the mutants. The latter would open the possibility of obtaining a more in-depth mechanistic understanding of the metabolites. The presented method is the first MS-based method to screen CYP BM3 mutant libraries for diversity in combination with a chemometrical approach to interpret results and visualize differences between the tested mutants.

  7. Research Focus towards biomolecular medicines development: An overview

    Directory of Open Access Journals (Sweden)

    K Ramalingam


    Full Text Available Research towards molecular medicines development for noninfectious diseases such as cardio-vascular diseases, cancer, diabetes, neuro-degenerative diseases and musculo-skeletal joint inflammatory disorders (arthritis needs a fresh impetus, in view of the developments in the assessment of the therapeutic proteins such as interferons, cytokines, interleukins, erythropoietin H, somatostatin, defensins, tumor necrosis factor, monoclonal antibodies, polyclonal antibodies, lectins etc. The new therapeutic strategies like gene therapy and cell based/stem cell therapy augment the efficacy of the various bimolecular proteins and their application towards clinical management of the diseases. The above research areas also imply a shift in the existing paradigm of both the clinical and therapeutic evaluation.

  8. Towards a calculus of biomolecular complexes at equilibrium. (United States)

    Mjolsness, Eric


    An overview is presented of the construction and use of algebraic partition functions to represent the equilibrium statistical mechanics of multimolecular complexes and their action within a larger regulatory network. Unlike many applications of equilibrium statistical mechanics, multimolecular complexes may operate with various subsets of their components present and connected to the others, the rest remaining in solution. Thus they are variable-structure systems. This aspect of their behavior may be accounted for by the use of 'fugacity' variables as a representation within the partition functions. Four principles are proposed by which the combinatorics of molecular complex construction can be reflected in the construction of their partition functions. The corresponding algebraic operations on partition functions are multiplication, addition, function composition and a less commonly used operation called contraction. Each has a natural interpretation in terms of probability distributions on multimolecular structures. Possible generalizations to nonequilibrium statistical mechanics are briefly discussed.

  9. The urgent need for universally applicable simple screening procedures and diagnostic criteria for gestational diabetes mellitus - lessons from projects funded by the World Diabetes Foundation

    DEFF Research Database (Denmark)

    Nielsen, Karoline Kragelund; de Courten, Maximilian; Kapur, Anil


    Background: To address the risks of adverse pregnancy outcomes and future type 2 diabetes associated with gestational diabetes mellitus (GDM), its early detection and timely treatment is essential. In the absence of an international consensus, multiple different guidelines on screening...... and diagnosis of GDM have existed for a long time. This may be changing with the publication of the recommendations by the International Association of Diabetes and Pregnancy Study Groups. However, none of these guidelines take into account evidence from or ground realities of resource-poor settings. Objective......: This study aimed to investigate whether GDM projects supported by the World Diabetes Foundation in developing countries utilize any of the internationally recommended guidelines for screening and diagnosis of GDM, explore experiences on applicability and usefulness of the guidelines and barriers if any...

  10. Revisions of the Fish Invasiveness Screening Kit (FISK) for its application in warmer climatic zones, with particular reference to peninsular Florida. (United States)

    Lawson, Larry L; Hill, Jeffrey E; Vilizzi, Lorenzo; Hardin, Scott; Copp, Gordon H


    The initial version (v1) of the Fish Invasiveness Scoring Kit (FISK) was adapted from the Weed Risk Assessment of Pheloung, Williams, and Halloy to assess the potential invasiveness of nonnative freshwater fishes in the United Kingdom. Published applications of FISK v1 have been primarily in temperate-zone countries (Belgium, Belarus, and Japan), so the specificity of this screening tool to that climatic zone was not noted until attempts were made to apply it in peninsular Florida. To remedy this shortcoming, the questions and guidance notes of FISK v1 were reviewed and revised to improve clarity and extend its applicability to broader climatic regions, resulting in changes to 36 of the 49 questions. In addition, upgrades were made to the software architecture of FISK to improve overall computational speed as well as graphical user interface flexibility and friendliness. We demonstrate the process of screening a fish species using FISK v2 in a realistic management scenario by assessing the Barcoo grunter Scortum barcoo (Terapontidae), a species whose management concerns are related to its potential use for aquaponics in Florida. The FISK v2 screening of Barcoo grunter placed the species into the lower range of medium risk (score = 5), suggesting it is a permissible species for use in Florida under current nonnative species regulations. Screening of the Barcoo grunter illustrates the usefulness of FISK v2 as a proactive tool serving to inform risk management decisions, but the low level of confidence associated with the assessment highlighted a dearth of critical information on this species.

  11. The universal statistical distributions of the affinity, equilibrium constants, kinetics and specificity in biomolecular recognition.

    Directory of Open Access Journals (Sweden)

    Xiliang Zheng


    Full Text Available We uncovered the universal statistical laws for the biomolecular recognition/binding process. We quantified the statistical energy landscapes for binding, from which we can characterize the distributions of the binding free energy (affinity, the equilibrium constants, the kinetics and the specificity by exploring the different ligands binding with a particular receptor. The results of the analytical studies are confirmed by the microscopic flexible docking simulations. The distribution of binding affinity is Gaussian around the mean and becomes exponential near the tail. The equilibrium constants of the binding follow a log-normal distribution around the mean and a power law distribution in the tail. The intrinsic specificity for biomolecular recognition measures the degree of discrimination of native versus non-native binding and the optimization of which becomes the maximization of the ratio of the free energy gap between the native state and the average of non-native states versus the roughness measured by the variance of the free energy landscape around its mean. The intrinsic specificity obeys a Gaussian distribution near the mean and an exponential distribution near the tail. Furthermore, the kinetics of binding follows a log-normal distribution near the mean and a power law distribution at the tail. Our study provides new insights into the statistical nature of thermodynamics, kinetics and function from different ligands binding with a specific receptor or equivalently specific ligand binding with different receptors. The elucidation of distributions of the kinetics and free energy has guiding roles in studying biomolecular recognition and function through small-molecule evolution and chemical genetics.

  12. The Universal Statistical Distributions of the Affinity, Equilibrium Constants, Kinetics and Specificity in Biomolecular Recognition (United States)

    Zheng, Xiliang; Wang, Jin


    We uncovered the universal statistical laws for the biomolecular recognition/binding process. We quantified the statistical energy landscapes for binding, from which we can characterize the distributions of the binding free energy (affinity), the equilibrium constants, the kinetics and the specificity by exploring the different ligands binding with a particular receptor. The results of the analytical studies are confirmed by the microscopic flexible docking simulations. The distribution of binding affinity is Gaussian around the mean and becomes exponential near the tail. The equilibrium constants of the binding follow a log-normal distribution around the mean and a power law distribution in the tail. The intrinsic specificity for biomolecular recognition measures the degree of discrimination of native versus non-native binding and the optimization of which becomes the maximization of the ratio of the free energy gap between the native state and the average of non-native states versus the roughness measured by the variance of the free energy landscape around its mean. The intrinsic specificity obeys a Gaussian distribution near the mean and an exponential distribution near the tail. Furthermore, the kinetics of binding follows a log-normal distribution near the mean and a power law distribution at the tail. Our study provides new insights into the statistical nature of thermodynamics, kinetics and function from different ligands binding with a specific receptor or equivalently specific ligand binding with different receptors. The elucidation of distributions of the kinetics and free energy has guiding roles in studying biomolecular recognition and function through small-molecule evolution and chemical genetics. PMID:25885453

  13. Raman spectroscopy detects biomolecular changes associated with nanoencapsulated hesperetin treatment in experimental oral carcinogenesis (United States)

    Gurushankar, K.; Gohulkumar, M.; Kumar, Piyush; Krishna, C. Murali; Krishnakumar, N.


    Recently it has been shown that Raman spectroscopy possesses great potential in the investigation of biomolecular changes of tumor tissues with therapeutic drug response in a non-invasive and label-free manner. The present study is designed to investigate the antitumor effect of hespertin-loaded nanoparticles (HETNPs) relative to the efficacy of native hesperetin (HET) in modifying the biomolecular changes during 7,12-dimethyl benz(a)anthracene (DMBA)-induced oral carcinogenesis using a Raman spectroscopic technique. Significant differences in the intensity and shape of the Raman spectra between the control and the experimental tissues at 1800-500 cm-1 were observed. Tumor tissues are characterized by an increase in the relative amount of proteins, nucleic acids, tryptophan and phenylalanine and a decrease in the percentage of lipids when compared to the control tissues. Further, oral administration of HET and its nanoparticulates restored the status of the lipids and significantly decreased the levels of protein and nucleic acid content. Treatment with HETNPs showed a more potent antitumor effect than treatment with native HET, which resulted in an overall reduction in the intensity of several biochemical Raman bands in DMBA-induced oral carcinogenesis being observed. Principal component and linear discriminant analysis (PC-LDA), together with leave-one-out cross validation (LOOCV) on Raman spectra yielded diagnostic sensitivities of 100%, 80%, 91.6% and 65% and specificities of 100%, 65%, 60% and 55% for classification of control versus DMBA, DMBA versus DMBA  +  HET, DMBA versus DMBA  +  HETNPs and DMBA  +  HET versus DMBA  +  HETNPs treated tissue groups, respectively. These results further demonstrate that Raman spectroscopy associated with multivariate statistical algorithms could be a valuable tool for developing a comprehensive understanding of the process of biomolecular changes, and could reveal the signatures of the

  14. Multiresolution persistent homology for excessively large biomolecular datasets

    Energy Technology Data Exchange (ETDEWEB)

    Xia, Kelin; Zhao, Zhixiong [Department of Mathematics, Michigan State University, East Lansing, Michigan 48824 (United States); Wei, Guo-Wei, E-mail: [Department of Mathematics, Michigan State University, East Lansing, Michigan 48824 (United States); Department of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824 (United States); Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824 (United States)


    Although persistent homology has emerged as a promising tool for the topological simplification of complex data, it is computationally intractable for large datasets. We introduce multiresolution persistent homology to handle excessively large datasets. We match the resolution with the scale of interest so as to represent large scale datasets with appropriate resolution. We utilize flexibility-rigidity index to access the topological connectivity of the data set and define a rigidity density for the filtration analysis. By appropriately tuning the resolution of the rigidity density, we are able to focus the topological lens on the scale of interest. The proposed multiresolution topological analysis is validated by a hexagonal fractal image which has three distinct scales. We further demonstrate the proposed method for extracting topological fingerprints from DNA molecules. In particular, the topological persistence of a virus capsid with 273 780 atoms is successfully analyzed which would otherwise be inaccessible to the normal point cloud method and unreliable by using coarse-grained multiscale persistent homology. The proposed method has also been successfully applied to the protein domain classification, which is the first time that persistent homology is used for practical protein domain analysis, to our knowledge. The proposed multiresolution topological method has potential applications in arbitrary data sets, such as social networks, biological networks, and graphs.

  15. Conformational thermodynamics of biomolecular complexes: The histogram-based method (United States)

    Das, Amit; Sikdar, Samapan; Ghosh, Mahua; Chakrabarti, J.


    Conformational changes in biomacromolecules govern majority of biological processes. Complete characterization of conformational contributions to thermodynamics of complexation of biomacromolecules has been challenging. Although, advances in NMR relaxation experiments and several computational studies have revealed important aspects of conformational entropy changes, efficient and large-scale estimations still remain an intriguing facet. Recent histogram-based method (HBM) offers a simple yet rigorous route to estimate both conformational entropy and free energy changes from same set of histograms in an efficient manner. The HBM utilizes the power of histograms which can be generated as accurately as desired from an arbitrarily large sample space from atomistic simulation trajectories. Here we discuss some recent applications of the HBM, using dihedral angles of amino acid residues as conformational variables, which provide good measure of conformational thermodynamics of several protein-peptide complexes, obtained from NMR, metal-ion binding to an important metalloprotein, interfacial changes in protein-protein complex and insight to protein function, coupled with conformational changes. We conclude the paper with a few future directions worth pursuing.

  16. Biomolecular Deuteration for Neutron Structural Biology and Dynamics. (United States)

    Haertlein, Michael; Moulin, Martine; Devos, Juliette M; Laux, Valerie; Dunne, Orla; Forsyth, V Trevor


    Neutron scattering studies provide important information in structural biology that is not accessible using other approaches. The uniqueness of the technique, and its complementarity with X-ray scattering, is greatest when full use is made of deuterium labeling. The ability to produce tailor-made deuterium-labeled biological macromolecules allows neutron studies involving solution scattering, crystallography, reflection, and dynamics to be optimized in a manner that has major impact on the scope, quality, and throughput of work in these areas. Deuteration facilities have now been developed at many neutron centres throughout the world; these are having a crucial effect on neutron studies in the life sciences and on biologically related studies in soft matter. This chapter describes methods that have been developed for the efficient production of deuterium-labeled samples for a wide range of neutron scattering applications. Examples are given that illustrate the use of these samples for each of the main techniques. Perspectives for biological deuterium labeling are discussed in relation to developments at current facilities and those that are planned in the future.

  17. Plucked Human Hair Shafts and Biomolecular Medical Research

    Directory of Open Access Journals (Sweden)

    Kevin Schembri


    Full Text Available The hair follicle is a skin integument at the boundary between an organism and its immediate environment. The biological role of the human hair follicle has lost some of its ancestral importance. However, an indepth investigation of this miniorgan reveals hidden complexity with huge research potential. An essential consideration when dealing with human research is the awareness of potential harm and thus the absolute need not to harm—a rule aptly qualified by the Latin term “primum non nocere” (first do no harm. The plucked hair shaft offers such advantages. The use of stem cells found in hair follicles cells is gaining momentum in the field of regenerative medicine. Furthermore, current diagnostic and clinical applications of plucked hair follicles include their use as autologous and/or three-dimensional epidermal equivalents, together with their utilization as surrogate tissue in pharmacokinetic and pharmacodynamics studies. Consequently, the use of noninvasive diagnostic procedures on hair follicle shafts, posing as a surrogate molecular model for internal organs in the individual patient for a spectrum of human disease conditions, can possibly become a reality in the near future.

  18. β2-Adrenoceptor affinity chromatography and its application in the screening of the active compounds from Semen Armeniacae Amarum

    Institute of Scientific and Technical Information of China (English)

    ZHENG XiaoHui; ZHAO XinFeng; YANG Rong; WANG ShiXiang; WEI YinMao; ZHENG JianBin


    β2-Adrenoceptor (β2-AR) was purified from the rabbit lung tissue by sepharose-salbutamol affinity chromatographic column. To prepare the β2-AR stationary phase, β2-AR was evenly immobilized on the surface of macro-pore silica with a mild chemical coupling method through covalent bond. The reten-tion properties of β2-AR stationary phase were characterized by four ligands, salbutamol sulfate, noradrenaline bitartrate, adrenaline hydrochloride and propranolol hydrochloride, to establish the β2-AR affinity chromatography. Then, the method was used to screen the active compounds from the total extracts of Semen Armeniacae Amarum. The results showed that β2-AR on the surface of the sta-tionary phase could keep its original bioactivity and selectivity. Amygdalin retained in the chroma-tographic column was proved to be the active compound of the total extracts of Semen Armeniacae Amarum. Compared with the existing chromatographic screening approaches, this method showed a good stability and high selectivity. The active compounds which could interact with β2-AR in traditional Chinese medicine (TCM) could be screened efficiently by this method, providing a new way to screen the active compounds in complicated samples such as TCM.

  19. Development and Application of a High-Throughput Screening Method to Evaluate Antifungal Activity against Trichophyton tonsurans. (United States)

    Preuett, Barry; Leeder, J Steven; Abdel-Rahman, Susan


    There exist relatively few drug classes on the market to treat dermatophyte infections. This investigation was designed to develop and validate high-throughput methodology for screening and confirmation of chemicals for activity against Trichophyton tonsurans. Growth characteristics were examined on two platforms (96- and 384-well) in three media at eight spore concentrations over a period of up to 120 h. Microspectrophotometry was used to automate plate reads. The 384-well platform was used to screen more than 7000 compounds from six chemical libraries. Z-scores for optical density relative to positive growth controls were used to flag compounds of interest and activity confirmed in separate assays. The final conditions selected for both screening and confirmation with minimum inhibitory concentration (MIC) determination were growth for 48 h at 32 °C in SabDex with 1 × 10(4) spores per reaction. Sensitivity and specificity averaged 99.2% (range, 95.2%-100%) and 99.8% (range, 99.1%-100%), respectively. MICs for known antifungals were similar to those reported by others using Clinical and Laboratory Standards Institute methods. Several novel compound classes were identified to have activity against T. tonsurans with potency comparable to known antifungals. A robust, reproducible assay is described that permits high-throughput screening in T. tonsurans.

  20. Biomolecular interactions in HCV nucleocapsid-like particles as revealed by vibrational spectroscopy (United States)

    Rodríguez-Casado, Arantxa; Molina, Marina; Carmona, Pedro


    Hepatitis C virus (HCV) occurs in the form of 55-65 nm spherical particles, but the structure of the virion remains to be clarified. Structural studies of HCV have been hampered by the lack of an appropriate cell culture system. However, structural analyses of HCV components can provide an essential framework for understanding of the molecular mechanism of virion assembly. This article reviews the potential of vibrational spectroscopy aimed at the knowledge of HCV structural biology, particularly regarding biomolecular interactions in nucleocapsid-like particles obtained in vitro.

  1. Force sensors based on piezoresistive and MOSFET cantilevers for biomolecular sensing


    Tosolini, Giordano


    Los procesos de reconocimiento biomolecular entre receptores y ligandos son muy importantes en biología. Estas biomoléculas pueden desarrollar complejos muy específicos y tener una variedad de funciones como replicación y transcripción genómica, actividad enzimática, respuesta inmune, señalamiento celular, etc. La complementariedad inequívoca mostrada por estos componentes biológicos es ampliamente utilizada para desarrollar biosensores. Dependiendo de la naturaleza de las señales que se conv...

  2. Fundamental behavior of a model biomolecular amphiphile system (United States)

    Haverstick, Kraig Leonard

    An interest in the fundamental interactions between protein components, in the form of either single amino acids or peptides, unifies the work represented in this thesis. These fundamental interactions drive protein folding, enzyme-substrate binding, and cell adhesion to extracellular ligands. The technology of lipidation was used to isolate these protein interactions. Lipidation of a water-soluble amino acid or peptide sequence confined the protein component to the air-water interface or to a self-assembled structure in water. Compression of the molecules at the air-water interface ordered them into a solid-like monolayer, and Langmuir-Blodgett deposition produced a surface modification with protein component presented in a controlled, orderly manner. These molecules have potential applications as biomaterials coatings or drug delivery devices. A method for determination of specific hydrogen bonding interactions through cocrystallization of two complementary peptide sequences is also described. In order to understand the effect of lipidation and lipid structure on peptide behavior, a comprehensive study of tail designs was first undertaken. Tail length, linkage group, linker, spacer length, and headgroup chirality, orientation, and terminal group were systematically varied in simple amino acid amphiphiles. Monolayer assembly, thermal stability, and structure were studied with Langmuir isotherms and Fourier transform infrared spectroscopy. Each part of the tail structure was found to affect monolayer behavior. With lipid effects better understood, peptide amphiphiles were designed, synthesized, and studied using peptide sequences of importance for cell adhesion. The sequences [IV-H1] from type IV collagen and Arg-Gly-Asp (RGD) were lipidated and characterized in monolayers by Langmuir isotherms and Fourier transform infrared spectroscopy. Biological functionality was determined by melanoma cell spreading assays. Peptide presentation was found to be critical for

  3. Biomolecular interactions probed by fluorescence resonance energy transfer (United States)

    Lange, Daniela Charlotte


    This thesis describes how a physical phenomenon, Fluorescence Resonance Energy Transfer (FRET), can be exploited for the study of interactions between biomolecules. The physical basis of this phenomenon is discussed and it is described how some of its characteristics can be exploited in measurement. A recently introduced method, photobleaching FRET microscopy, was implemented and its image analysis refined to suit our biological context. Further, a new technique is proposed, which combines FRET with confocal laser scanning microscopy to optimize resolution and to allow for 3D-studies in living cells. The first part of this thesis presents the application of FRET to the study of oligomerization of G-protein coupled receptors (GPCRs), which was performed at the Fraser Laboratories at McGill University in Montreal. It is demonstrated how FRET microscopy allowed us to circumvent problems of traditional biochemical approaches and provided the first direct evidence for GPCR oligomerization in intact cells. We found that somatostatin receptors (SSTRs) functionally interact by forming oligomers with their own kind, with different SSTR isoforms, and even with distantly related GPCRs, such as dopamine receptors, the latter of which is breaking with the dogma that GPCRs would only pair up with their own kind. The high sensitivity of the FRET technique allowed us to characterize these interactions under more physiological conditions, which lead to the observation that oligomerization is induced by receptor agonist. We further studied the differential effects of agonists and antagonists on receptor oligomerization, leading to a model for the molecular mechanism underlying agonist/antagonist function and receptor activation. The second part was carried out at the Neurobiology Laboratory of the VA Medical Center in Newington, CT. The objective was to further our understanding of Niemann- Pick type C disease, which is characterized by a defect in intracellular cholesterol

  4. Virological control of groundwater quality using biomolecular tests. (United States)

    Carducci, A; Casini, B; Bani, A; Rovini, E; Verani, M; Mazzoni, F; Giuntini, A


    Deep groundwater, even if generally protected, could be contaminated by surface or rain water infiltration through soil fractures, septic tanks, cesspits, land irrigation, disposal of wastewater and disposal of muds from depuration systems. The sanitary importance of such possible contamination is related to the different uses of the water and it is at the maximum level when it is intended for human use. Routine microbiological analyses do not consider viruses, only bacterial parameters, as contamination indicators. However, it is known that enteric viruses can survive a long time in deep aquifers and that they may not always be associated with bacterial indicators. The virological analysis of waters intended for drinking use is provided only as an occasional control exercised at the discretion of the sanitary authority. Technological difficulties with obtaining data about groundwater viral contamination led to a study to devise rapid and efficient methods for their detection and the application of these methods to samples from different sources. Four acid nucleic extraction techniques have been tested (classic proteinase K- phenol/chloroform, QIAamp Viral RNA Kit (Qiagen), SV Total RNA Isolation System (Promega) and NucleoSpin Virus L (Macherey-Nagel). Sensitivity and specificity of RT-PCR protocols for entero- (EV), hepatitis A (HAV) and small round structured (SRSV) viruses have been verified. Deep groundwater samples (100 L) were concentrated (2-step tangential flow ultrafiltration) and the concentrate contaminated with serial 10-fold dilutions of a known titre of poliovirus type 3. Extracted RNA was concentrated (microcon-100) and analysed by RT-PCR using specific EV primers and visualising amplification products by agarose gel electrophoresis. In addition, two different methods of RT-PCR for non-cultivable viruses have been tested: (a) RT-PCR and nested RT-PCR for HAV and (b) RT-PCR with generic primers and RT-PCR with specific primers for SRSV. Different

  5. Chinese Young Researcher Symposia on Pharmacology (Track 2) Establishment and application of an in vitro embryotoxicity screening test

    Institute of Scientific and Technical Information of China (English)

    YanCHANG; Hai-xiaLIN; Qi-bingMEI; Bei-liQIAN


    AIM Developmental toxicity testing to current international guidelines involves exposure of pregnant animals, mostly rats and rabbits, and subsequent assessment of toxic effects in their fetuses. Alternative methods have been developed since 1980s. The most complex assays in this area make distinctive and extensive use of isolated postimplantation rodent embryos which are cultured in vitro during the phase of major organogenesis. The objective of this study is to establish an in vitro embryotoxicity test----based on postimplatation 9.5d whole embryo culture (WEC) and 3T3 cell toxicity. The possibilities for their application as embryotoxicity screens have been investigated.

  6. The Cervical Cancer Screening Technique of Application and Progression%子宫颈癌筛查方法的应用及研究进展

    Institute of Scientific and Technical Information of China (English)

    张文娟; 东燕; 孙绪兰; 王萍; 曾燕


    Cervical cancer is a common gynecologic tumor and it is the second-leading cause of death from cancer in women worldwide. It is critical to construct a sustainable, reasonable and efficient general survey method for the early detection of precancerosis of Cervical Cancer. At present, cervical cancer screening technique includes: (a) cervical cytological screening (papanicolaou smear, TCT and DNA quantification); (b) visual inspection with acetic acid (VIA) and visual inspection with Lugol'S iodine (VH.I) ; (c) vaginoscopy; (d) HPV detection. The article is to summarize the application and progression of technique for cervical cancer screening.%子宫颈癌是妇科常见恶性肿瘤之一,发病率居女性恶性肿瘤第二位.建立可持续、合理、有效的普查方法,早期发现癌前病变是防治宫颈癌的关键.目前宫颈癌筛查方法有宫颈细胞学筛查(巴氏涂片、液基薄层细胞学检测、细胞DNA定量分析技术)、肉眼观察辅以醋酸白和Lugol碘溶液检测法、阴道镜检查、病毒-HPV检测,本文就当前各种筛查方法的应用及研究进展进行概括.

  7. A Teach-Discover-Treat Application of ZincPharmer: An Online Interactive Pharmacophore Modeling and Virtual Screening Tool.

    Directory of Open Access Journals (Sweden)

    David Ryan Koes

    Full Text Available The 2012 Teach-Discover-Treat (TDT community-wide experiment provided a unique opportunity to test prospective virtual screening protocols targeting the anti-malarial target dihydroorotate dehydrogenase (DHODH. Facilitated by ZincPharmer, an open access online interactive pharmacophore search of the ZINC database, the experience resulted in the development of a novel classification scheme that successfully predicted the bound structure of a non-triazolopyrimidine inhibitor, as well as an overall hit rate of 27% of tested active compounds from multiple novel chemical scaffolds. The general approach entailed exhaustively building and screening sparse pharmacophore models comprising of a minimum of three features for each bound ligand in all available DHODH co-crystals and iteratively adding features that increased the number of known binders returned by the query. Collectively, the TDT experiment provided a unique opportunity to teach computational methods of drug discovery, develop innovative methodologies and prospectively discover new compounds active against DHODH.

  8. Application of an ELISA-type screen printed electrode-based potentiometric assay to the detection of Cryptosporidium parvum oocysts. (United States)

    Laczka, Olivier; Skillman, Lucy; Ditcham, William G; Hamdorf, Brenton; Wong, Danny K Y; Bergquist, Peter; Sunna, Anwar


    We report a novel electrochemical method for the rapid detection of the parasitic protozoan, Cryptosporidium parvum. An antibody-based capture format was transferred onto screen-printed electrodes and the presence of horseradish peroxidase-labelled antibodies binding to the oocysts was potentiometrically detected. This method allowed the detection of 5 × 10(2)Cryptosporidium oocysts per mL in 60 min.

  9. Screening of the effective cellulose-degradable strain and its application in the production of cellulose bioethanol

    Institute of Scientific and Technical Information of China (English)


    Strains from the cellulose-containing environment were collected. Primary screening(by filter-paper Hutchison solid culture medium and sodium carboxymethylcellulose solid culture medium) and reelection(by filter-paper inorganic salt culture medium and sodium carboxymethylcellulose Congo red culture medium) indicated that five strains obtained were best suited for high performance cellulose degradation. Determination of sodium carboxymethylcellulose activity(CMCA) and filter paper activity(FPA) was accomplis...

  10. Photochemical functionalization of gallium nitride thin films with molecular and biomolecular layers. (United States)

    Kim, Heesuk; Colavita, Paula E; Metz, Kevin M; Nichols, Beth M; Sun, Bin; Uhlrich, John; Wang, Xiaoyu; Kuech, Thomas F; Hamers, Robert J


    We demonstrate that photochemical functionalization can be used to functionalize and photopattern the surface of gallium nitride crystalline thin films with well-defined molecular and biomolecular layers. GaN(0001) surfaces exposed to a hydrogen plasma will react with organic molecules bearing an alkene (C=C) group when illuminated with 254 nm light. Using a bifunctional molecule with an alkene group at one end and a protected amine group at the other, this process can be used to link the alkene group to the surface, leaving the protected amine exposed. Using a simple contact mask, we demonstrate the ability to directly pattern the spatial distribution of these protected amine groups on the surface with a lateral resolution of <12 mum. After deprotection of the amines, single-stranded DNA oligonucleotides were linked to the surface using a bifunctional cross-linker. Measurements using fluorescently labeled complementary and noncomplementary sequences show that the DNA-modified GaN surfaces exhibit excellent selectivity, while repeated cycles of hybridization and denaturation in urea show good stability. These results demonstrate that photochemical functionalization can be used as an attractive starting point for interfacing molecular and biomolecular systems with GaN and other compound semiconductors.

  11. A new approach to implement absorbing boundary condition in biomolecular electrostatics. (United States)

    Goni, Md Osman


    This paper discusses a novel approach to employ the absorbing boundary condition in conjunction with the finite-element method (FEM) in biomolecular electrostatics. The introduction of Bayliss-Turkel absorbing boundary operators in electromagnetic scattering problem has been incorporated by few researchers. However, in the area of biomolecular electrostatics, this boundary condition has not been investigated yet. The objective of this paper is twofold. First, to solve nonlinear Poisson-Boltzmann equation using Newton's method and second, to find an efficient and acceptable solution with minimum number of unknowns. In this work, a Galerkin finite-element formulation is used along with a Bayliss-Turkel absorbing boundary operator that explicitly accounts for the open field problem by mapping the Sommerfeld radiation condition from the far field to near field. While the Bayliss-Turkel condition works well when the artificial boundary is far from the scatterer, an acceptable tolerance of error can be achieved with the second order operator. Numerical results on test case with simple sphere show that the treatment is able to reach the same level of accuracy achieved by the analytical method while using a lower grid density. Bayliss-Turkel absorbing boundary condition (BTABC) combined with the FEM converges to the exact solution of scattering problems to within discretization error.

  12. Characterization of a nanoscale S-layer protein based template for biomolecular patterning. (United States)

    Wong, Wing Sze; Yung, Pun To


    Well organized template for biomolecular conjugation is the foundation for biosensing. Most of the current devices are fabricated using lithographic patterning processes and self-assembly monolayer (SAM) methods. However, the research toward developing a sub-10 nm patterned, self-regenerated template on various types of substrates is limited, mainly due to the limited functional groups of the building material. Bacterial surface layer proteins (S-layer proteins) can self-assemble into ordered lattice with regular pore sizes of 2-8 nm on different material supports and interfaces. The ordered structure can regenerate after extreme variations of solvent conditions. In this work, we developed a nanoscale biomolecular template based on S-layer proteins on gold surface for fabrication of sensing layer in biosensors. S-layer proteins were isolated from Bacillus cereus, Lysinibacillus sphaericus and Geobacillus stearothermophilus. Protein concentrations were measured by Bradford assay. The protein purities were verified by SDS-PAGE, showing molecular weights ranging from 97-135 kDa. The hydrophilicity of the substrate surface was measured after surface treatments of protein recrystallization. Atomic force microscopic (AFM) measurement was performed on substrate surface, indicating a successful immobilization of a monolayer of S-layer protein with 8-9 nm height on gold surface. The template can be applied on various material supports and acts as a self-regenerated sensing layer of biosensors in the future.

  13. Optimizing water hyperpolarization and dissolution for sensitivity-enhanced 2D biomolecular NMR (United States)

    Olsen, Greg; Markhasin, Evgeny; Szekely, Or; Bretschneider, Christian; Frydman, Lucio


    A recent study explored the use of hyperpolarized water, to enhance the sensitivity of nuclei in biomolecules thanks to rapid proton exchanges with labile amide backbone and sidechain groups. Further optimizations of this approach have now allowed us to achieve proton polarizations approaching 25% in the water transferred into the NMR spectrometer, effective water T1 times approaching 40 s, and a reduction in the dilution demanded for the cryogenic dissolution process. Further hardware developments have allowed us to perform these experiments, repeatedly and reliably, in 5 mm NMR tubes. All these ingredients - particularly the ⩾3000× 1H polarization enhancements over 11.7 T thermal counterparts, long T1 times and a compatibility with high-resolution biomolecular NMR setups - augur well for hyperpolarized 2D NMR studies of peptides, unfolded proteins and intrinsically disordered systems undergoing fast exchanges of their protons with the solvent. This hypothesis is here explored by detailing the provisions that lead to these significant improvements over previous reports, and demonstrating 1D coherence transfer experiments and 2D biomolecular HMQC acquisitions delivering NMR spectral enhancements of 100-500× over their optimized, thermally-polarized, counterparts.

  14. Biomolecular Systems of Disease Buried Across Multiple GWAS Unveiled by Information Theory and Ontology (United States)

    Lee, Younghee; Li, Jianrong; Gamazon, Eric; Chen, James L.; Tikhomirov, Anna; Cox, Nancy J.; Lussier, Yves A.


    A key challenge for genome-wide association studies (GWAS) is to understand how single nucleotide polymorphisms (SNPs) mechanistically underpin complex diseases. While this challenge has been addressed partially by Gene Ontology (GO) enrichment of large list of host genes of SNPs prioritized in GWAS, these enrichment have not been formally evaluated. Here, we develop a novel computational approach anchored in information theoretic similarity, by systematically mining lists of host genes of SNPs prioritized in three adult-onset diabetes mellitus GWAS. The “gold-standard” is based on GO associated with 20 published diabetes SNPs’ host genes and on our own evaluation. We computationally identify 69 similarity-predicted GO independently validated in all three GWAS (FDR<5%), enriched with those of the gold-standard (odds ratio=5.89, P=4.81e-05), and these terms can be organized by similarity criteria into 11 groupings termed “biomolecular systems”. Six biomolecular systems were corroborated by the gold-standard and the remaining five were previously uncharacterized. PMID:21347143

  15. The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes. (United States)

    van Zundert, G C P; Rodrigues, J P G L M; Trellet, M; Schmitz, C; Kastritis, P L; Karaca, E; Melquiond, A S J; van Dijk, M; de Vries, S J; Bonvin, A M J J


    The prediction of the quaternary structure of biomolecular macromolecules is of paramount importance for fundamental understanding of cellular processes and drug design. In the era of integrative structural biology, one way of increasing the accuracy of modeling methods used to predict the structure of biomolecular complexes is to include as much experimental or predictive information as possible in the process. This has been at the core of our information-driven docking approach HADDOCK. We present here the updated version 2.2 of the HADDOCK portal, which offers new features such as support for mixed molecule types, additional experimental restraints and improved protocols, all of this in a user-friendly interface. With well over 6000 registered users and 108,000 jobs served, an increasing fraction of which on grid resources, we hope that this timely upgrade will help the community to solve important biological questions and further advance the field. The HADDOCK2.2 Web server is freely accessible to non-profit users at

  16. Submicrometer Hall sensors for detection of magnetic nanoparticles in biomolecular sensing (United States)

    Mihajlovic, Goran; Xiong, P.; von Molnar, S.; Ohtani, K.; Ohno, H.; Field, M.; Sullivan, G. J.


    Significant progress has been made in the recent years in synthesis and biomolecular functionalization of magnetic nanoparticles. These magnetic bio-nanolabels can be utilized as protein or gene markers in biomolecular sensing assays, in contrast to the much larger micron sized magnetic beads that are usually limited to cell labeling. However, the low magnetic moments of individual nanoparticles (10^4-10^5 μB) render their sensitive detection still a challenging task. In order to address this issue we are developing miniaturized Hall sensors from InAs/AlSb quantum well semiconductor heterostructures with active Hall cross areas down to 300 nm x 300 nm. Our preliminary characterization measurements performed at room temperature show functional devices with magnetic field resolution < 100 μT/√Hz at frequencies above 100 Hz, yielding a moment sensitivity ˜ 10^5 μB. In addition to the progress in improving the moment sensitivity of the submicrometer Hall detectors, we will also present efforts in device integration with on-chip microcoils for the generation of local magnetic excitation fields. Results on nanoparticle detection will also be presented.

  17. The detection of specific biomolecular interactions with micro-Hall magnetic sensors (United States)

    Manandhar, Pradeep; Chen, Kan-Sheng; Aledealat, Khaled; Mihajlović, Goran; Yun, C. Steven; Field, Mark; Sullivan, Gerard J.; Strouse, Geoffrey F.; Bryant Chase, P.; von Molnár, Stephan; Xiong, Peng


    The detection of reagent-free specific biomolecular interactions through sensing of nanoscopic magnetic labels provides one of the most promising routes to biosensing with solid-state devices. In particular, Hall sensors based on semiconductor heterostructures have shown exceptional magnetic moment sensitivity over a large dynamic field range suitable for magnetic biosensing using superparamagnetic labels. Here we demonstrate the capability of such micro-Hall sensors to detect specific molecular binding using biotin-streptavidin as a model system. We apply dip-pen nanolithography to selectively biotinylate the active areas of InAs micro-Hall devices with nanoscale precision. Specific binding of complementarily functionalized streptavidin-coated superparamagnetic beads to the Hall crosses occurs via molecular recognition, and magnetic detection of the assembled beads is achieved at room temperature using phase sensitive micro-Hall magnetometry. The experiment constitutes the first unambiguous demonstration of magnetic detection of specific biomolecular interactions with semiconductor micro-Hall sensors, and the selective molecular functionalization and resulting localized bead assembly demonstrate the possibility of multiplexed sensing of multiple target molecules using a single device with an array of micro-Hall sensors.

  18. Effect of sintering temperatures and screen printing types on TiO2 layers in DSSC applications (United States)

    Supriyanto, Agus; Furqoni, Lutfi; Nurosyid, Fahru; Hidayat, Jojo; Suryana, Risa


    Dye-Sensitized Solar Cell (DSSC) is a candidate solar cell, which has a big potential in the future due to its eco-friendly material. This research is conducted to study the effect of sintering temperature and the type of screen-printing toward the characteristics of TiO2 layer as a working electrode in DSSC. TiO2 layers were fabricated using a screen-printing method with a mesh size of T-49, T-55, and T-61. TiO2 layers were sintered at temperatures of 600°C and 650°C for 60 min. DSSC structure was composed of TiO2 as semiconductors, ruthenium complex as dyes, and carbon as counter electrodes. The morphology of TiO2 layer was observed by using Nikon E2 Digital Camera Microscopy. The efficiencies of DSSC were calculated from the I-V curves. The highest efficiency is 0.015% at TiO2 layer fabricated with screen type T-61 and at a sintering temperature of 650°C.

  19. A High-Throughput Screening System for Arabidopsis Transcription Factors and Its Application to Med25-Dependent Transcriptional Regulation

    Institute of Scientific and Technical Information of China (English)

    Bin Ou; Minami Matsui; Hong-Ya Gu; Li-Jia Qu; Kang-Quan Yin; Sai-Nan Liu; Yan Yang; Tren Gu; Jennifer Man Wing Hui; Li Zhang; Jin Miao; Youichi Kondou


    T The activities of transcription factors (TFs) require interactions with specific DNA sequences and other regulatory proteins. To detect such interactions in Arabidopsis, we developed a high-throughput screening system with a Gateway-compatible Gal4-AD-TF library of 1589 Arabidopsis TFs, which can be easily screened by mating-based yeast-one-hybrid (Y1H) and yeast-two-hybrid (Y2H) methods. The efficiency of the system was validated by examining two well-characterized TF-DNA and TF-protein interactions: the CHE-CCA1 promoter interaction by Y1H and NPR1-TGAs interactions by Y2H. We used this system to identify eight TFs that interact with a Mediator subunit, Med25, a key regulator in JA signaling. We identified five TFs that interacted with the GCC-box cis-element in the promoter of PDF1.2, a downstream gene of Med25. We found that three of these TFs, all from the AP2-EREBP family, interact directly both with Med25 and the GCC-box of PDF1.2, suggesting that Med25 regulates PDF1.2 expression through these three TFs.These results demonstrate that this high-throughput Y1H/Y2H screening system is an efficient tool for studying transcriptional regulation networks in Arabidopsis. This system will be available for other Arabidopsis researchers, and thus it provides a vital resource for the Arabidopsis community.

  20. Application of computer-extracted breast tissue texture features in predicting false-positive recalls from screening mammography (United States)

    Ray, Shonket; Choi, Jae Y.; Keller, Brad M.; Chen, Jinbo; Conant, Emily F.; Kontos, Despina


    Mammographic texture features have been shown to have value in breast cancer risk assessment. Previous models have also been developed that use computer-extracted mammographic features of breast tissue complexity to predict the risk of false-positive (FP) recall from breast cancer screening with digital mammography. This work details a novel locallyadaptive parenchymal texture analysis algorithm that identifies and extracts mammographic features of local parenchymal tissue complexity potentially relevant for false-positive biopsy prediction. This algorithm has two important aspects: (1) the adaptive nature of automatically determining an optimal number of region-of-interests (ROIs) in the image and each ROI's corresponding size based on the parenchymal tissue distribution over the whole breast region and (2) characterizing both the local and global mammographic appearances of the parenchymal tissue that could provide more discriminative information for FP biopsy risk prediction. Preliminary results show that this locallyadaptive texture analysis algorithm, in conjunction with logistic regression, can predict the likelihood of false-positive biopsy with an ROC performance value of AUC=0.92 (pclinical implications of using prediction models incorporating these texture features may include the future development of better tools and guidelines regarding personalized breast cancer screening recommendations. Further studies are warranted to prospectively validate our findings in larger screening populations and evaluate their clinical utility.

  1. 论LED屏在舞蹈编导中的创新应用%On the innovative application of LED screen in the choreography

    Institute of Scientific and Technical Information of China (English)



    LED electronic screen as an information display media in technology era, with its incomparable advantages over traditional choreography and stage effect increasingly applied to modern dance choreographer. Firstly, related to the content of LED screen are summarized, followed by analysis of the coordinated application of LED and other elements, finally proposes the problems and its evasion mode of LED screen for choreography, aims to study and analyze the LED screen can be better used in modern dance choreographer, serve for the more perfect interpretation of dance art, and the better reflect of the connotation.%LED电子屏幕作为高科技时代的一种信息显示媒体,正以其传统舞美无法比拟的优势和舞台效果越来越多地应用到现代舞蹈的编导之中。本文首先对LED屏相关内容进行概述,其次分析了LED与其他元素的协调应用,最后提出LED屏应用于舞蹈编导中存在的问题及其规避方式,旨在通过研究和分析使LED屏能够更好地应用于现代舞蹈编导,服务于舞蹈艺术的更完美诠释和舞蹈内涵的更好体现。

  2. Thermo-responsive cell culture carriers based on poly(vinyl methyl ether)—the effect of biomolecular ligands to balance cell adhesion and stimulated detachment (United States)

    Teichmann, Juliane; Nitschke, Mirko; Pette, Dagmar; Valtink, Monika; Gramm, Stefan; Härtel, Frauke V.; Noll, Thomas; Funk, Richard H. W.; Engelmann, Katrin; Werner, Carsten


    Two established material systems for thermally stimulated detachment of adherent cells were combined in a cross-linked polymer blend to merge favorable properties. Through this approach poly(N-isopropylacrylamide) (PNiPAAm) with its superior switching characteristic was paired with a poly(vinyl methyl ether)-based composition that allows adjusting physico-chemical and biomolecular properties in a wide range. Beyond pure PNiPAAm, the proposed thermo-responsive coating provides thickness, stiffness and swelling behavior, as well as an apposite density of reactive sites for biomolecular functionalization, as effective tuning parameters to meet specific requirements of a particular cell type regarding initial adhesion and ease of detachment. To illustrate the strength of this approach, the novel cell culture carrier was applied to generate transplantable sheets of human corneal endothelial cells (HCEC). Sheets were grown, detached, and transferred onto planar targets. Cell morphology, viability and functionality were analyzed by immunocytochemistry and determination of transepithelial electrical resistance (TEER) before and after sheet detachment and transfer. HCEC layers showed regular morphology with appropriate TEER. Cells were positive for function-associated marker proteins ZO-1, Na+/K+-ATPase, and paxillin, and extracellular matrix proteins fibronectin, laminin and collagen type IV before and after transfer. Sheet detachment and transfer did not impair cell viability. Subsequently, a potential application in ophthalmology was demonstrated by transplantation onto de-endothelialized porcine corneas in vitro. The novel thermo-responsive cell culture carrier facilitates the generation and transfer of functional HCEC sheets. This paves the way to generate tissue engineered human corneal endothelium as an alternative transplant source for endothelial keratoplasty.

  3. Biomolecular characterization of wild sicilian oregano: phytochemical screening of essential oils and extracts, and evaluation of their antioxidant activities. (United States)

    Tuttolomondo, Teresa; La Bella, Salvatore; Licata, Mario; Virga, Giuseppe; Leto, Claudio; Saija, Antonella; Trombetta, Domenico; Tomaino, Antonio; Speciale, Antonio; Napoli, Edoardo M; Siracusa, Laura; Pasquale, Andrea; Curcuruto, Giusy; Ruberto, Giuseppe


    An extensive survey of wild Sicilian oregano was made. A total of 57 samples were collected from various sites, followed by taxonomic characterization from an agronomic perspective. Based on morphological and production characteristics obtained from the 57 samples, cluster analysis was used to divide the samples into homogeneous groups, to identify the best biotypes. All samples were analyzed for their phytochemical content, applying a cascade-extraction protocol and hydrodistillation, to obtain the non volatile components and the essential oils, respectively. The extracts contained thirteen polyphenol derivatives, i.e., four flavanones, seven flavones, and two organic acids. Their qualitative and quantitative characterization was carried out by LC/MS analyses. The essential oils were characterized using a combination of GC-FID and GC/MS analyses; a total of 81 components were identified. The major components of the oils were thymol, p-cymene, and γ-terpinene. Cluster analysis was carried out on both phytochemical profiles and resulted in the division of the oregano samples into different chemical groups. The antioxidant activity of the essential oils and extracts was investigated by the Folin-Ciocalteau (FC) colorimetric assay, by UV radiation-induced peroxidation in liposomal membranes (UV-IP test), and by determining the O(2)(∙-)-scavenging activity.

  4. Quadruple screen test (United States)

    Quad screen; Multiple marker screening; AFP plus; Triple screen test; AFP maternal; MSAFP; 4-marker screen; Down syndrome - quadruple; Trisomy 21 - quadruple; Turner syndrome - quadruple; Spina bifida - ...

  5. From the application of antibiotics to antibiotic residues in liquid manures and digestates: A screening study in one European center of conventional pig husbandry. (United States)

    Widyasari-Mehta, Arum; Hartung, Susen; Kreuzig, Robert


    In conventional pig husbandry, antibiotics are frequently applied. Together with excreta, antibiotic residues enter liquid manures finally used as organic soil fertilizers or input materials for biogas plants. Therefore, this first screening study was performed to survey the application patterns of antibiotics from fall 2011 until spring 2013. Manures and digestates were then analyzed for selected antibiotic residues from spring 2012 to 2013. The data analysis of veterinary drug application documents revealed the use of 34 different antibiotics belonging to 11 substance classes at 21 farms under study. Antibiotics, particularly tetracyclines, frequently administered to larger pig groups were detected in manure samples up to higher mg kg(-1) dry weight (DW) concentrations. Antibiotic residues in digestates, furthermore, show that a full removal capacity cannot be guaranteed through the anaerobic digestion process in biogas plants.

  6. Imaging and chemical surface analysis of biomolecular functionalization of monolithically integrated on silicon Mach-Zehnder interferometric immunosensors

    Energy Technology Data Exchange (ETDEWEB)

    Gajos, Katarzyna, E-mail: [M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków (Poland); Angelopoulou, Michailia; Petrou, Panagiota [Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR Demokritos, P. Grigoriou & Neapoleos St, Aghia Paraksevi 15310, Athens (Greece); Awsiuk, Kamil [M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków (Poland); Kakabakos, Sotirios [Institute of Nuclear & Radiological Sciences & Technology, Energy & Safety, NCSR Demokritos, P. Grigoriou & Neapoleos St, Aghia Paraksevi 15310, Athens (Greece); Haasnoot, Willem [RIKILT Wageningen UR, Akkermaalsbos 2, 6708 WB Wageningen (Netherlands); Bernasik, Andrzej [Faculty of Physics and Applied Computer Science, AGH University of Science and Technology, Mickiewicza 30, 30-059 Kraków (Poland); Academic Centre for Materials and Nanotechnology, AGH University of Science and Technology, Mickiewicza 30, 30-059 Kraków (Poland); Rysz, Jakub [M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków (Poland); Marzec, Mateusz M. [Academic Centre for Materials and Nanotechnology, AGH University of Science and Technology, Mickiewicza 30, 30-059 Kraków (Poland); Misiakos, Konstantinos; Raptis, Ioannis [Department of Microelectronics, Institute of Nanoscience and Nanotechnology, NCSR Demokritos, P. Grigoriou & Neapoleos St, Aghia Paraksevi 15310, Athens (Greece); Budkowski, Andrzej [M. Smoluchowski Institute of Physics, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków (Poland)


    Highlights: • Optimization of probe immobilization with robotic spotter printing overlapping spots. • In-situ inspection of microstructured surfaces of biosensors integrated on silicon. • Imaging and chemical analysis of immobilization, surface blocking and immunoreaction. • Insight with molecular discrimination into step-by-step sensor surface modifications. • Optimized biofunctionalization improves sensor sensitivity and response repeatability. - Abstract: Time-of-flight secondary ion mass spectrometry (imaging, micro-analysis) has been employed to evaluate biofunctionalization of the sensing arm areas of Mach-Zehnder interferometers monolithically integrated on silicon chips for the immunochemical (competitive) detection of bovine κ-casein in goat milk. Biosensor surfaces are examined after: modification with (3-aminopropyl)triethoxysilane, application of multiple overlapping spots of κ-casein solutions, blocking with 100-times diluted goat milk, and reaction with monoclonal mouse anti-κ-casein antibodies in blocking solution. The areas spotted with κ-casein solutions of different concentrations are examined and optimum concentration providing homogeneous coverage is determined. Coverage of biosensor surfaces with biomolecules after each of the sequential steps employed in immunodetection is also evaluated with TOF-SIMS, supplemented by Atomic force microscopy and X-ray photoelectron spectroscopy. Uniform molecular distributions are observed on the sensing arm areas after spotting with optimum κ-casein concentration, blocking and immunoreaction. The corresponding biomolecular compositions are determined with a Principal Component Analysis that distinguished between protein amino acids and milk glycerides, as well as between amino acids characteristic for Mabs and κ-casein, respectively. Use of the optimum conditions (κ-casein concentration) for functionalization of chips with arrays of ten Mach-Zehnder interferometers provided on-chips assays

  7. "Peak tracking chip" for label-free optical detection of bio-molecular interaction and bulk sensing. (United States)

    Bougot-Robin, Kristelle; Li, Shunbo; Zhang, Yinghua; Hsing, I-Ming; Benisty, Henri; Wen, Weijia


    A novel imaging method for bulk refractive index sensing or label-free bio-molecular interaction sensing is presented. This method is based on specially designed "Peak tracking chip" (PTC) involving "tracks" of adjacent resonant waveguide gratings (RWG) "micropads" with slowly evolving resonance position. Using a simple camera the spatial information robustly retrieves the diffraction efficiency, which in turn transduces either the refractive index of the liquids on the tracks or the effective thickness of an immobilized biological layer. Our intrinsically multiplex chip combines tunability and versatility advantages of dielectric guided wave biochips without the need of costly hyperspectral instrumentation. The current success of surface plasmon imaging techniques suggests that our chip proposal could leverage an untapped potential to routinely extend such techniques in a convenient and sturdy optical configuration toward, for instance for large analytes detection. PTC design and fabrication are discussed with challenging process to control micropads properties by varying their period (step of 2 nm) or their duty cycle through the groove width (steps of 4 nm). Through monochromatic imaging of our PTC, we present experimental demonstration of bulk index sensing on the range [1.33-1.47] and of surface biomolecule detection of molecular weight 30 kDa in aqueous solution using different surface densities. A sensitivity of the order of 10(-5) RIU for bulk detection and a sensitivity of the order of ∼10 pg mm(-2) for label-free surface detection are expected, therefore opening a large range of application of our chip based imaging technique. Exploiting and chip design, we expect as well our chip to open new direction for multispectral studies through imaging.

  8. Development of Screen-Printed Texture-Barrier Paste for Single-Side Texturization of Interdigitated Back-Contact Silicon Solar Cell Applications

    Directory of Open Access Journals (Sweden)

    Chi-Cheng Chen


    Full Text Available Continuous cost reduction of silicon-based solar cells is needed to lower the process time and increase efficiency. To achieve lower costs, screen-printed texture-barrier (SPTB paste was first developed for single-side texturization (ST of the interdigitated back-contact (IBC for silicon-based solar cell applications. The SPTB paste was screen-printed on silicon substrates. The SPTB paste was synthesized from intermixed silicate glass (75 wt %, a resin binder (ethyl cellulose ethoce: 20 wt %, and a dispersing agent (fatty acid: 5 wt %. The silicate glass is a necessity for contact formation during firing. A resin binder and a dispersing agent determine the rheology of the SPTB paste. In this work, by modulating various parameters, including post SPTB firing, alkali texturing, and removal of the SPTB, the ST of IBC silicon solar cells was achieved. Since the advantages of the SPTB paste include low toxicity and prompt formation of the texture-barrier, SPTB is potentially suited for simple fabrication at low-cost for solar cell applications. The cost of the SPTB is around $100/kg which is lower than the SiH4/NH3 gas ambient used in plasma-enhanced chemical vapor deposition (PECVD. Thus, the expensive Si3N4 film deposited by PECVD using SiH4 and NH3 gas ambient for silicon solar cells can be replaced by this SPTB.

  9. Hypertension screening (United States)

    Foulke, J. M.


    An attempt was made to measure the response to an announcement of hypertension screening at the Goddard Space Center, to compare the results to those of previous statistics. Education and patient awareness of the problem were stressed.

  10. Airport Screening (United States)

    ... cannot become radioactive from this procedure. However, some photographic film may need to be hand-screened because ... level. An American National Standards Institute/Health Physics Society industry standard states that the maxi- mum allowable ...

  11. Toxicology screen (United States)

    Toxicology screening is most often done using a blood or urine sample. However, it may be done soon after the person swallowed the medication, using stomach contents taken through gastric lavage (stomach pumping) or after vomiting.

  12. Applicability of DNA pools on 500 K SNP microarrays for cost-effective initial screens in genomewide association studies

    Directory of Open Access Journals (Sweden)

    Schalkwyk Leonard C


    Full Text Available Abstract Background Genetic influences underpinning complex traits are thought to involve multiple quantitative trait loci (QTLs of small effect size. Detection of such QTL associations requires systematic screening of large numbers of DNA markers within large sample populations. Using pooled DNA on SNP microarrays to screen for allelic frequency differences between groups such as cases and controls (called SNP Microarray and Pooling, or SNP-MaP has been validated as an efficient solution on both 10 k and 100 k platforms. We demonstrate that this approach can be effectively applied to the truly genomewide Affymetrix GeneChip® Mapping 500 K Array. Results In comparisons between five independent DNA pools (N ~200 per pool on separate Affymetrix GeneChip® Mapping 500 K Array sets, we show that, for SNPs with minor allele frequencies > 0.05, the reliability of the rank order of estimated allele frequencies, assessed as the average correlation between allele frequency estimates across the DNA pools, was 0.948 (average mean difference across the five pools = 0.069. Similarly, validity of the SNP-MaP approach was demonstrated by a rank-order correlation of 0.937 (average mean difference = 0.095 between the average DNA pool allele frequency estimates and the allele frequencies of an independent (CEPH sample of 60 unrelated individually genotyped subjects. Conclusion We conclude that SNP-MaP can be extended for use on the Affymetrix GeneChip® Mapping 500 K Array, providing a cost-effective, reliable and valid initial screen of 500 K SNP microarrays in genomewide association scans.

  13. An unbiased method to build benchmarking sets for ligand-based virtual screening and its application to GPCRs. (United States)

    Xia, Jie; Jin, Hongwei; Liu, Zhenming; Zhang, Liangren; Wang, Xiang Simon


    Benchmarking data sets have become common in recent years for the purpose of virtual screening, though the main focus had been placed on the structure-based virtual screening (SBVS) approaches. Due to the lack of crystal structures, there is great need for unbiased benchmarking sets to evaluate various ligand-based virtual screening (LBVS) methods for important drug targets such as G protein-coupled receptors (GPCRs). To date these ready-to-apply data sets for LBVS are fairly limited, and the direct usage of benchmarking sets designed for SBVS could bring the biases to the evaluation of LBVS. Herein, we propose an unbiased method to build benchmarking sets for LBVS and validate it on a multitude of GPCRs targets. To be more specific, our methods can (1) ensure chemical diversity of ligands, (2) maintain the physicochemical similarity between ligands and decoys, (3) make the decoys dissimilar in chemical topology to all ligands to avoid false negatives, and (4) maximize spatial random distribution of ligands and decoys. We evaluated the quality of our Unbiased Ligand Set (ULS) and Unbiased Decoy Set (UDS) using three common LBVS approaches, with Leave-One-Out (LOO) Cross-Validation (CV) and a metric of average AUC of the ROC curves. Our method has greatly reduced the "artificial enrichment" and "analogue bias" of a published GPCRs benchmarking set, i.e., GPCR Ligand Library (GLL)/GPCR Decoy Database (GDD). In addition, we addressed an important issue about the ratio of decoys per ligand and found that for a range of 30 to 100 it does not affect the quality of the benchmarking set, so we kept the original ratio of 39 from the GLL/GDD.

  14. [Measurement of serum PSA by DELFIA PSA kit and its application for mass screening. The Gunma Urological Oncology Study Group]. (United States)

    Imai, K; Watanabe, K; Higashi, H; Shinya, H; Okamura, K; Matsuo, Y; Yazima, H; Takezawa, Y; Yamanaka, H


    The significance of prostate specific antigen (PSA) measured by DELFIA PSA kit in the 1,177 serum samples examined by mass screening for prostate cancer was evaluated. All subjects were examined by questionnaire, digital rectal examination (DRE) and prostatic acid phosphatase (PAP) and the subjects in whom prostate cancer was suspected from abnormal DRE and/or elevated PAP were recommended to receive the secondary screening for the presence of prostate cancer. All serum specimens used for this study were kept in our serum bank. The cut-off value was investigated between non-cancer subjects (diagnosed as normal, voiding disturbance or BPH) and prostate cancer patients. When the cut-off value was 2.89 ng/ml, the sensitivity, specificity and accuracy as prostate marker was 80.6%, 90.0% and 89.4%, respectively. Therefore, the cut-off value was determined as 3.0 ng/ml. The significance of PSA was retrospectively evaluated compared to PAP in the subjects examined by our mass screening. Twenty eight of the 39 palpable prostate cancers which could not be detected from the PAP level were detected from the PSA level, namely the sensitivity of the detection using the PSA level is more excellent than that using PAP. However, the false negative rate obtained using PSA was high (30.3%) in the patients with stage B disease. The relationship among serum PSA concentration, prostate size estimated by DRE and age was investigated. PSA was increased with age and prostate size. This estimation should be confirmed by using an ultrasonography because the prostate size obtained by DRE is inaccurate as compared with that obtained by ultrasonography.

  15. A Bayesian Approach to Calibrating High-Throughput Virtual Screening Results and Application to Organic Photovoltaic Materials

    CERN Document Server

    Pyzer-Knapp, Edward O; Aspuru-Guzik, Alan


    A novel approach for calibrating quantum-chemical properties determined as part of a high-throughput virtual screen to experimental analogs is presented. Information on the molecular graph is extracted through the use of extended connectivity fingerprints, and exploited using a Gaussian process to calibrate both electronic properties such as frontier orbital energies, and optical gaps and device properties such as short circuit current density, open circuit voltage and power conversion efficiency. The Bayesian nature of this process affords a value for uncertainty in addition to each calibrated value. This allows the researcher to gain intuition about the model as well as the ability to respect its bounds.

  16. Screening of the effective cellulose-degradable strain and its application in the production of cellulose bioethanol

    Institute of Scientific and Technical Information of China (English)

    Peng-fei Gao; Dai-di Fan; Pei Ma; Yan-e Luo; Xiao-xuan Ma; Chen-hui Zhu; Jun-feng Hui


    Strains from the cellulose-containing environment were collected. Primary screening(by filter-paper Hutchison solid culture medium and sodium carboxymethylcellulose solid culture medium) and reelection(by filter-paper inorganic salt culture medium and sodium carboxymethylcellulosc Congo red coltnre medium) indicated that five strains obtained were best suited for high performance cellulose degradation. Determination of sodium carboxymethylcellulose activity(CMCA) and filter paper activity(FPA) was accomplished for each of the five. The strongest of the five in CMCA and FPA was applied to the production of cellulose bioethanol by separate hydrolysis and fermentation(SHF) and simultaneous saccharification and fermentation(SSF) respectively.

  17. Investigation of the Human Disease Osteogenesis Imperfecta: A Research-Based Introduction to Concepts and Skills in Biomolecular Analysis (United States)

    Mate, Karen; Sim, Alistair; Weidenhofer, Judith; Milward, Liz; Scott, Judith


    A blended approach encompassing problem-based learning (PBL) and structured inquiry was used in this laboratory exercise based on the congenital disease Osteogenesis imperfecta (OI), to introduce commonly used techniques in biomolecular analysis within a clinical context. During a series of PBL sessions students were presented with several…

  18. Biochemical and biomolecular aspects of oxidative stress due to acute and severe hypoxia in human muscle tissue. (United States)

    Corbucci, G G; Sessego, R; Velluti, C; Salvi, M


    Mitochondrial oxidative stress was investigated in severe and acute hypoxia and in reperfusion applied to human muscle tissues. The biochemical and biomolecular relationship between the response of the respiratory-chain enzymic complexes and the metabolism of specific hypoxia stress proteins (HSP) suggest an adaptive mechanism which antagonizes the oxidative damage due to acute and severe tissue hypoxia.

  19. Screening of point charge impurities in highly anisotropic metals: application to mu+-spin relaxation in underdoped cuprate superconductors. (United States)

    Shekhter, Arkady; Shu, Lei; Aji, Vivek; MacLaughlin, D E; Varma, C M


    We calculate the screening charge density distribution due to a point charge, such as that of a positive muon (mu+), placed between the planes of a highly anisotropic layered metal. In underdoped hole cuprates the screening charge converts the charge density in the metallic-plane unit cells in the vicinity of the mu+ to nearly its value in the insulating state. The current-loop-ordered state observed by polarized neutron diffraction then vanishes in such cells, and also in nearby cells over a distance of order the intrinsic correlation length of the loop-ordered state. This strongly suppresses the magnetic field at the mu+ site. We estimate this suppressed field in underdoped YBa2Cu3O6+x and La2-xSrxCuO4, and find consistency with the observed approximately 0.2 G field in the former case and the observed upper bound of approximately 0.2 G in the latter case. This resolves the controversy between the neutron diffraction and mu-spin relaxation experiments.

  20. HCC screening; HCC-Screening

    Energy Technology Data Exchange (ETDEWEB)

    Albrecht, T. [Charite-Unversitaetsmedizin,Freie Universitaet und Humboldt-Universitaet zu Berlin, Klinik und Hochschulambulanz fuer Radiologie und Nuklearmedizin,Campus Benjamin Franklin, Berlin (Germany)


    Hepatocellular carcinoma (HCC) is one of the most frequently diagnosed tumour diseases throughout the world. In the vast majority of cases those affected are high-risk patients with chronic viral hepatitis and/or liver cirrhosis, which means there is a clearly identifiable target group for HCC screening. With resection, transplantation, and interventional procedures for local ablation, following early diagnosis curative treatment options are available with which 5-year survival rates of over 60% can be reached. Such early diagnosis is a reality only in a minority of patients, however, and in the majority of cases the disease is already in an advanced stage at diagnosis. One of the objects of HCC screening is diagnosis in an early stage when curative treatment is still possible. Precisely this is achieved by screening, so that the proportion of patients treated with curative intent is decisively higher. There is not yet any clear evidence as to whether this leads to a lowering of the mortality of HCC. As lower mortality is the decisive indicator of success for a screening programme the benefit of HCC screening has so far been neither documented nor refuted. Nonetheless, in large regions of the world it is the practice for high-risk patients to undergo HCC screening in the form of twice-yearly ultrasound examination and determination of AFP. (orig.) [German] Das hepatozellulaere Karzinom (HCC) ist eine der weltweit haeufigsten Tumorerkrankungen. Es tritt in der grossen Mehrzahl der Faelle bei Hochrisikopatienten mit chronischer Virushepatitis bzw. Leberzirrhose auf, woraus sich eine klar identifizierbare Zielgruppe fuer das HCC-Screening ergibt. Mit der Resektion, der Transplantation und interventionellen lokal ablativen Verfahren stehen bei rechtzeitiger Diagnosestellung kurative Therapieoptionen zur Verfuegung, die 5-Jahres-Ueberlebensraten von >60% erreichen. Diese rechtzeitige Diagnosestellung erfolgt jedoch nur bei einer Minderzahl der Patienten, waehrend die

  1. Discovery of secondary metabolites in an extractive liquid-surface immobilization system and its application to high-throughput interfacial screening of antibiotic-producing fungi. (United States)

    Oda, Shinobu; Kameda, Arisa; Okanan, Masanori; Sakakibara, Yusuke; Ohashi, Shinichi


    An extractive liquid-surface immobilization (Ext-LSI) system, which consists of a hydrophobic organic solvent (an upper phase), a fungal cell-ballooned microsphere layer (a middle phase) and a liquid medium (a lower phase), is a unique interfacial cultivation system for fungi. The fungal cells growing at the interface between the organic and aqueous phases efficiently produce hydrophobic metabolites, which are continuously extracted into the organic phase, and/or hydrophilic metabolites that migrate into the aqueous phase without carbon catabolite repression and product and/or feed-back inhibitions. Application of the system to fermentation of Penicillium multicolor IAM 7153 and Trichoderma atroviride AG2755-5NM398 afforded remarkably different profiles of secondary metabolites in the organic phase compared with those in an aqueous phase in traditional submerged cultivation (SmC). Various hydrophobic metabolites exhibiting unique UV-visible spectra were accumulated into the organic phase. The system was applied to a novel interfacial screening system of antibiotic-producing fungi. Compared with the SmC, the interfacial cultivation system exhibited some interesting and important advantages, such as the higher accumulation of hydrophobic secondary metabolites, the lack of requirement for shaking and troublesome solvent extraction, and the small scale of the vessels (medium, 5 ml; dimethylsilicone oil, 1 ml), as well as the significantly different metabolite profiles. The interfacial screening system yielded a high incidence of antimicrobial activity, with 21.9% of the fungi tested exhibiting antifungal activity against Pichia anomala NBRC 10213. This novel interfacial high-throughput screening approach has the potential to discover new biologically active secondary metabolites even from strains previously found to be unproductive.

  2. Resolution-Adapted All-Atomic and Coarse-Grained Model for Biomolecular Simulations. (United States)

    Shen, Lin; Hu, Hao


    We develop here an adaptive multiresolution method for the simulation of complex heterogeneous systems such as the protein molecules. The target molecular system is described with the atomistic structure while maintaining concurrently a mapping to the coarse-grained models. The theoretical model, or force field, used to describe the interactions between two sites is automatically adjusted in the simulation processes according to the interaction distance/strength. Therefore, all-atomic, coarse-grained, or mixed all-atomic and coarse-grained models would be used together to describe the interactions between a group of atoms and its surroundings. Because the choice of theory is made on the force field level while the sampling is always carried out in the atomic space, the new adaptive method preserves naturally the atomic structure and thermodynamic properties of the entire system throughout the simulation processes. The new method will be very useful in many biomolecular simulations where atomistic details are critically needed.

  3. Biomolecular papain thin films grown by matrix assisted and conventional pulsed laser deposition: A comparative study (United States)

    György, E.; Pérez del Pino, A.; Sauthier, G.; Figueras, A.


    Biomolecular papain thin films were grown both by matrix assisted pulsed laser evaporation (MAPLE) and conventional pulsed laser deposition (PLD) techniques with the aid of an UV KrF∗ (λ =248 nm, τFWHM≅20 ns) excimer laser source. For the MAPLE experiments the targets submitted to laser radiation consisted on frozen composites obtained by dissolving the biomaterial powder in distilled water at 10 wt % concentration. Conventional pressed biomaterial powder targets were used in the PLD experiments. The surface morphology of the obtained thin films was studied by atomic force microscopy and their structure and composition were investigated by Fourier transform infrared spectroscopy. The possible physical mechanisms implied in the ablation processes of the two techniques, under comparable experimental conditions were identified. The results showed that the growth mode, surface morphology as well as structure of the deposited biomaterial thin films are determined both by the incident laser fluence value as well as target preparation procedure.

  4. Biomolecular Electrostatics Simulation by an FMM-based BEM on 512 GPUs

    CERN Document Server

    Yokota, Rio; Bardhan, Jaydeep P; Knepley, Matthew G; Barba, L A


    We present simulations of biomolecular electrostatics at a scale not reached before, thanks to both algorithmic and hardware acceleration. The algorithmic acceleration is achieved with the fast multipole method (FMM) in conjunction with a boundary element method (BEM) formulation of the continuum electrostatic model. The hardware acceleration is achieved through graphics processors, GPUs. We demonstrate the power of our algorithms and software for the calculation of the electrostatic interactions between biological molecules in solution. Computational experiments are presented simulating the electrostatics of protein--drug binding and several multi-million atom systems consisting of hundreds to thousands of copies of the problems, which models over 20 million atoms and has more than six billion unknowns, one iteration step requires only a few minutes on 512 GPU nodes. We achieved a sustained performance of 34.6TFlops for the entire BEM calculation. We are currently adapting our solver to model the linearized ...

  5. Towards local electromechanical probing of cellular and biomolecular systems in a liquid environment

    Energy Technology Data Exchange (ETDEWEB)

    Kalinin, Sergei V [Materials Sciences and Technology Division, Oak Ridge National Laboratory, Oak Ridge, TN 37931 (United States); Rodriguez, Brian J [Materials Sciences and Technology Division, Oak Ridge National Laboratory, Oak Ridge, TN 37931 (United States); Jesse, Stephen [Materials Sciences and Technology Division, Oak Ridge National Laboratory, Oak Ridge, TN 37931 (United States); Seal, Katyayani [Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, TN 37931 (United States); Proksch, Roger [Asylum Research, Santa Barbara, CA 93117 (United States); Hohlbauch, Sophia [Asylum Research, Santa Barbara, CA 93117 (United States); Revenko, Irene [Asylum Research, Santa Barbara, CA 93117 (United States); Thompson, Gary Lee [Department of Bioengineering, Clemson University, Clemson, SC 29634 (United States); Vertegel, Alexey A [Department of Bioengineering, Clemson University, Clemson, SC 29634 (United States)


    Electromechanical coupling is ubiquitous in biological systems, with examples ranging from simple piezoelectricity in calcified and connective tissues to voltage-gated ion channels, energy storage in mitochondria, and electromechanical activity in cardiac myocytes and outer hair cell stereocilia. Piezoresponse force microscopy (PFM) originally emerged as a technique to study electromechanical phenomena in ferroelectric materials, and in recent years has been employed to study a broad range of non-ferroelectric polar materials, including piezoelectric biomaterials. At the same time, the technique has been extended from ambient to liquid imaging on model ferroelectric systems. Here, we present results on local electromechanical probing of several model cellular and biomolecular systems, including insulin and lysozyme amyloid fibrils, breast adenocarcinoma cells, and bacteriorhodopsin in a liquid environment. The specific features of PFM operation in liquid are delineated and bottlenecks on the route towards nanometre-resolution electromechanical imaging of biological systems are identified.

  6. Biochemical Filter with Sigmoidal Response: Increasing the Complexity of Biomolecular Logic

    CERN Document Server

    Privman, Vladimir; Arugula, Mary A; Melnikov, Dmitriy; Bocharova, Vera; Katz, Evgeny


    The first realization of a designed, rather than natural, biochemical filter process is reported and analyzed as a promising network component for increasing the complexity of biomolecular logic systems. Key challenge in biochemical logic research has been achieving scalability for complex network designs. Various logic gates have been realized, but a "toolbox" of analog elements for interconnectivity and signal processing has remained elusive. Filters are important as network elements that allow control of noise in signal transmission and conversion. We report a versatile biochemical filtering mechanism designed to have sigmoidal response in combination with signal-conversion process. Horseradish peroxidase-catalyzed oxidation of chromogenic electron donor by hydrogen peroxide, was altered by adding ascorbate, allowing to selectively suppress the output signal, modifying the response from convex to sigmoidal. A kinetic model was developed for evaluation of the quality of filtering. The results offer improved...

  7. A Review of Salam Phase Transition in Protein Amino Acids Implication for Biomolecular Homochirality

    CERN Document Server

    Bai, F; Bai, Fan; Wang, Wenqing


    The origin of chirality, closely related to the evolution of life on the earth, has long been debated. In 1991, Abdus Salam suggested a novel approach to achieve biomolecular homochirality by a phase transition. In his subsequent publication, he predicted that this phase transition could eventually change D-amino acids to L-amino acids as C -H bond would break and H atom became a superconductive atom. Since many experiments denied the configuration change in amino acids, Salam hypothesis aroused suspicion. This paper is aimed to provide direct experimental evidence of a phase transition in alanine, valine single crystals but deny the configuration change of D- to L- enantiomers. New views on Salam phase transition are presented to revalidate its great importance in the origin of homochirality.

  8. Effect of temperature and magnetic field on the photocurrent response of biomolecular bulk-hetero junction (United States)

    Tajima, Hiroyuki; Sekiguchi, Yusuke; Matsuda, Masaki


    The photocurrent responses were investigated for the biomolecular bulk-hetero junction of chlorophyll α (Chl-α) and 1-(3-methoxycarbonyl)-propyl-1-phenyl-1-phenyl-(6,6)C61 (PCBM) in the temperature range between 300 K and 1.5 K under the magnetic field up to 8 T. The chopped-light photocurrent decreases on lowering the temperature. Below 10 K, photocurrent decrease was observed under the applied magnetic field. Decay of the photocurrent observed at 10 K was ascribed to the formation of the charged trap under light irradiation. The magnetic field effect (MFE) observed in this device was found to be very similar to that observed in P3HT:PCBM bulk-hetero junction at low temperatures.

  9. Gold nanoshells with gain-assisted silica core for ultra-sensitive bio-molecular sensors (United States)

    Tao, Yifei; Guo, Zhongyi; Zhang, Anjun; Zhang, Jingran; Wang, Benyang; Qu, Shiliang


    A novel bio-molecular nanostructured sensor composed of Au spherical nanoshell and gain-assisted silica-core has been proposed and investigated theoretically, which shows a superior performance compared to the existing structured sensor. Using quasi-static approximation calculation, it is found that the scattering efficiency and the quality factor of SPR can be enhanced greatly by introducing proper amount of gain. The simulated results demonstrate that our designed Au spherical nanoshell and gain-assisted silica-core can obtain as high as 166.7 nm/RIU for the sensitivity of refractive index, and the sensors' figure of merit is enhanced 2000 times nearly compared to that of g=0, which indicates that the designed spherical core-shell sensors have the powerful ability to detect a subtle change in the concentration of its background medium.

  10. Human rhinovirus 3C protease: generation of pharmacophore models for peptidic and nonpeptidic inhibitors and their application in virtual screening. (United States)

    Steindl, Theodora; Laggner, Christian; Langer, Thierry


    Three-dimensional pharmacophore models for peptidic and small organic nonpeptidic inhibitors of the human rhinovirus 3C protease were generated in a structure-based as well as in a ligand-based approach, using the software package Catalyst. The inhibitors possess an electrophilic moiety, often a Michael acceptor function, which covalently binds to a cysteine in the active site of the enzyme. Since this process presents the key step for virus inactivation, the creation of a new function in Catalyst was required in order to include this decisive functionality into the pharmacophore models. In the present study we focus on this feature definition process because it presents an innovative strategy to expand the pharmacophore description ability of the Catalyst software to also include covalent bonds between ligand and binding site. The resulting hypotheses were then used for virtual screening of 3D databases in order to verify their quality and to search for structurally diverse, possible new lead substances.

  11. Topics on distance correlation, feature screening and lifetime expectancy with application to Beaver Dam eye study data (United States)

    Kong, Jing

    This thesis includes 4 pieces of work. In Chapter 1, we present the work with a method for examining mortality as it is seen to run in families, and lifestyle factors that are also seen to run in families, in a subpopulation of the Beaver Dam Eye Study that has died by 2011. We find significant distance correlations between death ages, lifestyle factors, and family relationships. Considering only sib pairs compared to unrelated persons, distance correlation between siblings and mortality is, not surprisingly, stronger than that between more distantly related family members and mortality. Chapter 2 introduces a feature screening procedure with the use of distance correlation and covariance. We demonstrate a property for distance covariance, which is incorporated in a novel feature screening procedure based on distance correlation as a stopping criterion. The approach is further implemented to two real examples, namely the famous small round blue cell tumors data and the Cancer Genome Atlas ovarian cancer data Chapter 3 pays attention to the right censored human longevity data and the estimation of lifetime expectancy. We propose a general framework of backward multiple imputation for estimating the conditional lifetime expectancy function and the variance of the estimator in the right censoring setting and prove the properties of the estimator. In addition, we apply the method to the Beaver Dam eye study data to study human longevity, where the expected human lifetime are modeled with smoothing spline ANOVA based on the covariates including baseline age, gender, lifestyle factors and disease variables. Chapter 4 compares two imputation methods for right censored data, namely the famous Buckley-James estimator and the backward imputation method proposed in Chapter 3 and shows that backward imputation method is less biased and more robust with heterogeneity.

  12. Application of ED-optimality to screening experiments for analgesic compounds in an experimental model of neuropathic pain. (United States)

    Taneja, A; Nyberg, J; de Lange, E C M; Danhof, M; Della Pasqua, O


    In spite of the evidence regarding high variability in the response to evoked pain, little attention has been paid to its impact on the screening of drugs for inflammatory and neuropathic pain. In this study, we explore the feasibility of introducing optimality concepts to experimental protocols, enabling estimation of parameter and model uncertainty. Pharmacokinetic (PK) and pharmacodynamic data from different experiments in rats were pooled and modelled using nonlinear mixed effects modelling. Pain data on gabapentin and placebo-treated animals were generated in the complete Freund's adjuvant model of neuropathic pain. A logistic regression model was applied to optimise sampling times and dose levels to be used in an experimental protocol. Drug potency (EC(50)) and interindividual variability (IIV) were considered the parameters of interest. Different experimental designs were tested and validated by SSE (stochastic simulation and estimation) taking into account relevant exposure ranges. The pharmacokinetics of gabapentin was described by a two-compartment PK model with first order absorption (CL = 0.159 l h(-1), V(2) = 0.118 l, V(3) = 0.253 l, Ka = 0.26 h(-1), Q = 1.22 l h(-1)). Drug potency (EC(50)) for the anti-allodynic effects was estimated to be 1400 ng ml(-1). Protocol optimisation improved bias and precision of the EC50 by 6 and 11.9. %, respectively, whilst IIV estimates showed improvement of 31.89 and 14.91 %, respectively. Our results show that variability in behavioural models of evoked pain response leads to uncertainty in drug potency estimates, with potential impact on the ranking of compounds during screening. As illustrated for gabapentin, ED-optimality concepts enable analysis of discrete data taking into account experimental constraints.

  13. Label-free cardiac contractility monitoring for drug screening applications based on compact high-speed lens-free imaging (United States)

    Pauwelyn, Thomas; Reumers, Veerle; Vanmeerbeeck, Geert; Stahl, Richard; Janssens, Stefan; Lagae, Liesbet; Braeken, Dries; Lambrechts, Andy


    Cardiotoxicity is the major cause of drug withdrawal from the market, despite rigorous toxicity testing during the drug development process. Existing safety screening techniques, some of which are based on simplified cellular assays, others on electrical (impedance) or optical (fluorescent microscopy) measurements, are either too limited in throughput or offer too poor predictability of toxicity to be applied on large numbers of compounds in the early stage of drug development. We present a compact optical system for direct (label-free) monitoring of fast cellular movements that enable low cost and high throughput drug screening. Our system is based on a high-speed lens-free in-line holographic microscope. When compared to a conventional microscope, the system can combine adequate imaging resolution (5.5 μm pixel pitch) with a large field-of-view (63.4 mm2) and high speed (170 fps) to capture physical cell motion in real-time. This combination enables registration of cardiac contractility parameters such as cell contraction frequency, total duration, and rate and duration of both contraction and relaxation. The system also quantifies conduction velocity, which is challenging in existing techniques. Additionally, to complement the imaging hardware we have developed image processing software that extracts all the contractility parameters directly from the raw interference images. The system was tested with varying concentration of the drug verapamil and at 100 nM, showed a decrease in: contraction frequency (-23.3% +/- 13%), total duration (-21% +/- 5%), contraction duration (-19% +/- 6%) and relaxation duration (-21% +/- 8%). Moreover, contraction displacement ceased at higher concentrations.

  14. Versatile single-molecule multi-color excitation and detection fluorescence setup for studying biomolecular dynamics

    KAUST Repository

    Sobhy, M. A.


    Single-molecule fluorescence imaging is at the forefront of tools applied to study biomolecular dynamics both in vitro and in vivo. The ability of the single-molecule fluorescence microscope to conduct simultaneous multi-color excitation and detection is a key experimental feature that is under continuous development. In this paper, we describe in detail the design and the construction of a sophisticated and versatile multi-color excitation and emission fluorescence instrument for studying biomolecular dynamics at the single-molecule level. The setup is novel, economical and compact, where two inverted microscopes share a laser combiner module with six individual laser sources that extend from 400 to 640 nm. Nonetheless, each microscope can independently and in a flexible manner select the combinations, sequences, and intensities of the excitation wavelengths. This high flexibility is achieved by the replacement of conventional mechanical shutters with acousto-optic tunable filter (AOTF). The use of AOTF provides major advancement by controlling the intensities, duration, and selection of up to eight different wavelengths with microsecond alternation time in a transparent and easy manner for the end user. To our knowledge this is the first time AOTF is applied to wide-field total internal reflection fluorescence (TIRF) microscopy even though it has been commonly used in multi-wavelength confocal microscopy. The laser outputs from the combiner module are coupled to the microscopes by two sets of four single-mode optic fibers in order to allow for the optimization of the TIRF angle for each wavelength independently. The emission is split into two or four spectral channels to allow for the simultaneous detection of up to four different fluorophores of wide selection and using many possible excitation and photoactivation schemes. We demonstrate the performance of this new setup by conducting two-color alternating excitation single-molecule fluorescence resonance energy

  15. Differential geometry-based solvation and electrolyte transport models for biomolecular modeling: a review

    Energy Technology Data Exchange (ETDEWEB)

    Wei, Guowei; Baker, Nathan A.


    This chapter reviews the differential geometry-based solvation and electrolyte transport for biomolecular solvation that have been developed over the past decade. A key component of these methods is the differential geometry of surfaces theory, as applied to the solvent-solute boundary. In these approaches, the solvent-solute boundary is determined by a variational principle that determines the major physical observables of interest, for example, biomolecular surface area, enclosed volume, electrostatic potential, ion density, electron density, etc. Recently, differential geometry theory has been used to define the surfaces that separate the microscopic (solute) domains for biomolecules from the macroscopic (solvent) domains. In these approaches, the microscopic domains are modeled with atomistic or quantum mechanical descriptions, while continuum mechanics models (including fluid mechanics, elastic mechanics, and continuum electrostatics) are applied to the macroscopic domains. This multiphysics description is integrated through an energy functional formalism and the resulting Euler-Lagrange equation is employed to derive a variety of governing partial differential equations for different solvation and transport processes; e.g., the Laplace-Beltrami equation for the solvent-solute interface, Poisson or Poisson-Boltzmann equations for electrostatic potentials, the Nernst-Planck equation for ion densities, and the Kohn-Sham equation for solute electron density. Extensive validation of these models has been carried out over hundreds of molecules, including proteins and ion channels, and the experimental data have been compared in terms of solvation energies, voltage-current curves, and density distributions. We also propose a new quantum model for electrolyte transport.

  16. Principles of successful cancer screening. (United States)

    Smith, R A


    Screening for cancer is the application of various tests to apparently healthy individuals in order to identify who among them has occult disease, which may be either invasive disease or a precursor lesion. For any given cancer site, the potential of screening to reduce morbidity and mortality is based on well-defined criteria for the evaluation of screening effectiveness and on acceptable performance to be realized in the average community setting. Screening programs are most successful when they are organized into a system that leads to high rates of participation, high quality, and constant surveillance and evaluation. If the elements that contribute to a successful screening program are not well organized and integrated, then the fullest potential of screening will not be realized.

  17. Clinical Application of Screening for GJB2 Mutations before Cochlear Implantation in a Heterogeneous Population with High Rate of Autosomal Recessive Nonsyndromic Hearing Loss

    Directory of Open Access Journals (Sweden)

    Masoud Motasaddi Zarandy


    Full Text Available Clinical application of mutation screening and its effect on the outcome of cochlear implantation is widely debated. We investigated the effect of mutations in GJB2 gene on the outcome of cochlear implantation in a population with a high rate of consanguineous marriage and autosomal recessive nonsyndromic hearing loss. Two hundred and one children with profound prelingual sensorineural hearing loss were included. Forty-six patients had 35delG in GJB2. Speech awareness thresholds (SATs and speech recognition thresholds (SRTs improved following implantation, but there was no difference in performance between patients with GJB2-related deafness versus control (all >0.10. Both groups had produced their first comprehensible words within the same period of time following implantation (2.27 months in GJB2-related deaf versus 2.62 months in controls, =0.22. Although our findings demonstrate the need to uncover unidentified genetic causes of hereditary deafness, they do not support the current policy for genetic screening before cochlear implantation, nor prove a prognostic value.

  18. New soluble-formazan assay for HIV-1 cytopathic effects: application to high-flux screening of synthetic and natural products for AIDS-antiviral activity. (United States)

    Weislow, O S; Kiser, R; Fine, D L; Bader, J; Shoemaker, R H; Boyd, M R


    We have developed an effective and optimally safe microculture method for rapid and convenient assay of the in vitro cytopathic effects of human immunodeficiency virus (HIV-1) on human lymphoblastoid or other suitable host cells. The assay procedure is applicable to the evaluation of drug effects on in vitro infections induced directly in cultured host cells by cell-free HIV-1 or by coculture with H9 cells chronically infected with HIV-1. The assay uses a newly developed tetrazolium reagent that is metabolically reduced by viable cells to yield a soluble, colored formazan product measurable by conventional colorimetric techniques. This simple microassay minimizes the number of plate manipulations typically required with other assay methods and, coupled with computerized data collection and analysis, facilitates large-scale screening of agents for potential antiviral activity. To support and enhance the discovery of new anti-HIV-1 agents, the National Cancer Institute is offering investigators worldwide the opportunity to submit new candidate agents for anti-HIV-1 screening with this method.

  19. Higher-Order Level-Set Method and Its Application in Biomolecular Surfaces Construction

    Institute of Scientific and Technical Information of China (English)

    Chandrajit L. Bajaj; Guo-Liang Xu; Qin Zhang


    We present a general framework for a higher-order spline level-set (HLS) method and apply this to biomolecule surfaces construction. Starting from a first order energy functional, we obtain a general level set formulation of geometric partial differential equation, and provide an efficient approach to solving this partial differential equation using a C2 spline basis. We also present a fast cubic spline interpolation algorithm based on convolution and the Z-transform, which exploits the local relationship of interpolatory cubic spline coefficients with respect to given function data values. One example of our HLS method is demonstrated, which is the construction of biomolecule surfaces (an implicit salvation interface) with their individual atomic coordinates and solvated radii as prerequisites.

  20. Ionization of biomolecular targets by ion impact: input data for radiobiological applications (United States)

    de Vera, Pablo; Abril, Isabel; Garcia-Molina, Rafael; Solov'yov, Andrey V.


    In this work we review and further develop a semiempirical model recently proposed for the ion impact ionization of complex biological media. The model is based on the dielectric formalism, and makes use of a semiempirical parametrization of the optical energy-loss function of bioorganic compounds, allowing the calculation of single and total ionization cross sections and related quantities for condensed biological targets, such as liquid water, DNA and its components, proteins, lipids, carbohydrates or cell constituents. The model shows a very good agreement with experimental data for water, adenine and uracil, and allows the comparison of the ionization efficiency of different biological targets, and also the average kinetic energy of the ejected secondary electrons.

  1. The enzymology of mitochondrial fatty acid beta-oxidation and its application to follow-up analysis of positive neonatal screening results. (United States)

    Wanders, Ronald J A; Ruiter, Jos P N; IJLst, Lodewijk; Waterham, Hans R; Houten, Sander M


    Oxidation of fatty acids in mitochondria is a key physiological process in higher eukaryotes including humans. The importance of the mitochondrial beta-oxidation system in humans is exemplified by the existence of a group of genetic diseases in man caused by an impairment in the mitochondrial oxidation of fatty acids. Identification of patients with a defect in mitochondrial beta-oxidation has long remained notoriously difficult, but the introduction of tandem-mass spectrometry in laboratories for genetic metabolic diseases has revolutionalized the field by allowing the rapid and sensitive analysis of acylcarnitines. Equally important is that much progress has been made with respect to the development of specific enzyme assays to identify the enzyme defect in patients subsequently followed by genetic analysis. In this review, we will describe the current state of knowledge in the field of fatty acid oxidation enzymology and its application to the follow-up analysis of positive neonatal screening results.

  2. Unified Application of Vapor Screen Flow Visualization and Pressure Sensitive Paint Measurement Techniques to Vortex- and Shock Wave-Dominated Flow Fields (United States)

    Erickson, Gary E.


    Laser vapor screen (LVS) flow visualization and pressure sensitive paint (PSP) techniques were applied in a unified approach to wind tunnel testing of slender wing and missile configurations dominated by vortex flows and shock waves at subsonic, transonic, and supersonic speeds. The off-surface cross-flow patterns using the LVS technique were combined with global PSP surface static pressure mappings to characterize the leading-edge vortices and shock waves that coexist and interact at high angles of attack. The synthesis of LVS and PSP techniques was also effective in identifying the significant effects of passive surface porosity and the presence of vertical tail surfaces on the flow topologies. An overview is given of LVS and PSP applications in selected experiments on small-scale models of generic slender wing and missile configurations in the NASA Langley Research Center (NASA LaRC) Unitary Plan Wind Tunnel (UPWT) and 8-Foot Transonic Pressure Tunnel (8-Foot TPT).

  3. Unified Application Vapor Screen Flow Visualization and Pressure Sensitive Paint Measurement Techniques to Vortex- and Shock Wave-Dominated Flow Fields (United States)

    Erickson, Gary E.


    Laser vapor screen (LVS) flow visualization and pressure sensitive paint (PSP) techniques were applied in a unified approach to wind tunnel testing of slender wing and missile configurations dominated by vortex flows and shock waves at subsonic, transonic, and supersonic speeds. The off-surface cross-flow patterns using the LVS technique were combined with global PSP surface static pressure mappings to characterize the leading-edge vortices and shock waves that coexist and interact at high angles of attack (alpha). The synthesis of LVS and PSP techniques was also effective in identifying the significant effects of passive surface porosity and the presence of vertical tail surfaces on the flow topologies. An overview is given of LVS and PSP applications in selected experiments on small-scale models of generic slender wing and missile configurations in the NASA Langley Research Center (NASA LaRC) Unitary Plan Wind Tunnel (UPWT) and 8-Foot Transonic Pressure Tunnel (8-Foot TPT).

  4. Experimental on Application of Wind Screen Combined Grain Cleaning Device%原粮风筛组合清理装置应用试验

    Institute of Scientific and Technical Information of China (English)

    宗洋; 朱金林; 杨军伟; 谭保辉; 李进宝


    The traditional cleaning method cant achieve the purpose of environmental cleanup, cleaning grain warehouse and safe storage of raw grain, China Grain Reserves Corporation approve "the implementation plan of application and experiment project of wind screen combined grain cleaning device" by Henan branch to ensure the quality of raw grain into the warehouse.%传统的清理方式无法实现原粮环保清理、净粮入仓、安全储存的目的,中国储备粮管理总公司批复了河南分公司《原粮风筛组合清理装置应用试验项目实施方案》,以保证粮的入仓品质.

  5. Recycling wastes: its application in acoustic screens and construction materials; Residuos con necesidad de reciclado: su aplicacion en plantallas acusticas y como materiales de construccion

    Energy Technology Data Exchange (ETDEWEB)

    Santa Coloma, O.; Cortes, A.; Sanchez, J.A.


    The activities developed by man are origin of a great variety of wastes. These activities entail both the resource consumption and the generation of wastes. Both aspects are important because of the impact on the environment where man lives. If we focus on our attention on the consumption of natural resources, both economic aspects (every time the resources are more expensive) and its availability (it increases gradually the difficulty to get them). In this sense, it is very important to pro move the plans and programs necessary in order to minimize the wastes through the re utilization and recycling. Two of the options are the application of some wastes in the manufacture of acoustic screens and as construction materials. (Author)

  6. Development and application of a SYBR green RT-PCR for first line screening and quantification of porcine sapovirus infection

    Directory of Open Access Journals (Sweden)

    Mauroy Axel


    Full Text Available Abstract Background Sapoviruses are single stranded positive sense RNA viruses belonging to the family Caliciviridae. The virus is detected in different species including the human and the porcine species as an enteric pathogen causing asymptomatic to symptomatic enteritis. In this study, we report the development of a rapid real time qRT-PCR based on SYBR Green chemistry for the diagnosis of porcine sapovirus infection in swine. Results The method allows the detection of porcine sapoviruses and the quantification of the genomic copies present in stool samples. During its development, the diagnostic tool showed good correlation compared with the gold standard conventional RT-PCR and was ten-fold more sensitive. When the method was applied to field samples, porcine noroviruses from genogroup 2 genotype 11b were also detected. The method was also applied to swine samples from the Netherlands that were positive for PoSaV infection. Phylogenetic results obtained from the samples showed that PoSaV sequences were genetically related to the currently described genogroup III, to the proposed genogroup VII and also to the MI-QW19 sequence (close to the human SaV sequences. Conclusions A rapid, sensitive, and reliable diagnosis method was developed for porcine sapovirus diagnosis. It correlated with the gold standard conventional RT-PCR. Specificity was good apart for genogroup 2 genotype 11b porcine noroviruses. As a first line screening diagnosis method, it allows a quicker and easier decision on doubtful samples.

  7. STOPP (Screening Tool of Older Persons' potentially inappropriate Prescriptions): application to acutely ill elderly patients and comparison with Beers' criteria.

    LENUS (Irish Health Repository)

    Gallagher, Paul


    Introduction: STOPP (Screening Tool of Older Persons\\' potentially inappropriate Prescriptions) is a new, systems-defined medicine review tool. We compared the performance of STOPP to that of established Beers\\' criteria in detecting potentially inappropriate medicines (PIMs) and related adverse drug events (ADEs) in older patients presenting for hospital admission. METHODS: we prospectively studied 715 consecutive acute admissions to a university teaching hospital. Diagnoses, reason for admission and concurrent medications were recorded. STOPP and Beers\\' criteria were applied. PIMs with clear causal connection or contribution to the principal reason for admission were determined. RESULTS: median patient age (interquartile range) was 77 (72-82) years. Median number of prescription medicines was 6 (range 0-21). STOPP identified 336 PIMs affecting 247 patients (35%), of whom one-third (n = 82) presented with an associated ADE. Beers\\' criteria identified 226 PIMs affecting 177 patients (25%), of whom 43 presented with an associated ADE. STOPP-related PIMs contributed to 11.5% of all admissions. Beers\\' criteria-related PIMs contributed to significantly fewer admissions (6%). CONCLUSION: STOPP criteria identified a significantly higher proportion of patients requiring hospitalisation as a result of PIM-related adverse events than Beers\\' criteria. This finding has significant implications for hospital geriatric practice.

  8. Spray-Deposited Large-Area Copper Nanowire Transparent Conductive Electrodes and Their Uses for Touch Screen Applications. (United States)

    Chu, Hsun-Chen; Chang, Yen-Chen; Lin, Yow; Chang, Shu-Hao; Chang, Wei-Chung; Li, Guo-An; Tuan, Hsing-Yu


    Large-area conducting transparent conducting electrodes (TCEs) were prepared by a fast, scalable, and low-cost spray deposition of copper nanowire (CuNW) dispersions. Thin, long, and pure copper nanowires were obtained via the seed-mediated growth in an organic solvent-based synthesis. The mean length and diameter of nanowires are, respectively, 37.7 μm and 46 nm, corresponding to a high-mean-aspect ratio of 790. These wires were spray-deposited onto a glass substrate to form a nanowire conducting network which function as a TCE. CuNW TCEs exhibit high-transparency and high-conductivity since their relatively long lengths are advantageous in lowering in the sheet resistance. For example, a 2 × 2 cm(2) transparent nanowire electrode exhibits transmittance of T = 90% with a sheet resistance as low as 52.7 Ω sq(-1). Large-area sizes (>50 cm(2)) of CuNW TCEs were also prepared by the spray coating method and assembled as resistive touch screens that can be integrated with a variety of devices, including LED lighting array, a computer, electric motors, and audio electronic devices, showing the capability to make diverse sizes and functionalities of CuNW TCEs by the reported method.

  9. Electrochemical Sensors Based on Screen-Printed Electrodes: The Use of Phthalocyanine Derivatives for Application in VFA Detection (United States)

    Ndiaye, Amadou L.; Delile, Sébastien; Brunet, Jérôme; Varenne, Christelle; Pauly, Alain


    Here, we report on the use of electrochemical methods for the detection of volatiles fatty acids (VFAs), namely acetic acid. We used tetra-tert-butyl phthalocyanine (PcH2-tBu) as the sensing material and investigated its electroanalytical properties by means of cyclic voltammetry (CV) and square wave voltammetry (SWV). To realize the electrochemical sensing system, the PcH2-tBu has been dropcast-deposited on carbon (C) orgold (Au)screen-printed electrodes (SPEs) and characterized by cyclic voltammetry and scanning electron microscopy (SEM). The SEM analysis reveals that the PcH2-tBu forms mainly aggregates on the SPEs. The modified electrodes are used for the detection of acetic acid and present a linear current increase when the acetic acid concentration increases. The Cmodified electrode presents a limit of detection (LOD) of 25.77 mM in the range of 100 mM–400 mM, while the Aumodified electrode presents an LOD averaging 40.89 mM in the range of 50 mM–300 mM. When the experiment is realized in a buffered condition, theCmodified electrode presents a lower LOD, which averagesthe 7.76 mM. A pronounced signal decay attributed to an electrode alteration is observed in the case of the gold electrode. This electrode alteration severely affects the coating stability. This alteration is less perceptible in the case of the carbon electrode. PMID:27598214

  10. The application of the Escherichia coli giant spheroplast for drug screening with automated planar patch clamp system

    Directory of Open Access Journals (Sweden)

    Kyoko Kikuchi


    Full Text Available Kv2.1, the voltage-gated ion channel, is ubiquitously expressed in variety of tissues and dysfunction of this ion channel is responsible for multiple diseases. Electrophysiological properties of ion channels are so far characterized with eukaryotic cells using the manual patch clamp which requires skilful operators and expensive equipments. In this research, we created a simple and sensitive drug screen method using bacterial giant spheroplasts and the automated patch clamp which does not require special skills. We expressed a eukaryotic voltage-gated ion channel Kv2.1 in Escherichia coli using prokaryotic codon, and prepared giant spheroplasts large enough for the patch clamp. Human Kv2.1 currents were successfully recorded from giant spheroplasts with the automated system, and Kv2.1-expressed E. coli spheroplasts could steadily reacted to the dose–response assay with TEA and 4-AP. Collectively, our results indicate for the first time that the bacterial giant spheroplast can be applied for practical pharmaceutical assay using the automated patch clamp.

  11. Benefits and pitfalls of the application of screening methods for the analysis of pesticide residues in fruits and vegetables. (United States)

    Malato, Octavio; Lozano, Ana; Mezcua, Milagros; Agüera, Ana; Fernandez-Alba, Amadeo R


    The goal of this study was to expand knowledge on the performance of screening methods based on accurate mass measurements using a liquid chromatography electrospray quadrupole time-of-flight mass spectrometry (LC-ESI-QTOF-MS) system operating in full scan mode and with automatic identification based on the use accurate-mass databases. The study involved the analysis of 97 pesticides, in five matrices (tomato, pepper, zucchini, orange and leek) and at three concentration levels (20, 50 and 100 μg kg(-1)). Aspects concerning optimization of the search parameters, sensitivity, matrix effects, efficiency of the algorithm search, usefulness of fragment ions, etc., are evaluated in deep. Sensitivity requirements have been identified as the main obstacle affecting the automatic identification of pesticides, especially in complex matrices, where the ionization suppression reduces the detectability of analytes. In addition, we have detected some failures in the software used for automatic data processing in terms of analysis of isobaric compounds, use of isotopic clusters, spectral deconvolution and data processing speed that hamper the correct identification in some pesticide/matrix combinations. These drawbacks should be improved in the future for its effective implementation in routine residue analysis.

  12. Penicillin-binding protein 3 of Streptococcus pneumoniae and its application in screening of β-lactams in milk. (United States)

    Zhang, Jing; Wang, Zhanhui; Wen, Kai; Liang, Xiao; Shen, Jianzhong


    The soluble form of penicillin-binding protein 3 (sPBP3(∗)) from Streptococcus pneumoniae was expressed in Escherichia coli as a six-histidine fusion protein. The protein was purified and used to develop a microplate assay in direct competitive format for the detection of penicillins and cephalosporins in milk. The assay was based on competitive inhibition of the binding of horseradish peroxidase-labeled ampicillin (HRP-Amp) to the sPBP3(∗) by free β-lactam antibiotics in milk. Under optimized conditions, most of the β-lactam antibiotics (11 penicillins and 16 cephalosporins) could be detected at concentrations corresponding to the maximum residue limits (MRLs) set by the European Union. Analysis of spiked milk samples showed that acceptable recoveries ranged from 74.06 to 106.31% in skimmed milk and from 63.97 to 107.26% in whole milk, with coefficients of variation (CVs) less than 16%. With the high sensitivity and wide-range affinities to penicillins and cephalosporins, the developed assay based on sPBP3(∗) exhibited the potential to be a screening assay for fast detection of β-lactam antibiotics in milk.

  13. An UPLC-ESI-MS/MS Assay Using 6-Aminoquinolyl-N-Hydroxysuccinimidyl Carbamate Derivatization for Targeted Amino Acid Analysis: Application to Screening of Arabidopsis thaliana Mutants

    Directory of Open Access Journals (Sweden)

    Carolina Salazar


    Full Text Available In spite of the large arsenal of methodologies developed for amino acid assessment in complex matrices, their implementation in metabolomics studies involving wide-ranging mutant screening is hampered by their lack of high-throughput, sensitivity, reproducibility, and/or wide dynamic range. In response to the challenge of developing amino acid analysis methods that satisfy the criteria required for metabolomic studies, improved reverse-phase high-performance liquid chromatography-mass spectrometry (RPHPLC-MS methods have been recently reported for large-scale screening of metabolic phenotypes. However, these methods focus on the direct analysis of underivatized amino acids and, therefore, problems associated with insufficient retention and resolution are observed due to the hydrophilic nature of amino acids. It is well known that derivatization methods render amino acids more amenable for reverse phase chromatographic analysis by introducing highly-hydrophobic tags in their carboxylic acid or amino functional group. Therefore, an analytical platform that combines the 6-aminoquinolyl-N-hydroxysuccinimidyl carbamate (AQC pre-column derivatization method with ultra performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UPLC-ESI-MS/MS is presented in this article. For numerous reasons typical amino acid derivatization methods would be inadequate for large scale metabolic projects. However, AQC derivatization is a simple, rapid and reproducible way of obtaining stable amino acid adducts amenable for UPLC-ESI-MS/MS and the applicability of the method for high-throughput metabolomic analysis in Arabidopsis thaliana is demonstrated in this study. Overall, the major advantages offered by this amino acid analysis method include high-throughput, enhanced sensitivity and selectivity; characteristics that showcase its utility for the rapid screening of the preselected plant metabolites without compromising the quality of the

  14. Polymerase chain reaction-based screening method applicable universally to environmental haloarchaea and halobacteria for identifying polyhydroxyalkanoate producers among them. (United States)

    Mahansaria, Riddhi; Choudhury, Jayanta Debabrata; Mukherjee, Joydeep


    The existing techniques for detection of polyhydroxyalkanoates (PHA) in halophilic archaea/bacteria are either imprecise or require prior PHA production before screening. The proposed method involves amplification of the approximately 280-300 bp conserved region of Class III PHA synthase (phaC) gene of halophiles using the primers codehopCF and codehopCR (Han et al. Appl Environ Microb 76:7811-7819, 2010). In this study, the best reaction condition was ascertained after repeated trials. This developed method was tested on nine haloarchaeal and halobacterial type strains and 28 environmental halophilic archaea and bacteria isolated from the salt pans of the east and west coasts of India. 29 strains were found to be phaC-positive, while eight were found to be phaC-negative although they appeared PHA positive through conventional Nile Red staining. 16S rRNA-based phylogenetic analysis identified 9 haloarchaeal and 9 halobacterial species as novel PHA producers. Multiple sequence alignment of the phaC gene-derived amino acid sequences showed that only 7 amino acid residues were conserved within all four classes of phaC enzymes, whereas 61 amino acids were identical among the phaC enzyme specific to the haloarchaeal and halobacterial strains presently investigated. All phaC-positive strains produced PHA in standard nutrient deficient medium, whereas the phaC-negative strains did not accumulate any PHA as detected by gas chromatography and nuclear magnetic resonance analyses, thus proving the precision of the developed method and elimination of false positives seen with the traditional Nile Red staining procedure.

  15. [Applications in gynecology-obstetrics of the first legal cases concerning HIV transmission by blood transfusion and errors in screening]. (United States)

    Pierre, F; Soutoul, J H


    The intention of the authors in this paper is to provide a preliminary report on what is going on in order to inform gynaecologists and obstetricians of the initial legal steps concerning the transmission of HIV by blood transfusion and the defects in screening for the infection which could have been caught by a pregnant woman; where there was a possibility of a false-positive diagnosis from the serum which could have brought about a termination of pregnancy unnecessarily. Two decisions have been analysed, the one according to the old administrative law and the other according to the more recent judgement, involving pregnancy and other decisions which were not directly concerned with the specialty. These can be instructive for practitioners because these circumstance may come up again. It is worth looking at the case papers where medical responsibility can be invoked involving the professional insurance agencies. These cases will increase in numbers in the future. The authors analysed in the light of the decisions that had been made, possible penal, civil and administrative liabilities that could threaten gynaecologists and obstetricians in this field. The study ends by pointing out what can be done to lessen these medico-legal risks by avoiding blood loss in operations, by finding other ways than blood transfusions towards the end of pregnancy, but above all, by reducing and controlling the number of blood transfusions carefully. This has to be done in collaboration with the transfusion centres and the laboratories where the blood is tested. Judges will have to work out where the responsibility lies if the cases come before them.

  16. A device design of an integrated CMOS poly-silicon biosensor-on-chip to enhance performance of biomolecular analytes in serum samples. (United States)

    Pei-Wen, Yen; Che-Wei, Huang; Yu-Jie, Huang; Min-Cheng, Chen; Hsin-Hao, Liao; Shey-Shi, Lu; Chih-Ting, Lin


    For on-site clinical diagnosis of biomolecules, the detection performances of most point-of-care (POC) biosensor devices are limited by undesired cross-detection of other non-analyte proteins in patient serum samples and other complex samples. To conquer this obstacle, this work presents a fully integrated bottom-gate poly-silcion nanowire (polySi NW) biosensor system-on-chip (SoC) to enhance the detection performance of cardiac-specific troponin-I (cTnI) concentration levels in serum samples. By applying proper electrical potential at the bottom gate under polySi NW biosensor, the biosensor response to cTnI biomarker can be improved by at least 16 fold in 50% phantom serum samples. The experimental result shows its detection range is from 3.2 × 10(-13)M(mol l(-1)) to 3.2 × 10(-10)M. This enhancement can be attributed to the electrostatic interactions between target biomolecules and voltage-applied bottom gate electrodes. This is the first time that a polySi NW CMOS biosensor chip has shown feasibilities to detect specific biomarkers in serum samples. Therefore, the developed technology paves the way toward on-field applications of CMOS compatible SiNW biosensing technologies and it can be employed for future biomolecular analysis in on-site serum diagnosis applications.

  17. Screening-engineered Field-effect Photovoltaics and Synthesis, Characterization, and Applications of Carbon-based and Related Nanomaterials


    Regan, William Raymond


    Carbon nanomaterials, and especially graphene (a 2D carbon allotrope), possess unique electronic, optical, and mechanical properties and allow access to both new physical phenomena and reinventions of familiar technologies. In the first part of this thesis (chapter 2), the low carrier density and high conductivity of graphene are used to repurpose the electric field effect (used for many decades in transistors) into a universally-applicable doping method for electrically-contacted semiconduct...

  18. Mathematical Models of the Sinusoidal Screen Family

    Directory of Open Access Journals (Sweden)

    Tajana Koren


    Full Text Available In this paper we will define a family of sinusoidal screening elements and explore the possibilities of their application in graphic arts, securities printing and design solutions in photography and typography editing. For this purpose mathematical expressions of sinusoidal families were converted into a Postscript language. The introduction of a random variable results in a countless number of various mutations which cannot be repeated without knowing the programming code itself. The use of the family of screens in protection of securities is thus of great importance. Other possible application of modulated sinusoidal screens is related to the large format color printing. This paper will test the application of sinusoidal screens in vector graphics, pixel graphics and typography. The development of parameters in the sinusoidal screen element algorithms gives new forms defined within screening cells with strict requirements of coverage implementation. Individual solutions include stochastic algorithms, as well as the autonomy of screening forms in regard to multicolor printing channels.

  19. Tibialis anterior muscle needle biopsy and sensitive biomolecular methods: a useful tool in myotonic dystrophy type 1

    Directory of Open Access Journals (Sweden)

    S. Iachettini


    Full Text Available Myotonic dystrophy type 1 (DM1 is a neuromuscular disorder caused by a CTG repeat expansion in 3’UTR of DMPK gene. This mutation causes accumulation of toxic RNA in nuclear foci leading to splicing misregulation of specific genes. In view of future clinical trials with antisense oligonucleotides in DM1 patients, it is important to set up sensitive and minimally-invasive tools to monitor the efficacy of treatments on skeletal muscle. A tibialis anterior (TA muscle sample of about 60 mg was obtained from 5 DM1 patients and 5 healthy subjects through a needle biopsy. A fragment of about 40 mg was used for histological examination and a fragment of about 20 mg was used for biomolecular analysis. The TA fragments obtained with the minimally-invasive needle biopsy technique is enough to perform all the histopathological and biomolecular evaluations useful to monitor a clinical trial on DM1 patients.

  20. Tibialis anterior muscle needle biopsy and sensitive biomolecular methods: a useful tool in myotonic dystrophy type 1. (United States)

    Iachettini, S; Valaperta, R; Marchesi, A; Perfetti, A; Cuomo, G; Fossati, B; Vaienti, L; Costa, E; Meola, G; Cardani, R


    Myotonic dystrophy type 1 (DM1) is a neuromuscular disorder caused by a CTG repeat expansion in 3'UTR of DMPK gene. This mutation causes accumulation of toxic RNA in nuclear foci leading to splicing misregulation of specific genes. In view of future clinical trials with antisense oligonucleotides in DM1 patients, it is important to set up sensitive and minimally-invasive tools to monitor the efficacy of treatments on skeletal muscle. A tibialis anterior (TA) muscle sample of about 60 mg was obtained from 5 DM1 patients and 5 healthy subjects through a needle biopsy. A fragment of about 40 mg was used for histological examination and a fragment of about 20 mg was used for biomolecular analysis. The TA fragments obtained with the minimally-invasive needle biopsy technique is enough to perform all the histopathological and biomolecular evaluations useful to monitor a clinical trial on DM1 patients.

  1. Development and application of rapid screening technology and its evaluation and authentication profiles%快速筛选技术的评价验证

    Institute of Scientific and Technical Information of China (English)

    赵博; 张庆合; 李红梅


    快速筛选技术是指包括样品制备在内,能够在较短时间内出具检测结果的行为,也称之为快速检测技术。随着我国食品安全问题广受关注,快速筛选技术便成为研究的重点。快速检测目前主要应用于食品中农、兽药残留,微生物致病菌,营养成分,不明污染物等针对食品安全的现场快速检测及常规检测。本文介绍了分子光谱法、免疫分析方法、酶抑制法和生物传感器等几种快速筛选技术的研究进展以及在食品安全检测等领域的应用。随着快速筛选技术的不断发展使得快速检测方法及其相关仪器产品种类越来越多且原理复杂,快速检测方法的质量控制和方法验证显得尤为重要。本文重点阐述了快速筛选技术与方法的评价验证,其主要技术参数包括:敏感度、阴性和阳性界限值的准确性、选择性和特异性、检出限、定量限、重复性和再现性等,并对其发展前景进行了展望。%Rapid screening technology means, including sample preparation, a kind of technology to be able to issue the test results in a short time. It was also defined as rapid detection technology. It was mainly used in food, pesticide, veterinary drug residues, microbial pathogens, nutrients, and unknown contaminants, etc. Rapid screening technology had become the focus of research as well as the food safety in our country. Several technologies of the rapid screening method were mainly introduced, including molecular spectrometry, immunoassay, enzyme inhibition method, and biological sensors,etc. With the continuous development of rapid screening technology, rapid detection methods and related equipment products appeared more and more, and their quality control and validation method turned to be particularly important. In this paper, the development and application of the rapid screening technology in food safety were expounded as well as its evaluation methods

  2. Nutritional screening tools application in a general hospital: a comparative study Aplicação de instrumentos de triagem nutricional em hospital geral: um estudo comparativo

    Directory of Open Access Journals (Sweden)

    Janaína Damasceno Bezerra


    Full Text Available Introduction: There are many nutritional screening tools and it becomes difficult to choose which one is the best to be used in clinical nutrition practice. Objective: To compare five nutritional screening tools (MST, NRS-2002, MUST, MNA and MNA-SF in adults and elderly hospitalized. Materials and Methods: A cross-sectional study, with the application of nutritional screening tools in adult and elderly patients in the first 48 hours of hospitalization was performed. Nutritional risk occurrence between adult and elderly patients was compared. Statistical analyses were performed using descriptive data and a non-parametric test (Man Whitney. Results: We evaluated 77 patients, 51 (66.2% adults and 26 (33.8% elderly, aged 53.6 (standard deviation of 17.9 years, with female predominance (53.2%. The main reasons for hospitalization were neoplasia and nephrolithotripsy. Overall, one quarter of patients was at nutritional risk. Nutritional risk in adults was detected with similarity by MUST and MST. However it was underestimated by NRS-2002. The MNA and MNA-SF, exclusively for the elderly, also had similar result to detect nutritional risk. In relation to the time of application, the MNA was the instrument with longer application time. Conclusion: Considering the higher detection of patients with nutritional risk, the easiness and the lower application time, we suggest, respectively, MUST and MNA-SF to be used in adult and elderly patients admitted in this hospital.Introdução: Com inúmeros instrumentos de triagem nutricional existentes, é difícil eleger o mais adequado para os protocolos de nutrição hospitalar. Objetivo: Comparar cinco instrumentos de triagem nutricional (MST, NRS-2002, MUST, MNA e MNA-SF em adultos e idosos hospitalizados. Materiais e Métodos: Nesse estudo transversal, cinco instrumentos de triagem nutricional foram aplicados aos pacientes nas primeiras 48 horas de internação hospitalar. A ocorrência de risco nutricional

  3. Differentiation of AmpC beta-lactamase binders vs. decoys using classification kNN QSAR modeling and application of the QSAR classifier to virtual screening (United States)

    Hsieh, Jui-Hua; Wang, Xiang S.; Teotico, Denise; Golbraikh, Alexander; Tropsha, Alexander


    The use of inaccurate scoring functions in docking algorithms may result in the selection of compounds with high predicted binding affinity that nevertheless are known experimentally not to bind to the target receptor. Such falsely predicted binders have been termed `binding decoys'. We posed a question as to whether true binders and decoys could be distinguished based only on their structural chemical descriptors using approaches commonly used in ligand based drug design. We have applied the k-Nearest Neighbor ( kNN) classification QSAR approach to a dataset of compounds characterized as binders or binding decoys of AmpC beta-lactamase. Models were subjected to rigorous internal and external validation as part of our standard workflow and a special QSAR modeling scheme was employed that took into account the imbalanced ratio of inhibitors to non-binders (1:4) in this dataset. 342 predictive models were obtained with correct classification rate (CCR) for both training and test sets as high as 0.90 or higher. The prediction accuracy was as high as 100% (CCR = 1.00) for the external validation set composed of 10 compounds (5 true binders and 5 decoys) selected randomly from the original dataset. For an additional external set of 50 known non-binders, we have achieved the CCR of 0.87 using very conservative model applicability domain threshold. The validated binary kNN QSAR models were further employed for mining the NCGC AmpC screening dataset (69653 compounds). The consensus prediction of 64 compounds identified as screening hits in the AmpC PubChem assay disagreed with their annotation in PubChem but was in agreement with the results of secondary assays. At the same time, 15 compounds were identified as potential binders contrary to their annotation in PubChem. Five of them were tested experimentally and showed inhibitory activities in millimolar range with the highest binding constant Ki of 135 μM. Our studies suggest that validated QSAR models could complement

  4. Application of FISK, an invasiveness screening tool for non-native freshwater fishes, in the Murray-Darling Basin (southeastern Australia). (United States)

    Vilizzi, Lorenzo; Copp, Gordon H


    The Fish Invasiveness Scoring Kit (FISK) is currently one of the most popular pre-screening tools for freshwater fishes. A recent upgrade has ensured its wider climatic relevance to countries with subtropical regions. This enhancement is of particular importance to Australia, which encompasses tropical, arid, and temperate zones, and where the introduction of non-native fish species poses a significant risk to biodiversity. In this study, 55 fish species previously evaluated in a U.K.-based calibration of FISK are reassessed for their potential invasiveness in the Murray-Darling Basin (MDB; southeastern Australia), the continent's largest catchment encompassing arid and temperate climates. Approximately half of the species were classed as "medium risk" and the other half as "high risk," and the ≥19 threshold previously identified from the calibration study was confirmed. The three highest scoring species (common carp Cyprinus carpio carpio, goldfish Carassius auratus, and eastern mosquitofish Gambusia holbrooki) were those already present and invasive in the area, whereas nearly half of the tropical and subtropical species had lower scores compared to U.K. assessments, possibly because of climate change predictions of drier conditions across the MDB. There were some discordances between FISK and two Australian-based assessment protocols, one of which is qualitative and the other represents a simplified version of FISK. Notably, the Australian origins of FISK should provide for an additional reason for further applications of the tool in other RA areas (i.e., drainage basins) of the continent, ultimately encouraging adoption as the country's reference screening tool for management and conservation purposes.

  5. 基于信息甄别的预订货策略研究%The Application of Information Screening in Early Order Commitment

    Institute of Scientific and Technical Information of China (English)

    蒋龙珠; 江志斌; 储熠斌; 耿娜


    以一个制造商一个经销商组成的二级供应链为研究对象,在信息不对称条件下从制造商的角度,基于信息经济学理论建立了供应链的利润函数的信息甄别解析模型.提出了预订货激励契约.对其有效原因进行了分析并解释了契约关键参数的意义.得出了制造商的最优产量决策机制.结论表明:在信息不对称条件下,制造商可利用预订货价改变经销商的利润函数结构,通过信息甄别机制对经销商的预订购量进行判断以获得真实的市场需求信息.%A two-stage supply chain of one manufacture and one agency are studied under the condition of asymmetric information from the view of manufacture. By application of information screening in Early Order Commitment ( EOC) , the analytic models of the supply chain profit function is proposed based on the information economics theory. An incentive contract is proposed, analyzed its effect, explain its key index, and given out the optimal production volume. Conclusions demonstrate that the manufacture can re-structure the agency' s profit function by means of EOC price, and get the credible demand information from screening the agency' s purchase quantity under asymmetric information condition.

  6. Development of polarizable models for molecular mechanical calculations. 3. Polarizable water models conforming to Thole polarization screening schemes. (United States)

    Wang, Jun; Cieplak, Piotr; Cai, Qin; Hsieh, Meng-Juei; Wang, Junmei; Duan, Yong; Luo, Ray


    As an integrated step toward a coherent polarizable force field for biomolecular modeling, we analyzed four polarizable water models to evaluate their consistencies with the Thole polarization screening schemes utilized in our latest Amber polarizable force field. Specifically, we studied the performance of both the Thole linear and exponential schemes in these water models to assess their abilities to reproduce experimental water properties. The analysis shows that the tested water models reproduce most of the room-temperature properties of liquid water reasonably well but fall short of reproducing the dynamic properties and temperature-dependent properties. This study demonstrates the necessity to further fine-tune water polarizable potentials for more robust polarizable force fields for biomolecular simulations.

  7. Designer DNA Architectures: Applications in Nanomedicine


    Arun Richard Chandrasekaran


    DNA has been used as a material for the construction of nanoscale objects. These nanostructures are programmable and allow the conjugation of biomolecular guests to improve their functionality. DNA nanostructures display a wide variety of characteristics, such as cellular permeabil‐ ity, biocompatibility and stability, and responsiveness to external stimuli, making them excellent candidates for applications in nanomedicine.

  8. Designer DNA Architectures: Applications in Nanomedicine

    Directory of Open Access Journals (Sweden)

    Arun Richard Chandrasekaran


    Full Text Available DNA has been used as a material for the construction of nanoscale objects. These nanostructures are programmable and allow the conjugation of biomolecular guests to improve their functionality. DNA nanostructures display a wide variety of characteristics, such as cellular permeabil‐ ity, biocompatibility and stability, and responsiveness to external stimuli, making them excellent candidates for applications in nanomedicine.

  9. Lipid phase behavior studied with a quartz crystal microbalance: A technique for biophysical studies with applications in screening (United States)

    Peschel, Astrid; Langhoff, Arne; Uhl, Eva; Dathathreyan, Aruna; Haindl, Susanne; Johannsmann, Diethelm; Reviakine, Ilya


    Quartz crystal microbalance (QCM) is emerging as a versatile tool for studying lipid phase behavior. The technique is attractive for fundamental biophysical studies as well applications because of its simplicity, flexibility, and ability to work with very small amounts of material crucial for biomedical studies. Further progress hinges on the understanding of the mechanism, by which a surface-acoustic technique such as QCM, senses lipid phase changes. Here, we use a custom-built instrument with improved sensitivity to investigate phase behavior in solid-supported lipid systems of different geometries (adsorbed liposomes and bilayers). We show that we can detect a model anesthetic (ethanol) through its effect on the lipid phase behavior. Further, through the analysis of the overtone dependence of the phase transition parameters, we show that hydrodynamic effects are important in the case of adsorbed liposomes, and viscoelasticity is significant in supported bilayers, while layer thickness changes make up the strongest contribution in both systems.

  10. Breast cancer screening (United States)

    Mammogram - breast cancer screening; Breast exam - breast cancer screening; MRI - breast cancer screening ... performed to screen women to detect early breast cancer when it is more likely to be cured. ...

  11. ISSA (iterative screening and structure analysis)—a new reduction method and its application to the tropospheric cloud chemical mechanism RACM/CAPRAM2.4 (United States)

    Mauersberger, G.

    An automated reduction method ISSA (iterative screening and structure analysis) has been developed. It is aimed at the analysis of complex atmospheric chemical multiphase mechanisms and produces reduced mechanisms for specifiable application purposes. Cyclic and non-cyclic reactions identified by a structure analysis are separately evaluated. The normalized valuation coefficients are calculated in a box model framework by using time-averaged reaction rates. Starting with a set of target species, important reactions and species are selected together in an iteration procedure. So, only one threshold value fixed for all box model scenarios is necessary. For every scenario a specific reduced mechanism is obtained. The sum of reactions and species included in the specific reduced mechanisms generates then the ISSA-reduced mechanism. All reactants in the reduced mechanism are included in the verification procedure where the concentrations simulated with the full and the reduced mechanism are compared. The maximum relative deviation of daily maxima was found to be a suitable deviation measure for atmospheric trace species concentrations. An application of the ISSA method to the large cloud chemical mechanism RACM/CAPRAM2.4 resulted in reduction rates of 55% for reactions (46% gas phase, 60% liquid phase), 23% for species, and 23% for phase transfers. The deviation between full and reduced mechanism averaged over all scenarios and reactants was 2.5%. The liquid-phase part of this application was compared with a condensed version of the CAPARAM2.4 mechanism developed simultaneously with the full version. It was found that these two reduced versions of CAPRAM2.4 differ significantly. Whereas the condensed version achieves good verification results only for the target species, the ISSA-reduced version reproduce very well the complete full mechanism results and should be useful for future large-scale models, which will include both detailed microphysics and complex (reduced

  12. A coarse-grained model for the simulations of biomolecular interactions in cellular environments

    Energy Technology Data Exchange (ETDEWEB)

    Xie, Zhong-Ru; Chen, Jiawen; Wu, Yinghao, E-mail: [Department of Systems and Computational Biology, Albert Einstein College of Medicine of Yeshiva University, 1300 Morris Park Avenue, Bronx, New York 10461 (United States)


    The interactions of bio-molecules constitute the key steps of cellular functions. However, in vivo binding properties differ significantly from their in vitro measurements due to the heterogeneity of cellular environments. Here we introduce a coarse-grained model based on rigid-body representation to study how factors such as cellular crowding and membrane confinement affect molecular binding. The macroscopic parameters such as the equilibrium constant and the kinetic rate constant are calibrated by adjusting the microscopic coefficients used in the numerical simulations. By changing these model parameters that are experimentally approachable, we are able to study the kinetic and thermodynamic properties of molecular binding, as well as the effects caused by specific cellular environments. We investigate the volumetric effects of crowded intracellular space on bio-molecular diffusion and diffusion-limited reactions. Furthermore, the binding constants of membrane proteins are currently difficult to measure. We provide quantitative estimations about how the binding of membrane proteins deviates from soluble proteins under different degrees of membrane confinements. The simulation results provide biological insights to the functions of membrane receptors on cell surfaces. Overall, our studies establish a connection between the details of molecular interactions and the heterogeneity of cellular environments.

  13. Indirect readout in protein-peptide recognition: a different story from classical biomolecular recognition. (United States)

    Yu, Hua; Zhou, Peng; Deng, Maolin; Shang, Zhicai


    Protein-peptide interactions are prevalent and play essential roles in many living activities. Peptides recognize their protein partners by direct nonbonded interactions and indirect adjustment of conformations. Although processes of protein-peptide recognition have been comprehensively studied in both sequences and structures recently, flexibility of peptides and the configuration entropy penalty in recognition did not get enough attention. In this study, 20 protein-peptide complexes and their corresponding unbound peptides were investigated by molecular dynamics simulations. Energy analysis revealed that configurational entropy penalty introduced by restriction of the degrees of freedom of peptides in indirect readout process of protein-peptide recognition is significant. Configurational entropy penalty has become the main content of the indirect readout energy in protein-peptide recognition instead of deformation energy which is the main source of the indirect readout energy in classical biomolecular recognition phenomena, such as protein-DNA binding. These results provide us a better understanding of protein-peptide recognition and give us some implications in peptide ligand design.

  14. A starting point for fluorescence-based single-molecule measurements in biomolecular research. (United States)

    Gust, Alexander; Zander, Adrian; Gietl, Andreas; Holzmeister, Phil; Schulz, Sarah; Lalkens, Birka; Tinnefeld, Philip; Grohmann, Dina


    Single-molecule fluorescence techniques are ideally suited to provide information about the structure-function-dynamics relationship of a biomolecule as static and dynamic heterogeneity can be easily detected. However, what type of single-molecule fluorescence technique is suited for which kind of biological question and what are the obstacles on the way to a successful single-molecule microscopy experiment? In this review, we provide practical insights into fluorescence-based single-molecule experiments aiming for scientists who wish to take their experiments to the single-molecule level. We especially focus on fluorescence resonance energy transfer (FRET) experiments as these are a widely employed tool for the investigation of biomolecular mechanisms. We will guide the reader through the most critical steps that determine the success and quality of diffusion-based confocal and immobilization-based total internal reflection fluorescence microscopy. We discuss the specific chemical and photophysical requirements that make fluorescent dyes suitable for single-molecule fluorescence experiments. Most importantly, we review recently emerged photoprotection systems as well as passivation and immobilization strategies that enable the observation of fluorescently labeled molecules under biocompatible conditions. Moreover, we discuss how the optical single-molecule toolkit has been extended in recent years to capture the physiological complexity of a cell making it even more relevant for biological research.

  15. Toxicity evaluation of PEDOT/biomolecular composites intended for neural communication electrodes

    Energy Technology Data Exchange (ETDEWEB)

    Asplund, M; Thaning, E; Von Holst, H [Division of Neuronic Engineering, School of Technology and Health, Royal Institute of Technology, SE-14152 Huddinge (Sweden); Lundberg, J [Section for Neuroradiology, R2:02 NKK-lab, Department of Clinical Neuroscience, Karolinska Institutet, Karolinska University Hospital, Solna, SE-171 76, Stockholm (Sweden); Sandberg-Nordqvist, A C [Section of Clinical CNS Research, Department of Clinical Neuroscience, Karolinska Institutet, Karolinska University Hospital, Solna, SE-171 76, Stockholm (Sweden); Kostyszyn, B [Center for Hearing and Communication Research, Department of Clinical Neuroscience, Karolinska Institutet, Karolinska University Hospital, M1:01, SE-171 76 Stockholm (Sweden); Inganaes, O, E-mail: maria.asplund@sth.kth.s [Biomolecular and Organic Electronics, IFM, Linkoeping University, SE-581 83 Linkoeping (Sweden)


    Electrodes coated with the conducting polymer poly(3,4-ethylene dioxythiophene) (PEDOT) possess attractive electrochemical properties for stimulation or recording in the nervous system. Biomolecules, added as counter ions in electropolymerization, could further improve the biomaterial properties, eliminating the need for surfactant counter ions in the process. Such PEDOT/biomolecular composites, using heparin or hyaluronic acid, have previously been investigated electrochemically. In the present study, their biocompatibility is evaluated. An agarose overlay assay using L929 fibroblasts, and elution and direct contact tests on human neuroblastoma SH-SY5Y cells are applied to investigate cytotoxicity in vitro. PEDOT:heparin was further evaluated in vivo through polymer-coated implants in rodent cortex. No cytotoxic response was seen to any of the PEDOT materials tested. The examination of cortical tissue exposed to polymer-coated implants showed extensive glial scarring irrespective of implant material (Pt:polymer or Pt). However, quantification of immunological response, through distance measurements from implant site to closest neuron and counting of ED1+ cell density around implant, was comparable to those of platinum controls. These results indicate that PEDOT:heparin surfaces were non-cytotoxic and show no marked difference in immunological response in cortical tissue compared to pure platinum controls.

  16. Biomolecular characterization of the levansucrase of Erwinia amylovora, a promising biocatalyst for the synthesis of fructooligosaccharides. (United States)

    Caputi, Lorenzo; Nepogodiev, Sergey A; Malnoy, Mickael; Rejzek, Martin; Field, Robert A; Benini, Stefano


    Erwinia amylovora is a plant pathogen that affects Rosaceae, such as apple and pear. In E. amylovora the fructans, produced by the action of a levansucrase (EaLsc), play a role in virulence and biofilm formation. Fructans are bioactive compounds, displaying health-promoting properties in their own right. Their use as food and feed supplements is increasing. In this study, we investigated the biomolecular properties of EaLsc using HPAEC-PAD, MALDI-TOF MS, and spectrophotometric assays. The enzyme, which was heterologously expressed in Escherichia coli in high yield, was shown to produce mainly fructooligosaccharides (FOSs) with a degree of polymerization between 3 and 6. The kinetic properties of EaLsc were similar to those of other phylogenetically related Gram-negative bacteria, but the good yield of FOSs, the product spectrum, and the straightforward production of the enzyme suggest that EaLsc is an interesting biocatalyst for future studies aimed at producing tailor-made fructans.

  17. Bridge- and Solvent-Mediated Intramolecular Electronic Communications in Ubiquinone-Based Biomolecular Wires (United States)

    Liu, Xiao-Yuan; Ma, Wei; Zhou, Hao; Cao, Xiao-Ming; Long, Yi-Tao


    Intramolecular electronic communications of molecular wires play a crucial role for developing molecular devices. In the present work, we describe different degrees of intramolecular electronic communications in the redox processes of three ubiquinone-based biomolecular wires (Bis-CoQ0s) evaluated by electrochemistry and Density Functional Theory (DFT) methods in different solvents. We found that the bridges linkers have a significant effect on the electronic communications between the two peripheral ubiquinone moieties and solvents effects are limited and mostly depend on the nature of solvents. The DFT calculations for the first time indicate the intensity of the electronic communications during the redox processes rely on the molecular orbital elements VL for electron transfer (half of the energy splitting of the LUMO and LUMO+1), which is could be affected by the bridges linkers. The DFT calculations also demonstrates the effect of solvents on the latter two-electron transfer of Bis-CoQ0s is more significant than the former two electrons transfer as the observed electrochemical behaviors of three Bis-CoQ0s. In addition, the electrochemistry and theoretical calculations reveal the intramolecular electronic communications vary in the four-electron redox processes of three Bis-CoQ0s.

  18. Amplified Immunoassay of Human IgG Using Real-time Biomolecular Interaction Analysis (BIA) Technology

    Institute of Scientific and Technical Information of China (English)

    PEI,Ren-Jun(裴仁军); CUI,Xiao-Qiang(崔小强); YANG,Xiu-Rong(杨秀荣); WANG,Er-Kang(汪尔康)


    An automated biomolecular interaction analysis instrument (BIAcore) based on surface plasmon resonance (SPR) has been used to determine human immunoglobulin G (IgG) in real time. Polyclonal anti-human IgG antibody was covalently immobilized to a carboxymethyldextran-modified gold film surface. The samples of human IgG prepared in HBS buffer were poured over the immobilized surface. The signal amplification antibody was applied to amplify the response signal. After each measurement, the surface was regenerated with 0.1 mol/L H3PO4. The assay was rapid, requiring only 30 min for antibody immobilization and 20 min for each subsequent process of immune binding, antibody amplification and regeneration. The antibody immobilized surface had good response to human IgG in the range of 0.12-60 nmol/L with a detection limit of 60 pmoL/L. The same antibody immobilized surface could be used for more than 110 cycles of binding, amplificafion and regeneration. The results demonstrate that the sensitivity, specificity and reproducibility of amplified immunoassay using real-time BIA technology are satisfactory.

  19. A method for rapid quantitative assessment of biofilms with biomolecular staining and image analysis. (United States)

    Larimer, Curtis; Winder, Eric; Jeters, Robert; Prowant, Matthew; Nettleship, Ian; Addleman, Raymond Shane; Bonheyo, George T


    The accumulation of bacteria in surface-attached biofilms can be detrimental to human health, dental hygiene, and many industrial processes. Natural biofilms are soft and often transparent, and they have heterogeneous biological composition and structure over micro- and macroscales. As a result, it is challenging to quantify the spatial distribution and overall intensity of biofilms. In this work, a new method was developed to enhance the visibility and quantification of bacterial biofilms. First, broad-spectrum biomolecular staining was used to enhance the visibility of the cells, nucleic acids, and proteins that make up biofilms. Then, an image analysis algorithm was developed to objectively and quantitatively measure biofilm accumulation from digital photographs and results were compared to independent measurements of cell density. This new method was used to quantify the growth intensity of Pseudomonas putida biofilms as they grew over time. This method is simple and fast, and can quantify biofilm growth over a large area with approximately the same precision as the more laborious cell counting method. Stained and processed images facilitate assessment of spatial heterogeneity of a biofilm across a surface. This new approach to biofilm analysis could be applied in studies of natural, industrial, and environmental biofilms.

  20. Review of Transducer Principles for Label-Free Biomolecular Interaction Analysis

    Directory of Open Access Journals (Sweden)

    Janos Vörös


    Full Text Available Label-free biomolecular interaction analysis is an important technique to study the chemical binding between e.g., protein and protein or protein and small molecule in real-time. The parameters obtained with this technique, such as the affinity, are important for drug development. While the surface plasmon resonance (SPR instruments are most widely used, new types of sensors are emerging. These developments are generally driven by the need for higher throughput, lower sample consumption or by the need of complimentary information to the SPR data. This review aims to give an overview about a wide range of sensor transducers, the working principles and the peculiarities of each technology, e.g., concerning the set-up, sensitivity, sensor size or required sample volume. Starting from optical technologies like the SPR and waveguide based sensors, acoustic sensors like the quartz crystal microbalance (QCM and the film bulk acoustic resonator (FBAR, calorimetric and electrochemical sensors are covered. Technologies long established in the market are presented together with those newly commercially available and with technologies in the early development stage. Finally, the commercially available instruments are summarized together with their sensitivity and the number of sensors usable in parallel and an outlook for potential future developments is given.

  1. Rapid, Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components. (United States)

    Pardee, Keith; Green, Alexander A; Takahashi, Melissa K; Braff, Dana; Lambert, Guillaume; Lee, Jeong Wook; Ferrante, Tom; Ma, Duo; Donghia, Nina; Fan, Melina; Daringer, Nichole M; Bosch, Irene; Dudley, Dawn M; O'Connor, David H; Gehrke, Lee; Collins, James J


    The recent Zika virus outbreak highlights the need for low-cost diagnostics that can be rapidly developed for distribution and use in pandemic regions. Here, we report a pipeline for the rapid design, assembly, and validation of cell-free, paper-based sensors for the detection of the Zika virus RNA genome. By linking isothermal RNA amplification to toehold switch RNA sensors, we detect clinically relevant concentrations of Zika virus sequences and demonstrate specificity against closely related Dengue virus sequences. When coupled with a novel CRISPR/Cas9-based module, our sensors can discriminate between viral strains with single-base resolution. We successfully demonstrate a simple, field-ready sample-processing workflow and detect Zika virus from the plasma of a viremic macaque. Our freeze-dried biomolecular platform resolves important practical limitations to the deployment of molecular diagnostics in the field and demonstrates how synthetic biology can be used to develop diagnostic tools for confronting global health crises. PAPERCLIP.

  2. Biomolecular Nano-Flow-Sensor to Measure Near-Surface Flow

    Directory of Open Access Journals (Sweden)

    Noji Hiroyuki


    Full Text Available Abstract We have proposed and experimentally demonstrated that the measurement of the near-surface flow at the interface between a liquid and solid using a 10 nm-sized biomolecular motor of F1-ATPase as a nano-flow-sensor. For this purpose, we developed a microfluidic test-bed chip to precisely control the liquid flow acting on the F1-ATPase. In order to visualize the rotation of F1-ATPase, several hundreds nanometer-sized particle was immobilized at the rotational axis of F1-ATPase to enhance the rotation to be detected by optical microscopy. The rotational motion of F1-ATPase, which was immobilized on an inner surface of the test-bed chip, was measured to obtain the correlation between the near-surface flow and the rotation speed of F1-ATPase. As a result, we obtained the relationship that the rotation speed of F1-ATPase was linearly decelerated with increasing flow velocity. The mechanism of the correlation between the rotation speed and the near-surface flow remains unclear, however the concept to use biomolecule as a nano-flow-sensor was proofed successfully. (See supplementary material 1 Electronic supplementary material The online version of this article (doi:10.1007/s11671-009-9479-3 contains supplementary material, which is available to authorized users. Click here for file

  3. Drug Transport Microdevice Mimicking an Idealized Nanoscale Bio-molecular Motor

    Institute of Scientific and Technical Information of China (English)

    Jae Hwan Lee; Ramana M. Pidaparti


    Molecular motors are nature's nano-devices and the essential agents of movement that are an integral part of many living organisms.The supramolecular motor,called Nuclear Pore Complex (NPC),controls the transport of all cellular material between the cytoplasm and the nucleus that occurs naturally in biological cells of many organisms.In order to understand the design characteristics of the NPC,we developed a microdevice for drug/fluidic transport mimicking the coarse-grained representation of the NPC geometry through computational fluid dynamic analysis and optimization.Specifically,the role of the central plug in active fluidic/particle transport and passive transport (without central plug) was investigated.Results of flow rate,pressure and velocity profiles obtained from the models indicate that the central plug plays a major role in transport through this biomolecular machine.The results of this investigation show that fluidic transport and flow passages are important factors in designing NPC based nano- and micro-devices for drug delivery.

  4. A Starting Point for Fluorescence-Based Single-Molecule Measurements in Biomolecular Research

    Directory of Open Access Journals (Sweden)

    Alexander Gust


    Full Text Available Single-molecule fluorescence techniques are ideally suited to provide information about the structure-function-dynamics relationship of a biomolecule as static and dynamic heterogeneity can be easily detected. However, what type of single-molecule fluorescence technique is suited for which kind of biological question and what are the obstacles on the way to a successful single-molecule microscopy experiment? In this review, we provide practical insights into fluorescence-based single-molecule experiments aiming for scientists who wish to take their experiments to the single-molecule level. We especially focus on fluorescence resonance energy transfer (FRET experiments as these are a widely employed tool for the investigation of biomolecular mechanisms. We will guide the reader through the most critical steps that determine the success and quality of diffusion-based confocal and immobilization-based total internal reflection fluorescence microscopy. We discuss the specific chemical and photophysical requirements that make fluorescent dyes suitable for single-molecule fluorescence experiments. Most importantly, we review recently emerged photoprotection systems as well as passivation and immobilization strategies that enable the observation of fluorescently labeled molecules under biocompatible conditions. Moreover, we discuss how the optical single-molecule toolkit has been extended in recent years to capture the physiological complexity of a cell making it even more relevant for biological research.

  5. iGNM 2.0: the Gaussian network model database for biomolecular structural dynamics. (United States)

    Li, Hongchun; Chang, Yuan-Yu; Yang, Lee-Wei; Bahar, Ivet


    Gaussian network model (GNM) is a simple yet powerful model for investigating the dynamics of proteins and their complexes. GNM analysis became a broadly used method for assessing the conformational dynamics of biomolecular structures with the development of a user-friendly interface and database, iGNM, in 2005. We present here an updated version, iGNM 2.0, which covers more than 95% of the structures currently available in the Protein Data Bank (PDB). Advanced search and visualization capabilities, both 2D and 3D, permit users to retrieve information on inter-residue and inter-domain cross-correlations, cooperative modes of motion, the location of hinge sites and energy localization spots. The ability of iGNM 2.0 to provide structural dynamics data on the large majority of PDB structures and, in particular, on their biological assemblies makes it a useful resource for establishing the bridge between structure, dynamics and function.

  6. Colloid-in-liquid crystal gels that respond to biomolecular interactions. (United States)

    Agarwal, Ankit; Sidiq, Sumyra; Setia, Shilpa; Bukusoglu, Emre; de Pablo, Juan J; Pal, Santanu Kumar; Abbott, Nicholas L


    This paper advances the design of stimuli-responsive materials based on colloidal particles dispersed in liquid crystals (LCs). Specifically, thin films of colloid-in-liquid crystal (CLC) gels undergo easily visualized ordering transitions in response to reversible and irreversible (enzymatic) biomolecular interactions occurring at the aqueous interfaces of the gels. In particular, LC ordering transitions can propagate across the entire thickness of the gels. However, confinement of the LC to small domains with lateral sizes of ∼10 μm does change the nature of the anchoring transitions, as compared to films of pure LC, due to the effects of confinement on the elastic energy stored in the LC. The effects of confinement are also observed to cause the response of individual domains of the LC within the CLC gel to vary significantly from one to another, indicating that manipulation of LC domain size and shape can provide the basis of a general and facile method to tune the response of these LC-based physical gels to interfacial phenomena. Overall, the results presented in this paper establish that CLC gels offer a promising approach to the preparation of self-supporting, LC-based stimuli-responsive materials.

  7. AFMPB: An adaptive fast multipole Poisson-Boltzmann solver for calculating electrostatics in biomolecular systems (United States)

    Lu, Benzhuo; Cheng, Xiaolin; Huang, Jingfang; McCammon, J. Andrew


    A Fortran program package is introduced for rapid evaluation of the electrostatic potentials and forces in biomolecular systems modeled by the linearized Poisson-Boltzmann equation. The numerical solver utilizes a well-conditioned boundary integral equation (BIE) formulation, a node-patch discretization scheme, a Krylov subspace iterative solver package with reverse communication protocols, and an adaptive new version of the fast multipole method in which the exponential expansions are used to diagonalize the multipole-to-local translations. The program and its full description, as well as several closely related libraries and utility tools are available at and a mirror site at This paper is a brief summary of the program: the algorithms, the implementation and the usage. Restrictions: Only three or six significant digits options are provided in this version. Unusual features: Most of the codes are in Fortran77 style. Memory allocation functions from Fortran90 and above are used in a few subroutines. Additional comments: The current version of the codes is designed and written for single core/processor desktop machines. Check for updates and changes. Running time: The running time varies with the number of discretized elements (N) in the system and their distributions. In most cases, it scales linearly as a function of N.

  8. PARENT: A Parallel Software Suite for the Calculation of Configurational Entropy in Biomolecular Systems. (United States)

    Fleck, Markus; Polyansky, Anton A; Zagrovic, Bojan


    Accurate estimation of configurational entropy from the in silico-generated biomolecular ensembles, e.g., from molecular dynamics (MD) trajectories, is dependent strongly on exhaustive sampling for physical reasons. This, however, creates a major computational problem for the subsequent estimation of configurational entropy using the Maximum Information Spanning Tree (MIST) or Mutual Information Expansion (MIE) approaches for internal molecular coordinates. In particular, the available software for such estimation exhibits serious limitations when it comes to molecules with hundreds or thousands of atoms, because of its reliance on a serial program architecture. To overcome this problem, we have developed a parallel, hybrid MPI/openMP C++ implementation of MIST and MIE, called PARENT, which is particularly optimized for high-performance computing and provides efficient estimation of configurational entropy in different biological processes (e.g., protein-protein interactions). In addition, PARENT also allows for a detailed mapping of intramolecular allosteric networks. Here, we benchmark the program on a set of 1-μs-long MD trajectories of 10 different protein complexes and their components, demonstrating robustness and good scalability. A direct comparison between MIST and MIE on the same dataset demonstrates a superior convergence behavior for the former approach, when it comes to total simulation length and configurational-space binning.

  9. Affinity analysis for biomolecular interactions based on magneto-optical relaxation measurements (United States)

    Aurich, Konstanze; Nagel, Stefan; Heister, Elena; Weitschies, Werner


    Magneto-optical relaxation measurements of magnetically labelled biomolecules are a promising tool for immunometric analyses. Carcinoembryonic antigen (CEA) and its polyclonal and monoclonal antibodies (anti-CEA) were utilized as a model system for affinity analysis of the interaction between antibody and antigen. For this purpose antibodies were coupled with magnetic nanoparticles (MNPs). Aggregation of these antibody sensors due to interactions with the CEA was observed subsequently by measuring the relaxation time of the birefringence of a transmitted laser beam that occurs in a pulsed magnetic field. A kinetic model of chain-like aggregation developed for these purposes enables the rapid and simple calculation of the kinetic parameters of the underlying protein interaction. From the known antigen concentration and the increase in particle size during the interaction we are able to estimate the unknown parameters with standard methods for the statistical description of stepwise polymerization. This novel affinity analysis was successfully applied for the antigen-antibody interaction described herein and can be applied to other biomolecular interactions. First efforts have been made to establish magneto-optical relaxation measurements in body fluids.

  10. Extension of the GLYCAM06 Biomolecular Force Field to Lipids, Lipid Bilayers and Glycolipids. (United States)

    Tessier, Matthew B; Demarco, Mari L; Yongye, Austin B; Woods, Robert J


    GLYCAM06 is a generalisable biomolecular force field that is extendible to diverse molecular classes in the spirit of a small-molecule force field. Here we report parameters for lipids, lipid bilayers and glycolipids for use with GLYCAM06. Only three lipid-specific atom types have been introduced, in keeping with the general philosophy of transferable parameter development. Bond stretching, angle bending, and torsional force constants were derived by fitting to quantum mechanical data for a collection of minimal molecular fragments and related small molecules. Partial atomic charges were computed by fitting to ensemble-averaged quantum-computed molecular electrostatic potentials.In addition to reproducing quantum mechanical internal rotational energies and experimental valence geometries for an array of small molecules, condensed-phase simulations employing the new parameters are shown to reproduce the bulk physical properties of a DMPC lipid bilayer. The new parameters allow for molecular dynamics simulations of complex systems containing lipids, lipid bilayers, glycolipids, and carbohydrates, using an internally consistent force field. By combining the AMBER parameters for proteins with the GLYCAM06 parameters, it is also possible to simulate protein-lipid complexes and proteins in biologically relevant membrane-like environments.

  11. High-Throughput, Protein-Targeted Biomolecular Detection Using Frequency-Domain Faraday Rotation Spectroscopy. (United States)

    Murdock, Richard J; Putnam, Shawn A; Das, Soumen; Gupta, Ankur; Chase, Elyse D Z; Seal, Sudipta


    A clinically relevant magneto-optical technique (fd-FRS, frequency-domain Faraday rotation spectroscopy) for characterizing proteins using antibody-functionalized magnetic nanoparticles (MNPs) is demonstrated. This technique distinguishes between the Faraday rotation of the solvent, iron oxide core, and functionalization layers of polyethylene glycol polymers (spacer) and model antibody-antigen complexes (anti-BSA/BSA, bovine serum albumin). A detection sensitivity of ≈10 pg mL(-1) and broad detection range of 10 pg mL(-1) ≲ cBSA ≲ 100 µg mL(-1) are observed. Combining this technique with predictive analyte binding models quantifies (within an order of magnitude) the number of active binding sites on functionalized MNPs. Comparative enzyme-linked immunosorbent assay (ELISA) studies are conducted, reproducing the manufacturer advertised BSA ELISA detection limits from 1 ng mL(-1) ≲ cBSA ≲ 500 ng mL(-1) . In addition to the increased sensitivity, broader detection range, and similar specificity, fd-FRS can be conducted in less than ≈30 min, compared to ≈4 h with ELISA. Thus, fd-FRS is shown to be a sensitive optical technique with potential to become an efficient diagnostic in the chemical and biomolecular sciences.

  12. 糖尿病足筛查表格的设计及应用%The design and application of diabetic foot screening form

    Institute of Scientific and Technical Information of China (English)

    欧召容; 梁赤波


    Objective To detect risk factors of diabetic foot through diabetic foot screening,and take countermeasures timely to reduce the incidence of diabetic foot.Methods Designed diabetic foot screening form according to the diagnostic criteria,prevention strategies of diabetic foot,and document literature.Applied diabetic foot screen to 358 cases of diabetic under the charge of Changan Community Health Service Center,who were randomly divided into control group and observation group based on dangerous level,with 179 cases in each group.Two groups were under observation for 1 year respectively.Control group received conventional management,while observation group received hierarchical management according to dangerous level.Results Screening results:① the risk of diabetic foot occurred in 277 patients (77.4%) in this study,multiple risk factors in 183 cases,single risk factor in 94 cases.② There were 51 cases of high-risk foot,77 cases of moderate-risk foot,149 cases of low-risk foot,and 81 cases of normal foot.There was statistically significant difference in the incidence of diabetic foot (high,moderate and low risk foot) before and after the intervention in observation group (P < 0.01),no statistically significant difference in control group (P > 0.05).Conclusions Patients with diabetic have a high risk of diabetic foot.So it is necessary to strengthen community screening of diabetic foot,and carry out appropriate management according to dangerous level to prevent the occurrence of diabetic foot.Diabetic foot screening table is simple,convenient,economic and applicable in clinical application,worthy of clinical promotion.%目的 通过对糖尿病足的筛查,早期发现糖尿病足的危险因素,针对病因及时采取针对性的措施,减少糖尿病足的发生.方法 依据糖尿病足的诊断标准和预防策略这两根主线,再结合查阅文献资料设计糖尿病足的筛查表.对长安社区纳入管理的358例糖尿病患者进行糖尿

  13. Application of DNA Hybridization Biosensor as a Screening Method for the Detection of Genetically Modified Food Components

    Directory of Open Access Journals (Sweden)

    Marian Filipiak


    Full Text Available An electrochemical biosensor for the detection of genetically modified food components is presented. The biosensor was based on 21-mer single-stranded oligonucleotide (ssDNA probe specific to either 35S promoter or nos terminator, which are frequently present in transgenic DNA cassettes. ssDNA probe was covalently attached by 5’-phosphate end to amino group of cysteamine self-assembled monolayer (SAM on gold electrode surface with the use of activating reagents – water soluble 1-ethyl-3(3’- dimethylaminopropyl-carbodiimide (EDC and N-hydroxy-sulfosuccinimide (NHS. The hybridization reaction on the electrode surface was detected via methylene blue (MB presenting higher affinity to ssDNA probe than to DNA duplex. The electrode modification procedure was optimized using 19-mer oligoG and oligoC nucleotides. The biosensor enabled distinction between DNA samples isolated from soybean RoundupReady® (RR soybean and non-genetically modified soybean. The frequent introduction of investigated DNA sequences in other genetically modified organisms (GMOs give a broad perspectives for analytical application of the biosensor.

  14. A smartphone-based colorimetric reader for bioanalytical applications using the screen-based bottom illumination provided by gadgets. (United States)

    Vashist, Sandeep Kumar; van Oordt, Thomas; Schneider, E Marion; Zengerle, Roland; von Stetten, Felix; Luong, John H T


    A smartphone-based colorimetric reader (SBCR) was developed using a Samsung Galaxy SIII mini, a gadget (iPAD mini, iPAD4 or iPhone 5s), integrated with a custom-made dark hood and base holder assembly. The smartphone equipped with a back camera (5 megapixels resolution) was used for colorimetric imaging via the hood and base-holder assembly. A 96- or 24-well microtiter plate (MTP) was positioned on the gadget's screensaver that provides white light-based bottom illumination only in the specific regions corresponding to the bottom of MTP's wells. The pixel intensity of the captured images was determined by an image processing algorithm. The developed SBCR was evaluated and compared with a commercial MTP reader (MTPR) for three model assays: our recently developed human C-reactive protein sandwich enzyme-linked immunosorbent assay (ELISA), horseradish peroxidase direct ELISA, and bicinchoninic acid protein estimation assay. SBCR had the same precision, dynamic range, detection limit and sensitivity as MTPR for all three assays. With advanced microfabrication and data processing, SBCR will become more compact, lighter, inexpensive and enriched with more features. Therefore, SBCR with a remarkable computing power could be an ideal point-of-care (POC) colorimetric detection device for the next-generation of cost-effective POC diagnostics, immunoassays and diversified bioanalytical applications.

  15. Real-Time, Label-Free Detection of Biomolecular Interactions in Sandwich Assays by the Oblique-Incidence Reflectivity Difference Technique

    Directory of Open Access Journals (Sweden)

    Yung-Shin Sun


    Full Text Available One of the most important goals in proteomics is to detect the real-time kinetics of diverse biomolecular interactions. Fluorescence, which requires extrinsic tags, is a commonly and widely used method because of its high convenience and sensitivity. However, in order to maintain the conformational and functional integrality of biomolecules, label-free detection methods are highly under demand. We have developed the oblique-incidence reflectivity difference (OI-RD technique for label-free, kinetic measurements of protein-biomolecule interactions. Incorporating the total internal refection geometry into the OI-RD technique, we are able to detect as low as 0.1% of a protein monolayer, and this sensitivity is comparable with other label-free techniques such as surface plasmon resonance (SPR. The unique advantage of OI-RD over SPR is no need for dielectric layers. Moreover, using a photodiode array as the detector enables multi-channel detection and also eliminates the over-time signal drift. In this paper, we demonstrate the applicability and feasibility of the OI-RD technique by measuring the kinetics of protein-protein and protein-small molecule interactions in sandwich assays.

  16. Data Mining Approaches for Genomic Biomarker Development: Applications Using Drug Screening Data from the Cancer Genome Project and the Cancer Cell Line Encyclopedia. (United States)

    Covell, David G


    Developing reliable biomarkers of tumor cell drug sensitivity and resistance can guide hypothesis-driven basic science research and influence pre-therapy clinical decisions. A popular strategy for developing biomarkers uses characterizations of human tumor samples against a range of cancer drug responses that correlate with genomic change; developed largely from the efforts of the Cancer Cell Line Encyclopedia (CCLE) and Sanger Cancer Genome Project (CGP). The purpose of this study is to provide an independent analysis of this data that aims to vet existing and add novel perspectives to biomarker discoveries and applications. Existing and alternative data mining and statistical methods will be used to a) evaluate drug responses of compounds with similar mechanism of action (MOA), b) examine measures of gene expression (GE), copy number (CN) and mutation status (MUT) biomarkers, combined with gene set enrichment analysis (GSEA), for hypothesizing biological processes important for drug response, c) conduct global comparisons of GE, CN and MUT as biomarkers across all drugs screened in the CGP dataset, and d) assess the positive predictive power of CGP-derived GE biomarkers as predictors of drug response in CCLE tumor cells. The perspectives derived from individual and global examinations of GEs, MUTs and CNs confirm existing and reveal unique and shared roles for these biomarkers in tumor cell drug sensitivity and resistance. Applications of CGP-derived genomic biomarkers to predict the drug response of CCLE tumor cells finds a highly significant ROC, with a positive predictive power of 0.78. The results of this study expand the available data mining and analysis methods for genomic biomarker development and provide additional support for using biomarkers to guide hypothesis-driven basic science research and pre-therapy clinical decisions.

  17. Data Mining Approaches for Genomic Biomarker Development: Applications Using Drug Screening Data from the Cancer Genome Project and the Cancer Cell Line Encyclopedia.

    Directory of Open Access Journals (Sweden)

    David G Covell

    Full Text Available Developing reliable biomarkers of tumor cell drug sensitivity and resistance can guide hypothesis-driven basic science research and influence pre-therapy clinical decisions. A popular strategy for developing biomarkers uses characterizations of human tumor samples against a range of cancer drug responses that correlate with genomic change; developed largely from the efforts of the Cancer Cell Line Encyclopedia (CCLE and Sanger Cancer Genome Project (CGP. The purpose of this study is to provide an independent analysis of this data that aims to vet existing and add novel perspectives to biomarker discoveries and applications. Existing and alternative data mining and statistical methods will be used to a evaluate drug responses of compounds with similar mechanism of action (MOA, b examine measures of gene expression (GE, copy number (CN and mutation status (MUT biomarkers, combined with gene set enrichment analysis (GSEA, for hypothesizing biological processes important for drug response, c conduct global comparisons of GE, CN and MUT as biomarkers across all drugs screened in the CGP dataset, and d assess the positive predictive power of CGP-derived GE biomarkers as predictors of drug response in CCLE tumor cells. The perspectives derived from individual and global examinations of GEs, MUTs and CNs confirm existing and reveal unique and shared roles for these biomarkers in tumor cell drug sensitivity and resistance. Applications of CGP-derived genomic biomarkers to predict the drug response of CCLE tumor cells finds a highly significant ROC, with a positive predictive power of 0.78. The results of this study expand the available data mining and analysis methods for genomic biomarker development and provide additional support for using biomarkers to guide hypothesis-driven basic science research and pre-therapy clinical decisions.

  18. Debye screening (United States)

    Brydges, David C.; Federbush, Paul


    The existence and exponential clustering of correlation functions for a classical coulomb system at low density or high temperature are proven using methods from constructive quantum field theory, the sine gordon transformation and the Glimm, Jaffe, Spencer expansion about mean field theory. This is a vindication of a belief of long standing among physicists, known as Debye screening. That is, because of special properties of the coulomb potential, the configurations of significant probability are those in which the long range parts of r -1 are mostly cancelled, leaving an effective exponentially decaying potential acting between charge clouds. This paper generalizes a previous paper of one of the authors in which these results were obtained for a special lattice system. The present treatment covers the continuous mechanics situation, with essentially arbitrary short range forces and charge species. Charge symmetry is not assumed.

  19. Screening in Hot Non-Abelian Plasma

    CERN Document Server

    Petreczky, P


    This thesis is devoted to the study of the screening masses in hot non-Abelian theories. Section 1 contain a brief introduction to the topic. In section 2 a detailed overview of the screening phenomena and their applications is given. In section 3 the screening masses are defined through the coupled gap equations. Section 4 deals with the determination of the screening masses of hot SU(2) gauge theory in the framework of the 3d lattice adjoint Higgs model considered as an effective theory. Finally in section 5 the screening masses of hot SU(2) Higgs model are examined.

  20. 胸片和临床症状肺结核筛查的应用价值%Application Value of Chest X-Ray and Clinical Symptoms of Pulmonary Tuberculosis Screening

    Institute of Scientific and Technical Information of China (English)



    Objective: To evaluate the value of clinical application of chest X-ray and clinical symptoms of pulmonary TB screening. Methods:All objects by symptoms, chest X-ray screening questionnaire (CXR), and (or) sputum smear or culture. Results:There were abnormal CXR sensitivity was 94%, specificity was 73%. The sensitivity of screening with symptoms was 90%, the specificity was 32%. Smear microscopy failed to increase the suspicious patients, joint symptoms and CXR screening sensitivity was 100%, specificity was 65%. Conclusion:Only by CXR screening showed that the accuracy of screening compared with symptoms of high, combined with CXR and symptom screening has the highest sensitivity.%目的:评估胸片和临床症状对肺TB筛查的应用价值。方法:所有对象经症状问卷筛查、胸片(CXR)、和(或)痰涂片或培养。结果:存在CXR异常者敏感性为94%,特异性为73%。症状筛查结合的敏感性为90%,特异性为32%。涂片显微镜检查未能增加可疑病人,联合症状和CXR筛查敏感性达100%,特异性达65%。结论:仅用CXR筛查即呈现较单纯症状筛查高的准确度,联合CXR和症状筛查有最高的敏感性。

  1. Comparison of Four Kinds of Nutritional Screening Tools in Clinical Application of General Surgery Pa-tients Application%4种营养筛查工具在普外科患者中应用的比较

    Institute of Scientific and Technical Information of China (English)

    包学智; 田伟军


    目的:使用NRS2002和SGA、MNA、NRI 4种工具对普外科入院患者进行营养状态调查,比较4种工具的适用性和一致性以及每种工具所得筛查结果和临床结局的关系。方法:采用连续取样方法选取天津医科大学总医院普外科收治的125名患者为研究对象,当患者入院第2 d分别应用NRS2002和SGA、MNA、NRI进行营养筛查和评估,并比较每种工具所得筛查结果和临床结局的关系。结果:入院NRS2002、SGA及MNA适用性91.91%,NRI适用性91.18%,4种方法对患者营养风险的评价具有一致性。将BMI≤18.5或ALB≤30 g/L作为营养不良的一个标准,4种评价工具与该标准的一致性较差。NRS2002、SGA筛查结果和临床结局的关系最为密切。结论:4种营养评价工具均适用于普外科营养不足的筛查。NRS2002、SGA筛查结果和临床结局的关系最为密切。%Objective NRS2002, SGA, MNA and NRI are used to screen nutritional risk of general surgery hospitalized patients, then to compare their applicability and consistency and analyze the effect in clinical out⁃comes of NRS results with respect to each tool. Methods The 125 patients hospitalized in General Hospital of Tianjin Medical University from June to September 2014 were chosen as object of study, to screen and evalu⁃ate nutritional risk of patients by NRS 2002, SGA, MNA and NRI, respectively, on the second hospital day. Then to compare the consistency of NRS results with respect to the four tools on clinical outcomes. Results The applicabilities of hospital NRS2002, SGA, MNA and NRI were alternatively 91.91%,91.91%,91.91% and 91.18%.The evaluation of patients’NRS corresponding to different four tools was consistent. Let BMI≤18.5 or ALB≤30 g/L be one standard of malnutrition, the consistency of four evaluation tools and the standard was poor. The effects of screening results of NRS2002 and SGA on clinical outcomes were most closely related. Conclusion

  2. Screening and identification of phospholipase-producing strains and their applications%产磷脂酶菌株的筛选鉴定及其应用

    Institute of Scientific and Technical Information of China (English)

    姜芳燕; 王金梅; 戴大章; 李春


    采用磷脂平板初筛和摇瓶复筛,从富油土样中筛选得到一株产磷脂酶菌株BIT-18.经菌株形态特征、生理生化特征及16S rRNA序列分析,鉴定其为荧光假单胞菌(Pseudomonas fluorescens).以磷脂标准品(1-棕榈酰-2-油酰-Sn-甘油-3-磷脂酰胆碱)为底物,通过气相色谱分析反应产物的脂肪酸成分,定性鉴定P.fluorescens BIT-18表达的磷脂酶为B型磷脂酶.该酶为低温酶,最适温度和pH值分别为25℃和6.5,低浓度的金属离子有利于其酶促反应进行.以磷脂酶B为催化剂在自制间歇式反应器中对大豆油进行酶法脱胶,在加酶量500 U·kg-,加水量2%,温度40℃,pH 4.7的条件下反应6h,脱胶油磷含量由90.1 mg·kg-降至4.6 mg· kg-1,脱胶率高达94.9%,显示出良好的应用前景.%Using soybean phospholipids as substrates, one strain which expressed phospholipase was screened out from the oil-rich soil sample by preliminary screening of plate cultivation and re-screening of shake flask fermentation. According to the morphological characteristics, physiochemical properties, and 16S rRNA sequences, the strain BIT-18 was identified as Pseudomonas fluorescens. Synthetic phosphatecholine (l-palmitoyl-2-oleoyl phosphatecholine) was used as substrate, then the fatty acid compositions of hydrolyzates were analyzed by gas chromatography, and the phospholipase from BIT-18 was determined as phospholipase B. This enzyme could not tolerate a high temperature. The optimal conditions for the enzymatic reaction were 251 and pH 6. 5, and low concentrations of metal ions were good for trigging its reaction. The phospholipase B from BIT-18 was used as catalyst for the degumming of soybean oil in a self-made batch reactor. The optimal conditions were phospholipase B dosage of 500 U · kg-1 and 2% water, and reaction at 40℃ , pH 4. 7 for 6 h. The residual phosphorus content of degummed oil decreased from 90. 1 mg · kg-1 to 4. 6 mg · kg-1, with the degumming rate as

  3. An Analysis of Biomolecular Force Fields for Simulations of Polyglutamine in Solution

    Energy Technology Data Exchange (ETDEWEB)

    Fluitt, Aaron M. [Univ. of Chicago, IL (United States); de Pablo, Juan J. [Argonne National Lab. (ANL), Argonne, IL (United States)


    Polyglutamine (polyQ) peptides are a useful model system for biophysical studies of protein folding and aggregation, both for their intriguing aggregation properties and their own relevance to human disease. The genetic expansion of a polyQ tract triggers the formation of amyloid aggregates associated with nine neurodegenerative diseases. Several clearly identifiable and separable factors, notably the length of the polyQ tract, influence the mechanism of aggregation, its associated kinetics, and the ensemble of structures formed. Atomistic simulations are well positioned to answer open questions regarding the thermodynamics and kinetics of polyQ folding and aggregation. The additional, explicit representation of water permits deeper investigation of the role of solvent dynamics, and it permits a direct comparison of simulation results with infrared spectroscopy experiments. The generation of meaningful simulation results hinges on satisfying two essential criteria: achieving sufficient conformational sampling to draw statistically valid conclusions, and accurately reproducing the intermolecular forces that govern system structure and dynamics. In this work, we examine the ability of 12 biomolecular force fields to reproduce the properties of a simple, 30-residue polyQ peptide (Q30) in explicit water. In addition to secondary and tertiary structure, we consider generic structural properties of polymers that provide additional dimensions for analysis of the highly degenerate disordered states of the molecule. We find that the 12 force fields produce a wide range of predictions. We identify AMBER ff99SB, AMBER ff99SB*, and OPLS-AA/L to be most suitable for studies of polyQ folding and aggregation.

  4. g_contacts: Fast contact search in bio-molecular ensemble data (United States)

    Blau, Christian; Grubmuller, Helmut


    Short-range interatomic interactions govern many bio-molecular processes. Therefore, identifying close interaction partners in ensemble data is an essential task in structural biology and computational biophysics. A contact search can be cast as a typical range search problem for which efficient algorithms have been developed. However, none of those has yet been adapted to the context of macromolecular ensembles, particularly in a molecular dynamics (MD) framework. Here a set-decomposition algorithm is implemented which detects all contacting atoms or residues in maximum O(Nlog(N)) run-time, in contrast to the O(N2) complexity of a brute-force approach. Catalogue identifier: AEQA_v1_0 Program summary URL: Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, No. of lines in distributed program, including test data, etc.: 8945 No. of bytes in distributed program, including test data, etc.: 981604 Distribution format: tar.gz Programming language: C99. Computer: PC. Operating system: Linux. RAM: ≈Size of input frame Classification: 3, 4.14. External routines: Gromacs 4.6[1] Nature of problem: Finding atoms or residues that are closer to one another than a given cut-off. Solution method: Excluding distant atoms from distance calculations by decomposing the given set of atoms into disjoint subsets. Running time:≤O(Nlog(N)) References: [1] S. Pronk, S. Pall, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R. Shirts, J.C. Smith, P. M. Kasson, D. van der Spoel, B. Hess and Erik Lindahl, Gromacs 4.5: a high-throughput and highly parallel open source molecular simulation toolkit, Bioinformatics 29 (7) (2013).

  5. Biomolecularly capped uniformly sized nanocrystalline materials: glutathione-capped ZnS nanocrystals (United States)

    Torres-Martínez, Claudia L.; Nguyen, Liem; Kho, Richard; Bae, Weon; Bozhilov, Krassimir; Klimov, Victor; Mehra, Rajesh K.


    Micro-organisms such as bacteria and yeasts form CdS to detoxify toxic cadmium ions. Frequently, CdS particles formed in yeasts and bacteria were found to be associated with specific biomolecules. It was later determined that these biomolecules were present at the surface of CdS. This coating caused a restriction in the growth of CdS particles and resulted in the formation of nanometre-sized semiconductors (NCs) that exhibited typical quantum confinement properties. Glutathione and related phytochelatin peptides were shown to be the biomolecules that capped CdS nanocrystallites synthesized by yeasts Candida glabrata and Schizosaccharomyces pombe. Although early studies showed the existence of specific biochemical pathways for the synthesis of biomolecularly capped CdS NCs, these NCs could be formed in vitro under appropriate conditions. We have recently shown that cysteine and cysteine-containing peptides such as glutathione and phytochelatins can be used in vitro to dictate the formation of discrete sizes of CdS and ZnS nanocrystals. We have evolved protocols for the synthesis of ZnS or CdS nanocrystals within a narrow size distribution range. These procedures involve three steps: (1) formation of metallo-complexes of cysteine or cysteine-containing peptides, (2) introduction of stoichiometric amounts of inorganic sulfide into the metallo-complexes to initiate the formation of nanocrystallites and finally (3) size-selective precipitation of NCs with ethanol in the presence of Na+. The resulting NCs were characterized by optical spectroscopy, high-resolution transmission electron microscopy (HRTEM), x-ray diffraction and electron diffraction. HRTEM showed that the diameter of the ZnS-glutathione nanocrystals was 3.45+/-0.5 nm. X-ray diffraction and electron diffraction analyses indicated ZnS-glutathione to be hexagonal. Photocatalytic studies suggest that glutathione-capped ZnS nanocrystals prepared by our procedure are highly efficient in degrading a test model

  6. Enthalpy-entropy compensation in biomolecular halogen bonds measured in DNA junctions. (United States)

    Carter, Megan; Voth, Andrea Regier; Scholfield, Matthew R; Rummel, Brittany; Sowers, Lawrence C; Ho, P Shing


    Interest in noncovalent interactions involving halogens, particularly halogen bonds (X-bonds), has grown dramatically in the past decade, propelled by the use of X-bonding in molecular engineering and drug design. However, it is clear that a complete analysis of the structure-energy relationship must be established in biological systems to fully exploit X-bonds for biomolecular engineering. We present here the first comprehensive experimental study to correlate geometries with their stabilizing potentials for fluorine (F), chlorine (Cl), bromine (Br), or iodine (I) X-bonds in a biological context. For these studies, we determine the single-crystal structures of DNA Holliday junctions containing halogenated uracil bases that compete X-bonds against classic hydrogen bonds (H-bonds), estimate the enthalpic energies of the competing interactions in the crystal system through crystallographic titrations, and compare the enthalpic and entropic energies of bromine and iodine X-bonds in solution by differential scanning calorimetry. The culmination of these studies demonstrates that enthalpic stabilization of X-bonds increases with increasing polarizability from F to Cl to Br to I, which is consistent with the σ-hole theory of X-bonding. Furthermore, an increase in the X-bonding potential is seen to direct the interaction toward a more ideal geometry. However, the entropic contributions to the total free energies must also be considered to determine how each halogen potentially contributes to the overall stability of the interaction. We find that bromine has the optimal balance between enthalpic and entropic energy components, resulting in the lowest free energy for X-bonding in this DNA system. The X-bond formed by iodine is more enthalpically stable, but this comes with an entropic cost, which we attribute to crowding effects. Thus, the overall free energy of an X-bonding interaction balances the stabilizing electrostatic effects of the σ-hole against the competing

  7. Morbillivirus infection in cetaceans stranded along the Italian coastline: pathological, immunohistochemical and biomolecular findings. (United States)

    Di Guardo, Giovanni; Di Francesco, Cristina Esmeralda; Eleni, Claudia; Cocumelli, Cristiano; Scholl, Francesco; Casalone, Cristina; Peletto, Simone; Mignone, Walter; Tittarelli, Cristiana; Di Nocera, Fabio; Leonardi, Leonardo; Fernández, Antonio; Marcer, Federica; Mazzariol, Sandro


    Morbilliviruses are recognized as biological agents highly impacting the health and conservation status of free-ranging cetaceans worldwide, as clearly exemplified by the two Dolphin Morbillivirus (DMV) epidemics of 1990-1992 and 2006-2008 among Mediterranean striped dolphins (Stenella coeruleoalba). After these two epidemics, morbilliviral infection (MI) cases with peculiar neurobiological features were reported in striped dolphins stranded along the Spanish coastline. Affected cetaceans showed a subacute-to-chronic, non-suppurative encephalitis, with brain lesions strongly resembling those found in human "subacute sclerosing panencephalitis" and "old dog encephalitis". Brain was the only tissue in which morbilliviral antigen and/or genome could be detected. Beside a case of morbilliviral encephalitis in a striped dolphin's calf stranded in 2009, we observed 5 additional MI cases in 2 striped dolphins, 1 bottlenose dolphin (Tursiops truncatus) and 2 fin whales (Balaenoptera physalus), all stranded in 2011 along the Italian coastline. Noteworthy, 3 of these animals (2 striped dolphins and 1 bottlenose dolphin) showed immunohistochemical (IHC) and/or biomolecular (PCR) evidence of morbilliviral antigen and/or genome exclusively in their brain, with 1 striped dolphin and 1 bottlenose dolphin also exhibiting a non-suppurative encephalitis. Furthermore, simultaneous IHC and PCR evidence of a Toxoplasma gondii coinfection was obtained in 1 fin whale. The above results are consistent with those reported in striped dolphins after the two MI epidemics of 1990-92 and 2006-2008, with evidence of morbilliviral antigen and/or genome being found exclusively in the brain tissue from affected animals.

  8. Immunohistochemical Study to Evaluate the Prognostic Significance of Four Biomolecular Markers in Radiotherapy of Nasopharyngeal Carcinoma

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Yeon Joo; Lee, Seung Hee; Wu, Hong Gyun; Go, Heoun Jeong; Jeon, Yoon Kyung [Seoul National University College of Medicine, Seoul (Korea, Republic of)


    We performed an immunohistochemical study with pre-treatment biopsy specimens to evaluate the prognostic significance of four biomolecular markers which can be used as a predictive assay for radiotherapy (RT) treatment of nasopharyngeal carcinoma (NPC). From January 1998 through December 2006, 68 patients were histologically diagnosed as non-metastatic NPC and treated by RT. Only 38 patients had the paraffin block for the immunohistochemical study. Thirty-one patients had undifferentiated carcinoma and 7 patients had squamous cell carcinoma. Thirty two patients (84%) had advanced stage NPC (2002 AJCC Stage III{approx}IV). Immunohistochemical staining was performed for Met, COX-2, nm23-H1, and epidermal growth factor receptor (EGFR) expression using routine methods. The median follow-up time was 30 months (range, 11 to 83 months) for all patients, and 39 months (range, 19 to 83 months) for surviving patients. The 5-year overall survival (OS) rate of the patients with high Met extent ({>=}50%) was significantly lower than that of the patients with low Met extent (48% vs. 84%, p=0.02). In addition, Met extent was also a significant prognostic factor in multivariate analysis (p=0.01). No correlation was observed between Met extent and T stage, N stage, stage group, gender, age, and the response to chemotherapy or RT. Met extent showed moderate correlation with COX-2 expression (Pearson coefficient 0.496, p<0.01), but COX-2 expression did not affect OS. Neither nm23-H1 or EGFR expression was a prognostic factor for OS in this study. High Met extent ({>=}50%) might be an independent prognostic factor that predicts poor OS in NPC treated with RT.

  9. Evolução biomolecular homoquiral: a origem e a amplificação da quiralidade nas moléculas da vida Homochiral biomolecular evolution: the origin and the amplification of chirality in life molecules

    Directory of Open Access Journals (Sweden)

    José Augusto R. Rodrigues


    Full Text Available The fact that biologically relevant molecules exist only as one of the two enantiomers is a fascinating example of complete symmetry breaking of chirality and has long intrigued our curiosity. The origin of this selective chirality has remained a fundamental enigma with regard to the origin of life since the time of Pasteur, 160 years ago. The symmetry breaking processes, which include autocatalytic crystallization, asymmetric autocatalysis, spontaneous crystallization, adsorption and polymerization of amino acids on mineral surfaces, provide new insights into the origin of biomolecular homochirality.

  10. Quantum algorithms and mathematical formulations of biomolecular solutions of the vertex cover problem in the finite-dimensional hilbert space. (United States)

    Chang, Weng-Long; Ren, Ting-Ting; Feng, Mang


    In this paper, it is shown that the proposed quantum algorithm for implementing Boolean circuits generated from the DNA-based algorithm solving the vertex-cover problem of any graph G with m edges and n vertices is the optimal quantum algorithm. Next, it is also demonstrated that mathematical solutions of the same biomolecular solutions are represented in terms of a unit vector in the finite-dimensional Hilbert space. Furthermore, for testing our theory, a nuclear magnetic resonance (NMR) experiment of three quantum bits to solve the simplest vertex-cover problem is completed.

  11. Application of Touch Screen Panels in the Control System of Wood-based Board Production Lines%触摸屏在人造板生产线控制系统中的应用

    Institute of Scientific and Technical Information of China (English)



    The application of touch screen panels in the control system of wood-based board production lines is introduced. A touch screen panel, a man-machine interface, serves as a bridge for the bi-directional communication between operators and machines, suitable for the wide application and popularization in the control system of small and medium-sized wood-based board production lines.%介绍了触摸屏在人造板生产线控制系统中的应用。触摸屏这一人机界面作为操作人员和机器之间双向沟通的桥梁,适合在中小型人造板生产线控制系统中广泛推广应用。

  12. 胚胎植入前遗传学筛查的临床应用%Clinical Application of Preimplantation Genetic Screening

    Institute of Scientific and Technical Information of China (English)

    张倩; 郑叶; 颜军昊


    With the development of assisted reproductive technology and genetic analysis technology, the preimplantation genetic screening (PGS) is used to detect the numerical chromosomal abnormalities (aneuploid) in embryos, so as to improve pregnancy outcomes of in vitro fertilization-embryo transfer (IVF-ET). New methods and technologies have been used in PGS, such as blastocyst stage biopsy, comparative genomic hybridization, microarrays and next generation sequencing, which increase the diagnose accuracy and decrease the risk of misdiagnosis. At the same time, PGS is also facing many challenges. The clinical application of PGS was reviewed in this article.%随着辅助生殖技术和遗传学分析技术的发展,胚胎植入前遗传学筛查应用于胚胎染色体数目异常(非整倍体)检测,以期改善体外受精-胚胎移植的妊娠结局。新方法、新技术不断出现并应用于胚胎植入前遗传学筛查中,如囊胚期活检、比较基因组杂交技术、微阵列技术、第二代测序技术等,显著增加了诊断准确性,减少误诊风险。同时,胚胎植入前遗传学筛查的广泛应用也面临许多挑战。综述该领域的应用进展和面临的挑战。

  13. An Overview of High Throughput Biological Screening Methods and Its Application%高通量生物分析技术及应用研究进展

    Institute of Scientific and Technical Information of China (English)

    翟绪昭; 王广彬; 赵亮涛; 曾海娟; 李建武; 丁承超; 宋春美; 刘箐


    基因组学、蛋白组学、代谢组学等研究的兴起使得大量生物数据的快速获取和分析变得更加重要。传统的生物分析方法大多耗时、费力,已无法满足现代生命科学研究对海量生物信息的需要。高通量分析技术是快速获取大量生物信息的重要手段。对微阵列芯片、微流控芯片、焦磷酸测序、荧光偏振免疫分析、量子点荧光免疫分析等高通量生物分析技术进行了综述,简述了近几年高通量生物分析技术的研究重点和研究成果,并对其在食品安全、医学等方面的应用进行了简要介绍。%The emergence of genomics,proteomics,metabolomics and other molecular biology studies makes the rapid attainment and assessment of large amounts of biological data become extremely important. The traditional detection methods are time-consuming and laborious, and cannot satisfy the needs of contemporary biological science research for massive biological information. High Throughput Screening(HTS) methods are significant means of quick attainment of massive biological information. This paper will make an overview of microarray chip, microfluidic chip,pyrosequencing,fluorescence polarization immunoassay,quantum dot fluorescence immunoassay and multiple PCR, outline research focus and research results of HTS methods in recent years,and briefly introduce its application in food safety,medicine and other fields.

  14. Lung Cancer Screening (United States)

    ... Treatment Lung Cancer Prevention Lung Cancer Screening Research Lung Cancer Screening (PDQ®)–Patient Version What is screening? Go ... These are called diagnostic tests . General Information About Lung Cancer Key Points Lung cancer is a disease in ...

  15. Skin Cancer Screening (United States)

    ... Genetics of Skin Cancer Skin Cancer Screening Research Skin Cancer Screening (PDQ®)–Patient Version What is screening? ... These are called diagnostic tests . General Information About Skin Cancer Key Points Skin cancer is a disease ...

  16. Mental Health Screening Center (United States)

    ... Releases & Announcements Public Service Announcements Partnering with DBSA Mental Health Screening Center These online screening tools are not ... you have any concerns, see your doctor or mental health professional. Depression This screening form was developed from ...

  17. Testicular Cancer Screening (United States)

    ... Health Professional Testicular Cancer Treatment Testicular Cancer Screening Testicular Cancer Screening (PDQ®)–Patient Version What is screening? Go ... These are called diagnostic tests . General Information About Testicular Cancer Key Points Testicular cancer is a disease in ...

  18. Application of Sweat Patch Screening for 16 Drugs and Metabolites Using a Fast and Highly Selective LC-MS/MS Method

    NARCIS (Netherlands)

    Koster, Remco A.; Alffenaar, Jan-Willem C.; Greijdanus, Ben; VanDerNagel, Joanneke E. L.; Uges, Donald R. A.


    Background: To facilitate the monitoring of drug abuse by patients, a method was developed and validated for fast and highly selective screening for amphetamine, methamphetamine, 3,4-methylenedioxymethamphetamine, methylenedioxyamphetamine, methylenedioxyethylamphetamine, methylphenidate, cocaine, b

  19. A Bayesian Predictive Discriminant Analysis with Screened Data


    Hea-Jung Kim


    In the application of discriminant analysis, a situation sometimes arises where individual measurements are screened by a multidimensional screening scheme. For this situation, a discriminant analysis with screened populations is considered from a Bayesian viewpoint, and an optimal predictive rule for the analysis is proposed. In order to establish a flexible method to incorporate the prior information of the screening mechanism, we propose a hierarchical screened scale mixture of normal (HSS...

  20. Four Principles to Consider Before Advising Women on Screening Mammography

    DEFF Research Database (Denmark)

    Keen, John D; Juhl Jørgensen, Karsten


    This article reviews four important screening principles applicable to screening mammography in order to facilitate informed choice. The first principle is that screening may help, hurt, or have no effect. In order to reduce mortality and mastectomy rates, screening must reduce the rate of advanced...... might extend a woman's life is narrow, as many tumors that can form metastases will already have done so. Instead of encouraging screening mammography, physicians should help women make an informed decision as with any medical intervention....

  1. HPV基因分型检测在宫颈癌筛查中的应用%The Application of HPV Genotypes in Screening of Cervical Cancer

    Institute of Scientific and Technical Information of China (English)

    肖凤静; 苏明权; 杨柳; 马越云; 郝晓柯


    Objective: To explore the application value of HPV genotyped technology in screening of cervical cancer. Methods: Reverse dot blot hybridization was used to demonstrate the HPV genotypes, there were 23 genotypes including low-risk type and high-risk type. Results: In 98 samples, 38 cases were infected by HPV and the positive rate was 38.8%. The prevalence of HPV infection in the chronic cervicitis, CIN I, CIN II, CIN III and SCC was 30.4% (14/46), 15.4% (4/26), 71.4%(10/14), 75%(6/8) and 100% (4/4) respectively. The order of type-specific prevalence was HPV43, 11, 6, 31, 42 and 51 in the chronic cervicitis, HPV35, 16, 52, 53 and 59 in CIN I; HPV 16,6,11 and 51 in CIN II , HPV 16,18,31 and 53 in CIN III while the distribution order in SCC was HPV 1 6, followed by HPV52, 18, 33, 58, 59 and 66. Conclusions: Continuous HPV infection has a close relationship with cervical disease. Detection of HPV gene type provides great help for clinical screening, diagnosis, treatment and prognosis of cervical disease detection.%目的:探讨人乳头瘤病毒(human papilloma virus,HPV)基因分型技术在宫颈癌筛查中的临床应用价值.方法:采用反向斑点杂交法对HPV基因型进行分析,包括低危型(如6、11、42、43、44型等)和高危型(如16、18、31、33、35、MM4型等)共23个型别.结果:98例样本中检出HPV阳性者38例,23种基因型中共检出15种HPV型别,HPV总感染率38.8%(38/98).慢性宫颈炎患者中HPV感染率30.4% (14/46),检测到的HPV亚型主要是HPV43,11,6,42,31和51(其中HPV6,42,31,51检出率一致).CIN I患者HPV感染率15.4%(4/26),最常见的HPV亚型为HPV35,其次为HPV16,52,53和59(其中16,52,53,59检出率一致).CIN Ⅱ患者HPV感染率71.4%(10/14),以HPV16,6,11,51等亚型最常见.CINⅢ患者HPV感染率75%(6/8),HPV亚型以HPV16,18,31,53为主.SCC患者HPV阳性率为100%(4/4),HPV16检测率最高,其次为HPV52,18,33,58,59和66.结论:持续的HPV感染与宫颈疾病有着密切的关

  2. Unraveling the biomolecular snapshots of mitosis in healthy and cancer cells using plasmonically-enhanced Raman spectroscopy. (United States)

    Panikkanvalappil, Sajanlal R; Hira, Steven M; Mahmoud, Mahmoud A; El-Sayed, Mostafa A


    Owing to the dynamic and complex nature of mitosis, precise and timely executions of biomolecular events are critical for high fidelity cell division. In this context, visualization of such complex events at the molecular level can provide vital information on the biomolecular processes in abnormal cells. Here, we explored the plasmonically enhanced light scattering properties of functionalized gold nanocubes (AuNCs) together with surface-enhanced Raman spectroscopy (SERS) to unravel the complex and dynamic biological processes involved in mitosis of healthy and cancerous cells from its molecular perspectives. By monitoring various stages of mitosis using SERS, we noticed that relatively high rate of conversion of mitotic proteins from their α-helix structure to β-sheet conformation is likely in the cancer cells during meta-, ana-, and telophases. Unique biochemical modifications to the lipid and amino acid moieties, associated with the observed protein conformational modifications, were also identified. However, in healthy cells, the existence of proteins in their β conformation was momentary and was largely in the α-helix form. The role of abnormal conformational modifications of mitotic proteins on the development of anomalous mitotic activities was further confirmed by looking at plasmonic nanoparticle-induced cytokinesis failure in cancer cells. Our findings illustrate the vast possibilities of SERS in real-time tracking of complex, subtle, and momentary modifications of biomolecules in live cells, which could provide new insights to the role of protein conformation dynamics during mitosis on the development of cancer and many other diseases.

  3. Nanomechanical force transducers for biomolecular and intracellular measurements: is there room to shrink and why do it? (United States)

    Sirbuly, Donald J; Friddle, Raymond W; Villanueva, Joshua; Huang, Qian


    Over the past couple of decades there has been a tremendous amount of progress on the development of ultrasensitive nanomechanical instruments, which has enabled scientists to peer for the first time into the mechanical world of biomolecular systems. Currently, work-horse instruments such as the atomic force microscope and optical/magnetic tweezers have provided the resolution necessary to extract quantitative force data from various molecular systems down to the femtonewton range, but it remains difficult to access the intracellular environment with these analytical tools as they have fairly large sizes and complicated feedback systems. This review is focused on highlighting some of the major milestones and discoveries in the field of biomolecular mechanics that have been made possible by the development of advanced atomic force microscope and tweezer techniques as well as on introducing emerging state-of-the-art nanomechanical force transducers that are addressing the size limitations presented by these standard tools. We will first briefly cover the basic setup and operation of these instruments, and then focus heavily on summarizing advances in in vitro force studies at both the molecular and cellular level. The last part of this review will include strategies for shrinking down the size of force transducers and provide insight into why this may be important for gaining a more complete understanding of cellular activity and function.

  4. Application of whole-cell subtractive panning in phage display library screening%全细胞差减筛选法在噬菌体展示文库筛选中的应用

    Institute of Scientific and Technical Information of China (English)

    吴红珍; 张林波


    全细胞差减筛选法是近年来在细胞筛选的基础上发展起来的一项筛选技术,其利用成对的细胞,即两种不同状态的细胞对噬菌体展示文库进行差减筛选,主要用于筛选新的抗原表位、受体、配体、新型疫苗、肿瘤细胞的靶向活性肽、靶向基因载体及受体或酶的激动剂或抑制剂等.本文就其筛选的原理、优缺点、优化及其在噬菌体展示文库筛选中的应用作一综述.%Whole-cell subtractive panning is a screening technique developed based on whole-cell screening in recent years, which performs subtractive panning on phage display library by using couple cells, I.e. Two states of cells. It is mainly used for screening of novel antigenic epitopes, receptors, ligands, novel vaccines, the targeted active peptides of tumor cells, targeted gene vectors, and stimulants or antagonists of receptors or enzyme etc. The principle, advantages, disadvantages and optimization of the technique as well as its application in phage display library screening are reviewed in this paper.

  5. Application of microarray and functional-based screening methods for the detection of antimicrobial resistance genes in the microbiomes of healthy humans.

    Directory of Open Access Journals (Sweden)

    Roderick M Card

    Full Text Available The aim of this study was to screen for the presence of antimicrobial resistance genes within the saliva and faecal microbiomes of healthy adult human volunteers from five European countries. Two non-culture based approaches were employed to obviate potential bias associated with difficult to culture members of the microbiota. In a gene target-based approach, a microarray was employed to screen for the presence of over 70 clinically important resistance genes in the saliva and faecal microbiomes. A total of 14 different resistance genes were detected encoding resistances to six antibiotic classes (aminoglycosides, β-lactams, macrolides, sulphonamides, tetracyclines and trimethoprim. The most commonly detected genes were erm(B, blaTEM, and sul2. In a functional-based approach, DNA prepared from pooled saliva samples was cloned into Escherichia coli and screened for expression of resistance to ampicillin or sulphonamide, two of the most common resistances found by array. The functional ampicillin resistance screen recovered genes encoding components of a predicted AcrRAB efflux pump. In the functional sulphonamide resistance screen, folP genes were recovered encoding mutant dihydropteroate synthase, the target of sulphonamide action. The genes recovered from the functional screens were from the chromosomes of commensal species that are opportunistically pathogenic and capable of exchanging DNA with related pathogenic species. Genes identified by microarray were not recovered in the activity-based screen, indicating that these two methods can be complementary in facilitating the identification of a range of resistance mechanisms present within the human microbiome. It also provides further evidence of the diverse reservoir of resistance mechanisms present in bacterial populations in the human gut and saliva. In future the methods described in this study can be used to monitor changes in the resistome in response to antibiotic therapy.

  6. 24 CFR 983.255 - Tenant screening. (United States)


    ...) OFFICE OF ASSISTANT SECRETARY FOR PUBLIC AND INDIAN HOUSING, DEPARTMENT OF HOUSING AND URBAN DEVELOPMENT... suitability for tenancy. However, the PHA may opt to screen applicants for family behavior or suitability for... in 25 CFR part 5, subpart L, apply to tenant screening....

  7. Application of computer aids drug screening in new drug design and development%计算机模拟药物筛选在新药设计与开发中的应用

    Institute of Scientific and Technical Information of China (English)



    The development of computer technology, molecular pharmacology and molecular biology promoted the technique of in silico drug screening (virtual screening) used in the drug discovery. The in silico drug screening could be used for diversity screening and/or focussed screening. In present paper, the principles, characteristics and methods of computer aids drug screening were briefly described.

  8. Update: routine screening for antibodies to human immunodeficiency virus, civilian applicants for U.S. military service and U.S. Armed Forces, active and reserve components, January 2008-June 2013. (United States)


    This report contains an update through June 2013 on the results of screening for HIV infection among civilian applicants for military service and among members of the active and reserve components of the Armed Forces. Among civilian applicants, annual rates of prevalence of HIV infection showed a continuing downward trend. Rates among black, non-Hispanic applicants were higher than other racial/ethnic groups but have declined sharply since 2008. Among service members, annual rates have varied by service and component, with higher rates in the Army and Navy and lower rates in the Marine Corps and Air Force. Members of the Army and Air Force Reserves have had consistently higher rates than members of their respective active components. For both civilian applicants and service members, rates among men are notably higher than among women. The possible roles of unprotected sex and pre-deployment behaviors and the associated challenges to prevention of HIV infection are discussed.

  9. Effect of screen printing type on transparent TiO2 layer as the working electrode of dye sensitized solar cell (DSSC) for solar windows applications (United States)

    Nurosyid, F.; Furqoni, L.; Supriyanto, A.; Suryana, R.


    The working electrode based on semiconductor TiO2 DSSC has been fabricated by screen printing method. This study aim is to determine the effect of the screen type on TiO2 layer as the working electrode of DSSC. Screen used for deposition of TiO2 has the types of; T- 49, T-55 and T-61. TiO2 layer was sintered at temperature of 500°C. DSSC structure was composed of semiconductor TiO2 adsorbed dye, an electrolyte solution and a platinum counter electrode. TiO2 layer thickness was characterized by Scanning Electron Microscopy (SEM), while the absorbance was characterized using UV-Vis spectrophotometer and the electrical properties of DSSC were characterized by Keithley I-V measurement. TiO2 layer fabricated by screen T-49 had the biggest thickness that was 3.2 ± 0.3 μm and the highest UV-Vis absorbance wave at the peak wavelength of 315 nm with the absorbance value was 1.7. The I-V characterization showed that the sample fabricated by screen T-49 obtained the greatest efficiency that was 1.0 × 10-1%

  10. 营养风险筛查2002的临床应用和分析%Clinical application of Nutritional Risk Screening 2002

    Institute of Scientific and Technical Information of China (English)

    孙志慧; 胡若梅; 万津颖


    Objective To evaluate the clinical application of Nutritional Risk Screening 2002 (NRS 2002) in inpatients.Methods Totally 400 inpatients who were admitted to Tianjin Tianhe Hospital from Novem- ber 2008 to March 2009 were enrolled in this study.Physical examinations,including body height and body meas-urement,were performed the next morning after admission.The nutritional status was evaluated with NRS 2002.Results In all 400 inpatients.NRS 2002 was strongly practicable in 306 patients (76.5%) and weakly practica-ble in 94 patients (23.5%);Ninety-six patients (24.0%) had nutritional risks,which were most common in the department of internal medicine and the Department of neurology.The average age of patients with nutritional risks was (79.0±11.4) years,which was significantly higher than that of patients without nutritional risks [(58.1±15.8) years] (P<0.01).Conclusion NRS 2002 is effective and practicable in evaluating the nutritional status of inpatient.%目的 评估营养风险筛查2002 (NRS 2002)在住院患者营养筛查中的应用价值.方法 以2008年11月-2009年3月天津天和医院新住院患者400例为研究对象,在入院后第2天清晨测定身高、体重,详细记录病史及患者情况,采用NRS 2002对患者进行营养风险评价并进行分析.结果 400例患者中,306例为强适用(76.5%),94例为弱适用(23.5%);96例(24.0%)存在营养风险,其中普通内科(38.3%)和神经科(31.8%)患者的发生率居前两位.有营养风险患者的平均年龄为(79.0±11.4)岁,明显高于无营养风险患者的(58.1±15.8)岁(P<0.01).结论 NRS 2002可有效用于筛查住院患者的营养状况.

  11. Assessment of xenoestrogenic exposure by a biomarker approach: application of the E-Screen bioassay to determine estrogenic response of serum extracts

    Directory of Open Access Journals (Sweden)

    Weihe Pal


    Full Text Available Abstract Background Epidemiological documentation of endocrine disruption is complicated by imprecise exposure assessment, especially when exposures are mixed. Even if the estrogenic activity of all compounds were known, the combined effect of possible additive and/or inhibiting interaction of xenoestrogens in a biological sample may be difficult to predict from chemical analysis of single compounds alone. Thus, analysis of mixtures allows evaluation of combined effects of chemicals each present at low concentrations. Methods We have developed an optimized in vitro E-Screen test to assess the combined functional estrogenic response of human serum. The xenoestrogens in serum were separated from endogenous steroids and pharmaceuticals by solid-phase extraction followed by fractionation by high-performance liquid chromatography. After dissolution of the isolated fraction in ethanol-DMSO, the reconstituted extract was added with estrogen-depleted fetal calf serum to MCF-7 cells, the growth of which is stimulated by estrogen. After a 6-day incubation on a microwell plate, cell proliferation was assessed and compared with the effect of a 17-beta-estradiol standard. Results and conclusions To determine the applicability of this approach, we assessed the estrogenicity of serum samples from 30 pregnant and 60 non-pregnant Danish women thought to be exposed only to low levels of endocrine disruptors. We also studied 211 serum samples from pregnant Faroese women, whose marine diet included whale blubber that contain a high concentration of persistent halogenated pollutants. The estrogenicity of the serum from Danish controls exceeded the background in 22.7 % of the cases, while the same was true for 68.1 % of the Faroese samples. The increased estrogenicity response did not correlate with the lipid-based concentrations of individual suspected endocrine disruptors in the Faroese samples. When added along with the estradiol standard, an indication of an

  12. Prenatal screening and genetics

    NARCIS (Netherlands)

    Alderson, P.; Aro, A.R.; Dragonas, T.; Ettorre, E.; Hemminki, E.; Jalinoja, P.; Santalahti, P.; Tijmstra, T.


    Although the term 'genetic screening' has been used for decades, this paper discusses how, in its most precise meaning, genetic screening has not yet been widely introduced. 'Prenatal screening' is often confused with 'genetic screening'. As we show, these terms have different meanings, and we exami

  13. Stomach (Gastric) Cancer Screening (United States)

    ... Gastric Cancer Treatment Stomach Cancer Prevention Stomach Cancer Screening Research Stomach (Gastric) Cancer Screening (PDQ®)–Patient Version What is ... from the . There is no standard or routine screening test for stomach cancer. Several types of screening tests have been ...

  14. Prenatal screening and genetics

    DEFF Research Database (Denmark)

    Alderson, P; Aro, A R; Dragonas, T


    Although the term 'genetic screening' has been used for decades, this paper discusses how, in its most precise meaning, genetic screening has not yet been widely introduced. 'Prenatal screening' is often confused with 'genetic screening'. As we show, these terms have different meanings, and we ex...

  15. High throughput label-free platform for statistical bio-molecular sensing

    DEFF Research Database (Denmark)

    Bosco, Filippo; Hwu, En-Te; Chen, Ching-Hsiu


    Sensors are crucial in many daily operations including security, environmental control, human diagnostics and patient monitoring. Screening and online monitoring require reliable and high-throughput sensing. We report on the demonstration of a high-throughput label-free sensor platform utilizing...

  16. The influence of spirituality and religiosity on breast cancer screening delay in African American women: application of the Theory of Reasoned Action and Planned Behavior (TRA/TPB). (United States)

    Gullate, Mary


    African American women (AAW) are 25% more likely to present with late stage breast cancer and 20% more likely to die from their disease than Caucasian women. Researchers report that a treatment delay of 3 months is a significant factor in breast cancer mortality. Socioeconomic factors, lack of access and knowledge, spiritual and religious beliefs, fear and fatalism are reported as contributing factors to screening delays. Studies have primarily applied the Health Belief Model (HBM) and modified versions like the Champion HBM to preventive health practices. Neither have significant inclusion of spirituality or religiosity. The TRA/TPB focus on beliefs, intent and attitude as individual determinants of the likelihood of performing a specific behavior; but have not had wide utility in studies related to screening delays among AAW. This paper explores the utility of applying the TRA/TPB as the theoretical framework for determining cultural relevance of spirituality and religiosity to screening delays among AAW.

  17. Screening for Impaired Cognitive Domains in a Large Parkinson's Disease Population and Its Application to the Diagnostic Procedure for Parkinson's Disease Dementia

    Directory of Open Access Journals (Sweden)

    Kouichi Ohta


    Full Text Available Background: Dementia is a new focus of research on improved treatment for Parkinson's disease (PD. In 2007, a screening tool for PD dementia (PD-D was developed by the Movement Disorder Society (Level I testing, which still requires verification by a large population study. Methods: We conducted a cross-sectional and multicenter study including 13 institutions administering the Mini-Mental State Examination (MMSE and Montreal Cognitive Assessment (MoCA to 304 PD patients (mean age: 70.6 ± 8.3 years; mean Hoehn and Yahr stage: 2.7 ± 0.7. Results: In all, 34.5% of the patients had MMSE scores Conclusions: Level I testing with administration of the MMSE and MoCA is a practical and efficient screening tool for PD-D. However, the phonemic fluency and pentagon copying tests should be replaced by more specific/sensitive ones when screening for PD-D.

  18. Large-scale plasmonic microarrays for label-free high-throughput screening. (United States)

    Chang, Tsung-Yao; Huang, Min; Yanik, Ahmet Ali; Tsai, Hsin-Yu; Shi, Peng; Aksu, Serap; Yanik, Mehmet Fatih; Altug, Hatice


    Microarrays allowing simultaneous analysis of thousands of parameters can significantly accelerate screening of large libraries of pharmaceutical compounds and biomolecular interactions. For large-scale studies on diverse biomedical samples, reliable, label-free, and high-content microarrays are needed. In this work, using large-area plasmonic nanohole arrays, we demonstrate for the first time a large-scale label-free microarray technology with over one million sensors on a single microscope slide. A dual-color filter imaging method is introduced to dramatically increase the accuracy, reliability, and signal-to-noise ratio of the sensors in a highly multiplexed manner. We used our technology to quantitatively measure protein-protein interactions. Our platform, which is highly compatible with the current microarray scanning systems can enable a powerful screening technology and facilitate diagnosis and treatment of diseases.

  19. An application of Caenorhabditis elegans for drug screening%秀丽隐杆线虫(Caenorhabditis elegans)在药物筛选中的应用

    Institute of Scientific and Technical Information of China (English)

    杨再昌; 杨小生


    It is relatively simple and cheap for drug discovery by target-based screen in vitro, but the actions of drugs in vivo do not depend fully on the interactions between drugs and targets. Major reasons preventing many early candidates reaching market are the inappropriate ADME (absorption, distribution, metabolism and excretion) properties and drug-induced toxicity. Now more attentions were paid to the methods of drug screening in vivo. In recent years, C. elegans has been widely used as a drug screening model in drug discovery. The developments of screening for drugs increasing lifespan and antagonizing microbes using C. elegans-baszd assays were mainly discussed in this paper. With the advantages of easily culture, simple tissue structure, and being amenable to high-throughput screening (HTS), C. elegans may turn out to be invaluable in the development of novel screening methods in the future.%基于靶点的体外药物筛选操作相对简单,成本较低,但是由于药物在体内的作用并不仅仅取决于其与靶点的作用程度,吸收、分布、代谢、排泄特征和毒性均会对早期先导物能否进入临床使用产生极大的影响,因此,药物的体内筛选受到重视.本文重点综述了秀丽隐杆线虫(C.elegans)在抗衰老、抗感染药物筛选中的应用情况.秀丽隐杆线虫结构简单、易于培养和可实现高通量筛选,在未来的药物筛选中必将发挥更重要的作用.

  20. Dipolar recoupling NMR of biomolecular self-assemblies : determining inter- and intrastrand distances in fibrilized Alzheimer's {betta}-amyloid peptide.

    Energy Technology Data Exchange (ETDEWEB)

    Gregory, D. M.; Senzinger, T. L. S.; Burkoth, T. S.; Miller-Auer, H.; Lynn, D. G.; Meredith, S. C.; Botto, R. E.; Chemistry; Univ. of Chicago


    We demonstrate a new method for investigating the structure of self-associating biopolymers using dipolar recoupling NMR techniques. This approach was applied to the study of fibrillar {beta}-amyloid (A{beta}) peptides (the primary component of the plaques of Alzheimer's disease) containing only a single isotopic spin label ({sup 13}C), by employing the DRAWS (dipolar recoupling with a windowless sequence) technique to measure {sup 13}C-{sup 13}C distances. The 'single-label' approach simplified analysis of DRAWS data, since only interstrand contacts are present, without the possibility of any intrastrand contacts. As previously reported [T.L.S. Benzinger, D.M. Gregory, T.S. Burkoth, H. Miller-Auer, D.G. Lynn, R.E. Botto, S.C. Meredith, Proc. Natl. Acad. Sci. 95 (1998) 13407.], contacts of approximately 5 {angstrom} were observed at all residues studied, consistent with an extended parallel {beta}-sheet structure with each amino acid in exact register. Here, we propose that our strategy is completely generalizable, and provides a new approach for characterizing any iterative, self-associating biopolymer. Towards the end of generalizing and refining our approach, in this paper we evaluate several issues raised by our previous analyses. First, we consider the effects of double-quantum (DQ) transverse relaxation processes. Next, we discuss the effects of various multiple-spin geometries on modeling of DRAWS data. Several practical issues are also discussed: these include (1) the use of DQ filtering experiments, either to corroborate DRAWS data, or as a rapid screening assessment of the proper placement of isotopic spin labels; and (2) the comparison of solid samples prepared by either lyophilization or freezing. Finally, data obtained from the use of single labels is compared with that obtained in doubly {sup 13}C-labeled model compounds of known crystal structure. It is shown that such data are obtainable in far more complex peptide molecules. These

  1. Application of high throughput screening in drug development%高通量药物筛选在新药研究中的应用

    Institute of Scientific and Technical Information of China (English)



    The techniques used in the field of drug discovery have been quickly developed during the past decades. High throughput screening (HTS) is a new technique in drug discovery with the characteristics of efficiency, huge scale and automatically operation. The assay methods used in HTS are based on the molecular targets and cells. Screening results obtained from these methods indicate not only the bioactivities of compounds (samples) but also the mechanisms of actions of the compounds (samples). HTS has altered the strategy of drug development.

  2. The Model of Zebra Fish and Its Application to the Screening of Angiogenesis Inhibitor%斑马鱼模型及其在血管生成抑制剂筛选中的应用

    Institute of Scientific and Technical Information of China (English)

    冯康虎; 方鹏飞; 张文贤; 韩立文


    Since there are high genetic similarities between zebra fish and human, the model organisms of ze-bra fish are widely used to many studies about human physiology and pathology as well as the screening of new drugs, the paper is discussing the model of zebra fish and its application to the screening of angiogenesis inhibitor.%斑马鱼基因与人类高度相似,其模式生物正广泛应用到人体生理和病理的多项研究以及新型药物的筛选中,就目前斑马鱼模型及其在血管生成抑制剂筛选中的应用状况进行阐述。

  3. 抗性筛选在抗生素高产菌选育中的应用%Application of Antibiotic- Resistance Screening in Breeding of Antibiotic High-Yield Strains

    Institute of Scientific and Technical Information of China (English)

    戴菲; 李瑾; 黄运红; 付学琴; 龙中儿


    The resistance of bacteria to antibiotics has a certain correlation with its ability of producing antibiotics,which provides provide an effective way of directional selection of high-yield strains, namely antibiotic-resistance screening. The mechanism of antibiotic-resistance screening and its application in the mutation breeding of antibiotic high-yield strains were reviewed.%抗生素产生菌的产抗能力与其对抗生素的抗性之间具有一定的相关性,这为抗生素高产菌株的定向筛选提供了一种有效方法,即抗性筛选.综述了抗生素高产菌选育中抗性筛选的机理及其应用.

  4. Screening for abdominalt aortaaneurisme

    DEFF Research Database (Denmark)

    Lindholt, J S; Juul, Svend; Henneberg, E W;


    rupture. Ultrasonographic screening for AAA takes 10 minutes per scan, and the sensitivity and specificity are high. Ultrasonographic screening for AAA is a reliable, safe and inexpensive method for screening, and screening for AAA is discussed worldwide. One point four percent of deaths among men from 65...... on uncertain assumptions concerning prevalence, incidence and risk of rupture. Therefore a randomized trial screening of 65-73 year old males is taking place in the County of Viborg in Denmark. Udgivelsesdato: 1997-Mar-24...

  5. Screening for abdominalt aortaaneurisme

    DEFF Research Database (Denmark)

    Lindholt, Jes Sanddal; Juul, Søren; Henneberg, E W;


    rupture. Ultrasonographic screening for AAA takes 10 minutes per scan, and the sensitivity and specificity are high. Ultrasonographic screening for AAA is a reliable, safe and inexpensive method for screening, and screening for AAA is discussed worldwide. One point four percent of deaths among men from 65...... on uncertain assumptions concerning prevalence, incidence and risk of rupture. Therefore a randomized trial screening of 65-73 year old males is taking place in the County of Viborg in Denmark....

  6. 社区参与式研究在人群癌症筛查领域的应用%Application of Community-based Participation Research in Population-based Cancer Screening

    Institute of Scientific and Technical Information of China (English)

    丁璐; 王亚东; 王贵齐; 李鹏; 赵君; 刘茉; 杨文珍


    癌症是人类健康的头号杀手,人群筛查是癌症防控的基本手段。目前,癌症筛查已被纳入国家重大公共卫生服务项目,政府会针对不同癌症定期组织筛查。然而,在资金和技术得到保障的前提下,较低的人群筛查参与率逐渐成为影响癌症筛查效能的主要因素。社区参与式研究( community-based participatory research,CBPR)以社区参与理论为基础,可以有效地提高社区人群的癌症筛查参与率。本研究总结了国内外的人群癌症筛查参与现状和提高人群癌症筛查参与率的研究现状,详细阐述了社区参与式研究及其在该领域的应用现状,以期为各类公共卫生服务项目社区参与率的提高提供科学依据。%Cancer is the leading killer of human beings. Population -based screening is the basic means for cancer prevention and control. Cancer screening has been listed as a major public health project in China at present and relevant government departments regularly organizes screening for different cancers. However,under the premise of guaranteed fund and technology,the low participation rate of population -based screening has become the main factor influencing the efficiency of cancer screening. Based on the community participation theory,community-based participation research can effectively improve the participation rate of the community population-based cancer screening. In this study,we summarized the participation status of population-based cancer screening and its research status to improve the participation rate at home and abroad. We also elaborated the community-based participation research and its application status in this field,thus providing a scientific basis for improving the community participation of various kinds of public health service.

  7. 产后抑郁筛查量表中文版在产后抑郁筛查中的应用%Application of the Chinese version of the Postpartum Depression Screening Scale in the screening of postpartum depression

    Institute of Scientific and Technical Information of China (English)

    高明; 王智慧; 傅晓红; 陆丽艳


    Objective To compare the value of the Postpartum Depression Screening Scale (PDSS)and the Edinburgh Postnatal Depression scale (EPDS)in the screening of postpartum depression.Methods A total of 378women within 42 days postpartum completed PDSS,the Edinburgh Postnatal Depression Scale (EPDS)and Structured Clinical Interview for DSM-IV-TR Axis I Disorders-Patient Edition (SCID-I/P).The SCID-I/P was regarded the standard for postpartum depression diagnosis.Results The cut-of score for PDSS and EPDS was 76 and 13,respectively.Sensitivity of PDSS was 92.00%,and specificity was 95.25%,with positive predictive value of 77.02% and negative predictive value of 99.01%.Sensitivity of EPDS was 82.30%,and specificity was 81.33%,with positive predictive value of 44.73% and negative predictive value of 97.30%.The sensitivity,specificity and positive predictive value showed significantly difference between PDSS and EPDS (P<0.05),and negative predictive value had no statistical significant differece.Conclusion PDSS scale is more suitable for screening postpartum depression than EPDS scale.%目的 比较产后抑郁筛查量表(PDSS)和爱丁堡产后抑郁量表(EPDS)在产后抑郁筛查中的应用价值.方法 分别采用PDSS、爱丁堡产后抑郁量表(EPDS)及美国精神障碍诊断与统计手册第4版轴Ⅰ障碍定式临床检查患者版(SCID-I/P)对378例产后42 d的妇女进行评定,以SCID-I/P作为产后抑郁诊断标准.结果 将两种量表的临界值分别界定为76分和13分.PDSS的敏感性为92.00%,特异性为95.25%,阳性预测值为77.02%,阴性预测值为99.01%;EPDS的敏感性为82.26%,特异性为81.33%,阳性预测值为44.73%,阴性预测值为97.30%.两种量表特异性和敏感性差异比较有统计学意义(P<0.05).PDSS与EPDS阳性预测值比较差异有统计学意义(P<0.05),阴性预测值比较差异无统计学意义(P>0.05).结论 与EPDS比较,PDSS更适合产后抑郁的筛查.

  8. Design of LCD Tuch Screen Application Based on Nios Ⅱ%基于NiosⅡ的LCD触摸屏应用设计

    Institute of Scientific and Technical Information of China (English)



    为了实现触摸屏作为设备的人机接口界面,使用FPGA的SOPC技术,在FGPA中构建了NiosⅡ处理器系统作为触摸屏的控制器,编写NiosⅡ控制程序实现了触摸屏信息显示和触控功能.程序中设计了显示区域规划结构,为系统的信息显示和触控功能的实现提供了一种相对通用的方法,能够增加代码的重用性和通用性,简化了显示界面的程序设计过程,提高了系统性能和开发效率.%In order to achieve the touch screen as the man-machine interface equipment, using SOPC technology, NiosⅡ processor system in FGPA was builted as a touch screen controller. Screen display and touch screen capabilities have been realized by writing Nios II control procedures. The designed planning structure of Display Area has became a relatively common method to the information display and touch functions of the system. It can increase code reusability and versatility, simplify the program design process of display interface,and the system performance and development efficiency was improved.

  9. A New Method for Rapid Screening of End-Point PCR Products: Application to Single Genome Amplified HIV and SIV Envelope Amplicons.

    Directory of Open Access Journals (Sweden)

    Laurent Houzet

    Full Text Available PCR is the most widely applied technique for large scale screening of bacterial clones, mouse genotypes, virus genomes etc. A drawback of large PCR screening is that amplicon analysis is usually performed using gel electrophoresis, a step that is very labor intensive, tedious and chemical waste generating. Single genome amplification (SGA is used to characterize the diversity and evolutionary dynamics of virus populations within infected hosts. SGA is based on the isolation of single template molecule using limiting dilution followed by nested PCR amplification and requires the analysis of hundreds of reactions per sample, making large scale SGA studies very challenging. Here we present a novel approach entitled Long Amplicon Melt Profiling (LAMP based on the analysis of the melting profile of the PCR reactions using SYBR Green and/or EvaGreen fluorescent dyes. The LAMP method represents an attractive alternative to gel electrophoresis and enables the quick discrimination of positive reactions. We validate LAMP for SIV and HIV env-SGA, in 96- and 384-well plate formats. Because the melt profiling allows the screening of several thousands of PCR reactions in a cost-effective, rapid and robust way, we believe it will greatly facilitate any large scale PCR screening.

  10. Screening of lysosomal storage disorders: application of the online trapping-and-cleanup liquid chromatography/mass spectrometry method for mucopolysaccharidosis I. (United States)

    Ombrone, Daniela; Malvagia, Sabrina; Funghini, Silvia; Giocaliere, Elisa; Della Bona, Maria Luisa; Forni, Giulia; De Luca, Alessio; Villanelli, Fabio; Casetta, Bruno; Guerrini, Renzo; la Marca, Giancarlo


    In recent years, new treatments have become available to treat some lysosomal storage disorders (LSDs) and many studies suggest that there is a benefit with starting therapy early. Newborn screening should detect diseases early enough for prompt treatment. Some countries include additional conditions, such as some LSDs, into their newborn screening panels. Mucopolysaccharidosis Type I (MPS I) is an autosomal recessive disorder caused by the deficiency of α-L-iduronidase (IDUA) activity. Currently, enzyme replacement therapy (ERT) or bone marrow transplantation is available and this has raised a growing interest for the development of a newborn screening test. In 2009, we reported a new fast and simplified tandem mass spectrometry-based method for quantifying five enzyme activities on dried blood spots. Here, we describe the inclusion of IDUA activity determination for the simultaneous detection of six lysosomal storage diseases. We have defined reference normal ranges by testing 680 healthy newborns and 240 adults. The assay was checked through three confirmed MPS I patients whose IDUA activity was below the normal range. Reproducibility of the assays has been established by assessing the intra-day and inter-day assay imprecisions. This quick assay has been devised to be implemented in newborn screening by liquid chromatography tandem mass spectrometry.

  11. Hadronic Screening in Improved Taste

    CERN Document Server

    Gupta, Sourendu


    We present our results on meson and nucleon screening masses in finite temperature two flavour QCD using smeared staggered valence quarks and staggered thin-link sea quarks with different lattice spacings and quark masses. We investigate optimization of smearing by observing its effects on the infrared (IR) and ultraviolet (UV) components of gluon and quark fields. The application of smearing to screening at finite temperature also provides a transparent window into the mechanism of the interplay of smearing and chiral symmetry. The improved hadronic operators show that above the finite temperature cross over, T_c, screening masses are consistent with weak-coupling predictions. There is also evidence for a rapid opening up of a spectral gap of the Dirac operator immediately above T_c.

  12. Microelectroporation device for genomic screening

    Energy Technology Data Exchange (ETDEWEB)

    Perroud, Thomas D.; Renzi, Ronald F.; Negrete, Oscar; Claudnic, Mark R.


    We have developed an microelectroporation device that combines microarrays of oligonucleotides, microfluidic channels, and electroporation for cell transfection and high-throughput screening applications (e.g. RNA interference screens). Microarrays allow the deposition of thousands of different oligonucleotides in microscopic spots. Microfluidic channels and microwells enable efficient loading of cells into the device and prevent cross-contamination between different oligonucleotides spots. Electroporation allows optimal transfection of nucleic acids into cells (especially hard-to-transfect cells such as primary cells) by minimizing cell death while maximizing transfection efficiency. This invention has the advantage of a higher throughput and lower cost, while preventing cross-contamination compared to conventional screening technologies. Moreover, this device does not require bulky robotic liquid handling equipment and is inherently safer given that it is a closed system.


    Energy Technology Data Exchange (ETDEWEB)

    R. Schreiner


    The purpose of this report is to evaluate and document the screening of the clad degradation features, events, and processes (FEPs) with respect to modeling used to support the Total System Performance Assessment-License Application (TSPA-LA). This report also addresses the effect of certain FEPs on both the cladding and the commercial spent nuclear fuel (CSNF), DOE-owned spent nuclear fuel (DSNF), and defense high-level waste (DHLW) waste forms, as appropriate to address the effects on multiple materials and both components (FEPs,,,, and These FEPs are expected to affect the repository performance during the postclosure regulatory period of 10,000 years after permanent closure. Table 1-1 provides the list of cladding FEPs, including their screening decisions (include or exclude). The primary purpose of this report is to identify and document the analysis, screening decision, and TSPA-LA disposition (for included FEPs) or screening argument (for excluded FEPs) for these FEPs related to clad degradation. In some cases, where a FEP covers multiple technical areas and is shared with other FEP reports, this report may provide only a partial technical basis for the screening of the FEP. The full technical basis for shared FEPs is addressed collectively by the sharing FEP reports. The screening decisions and associated TSPA-LA dispositions or screening arguments from all of the FEP reports are cataloged in a project-specific FEPs database.

  14. Diffusion Monte Carlo applied to weak interactions - hydrogen bonding and aromatic stacking in (bio-)molecular model systems (United States)

    Fuchs, M.; Ireta, J.; Scheffler, M.; Filippi, C.


    Dispersion (Van der Waals) forces are important in many molecular phenomena such as self-assembly of molecular crystals or peptide folding. Calculating this nonlocal correlation effect requires accurate electronic structure methods. Usual density-functional theory with generalized gradient functionals (GGA-DFT) fails unless empirical corrections are added that still need extensive validation. Quantum chemical methods like MP2 and coupled cluster are more accurate, yet limited to rather small systems by their unfavorable computational scaling. Diffusion Monte Carlo (DMC) can provide accurate molecular total energies and remains feasible also for larger systems. Here we apply the fixed-node DMC method to (bio-)molecular model systems where dispersion forces are significant: (dimethyl-) formamide and benzene dimers, and adenine-thymine DNA base pairs. Our DMC binding energies agree well with data from coupled cluster (CCSD(T)), in particular for stacked geometries where GGA-DFT fails qualitatively and MP2 predicts too strong binding.

  15. Hybrid Quantum Mechanics/Molecular Mechanics/Coarse Grained Modeling: A Triple-Resolution Approach for Biomolecular Systems. (United States)

    Sokkar, Pandian; Boulanger, Eliot; Thiel, Walter; Sanchez-Garcia, Elsa


    We present a hybrid quantum mechanics/molecular mechanics/coarse-grained (QM/MM/CG) multiresolution approach for solvated biomolecular systems. The chemically important active-site region is treated at the QM level. The biomolecular environment is described by an atomistic MM force field, and the solvent is modeled with the CG Martini force field using standard or polarizable (pol-CG) water. Interactions within the QM, MM, and CG regions, and between the QM and MM regions, are treated in the usual manner, whereas the CG-MM and CG-QM interactions are evaluated using the virtual sites approach. The accuracy and efficiency of our implementation is tested for two enzymes, chorismate mutase (CM) and p-hydroxybenzoate hydroxylase (PHBH). In CM, the QM/MM/CG potential energy scans along the reaction coordinate yield reaction energies that are too large, both for the standard and polarizable Martini CG water models, which can be attributed to adverse effects of using large CG water beads. The inclusion of an atomistic MM water layer (10 Å for uncharged CG water and 5 Å for polarizable CG water) around the QM region improves the energy profiles compared to the reference QM/MM calculations. In analogous QM/MM/CG calculations on PHBH, the use of the pol-CG description for the outer water does not affect the stabilization of the highly charged FADHOOH-pOHB transition state compared to the fully atomistic QM/MM calculations. Detailed performance analysis in a glycine-water model system indicates that computation times for QM energy and gradient evaluations at the density functional level are typically reduced by 40-70% for QM/MM/CG relative to fully atomistic QM/MM calculations.

  16. 触摸屏和PLC在物料分拣系统中的应用%Application of Touch Screen and PLC in Material Sorting System

    Institute of Scientific and Technical Information of China (English)

    吴迎春; 徐连强; 张家骅


    介绍了物料自动分拣系统的组成及功能,根据其控制要求设计了PLC控制程序,用三菱触摸屏GT1055设计了人机交互界面;PLC程序可读性强、调试方便,触摸屏界面友好直观,系统运行稳定,并提高了物料分拣控制系统的灵活性.%This paper introduces the composition and function of automatic material sorting system and designs PLC program according to its control requirement, which is easy to be read and debugged. It also designs the human - machine interface with Mitsubishi GT1055 touch screen, This touch screen interface is friendly and intuitive. The material sorting control system operates stably and its flexibility is improved.

  17. Application of Touch Screen in the Pneumatic Line Training System%触摸屏在气动生产线实训系统中的应用

    Institute of Scientific and Technical Information of China (English)



    This paper in introduces the structure and function of pneumatic line teaching and training system,and mainly researches on the reform of the system based On MT4300 touch screen configuration,The touch screen is configured by EV5000 configuration software,which finally completes the monitoring and controlling of the feeding Station in the system.%本文在介绍了模块化生产线教学实训系统的结构和功能基础上,着重研究了运用MT4300触摸屏组态对该系统进行升级改造。通过EV5000组态软件实现触摸屏组态,完成对该系统上料站的监视与控制。


    Directory of Open Access Journals (Sweden)

    Marzena Matejczyk


    Full Text Available Escherichia coli K-12 GFP-based bacterial biosensors allowed the detection of cytotoxic and genotoxic effect of anticancer drug– cyclophosphamide and antidiabetic drug – metformin in PBS buffer and surface water. Experimental data indicated that recA::gfpmut2 genetic system was sensitive to drugs and drugs mixture applied in experiment. RecA promoter was a good bioindicator in cytotoxic and genotoxic effect screening of cyclophosphamide, metformin and the mixture of the both drugs in PBS buffer and surface water. The results indicated that E. coli K-12 recA::gfp mut2 strain could be potentially useful for first-step screening of cytotoxic and genotoxic effect of anticancer and antidiabetic pharmacist residues in water. Next steps in research will include more experimental analysis to validate recA::gfpmut2 genetic system in E. coli K-12 on different anticancer drugs.

  19. Application of Eukaryotic Elongation Factor-2 Kinase (eEF-2K) for Cancer Therapy: Expression, Purification, and High-Throughput Inhibitor Screening. (United States)

    Tavares, Clint D J; Devkota, Ashwini K; Dalby, Kevin N; Cho, Eun Jeong


    Protein kinases have emerged as an important class of therapeutic targets, as they are known to be involved in pathological pathways linked to numerous human disorders. Major efforts to discover kinase inhibitors in both academia and pharmaceutical companies have centered on the development of robust assays and cost-effective approaches to isolate them. Drug discovery procedures often start with hit identification for lead development, by screening a library of chemicals using an appropriate assay in a high-throughput manner. Considering limitations unique to each assay technique and screening capability, intelligent integration of various assay schemes and level of throughput, in addition to the choice of chemical libraries, is the key to success of this initial step. Here, we describe the purification of the protein kinase, eEF-2K, and the utilization of three biochemical assays in the course of identifying small molecules that block its enzymatic reaction.

  20. Achievement of constitutive fluorescent pLEXSY-egfp Leishmania braziliensis and its application as an alternative method for drug screening in vitro (United States)

    Bastos, Matheus Silva e; de Souza, Luciana Ângelo; Onofre, Thiago Souza; Silva, Abelardo; de Almeida, Márcia Rogéria; Bressan, Gustavo Costa; Fietto, Juliana Lopes Rangel


    BACKGROUND Gene reporter-fluorescent cells have emerged as alternative method for drug screening. OBJECTIVE Achievement of constitutive expression of fluorescent protein GFP by Leishmania braziliensis as alternative method for drug screening. METHODS L. braziliensis-GFP was generated using Leishmania tarentolae pLEXSY-egfp for constitutive expression of GFP. Fluorescent cells were selected and subjected to standardisation tests of anti-promastigote and anti-intracellular amastigote assays. FINDINGS Our results showed that L. braziliensis-GFP method is faster and more sensitive than Allamar Blue-resazurin. MAIN CONCLUSION Transfected parasites maintained stable fluorescence after successive in vitro passages and pLEXSY system can be used to achieve non-L. tarentolae fluorescent cells. PMID:28177050